ALBERT

Description: Cissus quadrangularis (Vitaceae) is a perennial climber endemic to Africa and is characterized by succulent angular stems. The plant grows in arid and semi-arid regions of Africa especially in the African savanna. The stem of C. quadrangularis has a wide range of applications in both human and animal medicine, but there is limited cytogenetic information available for this species. In this study, the chromosome number, genome size, and genome composition for C. quadrangularis were determined. Flow cytometry results indicated that the genome size of C. quadrangularis is approximately 2C = 1.410 pg. Fluorescence microscopy combined with DAPI stain showed the chromosome numbers to be 2n = 48. It is likely that C. quadrangularis has a tetraploid genome after considering the basic chromosome numbers in Cissus genus (n = 10, 11, or 12). A combination of low-throughput genome sequencing and bioinformatics analysis allowed identification and quantification of repetitive elements that make up about 52% of the C. quadrangularis genome, which was dominated by LTR-retrotransposons. Two LTR superfamilies were identified as Copia and Gypsy, with 24% and 15% of the annotated clusters, respectively. The comparison of repeat elements for C. quadrangularis, Vitis vinifera, and four other selected members in the Cissus genus revealed a high diversity in the repetitive element components, which could suggest recent amplification events in the Cissus genus. Our data provides a platform for further studies on the phylogeny and karyotype evolution in this genus and in the family Vitaceae.

Description: Background Sweet cherry (Prunus avium) is one of the most popular of the temperate fruits. Previous studies have demonstrated that there were several haplotypes in the chloroplast genome of sweet cherry cultivars. However, none of chloroplast genome of a sweet cherry cultivar were yet released, and the phylogenetic relationships among Prunus based on chloroplast genome data were unclear. Methods In this study, we assembled and annotated the complete chloroplast genome of a sweet cherry cultivar P. avium ‘Summit’ from high-throughput sequencing data. Gene Ontology (GO) terms were assigned to classify the function of the annotated genes. Maximum likelihood (ML) trees were constructed to reveal the phylogenetic relationships within Prunus species, using LSC (large single-copy) regions, SSC (small single-copy) regions, IR (inverted repeats) regions, CDS (coding sequences), intergenic regions, and whole cp genome datasets, respectively. Results The complete plastid genome was 157, 886 bp in length with a typical quadripartite structure of LSC (85,990 bp) and SSC (19,080 bp) regions, separated by a pair of IR regions (26,408 bp). It contained 131 genes, including 86 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNA genes. A total of 77 genes were assigned to three major GO categories, including molecular function, cellular component and biological process categories. Comparison with other Prunus species showed that P. avium ‘Summit’ was quite conserved in gene content and structure. The non-coding regions, ndhc-trnV, rps12-trnV and rpl32-trnL were the most variable sequences between wild Mazzard cherry and ‘Summit’ cherry. A total of 73 simple sequence repeats (SSRs) were identified in ‘Summit’ cherry and most of them were mononucleotide repeats. ML phylogenetic tree within Prunus species revealed four clades: Amygdalus, Cerasus, Padus, and Prunus. The SSC and IR trees were incongruent with results using other cp data partitions. These data provide valuable genetic resources for future research on sweet cherry and Prunus species.

Description: Use of virtual proxies of live animals are rapidly gaining ground in studies of animal behaviour. Such proxies help to reduce the number of live experimental animals needed to stimulate the behaviour of experimental individuals and to increase standardisation. However, using too simplistic proxies may fail to induce a desired effect and/or lead to quick habituation. For instance, in a predation context, prey often employ multimodal cues to detect predators or use specific aspects of predator behaviour to assess threat. In a live interaction, predator and prey often show behaviours directed towards each other, which are absent in virtual proxies. Here we compared the effectiveness of chemical and visual predator cues in the cooperatively breeding cichlid Neolamprologus pulcher, a species in which predation pressure has been the evolutionary driver of its sociality. We created playbacks of predators simulating an attack and tested their effectiveness in comparison to a playback showing regular activity and to a live predator. We further compared the effectiveness of predator odour and conspecific skin extracts on behaviours directed towards a predator playback. Regular playbacks of calmly swimming predators were less effective than live predators in stimulating a focal individual’s aggression and attention. However, playbacks mimicking an attacking predator induced responses much like a live predator. Chemical cues did not affect predator directed behaviour.

Description: Background and Objective Human papillomavirus (HPV) testing has become a preferred cervical cancer screening. However, most HPV infections are harmless and additional tests are required to screen HPV positive women. The objective of this study is to determine the optimal triage strategies for HPV positive women in China’s rural population. Methods A population-based screening was performed at seven rural counties of Jiangxi province, between October 2014 to January 2016. A total of 18,000 women aged 35–64 years were enrolled in this study. The primary screening was performed using CareHPV, HC-2, Cobas ®4,800 or HybriMax. Positive women were further screened with five triage tests: (1) Liquid-based cytology test (LBC); (2) conventional Pap cytology test (Pap smear); (3) HPV16, 18 detection; (4) viral load; and (5) visual inspection with acetic acid and Lugol’s iodine (VIA/VILI). Women who were tested positive were referred for colposcopy. The five triage tests were compared with respect to sensitivity, specificity, referral rate, cost and diagnostic time. Results Complete data were available for 17,782 women. The HPV prevalence was 13.6%. Referral rates for colposcopy were 4.5%, 2.8%, 2.8%, 6.6%, and 3.7% with LBC, Pap smear, HPV16/18, viral load, and VIA/VILI, respectively. The sensitivity of the above triage tests was 65.8%, 51.9%, 86.8%, 73.3%, and 41.7%, respectively. The specificity was 69.8%, 81.0%, 85.8%, 52.2% and 65.3%, respectively. The average time to diagnosis was significantly lower with HPV16/18, viral load and VIA/VILI than LBC and Pap smear. In addition, screening cost that leads to identify one HSIL+ woman was the lowest with viral load. Conclusion Our data indicate that HPV16/18 and viral load are the optimal triage strategies for HPV screening in China’s rural population.

Description: Classification on the basis of gene expression data derived from RNA-seq promises to become an important part of modern medicine. We propose a new classification method based on a model where the data is marginally negative binomial but dependent, thereby incorporating the dependence known to be present between measurements from different genes. The method, called qtQDA, works by first performing a quantile transformation (qt) then applying Gaussian quadratic discriminant analysis (QDA) using regularized covariance matrix estimates. We show that qtQDA has excellent performance when applied to real data sets and has advantages over some existing approaches. An R package implementing the method is also available on https://github.com/goknurginer/qtQDA.

Description: Yellow-bellied toad populations (Bombina variegata) show a wide fast–slow continuum of the life-history trait longevity ranging from 5 to 23 years. We investigated populations in Germany (n = 8) and Austria (n = 1) to determine their position within the continuum of longevity and the potential drivers of adult survival at the local and the continental scale. Intrinsic and extrinsic factors considered were local weather, nutritional state, allocation of ingested energy to somatic growth, pathogen prevalence, and geographical clines (latitude, altitude, and longitude). Capture-mark-recapture (CMR) monitoring and direct age assessment by skeletochronology allowed for reliable estimates of longevity and adult survival. Raw and corrected recapture rates as well as a probabilistic estimate of the lifespan of the eldest 1% adults of a cohort (CMR data) were used as surrogates for adult survival and thus longevity in a population. Additionally, survival rates were calculated from static life tables based on the age structure (skeletochronological data) of eight populations. Populations in Germany were short-lived with a maximum lifespan of annual cohorts varying from 5 to 8 years, whereas the population in Austria was long-lived with a cohort longevity of 13 to 23 years. We provide evidence that annual survival rates and longevity differ among years and between short- and long-lived populations, but there was no decrease of survival in older toads (i.e. absence of senescence). Variation of weather among years accounted for 90.7% of variance in annual survival rates of short-lived populations, whereas the sources of variation in the long-lived population remained unidentified. At the continental scale, longevity variation among B. variegata populations studied so far did not correspond to geographical clines or climate variation. Therefore, we propose that a population’s position within the fast–slow continuum integrates the response to local environmental stochasticity (extrinsic source of variation) and the efficiency of chemical antipredator protection determining the magnitude of longevity (intrinsic source of variation).

Description: This study focuses on the vegetation dynamic caused by global environmental change in the eastern margin of the Qinghai-Tibet Plateau (EMQTP). The Qinghai–Tibet Plateau (QTP) is one of the most sensitive areas responding to global environmental change, particularly global climate change, and has been recognized as a hotspot for coupled studies on changes in global terrestrial ecosystems and global climates. An important component of terrestrial ecosystems, vegetation dynamic has become a key issue in global environmental change, and numerous case studies have been conducted on vegetation dynamic trends using multi-source data and multi-scale methods across different study periods. The EMQTP is regarded as a transitional area located between the QTP and the Sichuan basin, and has special geographical and climatic conditions. Although this area is ecologically fragile and sensitive to climate change, few studies about vegetation dynamics have been carried out in this area. Thus, in this study, we used long-term series datasets of GIMMS 3g NDVI and VGT/PROBA-V NDVI to analyze the vegetation dynamics and phenological changes from 1982 to 2018. Validation was performed based on Landsat NDVI and Vegetation Index & Phenology (VIP) data. The results reveal that the year 1998 was a vital turning point in the start of growing season (SGS) in vegetation ecosystems. Before this turning point, the SGS had an average slope of 9.2 days/decade, and after, the average slope was 3.9 days/decade. The length of growing season (LGS) was slightly prolonged between 1982 to 2015. Additionally, the largest national alpine wetland grassland experienced significant vegetation degradation; in autumn, the degraded area accounted for 63.4%. Vegetation degradation had also appeared in the arid valleys of the Yalong River and the Jinsha River. Through validation analysis, we found that the main causes of vegetation degradation are the natural degradation of wetland grassland and human activities, specifically agricultural development and residential area expansion.

Description: The ecology and conservation status of many island-restricted bats remain largely unexplored. The free-tailed bat Mormopterus francoismoutoui is a small insectivorous tropical bat, endemic to Reunion Island (Indian Ocean). Despite being widely distributed on the island, the fine-scale genetic structure and evolutionary ecology of M. francoismoutoui remain under-investigated, and therefore its ecology is poorly known. Here, we used Illumina paired-end sequencing to develop microsatellite markers for M. francoismoutoui, based on the genotyping of 31 individuals from distinct locations all over the island. We selected and described 12 polymorphic microsatellite loci with high levels of heterozygosity, which provide novel molecular markers for future genetic population-level studies of M. francoismoutoui.

Description: Anthropogenic CO2 emissions are causing global ocean warming and ocean acidification. The early life stages of some marine fish are vulnerable to elevated ocean temperatures and CO2 concentrations, with lowered survival and growth rates most frequently documented. Underlying these effects, damage to different organs has been found as a response to elevated CO2 in larvae of several species of marine fish, yet the combined effects of acidification and warming on organ health are unknown. Yellowtail kingfish, Seriola lalandi, a circumglobal subtropical pelagic fish of high commercial and recreational value, were reared from fertilization under control (21 °C) and elevated (25 °C) temperature conditions fully crossed with control (500 µatm) and elevated (1,000 µatm) pCO2 conditions. Larvae were sampled at 11 days and 21 days post hatch for histological analysis of the eye, gills, gut, liver, pancreas, kidney and liver. Previous work found elevated temperature, but not elevated CO2, significantly reduced larval kingfish survival while increasing growth and developmental rate. The current histological analysis aimed to determine whether there were additional sublethal effects on organ condition and development and whether underlying organ damage could be responsible for the documented effects of temperature on survivorship. While damage to different organs was found in a number of larvae, these effects were not related to temperature and/or CO2 treatment. We conclude that kingfish larvae are generally vulnerable during organogenesis of the digestive system in their early development, but that this will not be exacerbated by near-future ocean warming and acidification.

Description: The prospective study including 166 participants aims to evaluate the association between seminal prosaposin and the outcomes of in vitro fertilization (IVF) cycles in humans. The generalized linear model (GLM) was used to analyze the associations between seminal prosaposin concentrations and normal fertilization rates and good embryos proportion. The generalized estimating equation (GEE) was used to evaluate the association between embryo parameters and the prosaposin concentrations. Each model was adjusted for age of the couples, female basal FSH, AFC and BMI, starting dose and oocyte yield of IVF cycles and smoker. GLM models suggested that prosaposin was significantly associated with fertilization rate (P = 0.005) and good embryo proportion (P = 0.038) while none of the semen parameters (sperm concentration, motility, progressive motility, normal morphology rate, postwash sperm concentration and motility) was significantly associated with the parameters in the cohort. Using GEE, it was also shown that prosaposin was positively associated with the occurrence of early cleavage and negatively associated with uneven cleavage pattern on day 3. In both the overall population and the normozoospermia patients, the prosaposin was significantly associated with pregnancy with adjustment with covariates. In conclusion, our data suggested that seminal prosaposin concentration could provide more information regarding normal fertilization and embryo development in IVF than traditional semen parameters.

Description: This article studies soil and plant phytoliths from the Eastern Serengeti Plains, specifically the Acacia-Commiphora mosaics from Oldupai Gorge, Tanzania, as present-day analogue for the environment that was contemporaneous with the emergence of the genus Homo. We investigate whether phytolith assemblages from recent soil surfaces reflect plant community structure and composition with fidelity. The materials included 35 topsoil samples and 29 plant species (20 genera, 15 families). Phytoliths were extracted from both soil and botanical samples. Quantification aimed at discovering relationships amongst the soil and plant phytoliths relative distributions through Chi–square independence tests, establishing the statistical significance of the relationship between categorical variables within the two populations. Soil assemblages form a spectrum, or cohort of co-ocurring phytolith classes, that will allow identifying environments similar to those in the Acacia-Commiphora ecozone in the fossil record.

Description: Purpose Renin-angiotensin system blockers (RASBs), which include angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin-2 receptor 1 blockers (ARBs), have been reported to be associated with lung cancer metastasis, radiotherapy and chemotherapy. Until now, very limited clinical data for RASBs’ diagnostic and prognostic effects has existed for lung cancer chemotherapy in Chinese patients. Methods There were a total of 678 lung cancer patients with hypertension, of which 461 (68%) were in the non-RASBs group and 217 (32%) were in the RASBs group. Patients’ gender, age, smoking status, histologic differentiation, tumor size, pathological grade, lymph node metastasis, pathological stage and progression-free survival (PFS) were retrospectively analyzed between these two groups. The clinical effects of ACEIs and ARBs in lung cancer patients were compared via t tests, and χ2 test, and potential prognostic factors for progression-free survival (PFS) were evaluated by Kaplan–Meier analysis. Results Significant differences were observed in lymph node metastasis between the RASBs and non-RASBs groups. The RASBs group (62.8% vs 71.7%, p = 0.037) and ARBs group (60.0% vs 71.7%, p = 0.030) had lower lymph node metastasis, and patients with RASBs had a lower pathological stage than those in non-RASBs groups (67.1% vs 77.4%, p = 0.044 ). The PFS of the RASBs (10.7 vs. 6.7 months, p = 0.040) and ACEIs (12.9 vs 6.7 months, p = 0.021) groups were longer than that of the non-RASBs group, while no statistical difference was shown between the ACEIs and ARBs groups. Moreover, the significant results of PFS were further confirmed in pathological stage III–IV patients. In the non-RASB group, 55% of patients took calcium channel blockers (CCBs), and the ACEIs group have a significantly longer PFS compared to the non-CCBs group (6.4 vs 12.9 months, p = 0.036). Conclusion In this study, we showed that the use of RASBs is a positive factor for pathological stage and prognosis of lung cancer patients. Therefore, it is necessary to actively evaluate medical history, especially the use of anti-hypertension medication, in patients with lung cancer and reflect medical history in the treatment and management plans of these patients.

