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  • 1
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    Large-scale model quality assessment for improving protein tertiary structure prediction (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-14
    Description: Motivation: Sampling structural models and ranking them are the two major challenges of protein structure prediction. Traditional protein structure prediction methods generally use one or a few quality assessment (QA) methods to select the best-predicted models, which cannot consistently select relatively better models and rank a large number of models well. Results: Here, we develop a novel large-scale model QA method in conjunction with model clustering to rank and select protein structural models. It unprecedentedly applied 14 model QA methods to generate consensus model rankings, followed by model refinement based on model combination (i.e. averaging). Our experiment demonstrates that the large-scale model QA approach is more consistent and robust in selecting models of better quality than any individual QA method. Our method was blindly tested during the 11th Critical Assessment of Techniques for Protein Structure Prediction (CASP11) as MULTICOM group. It was officially ranked third out of all 143 human and server predictors according to the total scores of the first models predicted for 78 CASP11 protein domains and second according to the total scores of the best of the five models predicted for these domains. MULTICOM’s outstanding performance in the extremely competitive 2014 CASP11 experiment proves that our large-scale QA approach together with model clustering is a promising solution to one of the two major problems in protein structure modeling. Availability and implementation : The web server is available at: http://sysbio.rnet.missouri.edu/multicom_cluster/human/ . Contact : chengji@missouri.edu
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-25
    Description: Motivation: Speed, accuracy and robustness of building protein fragment library have important implications in de novo protein structure prediction since fragment-based methods are one of the most successful approaches in template-free modeling (FM). Majority of the existing fragment detection methods rely on database-driven search strategies to identify candidate fragments, which are inherently time-consuming and often hinder the possibility to locate longer fragments due to the limited sizes of databases. Also, it is difficult to alleviate the effect of noisy sequence-based predicted features such as secondary structures on the quality of fragment. Results: Here, we present FRAGSION, a database-free method to efficiently generate protein fragment library by sampling from an Input–Output Hidden Markov Model. FRAGSION offers some unique features compared to existing approaches in that it (i) is lightning-fast, consuming only few seconds of CPU time to generate fragment library for a protein of typical length (300 residues); (ii) can generate dynamic-size fragments of any length (even for the whole protein sequence) and (iii) offers ways to handle noise in predicted secondary structure during fragment sampling. On a FM dataset from the most recent Critical Assessment of Structure Prediction, we demonstrate that FGRAGSION provides advantages over the state-of-the-art fragment picking protocol of ROSETTA suite by speeding up computation by several orders of magnitude while achieving comparable performance in fragment quality. Availability and implementation: Source code and executable versions of FRAGSION for Linux and MacOS is freely available to non-commercial users at http://sysbio.rnet.missouri.edu/FRAGSION/ . It is bundled with a manual and example data. Contact: chengji@missouri.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    Conditions for thermal instability in the Galactic Centre mini-spiral region (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-12
    Description: We explore the conditions for thermal instability to operate in the mini-spiral region of the Galactic Centre (Sgr A*), where both hot and cold media are known to coexist. The photoionization Cloudy calculations are performed for different physical states of plasma. We neglect the dynamics of the material and concentrate on studying the parameter ranges where thermal instability may operate, taking into account the past history of Sgr A*'s bolometric luminosity. We show that thermal instability does not operate at the present very low level of Sgr A* activity. However, Sgr A* was much more luminous in the past. For the highest luminosity states, the two-phase medium can be created up to 1.4 pc from the centre. Dust grains tend to suppress the instability, but the dust is destroyed in a strong radiation field and hot plasma. Clumpiness is thus induced in the high-activity period, and the cooling/heating timescales are long enough to preserve the past multi-phase structure. The instability enhances the clumpiness of the mini-spiral medium and creates the possibility for episodes of enhanced accretion of cold clumps towards Sgr A*. The mechanism determines the range of masses and sizes of clouds; under the conditions of Sgr A*, the likely values are 1–10 2  M for the cloud's typical mass.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    Tracking the weight of Hurricane Harveys stormwater using GPS data (2018)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2018-09-20
    Description: On 26 August 2017, Hurricane Harvey struck the Gulf Coast as a category four cyclone depositing ~95 km 3 of water, making it the wettest cyclone in U.S. history. Water left in Harvey’s wake should cause elastic loading and subsidence of Earth’s crust, and uplift as it drains into the ocean and evaporates. To track daily changes of transient water storage, we use Global Positioning System (GPS) measurements, finding a clear migration of subsidence (up to 21 mm) and horizontal motion (up to 4 mm) across the Gulf Coast, followed by gradual uplift over a 5-week period. Inversion of these data shows that a third of Harvey’s total stormwater was captured on land (25.7 ± 3.0 km 3 ), indicating that the rest drained rapidly into the ocean at a rate of 8.2 km 3 /day, with the remaining stored water gradually lost over the following 5 weeks at ~1 km 3 /day, primarily by evapotranspiration. These results indicate that GPS networks can remotely track the spatial extent and daily evolution of terrestrial water storage following transient, extreme precipitation events, with implications for improving operational flood forecasts and understanding the response of drainage systems to large influxes of water.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Oocyte-specific deletion of Pten causes premature activation of the primordial follicle pool (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-02-02
