ALBERT

Description: Schizophrenia is a very common psychiatric disorder. However, its etiology and pathogenesis is still unknown. Current theory saying that neurotransmitter imbalance such as serotonin or dopamine only provides limited effectiveness in schizophrenia treatment by drugs changing serotonin and dopamine concentration. Despite of such treatment, majority of schizophrenia patients still have very poor prognosis. Thus, the neurotransmitter imbalance theory is not correct. Here, I propose that schizophrenia is actually a TH2 dominant autoimmune disorder. The candidate of autoantigen could be acetylcholine receptors of CNS. My theory can explain the positive as well as negative symptoms of schizophrenia. By microarray analysis of PBMCS, one-tenth of the total 519 significantly expressed genes are immune-related genes. Among them, TH2 related genes are significantly up-regulated including IL-4, histidine decarboxylase, aldehyde dehydrogenase, CCR9, IgE Fc receptor, GATA2, serotonin receptor, phospholipase A2, and prostaglandin D2 synthase. Besides, TH1 and TH17 related genes are down-regulated including CXCL5, cathepsin C, and neutrophil related S100 binding proteins. The new theory sheds a light to better control this detrimental illness. Anti-inflammatory agents could be used to manage schizophrenia in the near future.

Description: Animal models are often used to obtain a better understanding of psychiatric, neurodegenerative, and neurodevelopmental disorders. Despite many years of research, these models have not led to many novel therapies or treatments. Translating results between species will always be difficult, and it is argued that inappropriate statistical analyses, failure to identify the experimental unit, lack of random assignment to treatment conditions, and unblinded assessment of outcomes contribute to the low rate of translating preclinical in vivo studies into successful therapies. It is known that these shortcomings can generate biased estimates, too many false positives and false negatives, and unreproducible results. These issues have been raised repeatedly, but have largely gone unheeded by scientists. Two recommendations are made to improve the situation.

Description: Mobile Platform Informatics (MPI) and Smartphone Informatics (SPI) methods like Mobile Image Ratiometry (MIR) are potentially transformative point-of-use instantaneous analysis tools that are useful across a variety of industries. In agriculture, MIR-compatible immuno test strips allow early detection of a number of biotic stressors before devastating crop losses occur. Here we describe a low-cost and easy-to-use Smartphone and/or tablet-based protocol (Mobile Assay Inc., www.mobileassay.com) for the detection and on-sight instantaneous analysis of B. cinerea, a fungus that causes significant damage to a variety of plants and flowers. Early detection and tracking of the B. cinerea fungus before the visible gray mold appears has the potential to increase agricultural productivity especially in the developing world.

Description: Here we show a new interaction mechanism of colliding population waves. It provides a stable coexistence of two similar but different species competing for the same limiting resource during their asexual propagation in a limited homogeneous environment under constant conditions. The revealed mechanism opens new opportunities in conservation biology.

Description: Two erectoid hominids from Sarstedt prompted a detailed examination of the course of the impressions of the Arteria meningea media and their characteristics within the line of hominidae.

Description: Genomic Replikin CountsTM of Infectious Salmon Anemia Virus (ISAV) in Canada Exceed the Counts in Lethal Outbreaks in Norway, Chile, and Scotland. Real-Time Tracking of the Evolution of the ISAV Genome and the Resultant Replikins Solid Phase ISAV Vaccine Make ISAV Pandemic Prevention Possible.

Description: Background: The modeling of interactions among transcription factors (TFs) and their respective target genes (TGs) into transcriptional regulatory networks is important for the complete understanding of regulation of biological processes. In the case of human TF-TG interactions, there is no database at present that explicitly provides such information even though many databases containing human TF-TG interaction data have been available. In an effort to provide researchers with a repository of TF-TG interactions from which such interactions can be directly extracted, we present here the Human Transcriptional Regulation Interactions database (HTRIdb).Description: The HTRIdb is an open-access database of experimentally validated interactions among human TFs and their TGs. HTRIdb can be searched via a user-friendly web interface and the retrieved TF-TG interactions data and the associated protein-protein interactions can be downloaded or interactively visualized as a network using the Cytoscape Web software. Moreover, users can improve the database quality by uploading their own interactions and indicating inconsistencies in the data. So far, HTRIdb has been populated with 283 TFs that regulate 11886 genes, totaling 18160 TF-TG interactions. HTRIdb is freely available at http://www.lbbc.ibb.unesp.br/htri.Conclusions: HTRIdb is a powerful user-friendly tool from which human experimentally validated TF-TG interactions can be easily extracted and used to construct transcriptional regulation interaction networks enabling researchers to decipher the regulation of biological processes.