Description: New fossil lungfish remains comprising two parasphenoids, tooth plates and scales from the Famennian Witpoort Formation of South Africa are described. From the parasphenoid material, which bears similarity to Oervigia and Sagenodus but is nevertheless unique, a new genus, Isityumzi mlomomde gen. et sp. nov. is erected. Tooth plates and scales from the same locality may be conspecific but are not yet assigned until further material becomes available. The tooth plates closely resemble those of some taxa in the Carboniferous genus Ctenodus. The new taxon is significant as only the second Devonian lungfish described from the African continent, and for hailing from the high-latitude (polar) Waterloo Farm environment situated close to 70° south during the Famennian.

Description: Background This study was designed to explore the profile and potential influencers of the vaginal microbiome (VMB) among asymptomatic pregnant Chinese women and its possible association with pregnancy outcomes. Methods A prospective study was conducted among pregnant Chinese women receiving regular prenatal care at a hospital in Shanghai, China from March 2017 to March 2018. Vaginal swabs were obtained from 113 asymptomatic pregnant women in mid-pregnancy and sequenced by the V3–V4 region of 16S rRNA on an Ion S5™ XL platform. Demographic characteristics and major pregnancy outcomes were collected through questionnaires and electronic medical records. Results The predominant vaginal community state types (CSTs) were CST I (45.1%) and CST III (31.9%). Participants were divided into a lactobacilli-dominant group (LD, CST I/II/III/I–III/V, n = 100, 88.5%) and a less lactobacilli-dominant group (LLD, CST IV-A/B, n = 13, 11.5%). Women in the LLD group showed an increased alpha diversity [median (interquartile range, IQR): 2.41 (1.67, 2.49) vs. 0.30 (0.17, 0.59), P 

Description: Restoration of keystone species is a primary strategy used to combat biodiversity loss and recover ecological services. This is particularly true for oceanic islands, which despite their small land mass, host a large fraction of the planet’s imperiled species. The endemic Opuntia spp. cacti are one example and a major focus for restoration in the Galápagos archipelago, Ecuador. These cacti are keystone species that support much of the unique vertebrate animal community in arid zones, yet human activities have substantially reduced Opuntia populations. Extreme aridity poses an obstacle for quickly restoring Opuntia populations though water-saving technologies may provide a solution. The aim of this study was to evaluate current restoration efforts and the utility of two water-saving technologies as tools for the early stages of restoring Opuntia populations in the Galápagos archipelago. We planted 1,425 seedlings between 2013 and 2018, of which 66% had survived by the end of 2018. Compared with no-technology controls, seedlings planted with Groasis Waterboxx® water-saving technology (polypropylene trays with water reservoir and protective refuge for germinants) had a greater rate of survival in their first two-years of growth on one island (Plaza Sur) and greater growth rate on four islands whereas the “Cocoon” water-saving technology (similar technology but made of biodegradable fiber) did not affect growth and actually reduced seedling survival. Survival and growth rate were also influenced by vegetation zone, elevation, and precipitation in ways largely contingent on island. Overall, our findings suggest that water-saving technologies are not always universally applicable but can substantially increase the survival and growth rate of seedlings in certain conditions, providing in some circumstances a useful tool for improving restoration outcomes for rare plants of arid ecosystems.

Description: In the Coregonus lavaretus complex may be found lacustrine sympatric pairs, which serves as an intriguing model for studying different aspects of fish evolutionary biology. One such sympatric whitefish pair inhabits Teletskoye Lake (West Siberia, Russia) and includes a “large” form (Coregonus lavaretus pidschian (Gmelin, 1789)) and a “small” form (C. l. pravdinellus (Dulkeit, 1949)). C. l. pravdinellus has a narrow trophic specialization and feeds on zooplankton, whereas the diet of C. l. pidschian is based on benthic prey. In the present study we aimed to address the question of how the gut microbial community reflects the divergence in diet of a sympatric pair of whitefish. Studied samples included the mucosa and content were collected for cardiac and pyloric stomach, anterior, middle, and posterior intestine, but only mucosa was collected for the pyloric caeca. In addition, water, sediment, macrophyte (environmental microbiota) and invertebrate (microbiota of prey) samples were collected in the same location. The V3–V4 region of the 16S rRNA genes was chosen for microbiome analysis and the software PICRUSt used to estimate the difference functional roles of the microbiota. The number of OTUs and Chao1 index in mucosa and content of cardiac and pyloric stomach were significantly different between whitefish. Significant differences were observed between whitefish for content from different parts of the intestine in terms of OTU number and Chao1 indices, whereas for mucosa from the same parts of intestine these differences were absent. No significant differences were found for diversity estimates of mucosa and content of different parts of the gut (there were a few exceptions) between whitefish. The form of whitefish and the segment of the digestive system were factors with a significant determinative effect on the structure of the microbiota from gut mucosa and content. The most dominant phyla in mucosa and content of cardiac and pyloric stomach was Proteobacteria (57.0–84.0%) for both whitefish. Throughout the intestine of C. l. pidschian the dominant phyla in mucosa were Proteobacteria (38.8%) and Firmicutes (15.6%), whereas for C. l. pravdinellus–Tenericutes (49.6%) and Proteobacteria (28.1%). For both forms, the phylum Spirochaetes was found in a significant amount (20.0–25.0%) in the mucosa of the posterior intestine. While for the content obtained from anterior, middle and posterior intestines, the dominant bacterial phyla were the same as those described for mucosa from the same parts of the intestine for both whitefish. The bacterial community of the prey and environment was significantly different from bacterial communities found for all parts of the gut mucosa for both whitefish, with the exception of the mucosa of the cardiac stomach. According to PICRUSt the highest level of differences between whitefish at the L3 level were found for the intestinal mucosa (75.3%), whereas the lowest one was registered for stomach content (38.8%).

Description: Background Management of recurrent ureteral stricture is challenging. Consensus on the best surgical choice has not been demonstrated. In this study, we aim to report our experience in treating recurrent ureteral stricture and demonstrate whether robot-assisted procedure for redo ureteral surgery is as effective as open procedure while remaining less invasive. Methods We retrospectively assessed 41 patients (22 robot-assisted surgeries and 19 open surgeries) who underwent consecutive robot-assisted and open procedures for redo ureteral surgery from January 2014 to 2018 in our institution. Perioperative outcomes, including demographics, operative time, estimated blood loss, complications, pain scores, success rate and cost, were compared between two groups. Results There was no significant intergroup difference in terms of age, body mass index, gender composition and American Society of Anesthesiologists scores. A total of 31 patients underwent redo pyeloplasty and ten underwent redo uretero-ureterostomy. Compared with open group, robot-assisted group showed shorter operative time (124.55 min vs. 185.11 min, p 〈 0.0001), less estimated blood loss (100.00 mL vs. 182.60 mL, p = 0.008) and higher cost (61161.77¥ vs. 39470.79¥, p 〈 0.0001). Complication rate and pain scores were similar between two groups. Median follow-up periods were 30 and 48 months for robot-assisted and open group respectively. Success rate in the robot-assisted (85.71%) and the open group (82.35%) was not significantly different. Conclusions Robot-assisted surgery for recurrent stricture after previous ureteral reconstruction is as effective as open procedure and is associated with shorter operative time and less estimated blood loss.

Description: Habitat loss and fragmentation are recognized as affecting the nature of biotic interactions, although we still know little about such changes for reptilian herbivores and their hindgut nematodes, in which endosymbiont interactions could range from mutualistic to commensal and parasitic. We investigated the potential cost and benefit of endosymbiont interactions between the spur-thighed tortoise (Testudo graeca L.) and adult oxyurid nematodes (Pharyngodonidae order Oxyurida) in scrublands of southern Spain. For this, we assessed the association between richness and abundance of oxyurid species with tortoises’ growth rates and body traits (weight and carapace length) across levels of habitat loss (low, intermediate and high). Furthermore, by using an intrapopulation ecological network approach, we evaluated the structure and diversity of tortoise–oxyurid interactions by focusing on oxyurid species infesting individual tortoises with different body traits and growth rates across habitats. Overall, tortoise body traits were not related to oxyurid infestation across habitats. Oxyurid richness and abundance however, showed contrasting relationships with growth rates across levels of habitat loss. At low habitat loss, oxyurid infestation was positively associated with growth rates (suggesting a mutualistic oxyurid–tortoise relationship), but the association became negative at high habitat loss (suggesting a parasitic relationship). Furthermore, no relationship was observed when habitat loss was intermediate (suggesting a commensal relationship). The network analysis showed that the oxyurid community was not randomly assembled but significantly nested, revealing a structured pattern for all levels of habitat loss. The diversity of interactions was lowest at low habitat loss. The intermediate level, however, showed the greatest specialization, which indicates that individuals were infested by fewer oxyurids in this landscape, whereas at high habitat loss individuals were the most generalized hosts. Related to the latter, connectance was greatest at high habitat loss, reflecting a more uniform spread of interactions among oxyurid species. At an individual level, heavier and larger tortoises tended to show a greater number of oxyurid species interactions. We conclude that there is an association between habitat loss and the tortoise–oxyurid interaction. Although we cannot infer causality in their association, we hypothesize that such oxyurids could have negative, neutral and positive consequences for tortoise growth rates. Ecological network analysis can help in the understanding of the nature of such changes in tortoise–oxyurid interactions by showing how generalized or specialized such interactions are under different environmental conditions and how vulnerable endosymbiont interactions might be to further habitat loss.

Description: Background This study sought to better understand the psychometric properties of the SARC-F, by examining the baseline and training-related relationships between the five SARC-F items and objective measures of muscle function. Each of the five items of the SARC-F are scored from 0 to 2, with total score of four or more indicative of likely sarcopenia. Methods This manuscript describes a sub-study of a larger step-wedge, randomised controlled 24-week progressive resistance and balance training (PRBT) program trial for Australian community dwelling older adults accessing government supported aged care. Muscle function was assessed using handgrip strength, isometric knee extension, 5-time repeated chair stand and walking speed over 4 m. Associations within and between SARC-F categories and muscle function were assessed using multiple correspondence analysis (MCA) and multinomial regression, respectively. Results Significant associations were identified at baseline between SARC-F total score and measures of lower-body muscle function (r =  − 0.62 to 0.57; p ≤ 0.002) in 245 older adults. MCA analysis indicated the first three dimensions of the SARC-F data explained 48.5% of the cumulative variance. The initial dimension represented overall sarcopenia diagnosis, Dimension 2 the ability to displace the body vertically, and Dimension 3 walking ability and falls status. The majority of the 168 older adults who completed the PRBT program reported no change in their SARC-F diagnosis or individual item scores (56.5–79.2%). However, significant associations were obtained between training-related changes in SARC-F total and item scores and changes in walking speed and chair stand test performance (r =  − 0.30 to 0.33; p 

Description: The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.

Description: To probe how non-human primates (NHPs) decode temporal dynamic stimuli, we used a two-alternative forced choice task (2AFC), where the cue was dynamic: a movie snippet drawn from an animation that transforms one image into another. When the cue was drawn from either the beginning or end of the animation, thus heavily weighted towards one (the target) of both images (the choice pair), then primates performed at high levels of accuracy. For a subset of trials, however, the cue was ambiguous, drawn from the middle of the animation, containing information that could be associated to either image. Those trials, rewarded randomly and independent of choice, offered an opportunity to study the strategy the animals used trying to decode the cue. Despite being ambiguous, the primates exhibited a clear strategy, suggesting they were not aware that reward was given non-differentially. More specifically, they relied more on information provided at the end than at the beginning of those cues, consistent with the recency effect reported by numerous serial position studies. Interestingly and counterintuitively, this effect became stronger for sessions where the primates were already familiar with the stimuli. In other words, despite having rehearsed with the same stimuli in a previous session, the animals relied even more on a decision strategy that did not yield any benefits during a previous session. In the discussion section we speculate on what might cause this behavioral shift towards stronger bias, as well as why this behavior shows similarities with a repetition bias in humans known as the illusory truth effect.

Description: Several squat lobster specimens of the genus Munidopsis were collected from an artificially placed carcass fall (cow bones) on Weijia Guyot in the western Pacific Ocean. Based on morphological comparisons and molecular analysis, three specimens were confirmed as juveniles of M. albatrossae Pequegnat & Pequegnat, 1973, which represents the first record of this species in the western Pacific. The other specimens collected are newly described as Munidopsis spinifrons sp. nov., which is distinguished from the closely related species in having a spinose rostrum and basal lateral eyespine on the eyestalk. The M. albatrossae from Weijia Guyot exhibited very low genetic distances when compared with a conspecific sample from Monterey Bay, USA, and the closely related species M. aries (A. Milne Edwards, 1880) from the northeastern Atlantic. A phylogenetic tree based on the mtCOI gene shows M. spinifrons sp. nov. as sister to M. vrijenhoeki Jones & Macpherson, 2007 and M. nitida (A. Milne Edwards, 1880), although M. vrijenhoeki presents a complex relationship with other species in the clade. The systematic status of the new species and the closely related species are discussed.

Description: Invasion facilitation, whereby one species has a positive effect on the establishment of another species, could help explain the rapid colonisation shown by some freshwater invasive species, but the underlying mechanisms remain unclear. We employed two-choice test arenas to test whether the presence of zebra mussel (Dreissena polymorpha) could facilitate the establishment of the killer shrimp (Dikerogammarus villosus). Killer shrimp preferred to settle on mats of zebra mussel, but this was unrelated to mat size, and was not different from attraction shown to artificial grass, suggesting that zebra mussel primarily provides substrate and refuge to the killer shrimp. Killer shrimp were strongly attracted to water scented by zebra mussel, but not to water scented by fish. Chemical attraction to the zebra mussel’s scent did not differ between sympatric and allopatric populations of killer shrimp, suggesting that chemical attraction is not an acquired or learned trait. Our study shows, for the first time, chemical attraction between two highly invasive freshwater species, thereby providing a plausible mechanism for invasion facilitation. This has implications for managing the spread of killer shrimp, and perhaps other freshwater invasive species, because chemical attraction could significantly increase establishment success in mutualistic systems. Failure to consider invasion facilitation may underestimate the risk of establishment, and likely also the impact of some aquatic invaders.

Description: In Oryza sativa, indica and japonica are pivotal subpopulations, and other subpopulations such as aus and aromatic are considered to be derived from indica or japonica. In this regard, Oryza sativa accessions are frequently viewed from the indica/japonica perspective. This study introduces a computational method for indica/japonica classification by applying phenotypic variables to the logistic regression model (LRM). The population used in this study included 413 Oryza sativa accessions, of which 280 accessions were indica or japonica. Out of 24 phenotypic variables, a set of seven phenotypic variables was identified to collectively generate the fully accurate indica/japonica separation power of the LRM. The resulting parameters were used to define the customized LRM. Given the 280 indica/japonica accessions, the classification accuracy of the customized LRM along with the set of seven phenotypic variables was estimated by 100 iterations of ten-fold cross-validations. As a result, the classification accuracy of 100% was achieved. This suggests that the LRM can be an effective tool to analyze the indica/japonica classification with phenotypic variables in Oryza sativa.

Description: Despite being classified as critically endangered, little work has been done on leopard protection in Pakistan. Once widely present throughout this region, leopards are now sparsely distributed, and possibly extinct from much of their previously recorded habitat. While leopards show morphological and genetic variation across their species range worldwide, resulting in the classification of nine different subspecies, the leopard genetic structure across Pakistan is unknown, with previous studies including only a very limited sampling. To clarify the genetic status of leopards in Pakistan we investigated the sequence variation in the subunit 5 of the mitochondrial gene NADH from 43 tissue samples and compared it with 238 sequences available from online databases. Phylogenetic analysis clearly separates the Pakistani leopards from the African and Arabian clades, confirming that leopards from Pakistan are members of the Asian clade. Furthermore, we identified two separate subspecies haplotypes within our dataset: P. p. fusca (N = 23) and P. p. saxicolor (N = 12).