    Description: In the mammalian ovary, progressive activation of primordial follicles from the dormant pool serves as the source of fertilizable ova. Menopause, or the end of female reproductive life, occurs when the primordial follicle pool is exhausted. However, the molecular mechanisms underlying follicle activation are poorly understood. We provide genetic evidence that in mice lacking PTEN (phosphatase and tensin homolog deleted on chromosome 10) in oocytes, a major negative regulator of phosphatidylinositol 3-kinase (PI3K), the entire primordial follicle pool becomes activated. Subsequently, all primordial follicles become depleted in early adulthood, causing premature ovarian failure (POF). Our results show that the mammalian oocyte serves as the headquarters of programming of follicle activation and that the oocyte PTEN-PI3K pathway governs follicle activation through control of initiation of oocyte growth.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reddy, Pradeep -- Liu, Lian -- Adhikari, Deepak -- Jagarlamudi, Krishna -- Rajareddy, Singareddy -- Shen, Yan -- Du, Chun -- Tang, Wenli -- Hamalainen, Tuula -- Peng, Stanford L -- Lan, Zi-Jian -- Cooney, Austin J -- Huhtaniemi, Ilpo -- Liu, Kui -- New York, N.Y. -- Science. 2008 Feb 1;319(5863):611-3. doi: 10.1126/science.1152257.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Biochemistry and Biophysics, Umea University, SE-901 87 Umea, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18239123" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Female ; Follicular Atresia ; Mice ; Mice, Transgenic ; Oocytes/cytology/growth & development/*physiology ; Organ Size ; Ovarian Follicle/cytology/*physiology ; Ovary/anatomy & histology/physiology ; Ovulation ; PTEN Phosphohydrolase/genetics/*physiology ; Phosphatidylinositol 3-Kinases/metabolism ; Phosphorylation ; Primary Ovarian Insufficiency/physiopathology ; Protein Kinases/metabolism ; Ribosomal Protein S6/metabolism ; Signal Transduction ; TOR Serine-Threonine Kinases
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Sensors, Vol. 19, Pages 4814: Phenomic and Physiological Analysis of Salinity Effects on Lettuce (2019)
    MDPI
    In: Sensors
    Details
    Publication Date: 2019
    Description: Salinity is a rising concern in many lettuce-growing regions. Lettuce (Lactuca sativa L.) is sensitive to salinity, which reduces plant biomass, and causes leaf burn and early senescence. We sought to identify physiological traits important in salt tolerance that allows lettuce adaptation to high salinity while maintaining its productivity. Based on previous salinity tolerance studies, one sensitive and one tolerant genotype each was selected from crisphead, butterhead, and romaine, as well as leaf types of cultivated lettuce and its wild relative, L. serriola L. Physiological parameters were measured four weeks after transplanting two-day old seedlings into 350 mL volume pots filled with sand, hydrated with Hoagland nutrient solution and grown in a growth chamber. Salinity treatment consisted of gradually increasing concentrations of NaCl and CaCl2 from 0 mM/0 mM at the time of transplanting, to 30 mM/15 mM at the beginning of week three, and maintaining it until harvest. Across the 10 genotypes, leaf area and fresh weight decreased 0–64% and 16–67%, respectively, under salinity compared to the control. Salinity stress increased the chlorophyll index by 4–26% in the cultivated genotypes, while decreasing it by 5–14% in the two wild accessions. Tolerant lines less affected by elevated salinity were characterized by high values of the chlorophyll fluorescence parameters Fv/Fm and instantaneous photosystem II quantum yield (QY), and lower leaf transpiration.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
    Published by MDPI
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  • 7
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    (U-Th)/He ages from zircons collected in the central Nepal Himalaya: summary (2020)
    PANGAEA
    Details
    Publication Date: 2024-01-20
    Keywords: Age, (U‐Th)/He dating; Age, error; Age, mineral; CN16-004; CN16-007; CN16-016; CN16-017; CN16-018; CN16-019; CN16-020; CN16-032; CN16-033; CN16-034; CN16-036; CN16-037; CN16-048; CN16-064; CN16-069; CN16-084; CN16-092; CN16-102; CN16-103; Comment; cooling age; ELEVATION; Event label; exhumation; Himalayas; LATITUDE; LONGITUDE; Nepal; ROCK; Rock sample; ZHe
    Type: Dataset
    Format: text/tab-separated-values, 57 data points
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  • 8
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    (U-Th)/He ages from Zircons collected in the central Nepal Himalaya: raw data (2020)
    PANGAEA
    Details
    Publication Date: 2024-01-20
    Keywords: Age, error; Age, mineral; alpha-ejection correction; CN16-004; CN16-007; CN16-016; CN16-017; CN16-018; CN16-019; CN16-020; CN16-032; CN16-033; CN16-034; CN16-036; CN16-037; CN16-048; CN16-064; CN16-069; CN16-084; CN16-092; CN16-102; CN16-103; cooling age; Event label; exhumation; Helium-4; Himalayas; Mass; Mass, standard error; Nepal; Ratio; ROCK; Rock sample; Sample code/label; Size; Thorium; Thorium/Uranium ratio; Uranium; ZHe
    Type: Dataset
    Format: text/tab-separated-values, 1197 data points
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  • 9
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    (U-Th)/He ages from zircons collected in the central Nepal Himalaya (2020)
    PANGAEA
    Details
    Publication Date: 2024-01-20
    Description: This dataset contains the results of 19 individual (U-Th)/He analyses using Zircons extracted from bedrock samples. The bedrock samples were collected from medium-high grade metamorphic rocks exposed along the Budhi Gandaki and Trishuli river valleys. They were collected in order to add to the already available thermochronometric datasets and better constrain the exhumation history of the central Himalayas. The measurements of the ages follow the general procedures outlined in Reiners (2005) and Reiners et al. (2004).
    Keywords: cooling age; exhumation; Himalayas; Nepal; ZHe
    Type: Dataset
    Format: application/zip, 2 datasets
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  • 10
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    Experimental evidence showing that no mitotically active female germline progenitors exist in postnatal mouse ovaries (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-07-09
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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