Description: Genome-wide association studies (GWAS) have become a standard method for finding genetic variations that contribute to common, complex diseases. Recently, it is suggested that these diseases may be caused by epistatic interactions of multiple genetic variations. Although tens of software tools have been developed for epistasis detection, few are able to infer pathway importance from the identified epistatic interactions. AntEpiSeeker is originally an algorithm for detecting epistatic interactions in case-control studies, using a two-stage ant colony optimization (ACO) algorithm. We have developed AntEpiSeeker2.0, which extends the AntEpiSeeker algorithm to inference of epistasis-associated pathways, based on a natural use of the ACO pheromones. By looking at pheromone distribution across pathways, epistasis-associated pathways can be easily identified. The effectiveness of AntEpiSeeker2.0 in inferring epistasis-associated pathways is demonstrated through a simulation study and a real data application. AntEpiSeeker 2.0 was designed to provide efficient inference of epistasis-associated pathways based on ant colony optimization and is freely available at http://lambchop.ads.uga.edu/antepiseeker2/.

Description: Natural agricultural production functions in open system, where energy and matter are exchanged freely between geosphere (especially pedosphere), biosphere, and atmosphere. The self regulation of biophysical processes in these spheres is crucial for global sustainability. However, modern farming practices have stressed the system to the extent that damaged C, N, and P cycles are threatening catastrophic consequences. High food-wastage coupled with high food price, high soil fertility zones but low crop productivity, and highly productive irrigated farming marred with ecological disasters are examples of global paradoxes associated with modern farming. High incidence of pesticide residues in soil and water bodies, low use efficiency of agricultural inputs, vulnerability to climate, and low conversion of energy by crops leaving high amount of residues and their subsequent burden on environment, and hunger and malnutrition in many parts of the world are threatening civilizations to crumble. Nanotechnology promises to break these vicious cycles, because technology is based on applying exact amounts of inputs for use by the crops, and only when they are required. Some of the examples are: nanofabricating nutrient ions to improve nutrient use efficiency, targeted use of nano-pesticides, holding of water and then releasing it at the time of crop need by nps, forecasting and elimination of diseases, packaging of food to improve shelf-life, protecting food during storage, DNA nanotechnology, smart treatment delivery systems, bioanalytical nanosensors, bioselective surfaces, nanobioprocessing, protection of the environment by the reduction and conversion of agricultural materials into valuable products, design and development of new nanocatalysts to convert vegetable oils into biobased fuels and biodegradable industrial solvents, and controlled ecological life support system.

Description: “A disruptive innovation is an innovation that helps create a new market and value network, and eventually goes on to disrupt an existing market and value network (over a few years or decades), displacing an earlier technology. The term is used in business and technology literature to describe innovations that improve a product or service in ways that the market does not expect.” -WikipediaOn April 3rd, 2012 Nature Precedings, Nature Publishing Group’s experiment in free pre-print publishing was shut down and no longer accepts submissions. According to the Nature Precedings website it was created in 2007 as “a place for researchers to share documents, including presentations, posters, white papers, technical papers, supplementary findings, and non-peer-reviewed manuscripts.” It was designed to “provide a rapid means for scientists to share preliminary findings, disseminate emerging results, solicit community feedback, and claim priority over discoveries.” It was designed in a way to “make such material easy to archive, share and cite.” Now that Nature Precedings is no more, a new disruptive open data-sharing platform (ODSP) for the life sciences is needed. Based, in part, by the model Nature Precedings established. Here I propose 5 qualities of an ideal ODSP and outline 10 benefits (see Table 1) to scientists for embracing such a potentially disruptive model.