Description: During systematic paleontological surveys in the Na Duong Basin in North Vietnam between 2009 and 2012, well-preserved fossilized cranial and postcranial remains belonging to at least 29 individuals of a middle to late Eocene (late Bartonian to Priabonian age (39–35 Ma)) alligatoroid were collected. Comparative anatomical study of the material warrants the diagnosis of a new taxon, Orientalosuchus naduongensis gen. et sp. nov. The combined presence of an enlarged fifth maxillary tooth, prominent preorbital ridges, a large supraoccipital exposure on the skull table, a palatine-pterygoid suture anterior to the posterior end of the suborbital fenestra, and a pterygoid forming a neck surrounding the choana is unique to this species. Unlike previous phylogenies, our parsimony analysis recovers a monophyletic Late Cretaceous to Paleogene East to Southeastern Asian alligatoroid group, here named Orientalosuchina. The group includes Orientalosuchus naduongensis, Krabisuchus siamogallicus, Eoalligator chunyii, Jiangxisuchus nankangensis and Protoalligator huiningensis, all of them sharing a medial shifted quadrate foramen aerum. The recognition of this clade indicates at least two separate dispersal events from North America to Asia: one during the Late Cretaceous by Orientalosuchina and one by the ancestor of Alligator sinensis during the Paleogene or Neogene, the timing of which is poorly constrained.

Description: A fundamental question in ecology is how the success of a taxon changes through time and what drives this change. This question is commonly approached using trajectories averaged over a group of taxa. Using results from probability theory, we show analytically and using examples that averaged trajectories will be more symmetric as the number of averaged trajectories increases, even if none of the original trajectories they were derived from is symmetric. This effect is not only based on averaging, but also on the introduction of noise and the incorporation of a priori known origination and extinction times. This implies that averaged trajectories are not suitable for deriving information about the processes driving the success of taxa. In particular, symmetric waxing and waning, which is commonly observed and interpreted to be linked to a number of different paleobiological processes, does not allow drawing any conclusions about the nature of the underlying process.

Description: Background Spatial genetic structure (SGS) analysis is a powerful approach to quantifying gene flow between trees, thus clarifying the functional connectivity of trees at population and landscape scales. The findings of SGS analysis may be useful for conservation and management of natural populations and plantations. Pinus cembroides is a widely distributed tree species, covering an area of about 2.5 million hectares in Mexico. The aim of this study was to examine five natural seed stands of P. cembroides in the Sierra Madre Occidental to determine the SGS at population (within the seed stand) and landscape (among seed stands) levels in order to establish guidelines for the conservation and management of the species. We hypothesized that P. cembroides, in which the seeds are dispersed by birds and mammals, creates weaker SGS than species with wind-dispersed seeds. Methods DNA fingerprinting was performed using the amplified fragment length polymorphism (AFLP) technique. In order to estimate the SGS at population and landscape levels, we measured the geographical (spatial) distance as the Euclidean distance. We also estimated the genetic distances between individuals using the pairwise kinship coefficient. Results The results showed non-significant autocorrelation in four out of five seed stands studied (i.e., a mainly random distribution in the space of the genetic variants of P. cembroides at population level). Discussion SGS was detected at the landscape scale, supporting the theory of isolation by distance as a consequence of restricted pollen and seed dispersal. However, the SGS may also have been generated by our sampling strategy. We recommended establishing a close network of seed stands of P. cembroides to prevent greater loss of local genetic variants and alteration of SGS. We recommend seed stands of P. cembroides of a minimum width of 225 m.

Description: Liver resection surgery is the most commonly used treatment strategy for patients diagnosed with hepatocellular carcinoma (HCC). However, there is still a chance for recurrence in these patients despite the survival benefits of this procedure. This study aimed to explore recurrence-related genes (RRGs) and establish a genomic-clinical nomogram for predicting postoperative recurrence in HCC patients. A total of 123 differently expressed genes and three RRGs (PZP, SPP2, and PRC1) were identified from online databases via Cox regression and LASSO logistic regression analyses and a gene-based risk model containing RRGs was then established. The Harrell’s concordance index (C-index), receiver operating characteristic (ROC) curves and calibration curves showed that the model performed well. Finally, a genomic-clinical nomogram incorporating the gene-based risk model, AJCC staging system, and Eastern Cooperative Oncology Group performance status was constructed to predict the 1-, 2-, and 3-year recurrence-free survival rates (RFS) for HCC patients. The C-index, ROC analysis, and decision curve analysis were good indicators of the nomogram’s performance. In conclusion, we identified three reliable RRGs associated with the recurrence of cancer and constructed a nomogram that performed well in predicting RFS for HCC patients. These findings could enrich our understanding of the mechanisms for HCC recurrence, help surgeons predict patients’ prognosis, and promote HCC treatment.

Description: The non-biomineralized artiopod Emeraldella brutoni Stein, Church & Robison, from the middle Cambrian (Drumian) Wheeler Formation in Utah represents the only confirmed occurrence of the genus Emeraldella outside of the stratigraphically older (Wuliuan) Burgess Shale Konservat-Lagerstätte in British Columbia. The hitherto known sole specimen of this species is preserved in dorsal view and lacks critical information on the ventral appendages. Here, we redescribe E. brutoni based on a new completely articulated specimen that illustrates the appendage organization in exceptional detail. The main body consists of a cephalic region covered by a semicircular head shield, a trunk including 10 tergites with expanded pleurae plus a cylindrical terminal segment, and a long articulated tailspine. The head carries a pair of elongate and flexible antennae, a pair of lateral eyes, and three pairs of post-antennal appendages. We report the presence of eyes in Emeraldella for the first time. The first post-antennal limb solely consists of an endopod with well-developed paired spiniform endites. The remaining cephalic appendages and those associated with all but the last trunk segments possess exopods terminating in paddle-shaped, distal lobes fringed with robust setae. The cylindrical terminal segment bears a pair of posteriorly oriented caudal flaps reminiscent of trunk exopods, and a styliform, possibly uniarticulate tailspine longer than the main body. The new data on E. brutoni suggests an exopodal origin for the paired caudal structures in Vicissicaudata, and improve our understanding of the fundamental organization of this major clade within Artiopoda.

Description: Background Heat shock protein 90 (HSP90) is a highly conserved chaperone with an approximate molecular weight of 90-kDa. It plays a critical role in maintaining stability and homeostasis of oncoproteins, helping cancer cells living in the unsuitable environmental conditions. The current study aims to inquire the difference of HSP90 expression in tumor tissues and normal tissues, analyze the correlation between HSP90 expression and the prognoses of patients with colorectal cancer (CRC), and investigate its role in CRC preliminarily. Methods Online analysis of HSP90 mRNA levels in different cancers was firstly done in Gene Expression Profiling Interactive Analysis. Then HSP90 expression was determined by immunohistochemistry between 99 CRC tissues and 81 normal tissues. Chi-square test or Fisher’s exact test was used to analyze the relationship between HSP90 and histopathologic characteristics. Kaplan–Meier analysis and Cox’s proportional hazards model were also done for further analysis of the prognostic values of HSP90. Pearson’s correlation coefficients between HSP90 expression values and other mRNA expression values were calculated based on The Cancer Genome Atlas dataset and bioinformatic analysis was done about these screened genes. Results Colorectal cancer tissues showed significantly higher expression of HSP90 than normal tissues (55.6% vs. 3.7%, P 〈 0.0001). Kaplan–Meier curves showed high HSP90 expression was associated with poor prognosis (P = 0.039) in CRC patients, and multivariate Cox proportional hazards regression model analysis also indicated that HSP90 expression (HR = 1.930, 95% CI [1.113–3.349], P = 0.019) linked to poor prognosis. Moreover, 85 genes were correlated with HSP90, which were involved in metabolic process and enriched in pathways of Proteasome and Base excision repair. Conclusions Our results suggested that HSP90 expression is inversely associated with survival outcomes and could be an independent prognostic factor for CRC patients. It mainly involved in metabolic process and exerted binding and catalytic activities.

Description: Background Styrax tonkinensis is a great potential biofuel as the species contains seeds with a particularly high oil content. Understanding the nutrient distribution in different parts of the fruit is imperative for the development and enhancement of S. tonkinensis as a biodiesel feedstock. Methods From 30 to 140 days after flowering (DAF), the development of S. tonkinensis fruit was tracked. The morphology change, nutrient content, and activity of associated enzymes in the continuum of the pericarp, seed coat, and kernel were analyzed. Results Between 30 and 70 DAF, the main locus of dry matter deposition shifted from the seed coat to the kernel. The water content within the pericarp remained high throughout development, but at the end (130 DAF later) decreased rapidly. The water content within both the seed coat and the kernel consistently declined over the course of the fruit development (30–110 DAF). Between 70 and 80 DAF, the deposition centers for sugar, starch, protein, potassium, and magnesium was transferred to the kernel from either the pericarp or the seed coat. The calcium deposition center was transferred first from pericarp to the seed coat and then to the kernel before it was returned to the pericarp. The sucrose to hexose ratio in the seed coat increased between 30 and 80 DAF, correlating with the accumulation of total soluble sugar, starch, and protein. In the pericarp, the sucrose to hexose ratio peaked at 40 and 100 DAF, correlating with the reserve deposition in the following 20–30 days. After 30 DAF, the chlorophyll concentration of both the pericarp and the seed coat dropped. The maternal unit (the pericarp and the seed coat) in fruit showed a significant positive linear relationship between chlorophyll b/a and the concentration of total soluble sugar. The potassium content had significant positive correlation with starch (ρ = 0.673, p = 0.0164), oil (ρ = 0.915, p = 0.000203), and protein content (ρ = 0.814, p = 0.00128), respectively. The concentration of magnesium had significant positive correlation with starch (ρ = 0.705, p = 0.0104), oil (ρ = 0.913, p = 0.000228), and protein content (ρ = 0.896, p = 0.0000786), respectively. Calcium content had a significant correlation with soluble sugar content (ρ = 0.585, p = 0.0457). Conclusions During the fruit development of S. tonkinensis, the maternal unit, that is, the pericarp and seed coat, may act a nutrient buffer storage area between the mother tree and the kernel. The stage of 70–80 DAF is an important time in the nutrient distribution in the continuum of the pericarp, seed coat, and kernel. Our results described the metabolic dynamics of the continuum of the pericarp, seed coat, and kernel and the contribution that a seed with high oil content offers to biofuel.

Description: The growth of Chlamydomonas reinhardtii microalgae cultures was successfully monitored, using classic off-line optical techniques (optical density and fluorescence) and on-line analysis of digital images. In this study, we found that the chlorophyll fluorescence ratio F685/F740 has a linear correlation with the logarithmic concentration of microalgae. By using digital images, the biomass concentration correlated with the luminosity of the images through an exponential equation and the length of penetration of a super luminescent blue beam (λ = 440 nm) through an inversely proportional function. The outcomes of this study are useful to monitor both research and industrial microalgae cultures.

Description: Objective To examine the long-term risk of stroke in women who have experienced symptomatic menopausal transition. Methods In this nationwide, population-based cohort study conducted from January 1, 2000 to December 31, 2013, we identified 22,058 women with no prior history of stroke, who experienced symptomatic menopausal transition at ≥45 years of age. Moreover, 22,058 women without symptomatic menopause were matched by propensity scores and enrolled as a comparison group. The propensity score was calculated by using all characteristic variables of each subject, including demographics (age and monthly income), comorbidities (hypertension, hyperlipidemia, diabetes mellitus, obesity, chronic kidney disease, coronary artery disease, congestive heart failure, chronic obstructive pulmonary disease, dysrhythmia, peripheral artery occlusive disease), Charlson’s comorbidity index score, clinic visit frequency, and long-term medications (antihypertensives, antidiabetic agents, statins, antiplatelets, aspirin, warfarin, and hormone replacement therapy). The primary endpoint was the development of stroke after the onset of symptomatic menopausal transition. The Fine and Gray’s proportional subhazards model was performed to assess the association between symptomatic menopausal transition and subsequent stroke. All subjects were followed up until December 31, 2013. Results During a mean follow-up of 8.5 years (standard deviation 4.7 years, maximum 14 years), 2,274 (10.31%) women with symptomatic menopausal transition, and 1,184 (5.37%) matched comparison participants developed stroke. The incidence rates were 11.17 per 1,000 person-years in the symptomatic menopausal transition group compared with 8.57 per 1,000 person-years in the comparison group. The risk of developing stroke was significantly higher in women with symptomatic menopausal transition (crude subhazard ratio, 1.31; 95% confidence interval (CI) [1.22–1.41]; P 〈 0.001). After adjusting for demographics, comorbidities, clinic visit frequency, and long-term medications, the risk of stroke remained statistically significant (adjusted subhazard ratio, 1.30; 95% CI [1.21–1.40]; P 〈 0.001). Moreover, subgroup analyses revealed no evidence for inconsistent effects for symptomatic menopausal transition on subsequent risk of stroke across all subgroups except age, comorbidities, hypertension, and use of antihypertensives. Women with early menopausal transition (before age 50), without comorbid condition, without hypertension, or without use of antihypertensives are at a higher risk of stroke. The longer duration of symptomatic menopausal transition was associated with higher risk of stroke (P for trend 〈 0.001). Conclusion In this large-scale retrospective cohort study, symptomatic menopausal transition was statistically significantly associated with a 30% increased risk of stroke. Further prospective studies are required to confirm our findings.

Description: Background Stand-up paddle boarding (SUP) is a rapidly growing global aquatic sport, with increasing popularity among participants within recreation, competition and rehabilitation. To date, few scientific studies have focused on SUP. Further, there is no research examining the biomechanics of the SUP paddle stroke. The purpose of this study was to investigate whether variations in kinematics existed among experienced and inexperienced SUP participants using three-dimensional motion analysis. This data could be of significance to participants, researchers, coaches and health practitioners to improve performance and inform injury minimization strategies. Methods A cross-sectional observational design study was performed with seven experienced and 19 inexperienced paddlers whereby whole-body kinematic data were acquired using a six-camera Vicon motion capture system. Participants paddled on a SUP ergometer while three-dimensional range of motion (ROM) and peak joint angles were calculated for the shoulders, elbows, hips and trunk. Mann–Whitney U tests were conducted on the non-normally distributed data to evaluate differences between level of expertise. Results Significant differences in joint kinematics were found between experienced and inexperienced participants, with inexperienced participants using greater overall shoulder ROM (78.9° ± 24.9° vs 56.6° ± 17.3°, p = 0.010) and less hip ROM than the experienced participants (50.0° ± 18.5° vs 66.4° ± 11.8°, p = 0.035). Experienced participants demonstrated increased shoulder motion at the end of the paddle stoke compared to the inexperienced participants (74.9° ± 16.3° vs 35.2° ± 28.5°, p = 0.001 minimum shoulder flexion) and more extension at the elbow (6.0° ± 9.2° minimum elbow flexion vs 24.8° ± 13.5°, p = 0.000) than the inexperienced participants. Discussion The results of this study indicate several significant kinematic differences between the experienced and inexperienced SUP participants. These variations in technique were noted in the shoulder, elbow and hip and are evident in other aquatic paddling sports where injury rates are higher in these joints. These finding may be valuable for coaches, therapists and participants needing to maximize performance and minimize injury risk during participation in SUP.

Description: The anthocyanin content in leaves can reveal valuable information about a plant’s physiological status and its responses to stress. Therefore, it is of great value to accurately and efficiently determine anthocyanin content in leaves. The selection of calibration method is a major factor which can influence the accuracy of measurement with visible and near infrared (NIR) spectroscopy. Three multivariate calibrations including principal component regression (PCR), partial least squares regression (PLSR), and back-propagation neural network (BPNN) were adopted for the development of determination models of leaf anthocyanin content using reflectance spectra data (450–600 nm) in Prunus cerasifera and then the performance of these models was compared for three multivariate calibrations. Certain principal components (PCs) and latent variables (LVs) were used as input for the back-propagation neural network (BPNN) model. The results showed that the best PCR and PLSR models were obtained by standard normal variate (SNV), and BPNN models outperformed both the PCR and PLSR models. The coefficient of determination (R2), the root mean square error of prediction (RMSEp), and the residual prediction deviation (RPD) values for the validation set were 0.920, 0.274, and 3.439, respectively, for the BPNN-PCs model, and 0.922, 0.270, and 3.489, respectively, for the BPNN-LVs model. Visible spectroscopy combined with BPNN was successfully applied to determine leaf anthocyanin content in P. cerasifera and the performance of the BPNN-LVs model was the best. The use of the BPNN-LVs model and visible spectroscopy showed significant potential for the nondestructive determination of leaf anthocyanin content in plants.

Description: Objective Ultrasound-guided lateral thoracolumbar interfascial plane block (US-TLIP block) is a novel regional technique for anesthesia or analgesia. However, there has been no prospective, randomized and controlled clinical trial investigating the perioperative analgesic effect of US-TLIP block on lumbar spinal fusion surgery. The aim of this study was to investigate the analgesic effect of bilateral single-shot US-TLIP in patients undergoing lumbar spinal fusion surgery. Methods A prospective and randomized comparative clinical study was conducted. A total of 60 patients (ASA classes: I–II), aged 21–74 years who were scheduled for lumbar spinal fusion surgery were randomized and divided into the TLIP group (Group T, n = 30) and control group (Group C, n = 30). The patients in Group T received preoperative bilateral single-shot US-TLIP with 30 ml of 0.375% ropivacaine at the third lumbar spine (L3) vertebral level, and the patients in Group C received an injection of 30 ml 0.9% saline through same technique. All patients received patient-controlled analgesia (PCA) after their operation. The frequency of PCA compressions and rescue analgesic administrations were recorded. Opioids (sufentanil and remifentanil), anesthetic consumption, the number of postoperative days spent in a hospital bed, overall hospital stay time and postoperative complications were recorded. The Visual Analogue Scale (VAS) and Bruggemann Comfort Scale (BCS) scores for pain and comfort assessment were recorded at 1, 12, 24, 36, and 48 hours postoperatively. Results Opioids and anesthetic consumption in the perioperative period decreased significantly in the TLIP group compared to the control group (P 

Description: It is assumed that the sequencing of ribosomes better reflects the active microbial community than the sequencing of the ribosomal RNA encoding genes. Yet, many studies exploring microbial communities in various environments, ranging from the human gut to deep oceans, questioned the validity of this paradigm due to the discrepancies between the DNA and RNA based communities. Here, we focus on an often neglected key step in the analysis, the reverse transcription (RT) reaction. Previous studies showed that RT may introduce biases when expressed genes and ribosmal rRNA are quantified, yet its effect on microbial diversity and community composition was never tested. High throughput sequencing of ribosomal RNA is a valuable tool to understand microbial communities as it better describes the active population than DNA analysis. However, the necessary step of RT may introduce biases that have so far been poorly described. In this manuscript, we compare three RT enzymes, commonly used in soil microbiology, in two temperature modes to determine a potential source of bias due to non-standardized RT conditions. In our comparisons, we have observed up to six fold differences in bacterial class abundance. A temperature induced bias can be partially explained by G-C content of the affected bacterial groups, thus pointing toward a need for higher reaction temperatures. However, another source of bias was due to enzyme processivity differences. This bias is potentially hard to overcome and thus mitigating it might require the use of one enzyme for the sake of cross-study comparison.

Description: The number of people suffering from eye fatigue induced by visual display terminal (VDT) viewing is expected to increase in the modern world. Eye dysfunction is suggested to induce a decrease in cognitive function, at least in the long term. Furthermore, considering other previous findings, it may be reasonable to think that acute or relatively short-term eye dysfunction attenuates cognitive function for not only older but also young individuals. Hence, clarification of the effect of eye fatigue induced by VDT viewing on cognitive performance is essential in order to maintain and/or improve our quality of life in the modern world regardless of age. The present study investigated the effect of eye fatigue induced by 1-h VDT viewing on cognitive performance, to test the hypothesis that such eye fatigue impairs cognitive performance in young individuals. A total of 19 healthy female university students voluntarily participated in this study. Before and after the 1-h VDT viewing or resting, the degree of eye fatigue and cognitive performance were evaluated. Refractive error measurement was performed to assess the degree of eye fatigue using a binocular auto refractometer, and a memory recognition task and Go/NoGo task were used to estimate cognitive performance. Response accuracy and reaction time were evaluated in the two tasks. Due to difficulty in interpreting the data of refractive error for one participant from the perspective of eye fatigue, the data for 18 participants were used for further analysis. The refractive error was significantly lower after than before the VDT viewing, but a corresponding change was not found before and after resting. Regarding cognitive performance, only the reaction time in the memory recognition task varied with the VDT viewing or resting. The reaction time was significantly longer after than before resting, without a corresponding difference before and after the VDT viewing. Thus, the 1-h VDT viewing induced eye fatigue, but relatively improved rather than attenuated reaction time in the memory recognition task. These results suggest that the effect of the increase in arousal level induced by the present VDT viewing on memory recognition compensated for the negative effect of 1-h resting of the eyes. We conclude that the acute eye fatigue induced by the 1-h VDT viewing does not have detrimental effects on cognition in young females at least under the present conditions.

Description: There is growing interest within regulatory agencies and toxicological research communities to develop, test, and apply new approaches, such as toxicogenomics, to more efficiently evaluate chemical hazards. Given the complexity of analyzing thousands of genes simultaneously, there is a need to identify reduced gene sets. Though several gene sets have been defined for toxicological applications, few of these were purposefully derived using toxicogenomics data. Here, we developed and applied a systematic approach to identify 1,000 genes (called Toxicogenomics-1000 or T1000) highly responsive to chemical exposures. First, a co-expression network of 11,210 genes was built by leveraging microarray data from the Open TG-GATEs program. This network was then re-weighted based on prior knowledge of their biological (KEGG, MSigDB) and toxicological (CTD) relevance. Finally, weighted correlation network analysis was applied to identify 258 gene clusters. T1000 was defined by selecting genes from each cluster that were most associated with outcome measures. For model evaluation, we compared the performance of T1000 to that of other gene sets (L1000, S1500, Genes selected by Limma, and random set) using two external datasets based on the rat model. Additionally, a smaller (T384) and a larger version (T1500) of T1000 were used for dose-response modeling to test the effect of gene set size. Our findings demonstrated that the T1000 gene set is predictive of apical outcomes across a range of conditions (e.g., in vitro and in vivo, dose-response, multiple species, tissues, and chemicals), and generally performs as well, or better than other gene sets available.

Description: The genus Cucurbita comprises many popular vegetable and ornamental plants, including pumpkins, squashes, and gourds, that are highly valued in China as well as in many other countries. During a survey conducted in Zhejiang province, Southeast China in 2016, severe symptoms of viral infection were observed on Cucurbita maxima Duch. ex Lam. Diseased plants showed symptoms such as stunting, mosaicking, Shoe string, blistering, yellowing, leaf deformation, and fruit distortion. Approximately, 50% of Cucurbita crops produced in Jinhua were diseased, causing an estimated yield loss of 35%. In this study, we developed a method using all known virus genomes from the NCBI database as a reference to map small RNAs to develop a diagnostic tool that could be used to diagnose virus diseases of C. maxima. 25 leaf samples from different symptomatic plants and 25 leaf samples from non-symptomatic plants were collected from the experimental field of Jihua National Agricultural Technology Garden for pathogen identification. Small RNAs from each set of three symptomatic and non-symptomatic samples were extracted and sequenced by Illumina sequencing. Twenty-four different viruses were detected in total. However, the majority of the small RNAs were from Zucchini yellow mosaic virus (ZYMV), Watermelon mosaic virus (WMV), and Cucumber mosaic virus (CMV). Mixed infections of these three viruses were diagnosed in leaf samples from diseased plants and confirmed by reverse transcription PCR (RT-PCR) using primers specific to these three viruses. Crude sap extract from symptomatic leaf samples was mechanically inoculated back into healthy C. maxima plants growing under greenhouse conditions. Inoculated plants developed the same disease symptoms as those observed in the diseased plants and a mixed infection of ZYMV, WMV, and CMV was detected again by RT-PCR, thus fulfilling Koch’s postulates. The diagnostic method developed in this study involves fewer bioinformatics processes than other diagnostic methods, does not require complex settings for bioinformatics parameters, provides a high level of sensitivity to rapidly diagnose plant samples with symptoms of virus diseases and can be performed cheaply. This method therefore has the potential to be widely applied as a diagnostic tool for viruses that have genome information in the NCBI database.

Description: The Asian clam, Corbicula fluminea, is a commonly consumed small freshwater bivalve in East Asia. However, available genetic information of this clam is still limited. In this study, the transcriptome of female C. fluminea was sequenced using the Illumina HiSeq 2500 platform. A total of 89,563 unigenes were assembled with an average length of 859 bp, and 36.7% of them were successfully annotated. Six members of Sox gene family namely SoxB1, SoxB2, SoxC, SoxD, SoxE and SoxF were identified. Based on these genes, the divergence time of C. fluminea was estimated to be around  476 million years ago. Furthermore, a total of 3,117 microsatellites were detected with a distribution density of 1:12,960 bp. Fifty of these microsatellites were randomly selected for validation, and 45 of them were successfully amplified with 31 polymorphic ones. The data obtained in this study will provide useful information for future genetic and genomic studies in C. fluminea.

Description: Intraspecific agonistic interactions are widespread across the animal kingdom, with many individual morphological and physiological characteristics playing important roles in the fate of disputes. Additionally, changes to environmental conditions can influence the outcomes of animal contests. The shore crab (Carcinus maenas) is a globally distributed species, present in numerous coastal and estuarine temperate systems around the world. Although shore crabs are highly tolerant to changes in temperature, this parameter has important physiological effects on the species’ ecology, while its effects on behavior are not fully understood. Our study aims to investigate how different individual characteristics (such as sex, color morphotype, carapace and chela morphology) and temperature conditions affect the dyadic interactions between shore crabs when disputing food resources. In general, the differences in carapace width between opponents, their sexes, color morphotypes and the temperature conditions interacted and were important predictors of the contest fate. We found that the body size and color morphotype of C. maenas determined the fate of dyadic disputes. However, the higher temperatures disrupted the well-established dominance of the larger red color morphotype individuals. Overall, the agonistic contest results suggest higher plasticity than previously acknowledged.

Description: Larvae, and especially fossil larvae, are challenging to deal with from a purely taxonomic view. Often one cannot determine which species the larvae belong to. Yet, larvae can still contribute to various scientific questions. Especially morphological traits of a fossil larva can be highly informative for reconstructing character evolution. Also the occurrence of specific larval types and larval characters in time and the disappearance of such forms can well be reconstructed also without being able to narrow down the phylogenetic relationship of a larva very far. Here, we report two new beetle larvae preserved in Baltic amber which are identified as representatives of Scraptiidae, based on an enlarged terminal end (‘9th abdomen segment’); this is only the third record of such larvae. In comparison to modern forms, the terminal ends of the two new fossil larvae is even larger in relation to the remaining body than in any known larva. Unfortunately, our knowledge of such larvae in the modern fauna is very limited. Still, one of the two already known fossil larvae of Scraptiidae also has a very long terminal end, but not as long as those of the two new fossils. These three fossil larvae therefore seem to possess a specific morphology not known from the modern fauna. This might either mean that they (1) represent a now extinct larval morphology, a phenomenon well known in other euarthropodan lineages, or that (2) these forms represent a part of the larval phase not known from modern day species as they have not been described yet; such cases occur in closely related lineages. In any case, the fossils expand the known diversity of larval morphologies.

Description: Genetic engineering has been used to decrease the lignin content and to change the lignin composition of switchgrass (Panicum virgatum L.) to decrease cell wall recalcitrance to enable more efficient cellulosic biofuel production. Previous greenhouse and field studies showed that downregulation of the gene encoding switchgrass caffeic acid O-methyltransferase (COMT) and overexpression of the switchgrass PvMYB4 (MYB4) gene effectively improved ethanol yield. To understand potential environmental impacts of cultivating these transgenic bioenergy crops in the field, we quantified the effects of field cultivation of transgenic switchgrass on soil organic carbon (SOC) dynamics. Total and active SOC as well as soil respiration were measured in soils grown with two COMT-downregulated transgenic lines (COMT2 and COMT3), three MYB4-overexpressed transgenic lines (L1, L6, and L8), and their corresponding non-transgenic controls. No differences in total SOC, dissolved organic carbon (DOC), and permanganate oxidizable carbon (POXC) were detected between transgenic and non-transgenic treatments for both COMT (10.4–11.1 g kg−1 for SOC, 60.0–64.8 mg kg−1 for DOC, and 299–384 mg kg−1 for POXC) and MYB4 lines (6.89–8.21 g kg−1 for SOC, 56.0–61.1 mg kg−1 for DOC, and 177–199 mg kg−1 for POXC). Soil CO2-carbon (CO2-C) production from the COMT2 transgenic line was not significantly different from its non-transgenic control. In contrast, the COMT3 transgenic line had greater soil CO2-C production than its non-transgenic control (210 vs. 165 µg g−1) after 72 days of laboratory incubation. Combining the improvement in ethanol yield and biomass production reported in previous studies with negligible change in SOC and soil respiration, COMT2 could be a better biofuel feedstock than COMT3 for environmental conservation and cost-effective biofuel production. On the other hand, MYB4 transgenic line L8 produced more biomass and total ethanol per hectare while it released more CO2-C than the control (253 vs. 207 µg g−1). Long-term in situ monitoring of transgenic switchgrass systems using a suite of soil and environmental variables is needed to determine the sustainability of growing genetically modified bioenergy crops.

Description: Model-based analyses of continuous trait evolution enable rich evolutionary insight. These analyses require a phylogenetic tree and a vector of trait values for the tree’s terminal taxa, but rarely do a tree and dataset include all taxa within a clade. Because the probability that a taxon is included in a dataset depends on ecological traits that have phylogenetic signal, missing taxa in real datasets should be expected to be phylogenetically clumped or correlated to the modelled trait. I examined whether those types of missing taxa represent a problem for model selection and parameter estimation. I simulated univariate traits under a suite of Brownian Motion and Ornstein-Uhlenbeck models, and assessed the performance of model selection and parameter estimation under absent, random, clumped or correlated missing taxa. I found that those analyses perform well under almost all scenarios, including situations with very sparsely sampled phylogenies. The only notable biases I detected were in parameter estimation under a very high percentage (90%) of correlated missing taxa. My results offer a degree of reassurance for studies of continuous trait evolution with missing taxa, but the problem of missing taxa in phylogenetic comparative methods still demands much further investigation. The framework I have described here might provide a starting point for future work.