Description: Innovative molecular tools allow neuroscientists to study neural circuitry associated with specific behaviors. Consequently, behavioral methods must be developed to interface with these new molecular tools in order for neuroscientists to identify the causal elements underlying behavior and decision-making processes. Here we present an apparatus and protocol for a novel Go/No-Go behavioral paradigm to study the brain attention and motivation/reward circuitry in awake, head-restrained rodents. This experimental setup allows: (1) Painless and stable restraint of the head and body; (2) Rapid acquisition to simple or complex operant tasks; (3) Repeated electrophysiological single and multiple unit recordings during ongoing behavior; (4) Pharmacological and viral manipulation of various brain regions via targeted guide cannula, and; (5) Optogenetic cell-type specific activation and silencing with simultaneous electrophysiological recording. In addition to the experimental advantages, the head-restraint system is relatively inexpensive and training parameters can be easily modulated to the specifications of the experimenter. The system runs on custom LabView software. In summary, our novel apparatus and protocol allows researchers to study and manipulate components of behavior, such as motivation, impulsivity, and reward-related working memory during an ongoing operant behavioral task without interference from non task-related behaviors. For more information on the custom apparatus, software or to collaborate please visit www.neuro-cloud.net/nature-precedings/dolzani.

Description: The genomes of all groups of viruses whose sequences are listed on Pubmed, specimens since 1918, analyzed by a software from Bioradar UK Ltd., contain Replikins which range in concentration from a Replikin Count (number of Replikins per 100 amino acids) of less than 1 to 30 (see accompanying communications for higher Counts in tuberculosis, malaria, and cancer, associated with higher lethality). Counts of less than 4.0 were found in ‘resting’ virus states; Counts greater than 4.0, found to be associated with rapid replication, were found invariably to accompany or to predict virus outbreaks, by as much as two years, in viral hosts examined from salmon, to birds, to livestock, to humans. X-ray diffraction showed Replikins to be on the surface of the hemagglutinin gene of influenza and to spread as the Count increased from 3.2 to 10.1, prior to, then during, the 2009 H1N1 influenza pandemic. The degree of lethality of these outbreaks was found to be a function of the statistically significant increase in Replikin Count, particularly in the influenza polymerase gene p B1 or its equivalent in other viruses. Prediction up to two years in advance of the outbreak, and the geographic location of the outbreak, now done in 7/7 trials (see Bogoch, Nature Precedings), has permitted the solid phase synthesis of Replikin vaccines in 7 days, with time to permit manufacture, adequate testing for safety and efficacy, and distribution freeze-dried to all populations. These completely synthetic Replikins vaccines so far have been shown to be effective against Taura Syndrome virus in shrimp, and H5N1 in chickens. Thus for the first time this new technology provides the practical possibility to prevent pandemics rather than just to react to them.

Description: We provide the first formalization true to the best of our knowledge to the problem of finding bicliques in a directed graph. The problem is addressed employing a two-stage approach based on an existing biclustering algorithm. This novel problem is useful in several biological applications of which we focus only on analyzing the viral-host protein interaction graphs. Strong and significant bicliques of HIV-1 and human proteins are derived using the proposed methodology, which provides insights into some novel regulatory functionalities in case of the acute immunodeficiency syndrome in human.

Description: Analysis of the electron salvation process data indicates that the electron transfer between the electron donor and acceptor is hindered by the electron salvation process. It is proposed that the electron transfer in the cell environment must be assisted by intermediate messenger called the “transport protein”.

Description: TRPC   channels   have   been   implicated   in   social   behaviors   (TRPC4)   and   anxiety   (TRPC5).   TRPC1   channels   are   widely  expressed  in  the  mammalian  brain.  TRPC1  subunits  form  heteromultimeric  channels  with  TRPC3,  4,  and   5  subunits  that  are  activated  following  Gq-­coupled  signaling  cascades.  Robust  expression  of  TRPC1  was  found   in  the  corticolimbic  areas  of  the  brain  including  the  prefrontal  cortex  (PFC),  striatum,  hippocampus  (HIP),  and  lateral septum (LS). Knock-out of TRPC1 in the brain was confirmed via immunoblots. Real-time  PCR  experiments  show  no  compensation  in  the  PFC  by  other  TRPC  channels  following  loss  of  TRPC1.  The   dense  expression  of  the  TRPC1  channels  in  the  PFC,  LS  and  HIP  led  us  to  examine  behaviors  associated  with   those  regions.  Here  we  show  no  differences  in  cocaine  mediated  behaviors  in  TRPC1-­/-­  compared  to  +/+  mice.