Description: Objective To analyze the relationship between tumor size and metastatic site in stage IV NSCLC patients. Methods A total of 40,196 stage IV NSCLC patients from 2010 to 2015 were screened by SEER database. Chi-square test was used to compare the characteristics of clinical variables. At the same time, multivariate Logistic regression analysis was used to evaluate the relationship between tumor size and organ metastasis. Results Regardless of tumor size, the proportion of bone metastasis and lung metastasis was higher and similar in patients with squamous cell carcinoma, while in patients with adenocarcinoma, bone metastasis accounted for the highest proportion. We found that whether the metastatic site was bone, brain, liver or lung, the proportion of patients with a tumor size of 3–7 cm was the highest. Multivariate regression analysis demonstrated that patients with a tumor size of 3–7 cm and a tumor size ≥7 cm were more likely to develop brain metastasis and lung metastasis compared with patients with a tumor size ≤3 cm (all P 

Description: Peroxisome proliferator-activated receptor γ (PPARγ) is a ligand-activated transcription factor that regulates lipid/glucose homeostasis and adipocyte differentiation. While the role of PPARγ in adipogenesis and diabetes has been extensively studied, little is known about PPARγ function during early embryonic development. Within zebrafish, maternally-loaded pparγ transcripts are present within the first 6 h post-fertilization (hpf), and de novo transcription of zygotic pparγ commences at ~48 hpf. Since maternal pparγ transcripts are elevated during a critical window of cell fate specification, the objective of this study was to test the hypothesis that PPARγ regulates gastrulation and dorsoventral patterning during zebrafish embryogenesis. To accomplish this objective, we relied on (1) ciglitazone as a potent PPARγ agonist and (2) a splice-blocking, pparγ-specific morpholino to knockdown pparγ. We found that initiation of ciglitazone—a potent human PPARγ agonist—exposure by 4 hpf resulted in concentration-dependent effects on dorsoventral patterning in the absence of epiboly defects during gastrulation, leading to ventralized embryos by 24 hpf. Interestingly, ciglitazone-induced ventralization was reversed by co-exposure with dorsomorphin, a bone morphogenetic protein signaling inhibitor that induces strong dorsalization within zebrafish embryos. Moreover, mRNA-sequencing revealed that lipid- and cholesterol-related processes were affected by exposure to ciglitazone. However, pparγ knockdown did not block ciglitazone-induced ventralization, suggesting that PPARγ is not required for dorsoventral patterning nor involved in ciglitazone-induced toxicity within zebrafish embryos. Our findings point to a novel, PPARγ-independent mechanism of action and phenotype following ciglitazone exposure during early embryonic development.

Description: Background The mechanics and energetics of spider locomotion have not been deeply investigated, despite their importance in the life of a spider. For example, the reproductive success of males of several species is dependent upon their ability to move from one area to another. The aim of this work was to describe gait patterns and analyze the gait parameters of Eupalaestrus weijenberghi (Araneae, Theraphosidae) in order to investigate the mechanics of their locomotion and the mechanisms by which they conserve energy while traversing different inclinations and surfaces. Methods Tarantulas were collected and marked for kinematic analysis. Free displacements, both level and on an incline, were recorded using glass and Teflon as experimental surfaces. Body segments of the experimental animals were measured, weighed, and their center of mass was experimentally determined. Through reconstruction of the trajectories of the body segments, we were able to estimate their internal and external mechanical work and analyze their gait patterns. Results Spiders mainly employed a walk-trot gait. Significant differences between the first two pairs and the second two pairs were detected. No significant differences were detected regarding the different planes or surfaces with respect to duty factor, time lags, stride frequency, and stride length. However, postural changes were observed on slippery surfaces. The mechanical work required for traversing a level plane was lower than expected. In all conditions, the external work, and within it the vertical work, accounted for almost all of the total mechanical work. The internal work was extremely low and did not rise as the gradient increased. Discussion Our results support the idea of considering the eight limbs functionally divided into two quadrupeds in series. The anterior was composed of the first two pairs of limbs, which have an explorative and steering purpose and the posterior was more involved in supporting the weight of the body. The mechanical work to move one unit of mass a unit distance is almost constant among the different species tested. However, spiders showed lower values than expected. Minimizing the mechanical work could help to limit metabolic energy expenditure that, in small animals, is relatively very high. However, energy recovery due to inverted pendulum mechanics only accounts for only a small fraction of the energy saved. Adhesive setae present in the tarsal, scopulae, and claw tufts could contribute in different ways during different moments of the step cycle, compensating for part of the energetic cost on gradients which could also help to maintain constant gait parameters.

Description: The giant panda (Ailuropoda melanoleuca) is one of the most endangered mammals, and its conservation has significant ecosystem and cultural service value. Cytosine DNA methylation (5mC) is a stable epigenetic modification to the genome and has multiple functions such as gene regulation. However, DNA methylome of giant panda and its function have not been reported as of yet. Bisulfite sequencing was performed on a 4-day-old male giant panda’s brain, liver and pancreatic tissues. We found that the whole genome methylation level was about 0.05% based on reads normalization and mitochondrial DNA was not methylated. Three tissues showed similar methylation tendency in the protein-coding genes of their genomes, but the brain genome had a higher count of methylated genes. We obtained 467 and 1,013 different methylation regions (DMR) genes in brain vs. pancreas and liver, while only 260 DMR genes were obtained in liver vs pancreas. Some lncRNA were also DMR genes, indicating that methylation may affect biological processes by regulating other epigenetic factors. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that low methylated promoter, high methylated promoter and DMR genes were enriched at some important and tissue-specific items and pathways, like neurogenesis, metabolism and immunity. DNA methylation may drive or maintain tissue specificity and organic functions and it could be a crucial regulating factor for the development of newborn cubs. Our study offers the first insight into giant panda’s DNA methylome, laying a foundation for further exploration of the giant panda’s epigenetics.

Description: Information regarding the records of Brazilian marine gastrotrichs is presented. We systematized and organized the existing information associated with approximately 23 species (belonging to the genera Aspidiophorus, Chaetonotus, Crasiella, Dactylopodola, Dendrodasys, Draculiciteria, Halichaetonotus, Heteroxenotrichula, Kryptodasys, Macrodasys, Pseudostomella, Ptychostomella, Urodasys and Xenotrichula) from the Brazilian coast (eight endemic) and their 1,581 records from 36 marine ecoregions of the world. A link is provided to an on-line interactive map where all occurrences for each species are shown, accompanied by geographic coordinates, oceans, countries, cities, granulometric characteristics and ecoregions. Furthermore, a critical analysis of the geographical distribution of Brazilian marine gastrotrichs, an estimate of the number of undescribed species, a summary of the existence and status of taxonomical collections are also presented.

Description: Metabolic syndrome is a cluster of the most dangerous heart attack risk factors (diabetes and raised fasting plasma glucose, abdominal obesity, high cholesterol and high blood pressure), and has become a major global threat to human health. A number of studies have demonstrated that hundreds of non-coding RNAs, including miRNAs and lncRNAs, are involved in metabolic syndrome-related diseases such as obesity, type 2 diabetes mellitus, hypertension, etc. However, these research results are distributed in a large number of literature, which is not conducive to analysis and use. There is an urgent need to integrate these relationship data between metabolic syndrome and non-coding RNA into a specialized database. To address this need, we developed a metabolic syndrome-associated non-coding RNA database (ncRNA2MetS) to curate the associations between metabolic syndrome and non-coding RNA. Currently, ncRNA2MetS contains 1,068 associations between five metabolic syndrome traits and 627 non-coding RNAs (543 miRNAs and 84 lncRNAs) in four species. Each record in ncRNA2MetS database represents a pair of disease-miRNA (lncRNA) association consisting of non-coding RNA category, miRNA (lncRNA) name, name of metabolic syndrome trait, expressive patterns of non-coding RNA, method for validation, specie involved, a brief introduction to the association, the article referenced, etc. We also developed a user-friendly website so that users can easily access and download all data. In short, ncRNA2MetS is a complete and high-quality data resource for exploring the role of non-coding RNA in the pathogenesis of metabolic syndrome and seeking new treatment options. The website is freely available at http://www.biomed-bigdata.com:50020/index.html

Description: Growing nectar- and pollen-rich flowering plant varieties in domestic gardens and other greenspace is an important pro-environmental behaviour that supports pollinating insects. Wildlife gardening is popular in the UK; however, public attitudes and behaviour relating to planting for pollinators are currently not well understood. We investigated these through questionnaires and interviews with customers in five garden centres in Sussex, southeast England, a relevant and useful consumer group representing horticulturally-engaged members of the public. Garden centre customers had strongly positive attitudes and were motivated to plant for bees and other pollinators: most (77%) grew pollinator-friendly varieties, while 64% would be more likely to buy a plant with a pollinator-friendly logo. Personal motivation to support pollinators was linked to a recent increase in personal and public awareness of their declines through (often negativistic) information from mass media sources. Practical implications of these findings in relation to the horticultural retail industry are discussed.

Description: Foxtail millet (Setaria italic L.) is an important food and fodder crop that is cultivated worldwide. Quantifying the effects of herbicides on foxtail millet is critical for safe herbicide application. In this study, we analyzed the effects of different fluroxypyr dosages on the growth parameters and physiological parametric of foxtail millet, that is, peroxidation characteristics, photosynthetic characteristics, and endogenous hormone production, by using multivariate statistical analysis. Indicators were screened via Fisher discriminant analysis, and the growth parameters, peroxidation characteristics, photosynthesis characteristics and endogenous hormones of foxtail millet at different fluroxypyr dosages were comprehensively evaluated by principal component analysis. On the basis of the results of principal component analysis, the cumulative contribution rate of the first two principal component factors was 93.72%. The first principal component, which explained 59.23% of total variance, was selected to represent the photosynthetic characteristics and endogenous hormones of foxtail millet. The second principal component, which explained 34.49% of total variance, represented the growth parameters of foxtail millet. According to the principal component analysis, the indexes were simplified into comprehensive index Z, and the mathematical model of comprehensive index Z was set as F = 0.592Z1 + 0.345Z2. The results showed that the comprehensive evaluation score of fluroxypyr at moderate concentrations was higher than at high concentrations. Consequently, one L (active ingredient, ai) ha−1 fluroxypyr exerted minimal effects on growth parameters, oxidase activity, photosynthetic activity, and endogenous hormones, and had highest value of comprehensive evaluation, which had efficient and safe benefits in foxtail millet field.

Description: Endometriosis is a chronic disease occurring during the reproductive stage of women. Although there is only limited association between endometriosis and gynecological cancers with regard to clinical features, the molecular basis of the relationship between these diseases is unexplored. We conducted a systematic study by integrating literature-based evidence, gene expression and large-scale cancer genomics data in order to reveal any genetic relationships between endometriosis and cancers in women. We curated 984 endometriosis-related genes from 3270 PubMed articles and then conducted a meta-analysis of the two public gene expression profiles related to endometriosis which identified Differential Expression of Genes (DEGs). Following an overlapping analysis, we identified 39 key endometriosis-related genes common in both literature and DEG analysis. Finally, the functional analysis confirmed that all the 39 genes were associated with the vital processes of tumour formation and cancer progression and that two genes (PGR and ESR1) were common to four cancers of women. From network analysis, we identified a novel linker gene, C3AR1, which had not been implicated previously in endometriosis. The shared genetic mechanisms of endometriosis and cancers in women identified in this study provided possible new avenues of multiple disease management and treatments through early diagnosis.

Description: Titanosauriform sauropod dinosaurs were once considered rare in the Upper Cretaceous of Asia, but a number of titanosauriforms from this stratigraphic interval have been discovered in China in recent years. In fact, all adequately known Cretaceous Asian sauropods are titanosauriforms, but only a few have been well studied, lending significance to any new anatomical information that can be extracted from Asia’s Cretaceous sauropod record. Here we give a detailed description of some titanosauriform bones recovered recently from the Upper Cretaceous Daijiaping Formation of Tianyuan County, Zhuzhou City, Hunan Province, southern China. The occurrence of this material in Hunan increases the known geographic range of titanosauriforms in eastern Asia. Although all of the specimens discussed in this paper can be assigned to Titanosauriformes at least tentatively, some bones display a limited number of features that are more typical of basal sauropods and/or derived diplodocoids, suggesting complex patterns of character evolution within Neosauropoda.

Description: The continued and general rise of antibiotic resistance in pathogenic microbes is a well-recognized global threat. Host defense peptides (HDPs), a component of the innate immune system have demonstrated promising potential to become a next generation antibiotic effective against a plethora of pathogens. While the effectiveness of antimicrobial HDPs has been extensively demonstrated in experimental studies, theoretical insights on the mechanism by which these peptides function is comparably limited. In particular, experimental studies of AMP mechanisms are limited in the number of different peptides investigated and the type of peptide parameters considered. This study makes use of the random forest algorithm for classifying the antimicrobial activity as well for identifying molecular descriptors underpinning the antimicrobial activity of investigated peptides. Subsequent manual interpretation of the identified important descriptors revealed that polarity-solubility are necessary for the membrane lytic antimicrobial activity of HDPs.

Description: Improved understanding of properties that mediate protein solubility and resistance to aggregation are important for developing biopharmaceuticals, and more generally in biotechnology and synthetic biology. Recent acquisition of large datasets for antibody biophysical properties enables the search for predictive models. In this report, machine learning methods are used to derive models for 12 biophysical properties. A physicochemical perspective is maintained in analysing the models, leading to the observation that models cluster largely according to charge (cross-interaction measurements) and hydrophobicity (self-interaction methods). These two properties also overlap in some cases, for example in a new interpretation of variation in hydrophobic interaction chromatography. Since the models are developed from differences of antibody variable loops, the next stage is to extend models to more diverse protein sets. Availability The web application for the sequence-based algorithms are available on the protein-sol webserver, at https://protein-sol.manchester.ac.uk/abpred, with models and virtualisation software available at https://protein-sol.manchester.ac.uk/software.

Description: Finite element analysis has been an increasingly widely applied biomechanical modeling method in many different science and engineering fields over the last decade. In the biological sciences, there are many examples of FEA in areas such as paleontology and functional morphology. Despite this common use, the modeling of trabecular bone remains a key issue because their highly complex and porous geometries are difficult to replicate in the solid mesh format required for many simulations. A common practice is to assign uniform model material properties to whole or portions of models that represent trabecular bone. In this study we aimed to demonstrate that a physical, element reduction approach constitutes a valid protocol for addressing this problem in addition to the wholesale mathematical approach. We tested a customized script for element reduction modeling on five exemplar trabecular geometry models of carnivoran temporomandibular joints, and compared stress and strain energy results of both physical and mathematical trabecular modeling to models incorporating actual trabecular geometry. Simulation results indicate that that the physical, element reduction approach generally outperformed the mathematical approach: physical changes in the internal structure of experimental cylindrical models had a major influence on the recorded stress values throughout the model, and more closely approximates values obtained in models containing actual trabecular geometry than solid models with modified trabecular material properties. In models with both physical and mathematical adjustments for bone porosity, the physical changes exhibit more weight than material properties changes in approximating values of control models. Therefore, we conclude that maintaining or mimicking the internal porosity of a trabecular structure is a more effective method of approximating trabecular bone behavior in finite element models than modifying material properties.

Description: Background Although the postural instability accompanying bilateral vestibular loss in human and quadrupeds during lateral head movements are well-known, it is still unclear whether or not lateral head turns would indeed activate the postural control system to maintain balance. This study aimed to examine the kinetic parameters in freely standing intact cats during head movements in order to further answer the above question. Methods Six intact cats were trained to stand, unrestrained on a force plate and perform voluntary head movements to the left and right positions in response to visual cues. Each trial was divided into two phases, quiet standing with the cat’s head maintaining a straight forward and lateral head position after voluntary head movements. Kinetic parameters including peak pressure and contact area under each limb as well as center of pressure (COP) displacements of the whole body were measured. Results Compared to the neutral head position, peak pressure and contact area of the left head position were significantly smaller for the left forelimb while greatly larger for the right forelimb. An exact opposite case of peak pressure and contact area in the forelimbs was found between the right and neutral head positions. In addition, the COP displacements altered oppositely to the head movements, and presented a significantly right shift in the left position and a significantly left shift in the right position. Conclusion These results demonstrate that the lateral displacement of the head in standing intact cats does activate the postural adjustment to maintain balance, which is consistent with the concept that vestibular input can contribute to postural balance during voluntary head turns.

Description: Environmental DNA (eDNA) is a powerful tool for monitoring the distribution of aquatic macro-organisms. However, environmental factors, including the water temperature and water quality, can affect the inhibition and/or degradation of eDNA, which complicates accurate estimations of eDNA concentrations and the detection of the presence/absence of species in natural habitats. Further very few eDNA studies have been conducted for reptiles, especially with respect to estimating their biomass and/or abundances. Here we examined the relationship between the visually-observed number of red-eared sliders (Trachemys scripta elegans) and eDNA concentrations across 100 ponds. Additionally, we evaluated the effect of water quality on red-eared slider eDNA concentration in these ponds. We found that there was a significant positive correlation between the observed number of red-eared sliders and the eDNA concentration in the ponds. On comparing various water quality indicators, including dissolved nitrogen, dissolved phosphorous, organic matter, and chlorophyll a (Chl. a), we found that only Chl. a had a negative correlation with the red-eared slider eDNA concentration, while we did not find any inhibition in the quantitative PCR. We conclude that concentrations of eDNA can potentially be used for estimating the abundance of the red-eared slider. Additionally, Chl. a might indirectly influence the degradation of eDNA through the microorganisms bonded to the phytoplankton in the ponds, as microbial activity is thought to decrease eDNA persistence.

Description: Background Understanding individual food preferences is critical for creating tailored strategies that promote healthy individual eating behaviors. Individual sensory liking appears to be an essential determinant of dietary intake. Taste preferences influence satisfaction and satiety, and may consequently influence weight status and psychological adjustment. The purpose of this study was to identify the association between taste preferences (sweet, salty, sweet & fatty, salty & fatty) and personality features. Methods The Millon Clinical Multiaxial Inventory-III (MCMI-III) was used for the assessment of personality traits and PrefQuest (PQ) was used for measuring recalled food preferences. A total of 137 participants were included in the study. The relationship between compulsive and antisocial features and taste preferences was assessed by hierarchical multiple linear regression, while controlling for age, gender, BMI, marital status, and educational level. Results The antisocial personality traits were a negative explanatory variable for sweet & fatty taste preference, R2 = .15, t(132) =  − 2.40, p = .018, 95% [−.57, −.06] and salty & fatty taste preference, R2 = .16, t(133) =  − 2.38, p = .019, 95% [−.07, −.01], while controlling for anthropological factors. In addition, men showed a higher preference than women for sweet & fatty food, such as chocolate or desserts, rsp = .19, p = .021, and for the salty & fatty food, rsp = .30, p 

Description: In this study, silver nanoparticles (NP) were synthesized by two methods: using an aqueous extract of Mentha spicata leaves and using citrate ions as stabilizing agent, and the cytotoxicity and anticancer activity of both NP were evaluated in vitro. The particles synthesized with the aqueous extract were spherical with a size ranging from 15 to 45 nm. These NP decreased cell viability in all of the cells studied; however, the IC50 could only be estimated in the Chang liver cells (IC50 = 21.37 µg/mL). These particles also decreased the generation of reactive oxygen species in Chang and SiHa cells. Additionally, the dispersions decreased the activity of caspase-3. There was no significant difference between the biological activities of the NP obtained with the aqueous extract and the NP synthesized using citrate ions. This study showed that an aqueous extract of M. spicata is an excellent alternative for the synthesis of silver NP. These NP showed cytotoxicity and anticancer activity in vitro. Although more experiments are required, the cell death occurs probably through a mechanism different from apoptosis.

Description: Solidago canadensis L. is a drought-tolerant, invasive plant, characterized by a large biomass of underground and aboveground parts. The aim of this study was to assess the accumulation of manganese (Mn) and copper (Cu) in the roots and rhizomes and the stems, leaves, and inflorescence parts in S. canadensis from two locations that differed in soil pH, organic carbon, and Mn and Cu concentrations. The concentration of the metals in the samples was determined by the AAS method; the pH was determined by the potentiometric method; and the content of organic carbon was determined using Tiurin’s method. The concentration of Mn and Cu in the roots of S. candensis correlated with the concentrations of the metals in the soil without regard to the soil condition or its organic carbon content. With a low soil pH and organic carbon content, Mn accumulation per 1 ramet in the aboveground parts of S. canadensis consisted over 50% of the total Mn content in the plant. In neutral or alkaline soils, the amount of Mn per 1 ramet accumulated in underground parts was over 60%. Regardless of the soil conditions, about 35% of Mn accumulated in rhizomes. Approximately 60% of copper accumulated in the underground parts of S. candensis (45% in rhizomes) without regard to the soil reaction or organic carbon content. The ability of the plant to accumulate large amounts of metals disposes Solidago canadensis as a candidate for the phytoremediation of soils contaminated with heavy metals.

Description: Background Proper glycemic control is an important goal of critical care medicine, including perioperative patient care that can influence patients’ prognosis. Insulin secretion from pancreatic β-cells is generally assumed to play a critical role in glycemic control in response to an elevated blood glucose concentration. Many animal and human studies have demonstrated that perioperative drugs, including volatile anesthetics, have an impact on glucose-stimulated insulin secretion (GSIS). However, the effects of the intravenous anesthetic propofol on glucose metabolism and insulin sensitivity are largely unknown at present. Methods The effect of propofol on insulin secretion under low glucose or high glucose was examined in mouse MIN6 cells, rat INS-1 cells, and mouse pancreatic β-cells/islets. Cellular oxygen or energy metabolism was measured by Extracellular Flux Analyzer. Expression of glucose transporter 2 (GLUT2), potassium channels, and insulin mRNA was assessed by qRT-PCR. Protein expression of voltage-dependent potassium channels (Kv2) was also assessed by immunoblot. Propofol’s effects on potassium channels including stromatoxin-1-sensitive Kv channels and cellular oxygen and energy metabolisms were also examined. Results We showed that propofol, at clinically relevant doses, facilitates insulin secretion under low glucose conditions and GSIS in MIN6, INS-1 cells, and pancreatic β-cells/islets. Propofol did not affect intracellular ATP or ADP concentrations and cellular oxygen or energy metabolism. The mRNA expression of GLUT2 and channels including the voltage-dependent calcium channels Cav1.2, Kir6.2, and SUR1 subunit of KATP, and Kv2 were not affected by glucose or propofol. Finally, we demonstrated that propofol specifically blocks Kv currents in β-cells, resulting in insulin secretion in the presence of glucose. Conclusions Our data support the hypothesis that glucose induces membrane depolarization at the distal site, leading to KATP channel closure, and that the closure of Kv channels by propofol depolarization in β-cells enhances Ca2+ entry, leading to insulin secretion. Because its activity is dependent on GSIS, propofol and its derivatives are potential compounds that enhance and initiate β-cell electrical activity.

Description: Vertebrate osteological collections provide comparative material for morphological analysis. Before being stored in the collection and studied by researchers, specimens are treated by preparators or curators and are cleaned. The preparation protocol employed ideally should not damage the material. Here, we explore the potential deformation of bones due to preparation using geometric morphometric methods. We focus both on intraspecific and interspecific variability. Our data on the scapular girdle of birds show that, at an intraspecific level, the effect of preparation on bone shape cannot be neglected. Paired and unpaired bones did not respond to the preparation process in the same way, possibly due to differences in function and their anatomical characteristics. Moreover, deformations due to preparation can be estimated by looking at the texture of the bone. At the interspecific level, we found no significant differences as the deformations induced by preparation are relatively small compared to differences among species. This study highlights the importance of carefully selecting preparation methods in order to avoid physical damage that could impact the shape of bones, especially for studies at the intraspecific level.

Description: Phenylalanine ammonia lyase (PAL) plays an important role in the biosynthesis of secondary metabolites regulating plant growth response. To date, the evolutionary history of the PAL family in Rosaceae plants remains unclear. In this study, we identified 16 PAL homologous genes in five Rosaceae plants (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Prunus persica, and Malus × domestica). We classified these PALs into three categories based on phylogenetic analysis, and all PALs were distributed on 13 chromosomes. We tracked gene duplication events and performed sliding window analysis. These results revealed the evolution of PALs in five Rosaceae plants. We predicted the promoter of the PbPALs by PLANT CARE online software, and found that the promoter region of both PbPAL1 and PbPAL3 have at least one AC element. The results of qRT-PCR analysis found that PbPAL1 and PbPAL2 were highly expressed in the stems and roots, while expression level of PbPAL3 was relatively low in different tissues. The expression of PbPAL1 and PbPAL2 increased firstly and then decreased at different developmental periods of pear fruit. Among them, the expression of PbPAL1 reached the highest level 55 days after flowering. Three PbPALs were induced by abiotic stress to varying degrees. We transfected PbPAL1 and PbPAL2 into Arabidopsis thaliana, which resulted in an increase in lignin content and thickening of the cell walls of intervascular fibres and xylem cells. In summary, this research laid a foundation for better understanding the molecular evolution of PALs in five Rosaceae plants. Furthermore, the present study revealed the role of PbPALs in lignin synthesis, and provided basic data for regulating lignin synthesis and stone cells development in pear plants.

Description: Background The aim of the ReproQuestionnaire (ReproQ) is to measure the client’s experience with maternity care, following WHO’s responsiveness model. To support quality improvement, ReproQ should be able to discriminate best from worst organisational units. Methods We sent questionnaires to 27,487 third-trimester pregnant women (response 31%) and to 37,230 women 6 weeks after childbirth (response 39%). For analysis we first summarized the ReproQ domain scores into three summary scores: total score (all eight domains), personal score (four personal domains), and setting score (four setting domains). Second, we estimated the proportion of variance across perinatal units attributable to the ‘actual’ difference across perinatal units using intraclass correlation coefficients (ICCs). Third, we assessed the ability of ReproQ to discriminate between perinatal units based on both a statistical approach using multilevel regression analyses, and a relevance approach based on the minimally important difference (MID). Finally, we compared the domain scores of the best and underperforming units. Results ICCs ranged between 0.004 and 0.025 for the summary scores, and between 0.002 and 0.125 for the individual domains. ReproQ was able to identify the best and worst performing units with both the statistical and relevance approach. The statistical approach was able to identify four underperforming units during childbirth (total score), while the relevance approach identified 10 underperforming units. Conclusions ReproQ, a valid and efficient measure of client experiences in maternity care, has the ability to discriminate well across perinatal units, and is suitable for benchmarking under routine conditions.

Description: Polymorphism among individuals of the same population has generally been linked to alternative reproductive tactics, where different morphs can exhibit differences in their morphological, ecological, and behavioral attributes. These differences may result in a divergence in diet between morphs due to differential exploitation of habitat, morphological differences that influence prey selection, or differential energy expenditure that results in different nutritional needs. The present study analyzes the morphology (morphometry and body mass) and diet of red and yellow male morphs in a population (El Enzuelado) of the lizard Sceloporus minor from central Mexico. No differences between morphs were found for any of the morphometric variables analyzed (snout-vent length, tail length, jaw length, jaw width, head length, head width, head height, tibia length, femur length, forearm length and ventral patch length). In both morphs, allometric growth was observed in all body features analyzed, as well as in morphometric features of the head across seasons. Analysis of stomach contents showed that the diet of red males was composed of 12 categories of prey, while that of yellow males was composed of 10 categories; those categories of diet not shared between morphs (e.g., Isoptera, Psocoptera) were consumed by their respective morph in very low proportions. Categories of diet with the highest values of food importance for both groups were Coleoptera, Orthoptera, and leaves; a similar pattern was seen across seasons. This, in turn, is reflected in low niche breadth values for each morph and a very high niche overlap. There were no significant differences between morphs overall, or between morphs per season, in the weight and volume of stomach contents or in the number of prey items found in stomachs; however, differences in these variables across all males (independent of morph) were recorded between seasons. Likewise, no significant correlations were found between body size (snout-vent length) and the volume of stomach contents for either morph or between lizard mandibular dimensions and the volume of stomach contents for red morph males. For the yellow morph, prey volume unexpectedly decreased significantly with jaw size rather than increasing as expected. Overall, this study adds new information about the morphology and feeding of males in this species, and suggests that in this population, color morphs lack the morphological and ecological differences found in some other species of polymorphic lizard.

Description: Objective To investigate the correlation between the single nucleotide polymorphisms (SNPs) in the toll-like receptor 4 (TLR4) gene and the susceptibility to chronic periodontitis. Design 241 Chinese subjects from the cohort of Beijing Shijingshan Community were recruited. Buccal swab samples, the whole unstimulated saliva and periodontal clinical parameters were collected. Human DNA extracted from buccal swab samples were used for genotyping eight SNPs of the TLR4 gene (rs11536889, rs1927906, rs1927911, rs2149356, rs4986790, rs4986791, rs2737190, rs787384) by the Sequenom MassARRAY system. Porphyromonas gingivalis (P. gingivalis) was detected from the deposition of the whole unstimulated saliva through polymerase chain reaction (PCR) method based on 16S rRNA. The correlation between SNPs of TLR4 and chronic periodontitis susceptibility in the whole subjects and the patients detected with P. gingivalis was investigated. Results The variants of rs4986790 and rs4986791 were not found in 241 Chinese subjects. Moreover, there was no significant difference in the distribution of theother6 SNPs of TLR4 between groups of none/mild -periodontitis and moderate/severe-periodontitis subjects. When combined with P. gingivalis infection, rs1927911 (TT/CC+CT), rs2149356 (TT/GG+GT) and rs2737190 (GG/AA+AG) were independent risk factors of chronic periodontitis. Conclusion Three SNPs of TLR4, i.e., rs1927911 (TT/CC+CT), rs2149356 (TT/GG+GT) and rs2737190 (GG/AA+AG), were associated with moderate/severe chronic periodontitis in Chinese population infected with P. gingivalis. P. gingivalis, which interacted with TLR4 gene plays an important role in the pathogenesis of periodontitis.

Description: Background Intragenomic variability in 16S rDNA is a limiting factor for taxonomic and diversity characterization of Bacteria, and studies on its occurrence in natural/environmental populations are scarce. In this work, direct DNA amplicon sequencing coupled with frequent-cutter restriction analysis allowed detection of intragenomic 16S rDNA variation in culturable endophytic bacteria from cacao seeds in a fast and attractive manner. Methods Total genomic DNA from 65 bacterial strains was extracted and the 16S rDNA hyper variable V5–V9 regions were amplified for enzyme digestion and direct Sanger-type sequencing. The resulting electropherograms were visually inspected and compared to the corresponding AluI-restriction profiles, as well as to complete genome sequences in databases. Restriction analysis were employed to substitute the need of amplicon cloning and re-sequencing. A specifically improved polyacrylamide-gradient electrophoresis allowed to resolve 5-bp differences in restriction fragment sizes. Chi-square analysis on 2 × 2 contingency table tested for the independence between the ‘number of AluI bands’ and ‘type of eletropherogram’. Results Two types of electropherograms were obtained: unique template, with single peaks per base (clean chromatograms), and heterogeneous template, with various levels of multiple peaks per base (mixed chromatograms). Statistics revealed significant interaction between number of restriction fragments and type of electropherogram for the same amplicons: clean or mixed ones associated to ≤5 or ≥6 bands, respectively. The mixed-template pattern combined with the AluI-restriction profiles indicated a high proportion of 49% of the culturable endophytes from a tropical environment showing evidence of intragenomic 16S rDNA heterogeneity. Conclusion The approach presented here was useful for a rapid, first-tier detection of intragenomic variation in culturable isolates, which can be applied in studies of other natural populations; a preliminary view of intragenomic heterogeneity levels can complement culture-dependent and -independent methods. Consequences of these findings in taxonomic and diversity studies in complex bacterial communities are discussed.