Description: Genomic Replikin Counts predict both the increase and the decrease of lethality of malaria

Description: The genomic Replikin Count of all the sequences on Pubmed of different strains of tuberculosis were analyzed. The lowest Counts occurred with species within the lowest drug resistance, the highest Counts with sequences of the highest drug resistance and lethality.

Description: For the broad spectrum of cognitive biological phenomena having ‘dual’ information sources, isolation from crosstalk between them requires more metabolic free energy than permitting correlation. This allows an evolutionary exaptation leading to dynamic global broadcasts at multiple scales, similar to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological systems. Entropy gradient models adapted from nonequilibrium thermodynamics lead to an index theorem in which analytic solutions of empirical equations describe different possible topological modes. Not only is the living state characterized by cognition at every scale and level of organization, but by multiple, shifting, tunable, cooperative broadcasts that link selected subsets of those structures to address problems. As for animal consciousness, the ‘stream’ of cognitive physiological broadcast is constrained by the riverbanks of embedding context, expressed in terms of systematic regularities of an enveloping environmental information source and the limitations imposed by developmental trajectory.

Description: Earlier studies have shown that the increased concentration of a new class of virus genomic peptides, Replikins, precedes and predicts virus outbreaks. We now find that the area in the genome of the highest concentration of Replikins, and the country in which this peak exists in scout viruses, have permitted in the past five years seven consecutive accurate predictions of the geographic localization of coming outbreaks, including those now realized in Mexico for H1N1, and in Cambodia for H5N1. Real-time Replikin analysis of the evolution of the virus genome identified both mutations and structural reorganization of the hemagglutinin and p B1 genes over several years before each outbreak. This information, together with the specific Replikin sequences so obtained, permitted solid-phase synthesis of Replikin vaccines in seven days, which blocked H5N1 in chickens. The information also now provides up to two years of time to thoroughly test and distribute vaccines to high risk individuals in the countries identified; thus for the first time, a quantitative genomic Replikins method to both predict initial outbreaks and to prevent the development of a pandemic.

Description: We developed an efficient “Combinatorial Strategy” for cloning different vectors with various clone sites. 1) Using originally existed clone sites from circular vectors to prepare the inserts, and if no appropriate sites are available, performing SDM to create compatible sites, to achieve maximal correct digestion of the inserts. 2) Different vectors were digested with various restriction endonucleases, and then dephosphorylated with CIP. 3) Top10 competent cells were used for transformation to increase the transformant colonies. Our results showed that, when blunt sites, or a Xba I site was adopted for ligation, the percentages of positive clones were about 50%. Whereas, when different sites, including one blunt and another Pst I sites, Not I and Xho I sites, the percentages of positive clones were nearly 100%. Using this strategy, most vectors could be successfully cloned through “one ligation, one transformation, three to five minipreps.”

Description: Alzheimer’s disease (AD) is one of the most prominent neurodegenerative disorders, particularly in elder persons over 65 age. It is characterized by progressive cognitive deterioration together with declining activities. Amyloid precursor protein (APP) cleaves at A-beta (Aβ) peptide by rate limiting factor of Beta-site APP cleaving enzyme (BACE-1) in amyloidogenic pathway. Elevated level of BACE-1 leads to the accumulation of an insoluble form of Aβ peptides (Senile Plaques), an important hallmark in the pathogenesis of Alzheimer disease. Five published inhibitors of BACE-1, thiazolidinediones, rosiglitazone, pioglitazone, Sc7 and tartaric acid are available with poor pharmacological properties and intolerable side effects. Therefore, a computational approach was undertaken to design novel inhibitors against human BACE-1. The crystal structure of human BACE-1 was retrieved from the protein data bank and optimized by applying OPLS force field in Maestro v9.2. An ASINEX database (115,000 ligands) was downloaded and compounds were prepared using LigPrep. The optimized ligand dataset was docked into the BACE-1 through sequential application of Glide HTVS, SP and XP methods that penalizes more stringently for minor steric classes subsequently. Finally, seven leads were reported and ranked based on XPGscore with better binding affinity and good pharmacological properties compared with existing inhibitors. Six leads were proposed for human BACE-1. Among the six, lead 1, with XPGscore -8.051Kcal/mol, would be intriguing for rational drug design against Alzheimer’s disease and would be highly encouraging for future Alzheimer’s therapy if tested in animal models.