Description: Anthropogenic threat maps are commonly used as a surrogate for the ecological integrity of rivers in freshwater conservation, but a clearer understanding of their relationships is required to develop proper management plans at large scales. Here, we developed and validated empirical models that link the ecological integrity of rivers to threat maps in a large, heterogeneous and biodiverse Andean–Amazon watershed. Through fieldwork, we recorded data on aquatic invertebrate community composition, habitat quality, and physical-chemical parameters to calculate the ecological integrity of 140 streams/rivers across the basin. Simultaneously, we generated maps that describe the location, extent, and magnitude of impact of nine anthropogenic threats to freshwater systems in the basin. Through seven-fold cross-validation procedure, we found that regression models based on anthropogenic threats alone have limited power for predicting the ecological integrity of rivers. However, the prediction accuracy improved when environmental predictors (slope and elevation) were included, and more so when the predictions were carried out at a coarser scale, such as microbasins. Moreover, anthropogenic threats that amplify the incidence of other pressures (roads, human settlements and oil activities) are the most relevant predictors of ecological integrity. We concluded that threat maps can offer an overall picture of the ecological integrity pattern of the basin, becoming a useful tool for broad-scale conservation planning for freshwater ecosystems. While it is always advisable to have finer scale in situ measurements of ecological integrity, our study shows that threat maps provide fast and cost-effective results, which so often are needed for pressing management and conservation actions.

Description: Background Genetic testing for BRCA1/2 germline mutations in hereditary breast/ovarian cancer patients requires screening for single nucleotide variants, small insertions/deletions and large genomic rearrangements (LGRs). These studies have long been run by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). The recent introduction of next-generation sequencing (NGS) platforms dramatically improved the speed and the efficiency of DNA testing for nucleotide variants, while the possibility to correctly detect LGRs by this mean is still debated. The purpose of this study was to establish whether and to which extent the development of an analytical algorithm could help us translating NGS sequencing via an Ion Torrent PGM platform into a tool suitable to identify LGRs in hereditary breast-ovarian cancer patients. Methods We first used NGS data of a group of three patients (training set), previously screened in our laboratory by conventional methods, to develop an algorithm for the calculation of the dosage quotient (DQ) to be compared with the Ion Reporter (IR) analysis. Then, we tested the optimized pipeline with a consecutive cohort of 85 uncharacterized probands (validation set) also subjected to MLPA analysis. Characterization of the breakpoints of three novel BRCA1 LGRs was obtained via long-range PCR and direct sequencing of the DNA products. Results In our cohort, the newly defined DQ-based algorithm detected 3/3 BRCA1 LGRs, demonstrating 100% sensitivity and 100% negative predictive value (NPV) (95% CI [87.6–99.9]) compared to 2/3 cases detected by IR (66.7% sensitivity and 98.2% NPV (95% CI [85.6–99.9])). Interestingly, DQ and IR shared 12 positive results, but exons deletion calls matched only in five cases, two of which confirmed by MLPA. The breakpoints of the 3 novel BRCA1 deletions, involving exons 16–17, 21–22 and 20, have been characterized. Conclusions Our study defined a DQ-based algorithm to identify BRCA1 LGRs using NGS data. Whether confirmed on larger data sets, this tool could guide the selection of samples to be subjected to MLPA analysis, leading to significant savings in time and money.

Description: Background Sacbrood virus (SBV) is one of the most pathogenic honeybee viruses that exhibits host specificity and regional variations. The SBV strains that infect the Chinese honeybee Apis cerana are called Chinese SBVs (CSBVs). Methods In this study, a CSBV strain named AmCSBV-SDLY-2016 (GenBank accession No. MG733283) infecting A. mellifera was identified by electron microscopy, its protein composition was analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis and agar gel immunodiffusion assay, and its nucleotide sequence was identified using a series of reverse-transcription polymerase chain reaction fragments of AmCSBV-SDLY-2016 generated using SBV/CSBV-specific primers. To investigate phylogenetic relationships of the CSBV isolates, a phylogenetic tree of the complete open reading frames (ORF) of the CSBV sequences was constructed using MEGA 6.0; then, the similarity and recombination events among the isolated CSBV strains were analyzed using SimPlot and RDP4 software, respectively. Results Sequencing results revealed the complete 8,794-nucleotide long complete genomic RNA of the strain, with a single large ORF (189–8,717) encoding 2,843 amino acids. Comparison of the deduced amino acid sequence with the SBV/CSBV reference sequences deposited in the GenBank database identified helicase, protease, and RNA-dependent RNA polymerase domains; the structural genes were located at the 5′ end, whereas the non-structural genes were found at the 3′ end. Multiple sequence alignment showed that AmCSBV-SDLY-2016 had a 17-amino acid (aa) and a single aa deletion at positions 711–729 and 2,128, respectively, as compared with CSBV-GD-2002, and a 16-aa deletion (positions 711–713 and 715–728) as compared with AmSBV-UK-2000. However, AmCSBV-SDLY-2016 was similar to the CSBV-JLCBS-2014 strain, which infects A. cerana. AmCSBV-SDLY-2016 ORF shared 92.4–97.1% identity with the genomes of other CSBV strains (94.5–97.7% identity for deduced amino acids). AmCSBV-SDLY-2016 was least similar (89.5–90.4% identity) to other SBVs but showed maximum similarity with the previously reported CSBV-FZ-2014 strain. The phylogenetic tree constructed from AmCSBV-SDLY-2016 and 43 previously reported SBV/CSBV sequences indicated that SBV/CSBV strains clustered according to the host species and country of origin; AmCSBV-SDLY-2016 clustered with other previously reported Chinese and Asian strains (AC genotype SBV, as these strains originated from A. cerana) but was separate from the SBV genomes originating from Europe (AM genotype SBV, originating from A. mellifera). A SimPlot graph of SBV genomes confirmed the high variability, especially between the AC genotype SBV and AM genotype SBV. This genomic diversity may reflect the adaptation of SBV to specific hosts, ability of CSBV to cross the species barrier, and the spatial distances that separate CSBVs from other SBVs.

Description: Background Dysregulated long non-coding RNAs (lncRNAs) may serve as potential biomarkers of cancers including breast cancer (BRCA). This study aimed to identify lncRNAs with strong prognostic value for BRCA. Methods LncRNA expression profiles of 929 tissue samples were downloaded from TANRIC database. We performed differential expression analysis between paired BRCA and adjacent normal tissues. Survival analysis was used to identify lncRNAs with prognostic value. Univariate and multivariate Cox regression analyses were performed to confirm the independent prognostic value of potential lncRNAs. Dysregulated signaling pathways associated with lncRNA expression were evaluated using gene set enrichment analysis. Results We found that a total of 398 lncRNAs were significantly differentially expressed between BRCA and adjacent normal tissues (adjusted P value = 1). Additionally, 381 potential lncRNAs were correlated Overall Survival (OS) (P value 〈 0.05). A total of 48 lncRNAs remained when differentially expressed lncRNAs overlapped with lncRNAs that had prognostic value. Among the 48 lncRNAs, one lncRNA (LINC01614) had stronger prognostic value and was highly expressed in BRCA tissues. LINC01614 expression was validated as an independent prognostic factor using univariate and multivariate analyses. Higher LINC01614 expression was observed in several molecular subgroups including estrogen receptors+, progesterone receptors+ and human epidermal growth factor receptor 2 (HER2)+ subgroup, respectively. Also, BRCA carrying one of four gene mutations had higher expression of LINC01614 including AOAH, CIT, HER2 and ODZ1. Higher expression of LINC01614 was positively correlated with several gene sets including TGF-β1 response, CDH1 signals and cell adhesion pathways. Conclusions A novel lncRNA LINC01614 was identified as a potential biomarker for prognosis prediction of BRCA. This study emphasized the importance of LINC01614 and further research should be focused on it.

Description: The genus Astrophiura, which ranks among the most extraordinary of modern brittle stars, is the type genus of the recently resurrected family Astrophiuridae within the order Ophiurida. On account of its absurdly enlarged and strongly modified lateral arm plates, Astrophiura bears a closer resemblance to a pentagonal starfish than to a typical ophiuroid. Although molecular evidence suggests an ancient origin of the Astrophiuridae, dating back at least to the Early Jurassic, not a single fossil astrophiurid has been reported so far. Here, we describe dissociated lateral arm plates from the Campanian of Cringleford near Norwich, UK, and the Maastrichtian of Rügen, Germany (both Upper Cretaceous) with unambiguous astrophiurid affinities and assign these to a new species, Astrophiura markbeneckei. This represents the first fossil record of the family. In addition, the Rügen material included lateral arm plates that superficially resemble those of A. markbeneckei sp. nov. but differ in having spine articulations that are typical of the ophionereidoid family Amphilimnidae. We assign these plates to a new genus and species, Astrosombra rammsteinensis, an extinct amphilimnid with morphological modifications similar to those of Astrophiura, and thus representing a remarkable case of parallel evolution amongst brittle stars looking like starfish.

Description: Data obtained using three different types of sampling gear is compared and combined to assess the size composition and density of a non-indigenous snow crab population Chionoecetes opilio in the previously free of alien species Kara Sea benthos. The Sigsbee trawl has small mesh and catches even recently settled crabs. The large bottom trawl is able to catch large crabs, but does not retain younger crabs, due to its large mesh. Video sampling allows the observation of larger crabs, although some smaller crabs can also be spotted. The combined use of such gear could provide full scope data of the existing size groups in a population. The density of the crabs was calculated from the video footage. The highest figures were in Blagopoluchiya Bay at 0.87 crabs/m2, where the settlement seems to be reaching its first peak of population growth after the introduction. High density in the Kara Gates Strait at 0.55 crabs/m2, could be due to the close proximity of the Barents Sea from where the crabs can enter by both larval dispersal and active adult migration. All size groups have been present in most sampled areas, which suggest successful settlement and growth of crabs over a number of years. Again, this was not the case in Blagopoluchiya Bay with high density of small crabs (

Description: Phenotypic differences between Campylobacter fetus fetus and C. fetus venerealis subspecies allow the differential diagnosis of bovine genital campylobacteriosis. The hydrogen sulfide production, for example, is a trait exclusive to C. fetus fetus and C. fetus venerealis biovar intermedius. This gas that can be biochemically tested can be produced from L-cysteine (L-Cys). Herein, we report a novel multiplex-PCR to differentiate C. fetus based on the evaluation of a deletion of an ATP-binding cassette-type L-Cys transporter that could be involved in hydrogen sulfide production, as previously described. A wet lab approach combined with an in silico whole genome data analysis showed complete agreement between this L-Cys transporter-PCR and the hydrogen sulfide production biochemical test. This multiplex-PCR may complement the tests currently employed for the differential diagnosis of C. fetus.

Description: The Formosan subterranean termite, Coptotermes formosanus Shiraki, is a serious pest worldwide. Juvenile hormone analog (and its analogs such as methoprene) can induce the transformation of the worker caste into soldier caste in C. formosanus. However, several factors, such as feeding substrate and colony origin, influence the proportion of solider formation. The molecular mechanism of worker to soldier transformation of C. formosanus is still not clear. RT-qPCR is a powerful tool for molecular studies. Accurate gene quantification by the relative quantification method requires a stable expressed gene as the reference gene. However, no reference genes were available for this species in the methoprene bioassay. To study the problem of gene response to methoprene by RT-qPCR we have to first screen reference genes in C. formosanus. Workers were fed with methoprene. Termites were collected during the methoprene bioassay and separated into head and thorax+abdomen. Expression profiles of 10 candidate reference genes in the two body part types were investigated using RT-qPCR. The results were analyzed by a set of established methods (geNorm, NormFinder, BestKeeper, and RefFinder) as well as comparative ΔCt method. Our results suggest that RPS18 is the most stably-expressed gene both in the head and thorax+abdomen for expression analysis in the methoprene bioassay of C. formosanus. The screening of suitable reference genes in C. formosanus establishes the foundation for the molecular study of soldier caste differentiation in this species.

Description: Verticillium dahliae causes disease symptoms in its host plants; however, due to its rapid variability, V. dahliae is difficult to control. To analyze the reason for this pathogenic differentiation, 22 V. dahliae strains with different virulence were isolated from a cotton farm. The genetic diversity of cotton varieties make cotton cultivars have different Verticillium wilt resistance, so the Xinluzao 7 (susceptible to V. dahliae), Zhongmian 35 (tolerant), and Xinluzao 33 (resistant) were used to investigate the pathogenicity of the strains in a green house. Vegetative compatibility groups (VCGs) assays, Internal Transcribed Spacer (ITS) PCR, and pathogenicity analysis showed that SHZ-4, SHZ-5, and SHZ-9 had close kinship and significantly different pathogenicity. Transcriptome sequencing of the three strains identified 19 of 146 unigenes in SHZ-4_vs_ SHZ-5, SHZ-5_vs_ SHZ-9, and SHZ-4_vs_ SHZ-9. In these unigenes, three proteinase and four polysaccharide degrading hydrolases were found to be associated with the pathogenicity. However, due to a number of differentially expressed genes in the transport, these unigenes not only played a role in nutrition absorption but might also contribute to the resistance of sugar-induced hyperosmosis. Moreover, the tolerance ability was positively related to the pathogenicity of V. dahliae. This resistance to sugar-induced hyperosmosis might help V. dahliae to access the nutrition of the host. The pathogenicity of V. dahliae correlated with the resistance of sugar-induced-hyperosmosis, which provides clues for the cultivation of V. dahliae resistant varieties.

Description: Background Long non-coding RNAs (lncRNAs) regulate endometrial secretion and uterine volume. However, there is little research on the role of lncRNAs in the uterus of Small Tail Han sheep (FecB++). Herein, RNA-seq was used to comparatively analyze gene expression profiles of uterine tissue between polytocous and monotocous sheep (FecB++) in follicular and luteal phases. Methods To identify lncRNA and mRNA expressed in the uterus, the expression of lncRNA and mRNA in the uterus of Small Tail Han sheep (FecB++) from the polytocous group (n = 6) and the monotocous group (n = 6) using RNA-sequencing and real-time polymerase chain reaction (RT-PCR). Identification of differentially expressed lncRNAs and mRNAs were performed between the two groups and two phases . Gene ontology (GO) and pathway enrichment analyses were performed to analyze the biological functions and pathways for the differentially expressed mRNAs. LncRNA-mRNA co-expression network was constructed to further analyses the function of related genes. Results In the follicular phase, 473 lncRNAs and 166 mRNAs were differentially expressed in polytocous and monotocous sheep; in the luteal phase, 967 lncRNAs and 505 mRNAs were differentially expressed in polytocous and monotocous sheep. GO and KEGG enrichment analysis showed that the differentially expressed lncRNAs and their target genes are mainly involved in ovarian steroidogenesis, retinol metabolism, the oxytocin signaling pathway, steroid hormone biosynthesis, and the Foxo signaling pathway. Key lncRNAs may regulate reproduction by regulating genes involved in these signaling pathways and biological processes. Specifically, UGT1A1, LHB, TGFB1, TAB1, and RHOA, which are targeted by MSTRG.134747, MSTRG.82376, MSTRG.134749, MSTRG.134751, and MSTRG.134746, may play key regulatory roles. These results offer insight into molecular mechanisms underlying sheep prolificacy.

Description: This work was aimed to investigate the effects of the different particle size of ground alfalfa hay on caecal microbial and archeal communities of rabbits. One hundred-twenty New Zealand rabbits (950.3 ± 8.82 g) were allocated into four treatments, with five replicates in each treatment and six rabbits in each replicate. The particle sizes of the alfalfa meal in the four treatment diets were 2,500, 1,000, 100 and 10 µm respectively, while the other ingredients were ground through a 2.5 mm sieve. High-throughput sequencing technology was applied to examine the differences in bacteria and methanogenic archaea diversity in the caecum of the four treatment groups of rabbits. A total of 745,946 bacterial sequences (a mean of 31,081 ± 13,901 sequences per sample) and 539,227 archaeal sequences (a mean of 22,468 ± 2,443 sequences per sample) were recovered from twenty-four caecal samples, and were clustered into 9,953 and 2,246 OTUs respectively. A total of 26 bacterial phyla with 465 genera and three archaeal phyla with 10 genera were identified after taxonomic summarization. Bioinformatic analyses illustrated that Firmicutes (58.69% ∼ 68.50%) and Bacteroidetes (23.96% ∼ 36.05%) were the two most predominant bacterial phyla and Euryarchaeota (over 99.9%) was the most predominant archaeal phyla in the caecum of all rabbits. At genus level, as the particle size of alfalfa decreased from 2,500 to 10 µm, the relative abundances of Ruminococcaceae UCG-014 (P 

Description: A wasp mimicking praying mantis (Mantodea) of the early evolving Mantoididae family was discovered in 2013 at a research station near the Amazon River in Northern Peru. This adult specimen exhibited a striking bright red/orange and black coloration pattern that was undocumented in all known praying mantis species. We tested the status of this new specimen using external morphology, male genital dissections, and geographic distribution. Our findings demonstrate the specimen to represent a new species, Vespamantoida wherleyi gen. nov. sp. nov., that is closely allied with a recently described species, Mantoida toulgoeti Roy, 2010, both of which are included within the newly erected genus. To support our actions, we present high resolution images of museum preserved and living specimens, morphological illustrations, a generic-level distribution map, and recorded video of the behavior of the holotype taken in the field at the time of collection. The bright red/orange coloration contrasted with black markings, the general appearance of a hymenopteran that includes a narrowed wasp waist, and the locomotory patterns and antennal movements mark this newly discovered species as unique among all hymenopteran mimicking Mantoididae as well as all other praying mantises.

Description: Although ontogeny influences dietary composition and trophic niche breadth in many anurans, its effects on diet have been little analyzed in sympatric species. In this study, we analyzed interspecific and ontogenetic variation in dietary composition and trophic niche width in an anuran community from a semi-arid environment. We found a more profound effect of species identity than body size on dietary composition, with the diet of four species dominated by formicids, that of two others by coleopterans and formicids, and that of the remaining species not dominated by specific prey types. We found ontogenetic changes in dietary composition in three of four species analyzed, in which consumption of some small insects decreased as predator size increased, regardless of species. Additionally, we did not find ontogenetic change in prey number consumed in any of the four species, but prey size increased with increasing predator size in all of them. Most species exhibited a narrow trophic niche, which was even narrower in adults in three of the four species analyzed. Costello’s modified plots revealed a high variation among individuals in termite consumption in Anaxyrus punctatus, and in more prey types in Spea multiplicata. Our results suggest that this community is not size-structured, and that ontogenetic diet shifts are mainly caused by passive sampling toward prey of different sizes. Finally, comparisons with previous data revealed an interpopulation pattern, in which trophic niche width contracts as aridity increases, possibly because of an increase in interspecific competition for trophic resources.

Description: The traditional terminology of ‘scythe’ or ‘sickle’ shaped is observed to be flawed as an effective descriptor for pectoral fin shape in pachycormids. The diversity of pachycormid pectoral fin shapes is assessed across the 14 recognised genera that preserve complete pectoral fins, and improved terms are defined to more effectively describe their form, supported by anatomical observation and aspect ratio analysis of individual fins, and corroborated by landmark analysis. Three clear and distinct pectoral fin structural morphotypes emerge (falceform, gladiform, falcataform), reflecting a diversity of pachycormid lifestyles throughout the Mesozoic, from agile pursuit predator to slow-cruising suspension feeder.

Description: The medicinal orchid genus Dendrobium belonging to the Orchidaceae family is a huge genus comprising about 800–1,500 species. To better illustrate the species status in the genus Dendrobium, a comparative analysis of 33 available chloroplast genomes retrieved from NCBI RefSeq database was compared with that of the first complete chloroplast genome of D. nobile from north-east India based on next-generation sequencing methods (Illumina HiSeq 2500-PE150). Our results provide comparative chloroplast genomic information for taxonomical identification, alignment-free phylogenomic inference and other statistical features of Dendrobium plastomes, which can also provide valuable information on their mutational events and sequence divergence.

Description: Background The problem of access to medical information, particularly in low-income countries, has been under discussion for many years. Although a number of developments have occurred in the last decade (e.g., the open access (OA) movement and the website Sci-Hub), everyone agrees that these difficulties still persist very widely, mainly due to the fact that paywalls still limit access to approximately 75% of scholarly documents. In this study, we compare the accessibility of recent full text articles in the field of ophthalmology in 27 established institutions located worldwide. Methods A total of 200 references from articles were retrieved using the PubMed database. Each article was individually checked for OA. Full texts of non-OA (i.e., “paywalled articles”) were examined to determine whether they were available using institutional and Hinari access in each institution studied, using “alternative ways” (i.e., PubMed Central, ResearchGate, Google Scholar, and Online Reprint Request), and using the website Sci-Hub. Results The number of full texts of “paywalled articles” available using institutional and Hinari access showed strong heterogeneity, scattered between 0% full texts to 94.8% (mean = 46.8%; SD = 31.5; median = 51.3%). We found that complementary use of “alternative ways” and Sci-Hub leads to 95.5% of full text “paywalled articles,” and also divides by 14 the average extra costs needed to obtain all full texts on publishers’ websites using pay-per-view. Conclusions The scant number of available full text “paywalled articles” in most institutions studied encourages researchers in the field of ophthalmology to use Sci-Hub to search for scientific information. The scientific community and decision-makers must unite and strengthen their efforts to find solutions to improve access to scientific literature worldwide and avoid an implosion of the scientific publishing model. This study is not an endorsement for using Sci-Hub. The authors, their institutions, and publishers accept no responsibility on behalf of readers.

Description: Background Although several risk factors for nosocomial diarrhea have been identified, the detail of association between these factors and onset of nosocomial diarrhea, such as degree of importance or temporal pattern of influence, remains unclear. We aimed to determine the association between risk factors and onset of nosocomial diarrhea using machine learning algorithms. Methods We retrospectively collected data of patients with acute cerebral infarction. Seven variables, including age, sex, modified Rankin Scale (mRS) score, and number of days of antibiotics, tube feeding, proton pump inhibitors, and histamine 2-receptor antagonist use, were used in the analysis. We split the data into a training dataset and independant test dataset. Based on the training dataset, we developed a random forest, support vector machine (SVM), and radial basis function (RBF) network model. By calculating an area under the curve (AUC) of the receiver operating characteristic curve using 5-fold cross-validation, we performed feature selection and hyperparameter optimization in each model. According to their final performances, we selected the optimal model and also validated it in the independent test dataset. Based on the selected model, we visualized the variable importance and the association between each variable and the outcome using partial dependence plots. Results Two-hundred and eighteen patients were included. In the cross-validation within the training dataset, the random forest model achieved an AUC of 0.944, which was higher than in the SVM and RBF network models. The random forest model also achieved an AUC of 0.832 in the independent test dataset. Tube feeding use days, mRS score, antibiotic use days, age and sex were strongly associated with the onset of nosocomial diarrhea, in this order. Tube feeding use had an inverse U-shaped association with the outcome. The mRS score and age had a convex downward and increasing association, while antibiotic use had a convex upward association with the outcome. Conclusion We revealed the degree of importance and temporal pattern of the influence of several risk factors for nosocomial diarrhea, which could help clinicians manage nosocomial diarrhea.

Description: In the Chinese Han population, prolonged exposure to hypoxic conditions can promote compensatory erythropoiesis which improves hypoxemia. However, Tibetans have developed unique phenotypes, such as downregulation of the hypoxia-inducible factor pathway through EPAS1 gene mutation, thus the mechanism of adaption of the Han population should be further studied. The results indicated that, under plateau hypoxic conditions, the plains population was able to acclimate rapidly to hypoxia through increasing EPAS1 mRNA expression and changing the hemoglobin conformation. Furthermore, the mutant genotype frequencies of the rs13419896, rs1868092 and rs4953354 loci in the EPAS1 gene were significantly higher in the Tibetan population than in the plains population. The EPAS1 gene expression level was lowest in the Han population carrying the A-A homozygous mutant of the rs13419896 locus but that it increased rapidly after these individuals entered the plateau. At this time, the hemoglobin content was lower in the homozygous mutant Han group than in the wild-type and heterozygous mutant populations, and the viscosity of blood was reduced in populations carrying the A-A haplotypes in rs13419896 and rs1868092 Among Tibetans, the group carrying homozygous mutations of the three SNPs also had lower hemoglobin concentrations than the wild-type. The Raman spectroscopy results showed that exposure of the Tibetan and Han population to hypoxic conditions changed the spatial conformation of hemoglobin and its binding ability to oxygen. The Tibetan population has mainly adapted to the plateau through genetic mutations, whereas some individuals adapt through changes in hemoglobin structure and function.

Description: Aim The target molecule regulatory function of microRNA-21 (miR-21) in multiple signalling pathways has become a main focus of genetic and pharmacological regulatory studies of various diseases. The identification of target genes for miRNA-21 in the development of hair follicles can provide new research pathways for the regulation of cell development. Methods In the present study, eight six-month-old ewes from Super Merino (SM) and Small Tailed Han (STH) sheep breeds were selected. Target prediction and dual-luciferase wild-type and mutant vectors were used to identify the target genes of miR-21. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) and bioinformatics analysis were conducted to analyze the effects of miR-21. Results The results show that the expressions of CNKSR2, KLF3 and TNPO1 were downregulated by miRNA-21 at rates of 36%, 26% and 48%, respectively. Moreover, there was a significant negative correlation between the expression of miR-21 and the three target genes in sheep with two extreme phenotypes. The expression of microRNA-21in October was significantly lower than that in January and February; while the expression of CNKSR2, KLF3 and TNPO1 in October was higher than that in January and February. Conclusions: These results suggest that CNKSR2, KLF3 and TNPO1 are three newly discovered target genes of miR-21 and might be involved in the effects of miR-21 on hair follicle development.

Description: Background DegS is a periplasmic serine protease that is considered to be the initiator of the σE stress response pathway, and this protein plays an important role in the regulation of the stress response in E. coli. However, knowledge of the biological function and global regulatory network of DegS in Vibrio cholerae remains limited. In this study, we aimed to characterize the molecular functions and further investigate the regulatory network of degS in V. cholerae. Methods A deletion mutant of degS was constructed in the V. cholerae HN375 strain. Bacterial colony morphology was observed by a plate-based growth experiment, and bacterial growth ability was observed by a growth curve experiment. High-throughput RNA sequencing (RNA-Seq) technology was used to analyze the differential transcriptomic profiles between the wild-type and degS mutant strains. Gene ontology (GO), pathway analysis and Gene-Act-network analysis were performed to explore the main functions of the differentially expressed genes. Quantitative real-time PCR (qRT-PCR) was performed to validate the reliability and accuracy of the RNA-Seq analysis. The complementation experiments were used to test the roles of degS and ropS in the small colony degS mutant phenotype. Results When degS was deleted, the degS mutant exhibited smaller colonies on various media and slower growth than the wild-type strain. A total of 423 differentially expressed genes were identified, including 187 genes that were upregulated in the degS mutant compared to the wild-type strain and 236 genes that were relatively downregulated. GO categories and pathway analysis showed that many differentially expressed genes were associated with various cellular metabolic pathways and the cell cycle. Furthermore, Gene-Act network analysis showed that many differentially expressed genes were involved in cellular metabolic pathways and bacterial chemotaxis. The cAMP-CRP-RpoS signaling pathway and the LuxPQ signal transduction system were also affected by the degS mutant. The expression patterns of nine randomly selected differentially expressed genes were consistent between the qRT-PCR and RNA-seq results. The complementation experiments showed that the small colony degS mutant phenotype could be partially restored by complementation with the pBAD24-degS or pBAD24-rpoS plasmid. Discussion These results suggest that the degS gene is important for normal growth of V. cholerae. Some of the differentially expressed genes were involved in various cellular metabolic processes and the cell cycle, which may be associated with bacterial growth. Several new degS-related regulatory networks were identified. In addition, our results suggested that the cAMP-CRP-RpoS signaling pathway may be involved in the small colony degS mutant phenotype. Overall, we believe that these transcriptomic data will serve as useful genetic resources for research on the functions of degS in V. cholerae.

Description: The conformational space of the ribose-phosphate backbone is very complex as it is defined in terms of six torsional angles. To help delimit the RNA backbone conformational preferences, 46 rotamers have been defined in terms of these torsional angles. In the present work, we use the ribose experimental and theoretical 13C′ chemical shifts data and machine learning methods to classify RNA backbone conformations into rotamers and families of rotamers. We show to what extent the experimental 13C′ chemical shifts can be used to identify rotamers and discuss some problem with the theoretical computations of 13C′ chemical shifts.

Description: Background Stable cesium (133Cs) naturally exists in the environment whereas recently deposited radionuclides (e.g., 137Cs) are not at equilibrium. Stable cesium has been used to understand the long-term behavior of radionuclides in plants, trees and mushrooms. We are interested in using 133Cs to predict the future transfer factor (TF) of radiocesium from contaminated logs to shiitake mushrooms in Eastern Japan. However, the current methodology to obtain a representative wood sample for 133Cs analysis involves mechanically breaking and milling the entire log (excluding bark) to a powder prior to analysis. In the current study, we investigated if sawdust obtained from cutting a log along its length at eight points is as robust but a faster alternative to provide a representative wood sample to determine the TF of 133Cs between logs and shiitake. Methods Oak logs with ready-to-harvest shiitake fruiting bodies were cut into nine 10-cm discs and each disc was separated into bark, sapwood and heartwood and the concentration of 133Cs was measured in the bark, sapwood, heartwood, sawdust (generated from cutting each disc) and fruiting bodies (collected separately from each disc), and the wood-to-shiitake TF was calculated. Results We found that the sawdust-to-shiitake TF of 133Cs did not differ (P = 0.223) compared to either the sapwood-to-shiitake TF or heartwood-to-shiitake TF, but bark did have a higher concentration of 133Cs (P 〈 0.05) compared to sapwood and heartwood. Stable cesium concentration in sawdust and fruiting bodies collected along the length of the logs did not differ (P 〉 0.05). Discussion Sawdust can be used as an alternative to determine the log-to-shiitake TF of 133Cs. To satisfy the goals of different studies and professionals, we have described two sampling methodologies (Methods I and II) in this paper. In Method I, a composite of eight sawdust samples collected from a log can be used to provide a representative whole-log sample (i.e., wood and bark), whereas Method II allows for the simultaneous sampling of two sets of sawdust samples—one set representing the whole log and the other representing wood only. Both methodologies can greatly reduce the time required for sample collection and preparation.

Description: Background The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Methods Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. Results—Discussion We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated.

Description: Background This study aimed to identify which maximum voluntary isometric contraction (MVIC) and sub-MVIC tests produce the highest activation of the erector spinae muscles and the greatest reduction in inter-individual variability, to put them forward as reference normalization maneuvers for future studies. Methods Erector spinae EMG activity was recorded in 38 healthy women during five submaximal and three maximal exercises. Results None of the three MVIC tests generated the maximal activation level in all the participants. The maximal activation level was achieved in 68.4% of cases with the test performed on the roman chair in the horizontal position (96.3 ± 7.3; p