Description: In this work I attempt to justify the claim that the discovery of statistically relevant brain correlates of consciousness supports Non-Reductive Physicalism. First I distinguish the main varieties of Reductive and Non-Reductive Physicalism, selecting the right one that is benefited by progress in brain sciences. Second, I discuss epistemological problems in the search of brain correlates of consciousness, focusing on the simultaneous occurrence of conscious activity, known by means of subjective report, and the corresponding brain activity, registered with the help of technology. Finally, I argue – using Salmon´s concept of Statistical Explanation – that statistics affords a distinction of causal (physical) from casual (illusory) correlations.

Description: Despite predictive success, population dynamics and evolutionary game theory still pose fundamental problems. Violation of the competitive exclusion principle in plankton communities provides an example. A promising solution of this ‘paradox of the plankton’ comes from theories involving cyclic competition, an evolutionary analogue of the classical rock-paper-scissors (RPS) game. However, modeling probabilistic RPS structures, one encounters a fundamental difficulty: the pairs rock-scissors, scissors-paper, and paper-rock possess representations in separate Kolmogorovian probability spaces, but a single global probability space for entire triplets does not exist. Populations that take part in cyclic competition should therefore involve probabilistic incompatibilities, analogous to those occurring in quantum mechanics. Here, using experimental data collected from 1990 to 2011 on the RPS cycles of lizards, we show that the incompatibilities are indeed unavoidable, and the data cannot be reconstructed from a single Kolmogorovian probability space. We then prove that the effect is genuinely quantum probabilistic, i.e. all the probabilities can be formulated in terms of a single density matrix and a set of non-commuting projectors. This formal quantum structure is dormant in games where probabilities of strategies do not entangle with probabilities of payoffs, and thus could be overlooked. In more realistic scenarios, involving games ‘with ace in a sleeve’, the non-Kolmogorovian structure can be activated. Surprisingly, lizards occasionally do play such games. In consequence, the formalism of evolutionary games, similarly to quantum mechanics, should begin with density matrix equations. Implications of our finding extend beyond lizard communities, given that RPS games are common in nature and higher dimensional RPS games may be even more common in ecosystems.

Description: A wide variety of chemicals having distinct odors are smelled by humans. Odor perception initiates in the nose, where it is detected by a large family of olfactory receptors (ORs). Based on divergence of evolutionary model a sequence of human ORs database has been proposed by D. Lancet et al (2000, 2006). It is quite impossible to infer whether a given sequence of nucleotides is a human OR or not, without any biological experimental validation. In our perspective, a proper quantitative understanding of these ORs is required to justify or nullify whether a given sequence is a human OR or not. In this paper, all human OR sequences have been quantified, and a set of clusters have been made using the quantitative results based on two different metrics. Using this proposed quantitative model, one can easily make probable justification or deterministic nullification whether a given sequence of nucleotides is a probable human OR homologue or not, without seeking any biological experiment. Of course a further biological experiment is essential to validate the probable human OR homologue.

Description: Drug Discovery is shifting focus from the industry to outside partners and in the process creating new bottlenecks, suggesting the need for a more disruptive overhaul. Technologies like high throughput screening (HTS) have moved to a larger number of academic and institutional laboratories in the US, with little apparent coordination or consideration of the outputs and creating a translational gap. While there have been collaborative public private partnerships in Europe to share pharmaceutical data, the USA has lagged behind. Sharing precompetitive computational models may be the next frontier to provide more confidence in the quality of the leads produced and attract investment. We suggest there needs to be an awareness of what research is going on in the screening centers, more collaboration and coordination. These efforts will shift the focus to finding the best researchers to fund and require a rethink of how to reward their collaborative efforts.

Description: Climate change has manifested differential impacts on various components of the earth system. The impact of climate change is not merely limited to the climatic variable. Climate change has resulted in complex, unforeseen consequences in the biosphere of earth. The silent but gradual changes arise out of varied responses of disease-causing organism to the combination of the disease-conducive environmental variables. The change is the same for both the target hosts plant as well as the animal kingdom. There is an urgent need to look into the changing disease dynamics and the disease pathogen genome sensitivity to the changes in climatic variables. The long memory of genetic makeup of disease pathogen to capture, inherit and evolve or mutate the changed or impacted gene due to climate change in generation after generation may invite a cascading effect on the next generation of biosphere. These silent but gradual changes in the genome of disease organism are rarely investigated or included in simulation models. This also enhances the risk of quantification of uncertainties of various disease simulation models. Thus, chances and lists of black swan events in life and food insecurity are on the rise.

Description: Climate change has manifested differential impacts on various components of the earth system. The impact of climate change is not merely limited to the climatic variable. Climate change has resulted in complex, unforeseen consequences in the biosphere of earth. The silent but gradual changes arise out of varied responses of disease-causing organism to the combination of the disease-conducive environmental variables. The change is the same for both the target hosts plant as well as the animal kingdom. There is an urgent need to look into the changing disease dynamics and the disease pathogen genome sensitivity to the changes in climatic variables. The long memory of genetic makeup of disease pathogen to capture, inherit and evolve or mutate the changed or impacted gene due to climate change in generation after generation may invite a cascading effect on the next generation of biosphere. These silent but gradual changes in the genome of disease organism are rarely investigated or included in simulation models. This also enhances the risk of quantification of uncertainties of various disease simulation models. Thus, chances and lists of black swan events in life and food insecurity are on the rise.

Description: Protein chemistry uses protein description and classification based on molecular mass and isoelectric point as general features. Enzymes are also compared by enzymatic reaction constants, namely Km and kcat values. Proteins are also studied by binding to different oligonucleotides. Here we suggest a simple experimental method for such a comparison of DNA binding proteins, which we call "nucleic acid-protein fingerprints". The experimental design of the method is based on an use of short oligonucleotides immobilized inside microarray of hydrogel cells – biochip. As a first stage, we solved a simple experimental task: what is the shortest single strand oligonucleotide to be recognized by protein? We tested binding of oligonucleotides from 2 to 12 bases, and we have obtained unexpected result that tetranucleotide one is long enough for specific protein binding. This 4-mer can contain two universal bases – 5-nitroindole nucleoside analogue (Ni) and only two meaningful bases, like A, G, T and C. The result obtained opens a way for constructing the simplest protein binding microarray. This microarray consists of 16 meaningful dinucleotides, like AA, AG, CT, GG etc. Physical sequences of all the nucleotides were NiNiAA, etc, where Ni is bound to gel through the amino linker. We prepared such an array and tested it for specific binding of several DNA/RNA binding proteins, labeled with fluorescent dyes like Texas Red of Bodipy. We tested RNase A and Binase for binding on the simplest microarray. It contains only 16 units, and there is a significant difference in the binding patterns. The microarray based on 3-mers must contains 64 units and must have much more specificity. The new principle of protein classification based on nucleic acid-protein recognition has been proposed and experimentally proved. Such an experimental approach must lead to a universal classification of specific DNA/RNA binding proteins.

Description: This paper presents a novel method to segment/decode DNA sequences based on n-gram statistical language model. Firstly, we find the length of most DNA “words” is 12 to 15 bps by analyzing the genomes of 12 model species. The bound of language entropy of DNA sequence is about 1.5674 bits. After building an n-gram biology languages model, we design an unsupervised ‘probability approach to word segmentation’ method to segment the DNA sequences. The benchmark of segmenting method is also proposed. In cross segmenting test, we find different genomes may use the similar language, but belong to different branches, just like the English and French/Latin. We present some possible applications of this method at last.

Description: For a broad spectrum of low level cognitive regulatory and other biological phenomena, isolation from signal crosstalk between them requires more metabolic free energy than permitting correlation. This allows an evolutionary exaptation leading to dynamic global broadcasts of interacting physiological processes at multiple scales. The argument is similar to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological subsystems. Not only is the living state characterized by cognition at every scale and level of organization, but by multiple, shifting, tunable, cooperative larger scale broadcasts that link selected subsets of functional modules to address problems. This multilevel dynamical viewpoint has implications for initiatives in translational medicine that have followed the implosive collapse of pharmaceutical industry ‘magic bullet’ research. In short, failure to respond to the inherently multilevel, multiscale nature of human pathophysiology will doom translational medicine to a similar implosion.

Description: For a long time ecologists have questioned the variations of biodiversity across the latitudinal gradient. Recently it has emerged that the changes in β-diversity are caused simply by changes in the sizes of species pools. I combined the species pool size and the fractal nature of ecosystems to clarify some general patterns of this gradient. Considering temperature, humidity and NPP as the main variables of an ecosystem niche and as the axis of the polygon in the Cartesian plane, it is possible to build fractal hypervolumes, whose the fractal dimension rises up to three, moving towards the equator. It follows that the best figure that graphically synthesizes the evolutionary forces that fit this ecosystem hypervolume is the fractal cauliflower.

Description: We studied the dispersion of Aedes aegypti during egg laying in natural conditions. Two independent experiments involving mosquitoes dispersing from urbanization towards adjacent un-urbanized areas were carried out and analyzed in statistical terms. We find relations between stochastic variables related to the egg laying mosquito activity (ELMA), useful to assess dispersion probabilities, despite the lack of knowledge of the total number of ovipositions in the zone. We propose to evaluate the activity as minus the logarithm of the fraction of negative ovitraps at different distances from buildings. We also estimate the average number of eggs laid per oviposition using a regression between the ELMA and the number of eggs found. Three zones with different oviposition activity were determined: a corridor surrounding the urbanized area, a second region between 10m and 25m and the third region extending from 30m to 45m from the urbanization. The landscape (plant cover) and the human activity in the area appear to have an influence in the dispersal of Aedes aegypti.

Description: Human CK2α2 is an enzyme that belongs to the Serine/Threonine protein kinase family which is involved in signal transduction. Over expression of CK2α2 causes kidney cancer therefore, human CK2α2 has been identified as a drug target for the development of potential antagonists against cancer therapy. The existing human CK2α2 inhibitors in clinical practice are having side effects like fatigue, diarrhea, nausea, anorexia and vomiting. High-throughput virtual screening is one of the most common method used to identify lead compounds was implemented in the present study to identify potential inhibitors of human CK2α2. The co-crystal structure of human CK2α2 was retrieved from the protein data bank. A 2D similarity search was performed for available five human CK2α2 inhibitors (Apigenin, VX680, Sunitinib, SUI4813 and CCK) taken from PDB and PubMed to acquire 1942 structural analogs. The 3D structural conversion and multiple confirmations for 1942 compounds were generated using LigPrep. The docking and scoring calculations were performed using Glide v5.7 which includes high throughput virtual screening (HTVS), Standard precision (SP) docking and extra precision (XP) docking. Obtained 39 leads were compared with docking scores of the existing inhibitors and proposed six leads having good binding affinity. The binding orientation of CK2α2-lead 1complex was correlating with native co-crystal structure. Hence, lead ‘1’ can be suggested as potent inhibitor against human CK2α2 involved in kidney cancer.

Description: Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication, and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and ``ancient” Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com.

Description: Peroxisome proliferator-activated receptor (PPAR γ) acts as a key regulator on adipocyte differentiation and glucose homeostasis. PPAR γ has been implicated in the pathology of type 2 diabetes. As human PPAR γ activity is considered important in improving insulin sensitivity, in silico screening was carried out to find potent agonists for human PPAR γ protein. The co-crystal structure of PPAR γ, solved through X-Ray diffraction method was retrieved from the protein data bank. Four PPAR γ agonists selected from literature were submitted to subsequent 2D searching protocol using Ligand.Info, which yielded 1699 structural analogs. The PPAR γ co-crystal structure and ligand dataset were preprocessed using protein preparation wizard and LigPrep, respectively. Further, docking was performed by using three phased docking protocol of Maestro v9.2 that implements Glide v5.7. The obtained thirteen leads through docking were compared with the existing inhibitors and seven leads with good binding affinity with PPAR γ were proposed. The binding orientations of the seven leads were coinciding well with the native co-crystal structure of human PPAR γ. Thus, the proposed seven leads can be suggested as potential agonists for improving insulin sensitivity in the treatment of type 2 diabetes mellitus if synthesized and validated in animal models

Description: Background: The consumption of diets high in calories and low in nutrient value is becoming increasingly common in modern society, which can lead to metabolic disorders like diabetes and obesity, and potentially to psychiatric disorders. We have performed studies to assess how the shift from a healthy diet rich in omega-3 fatty acids to a diet rich in saturated fatty acid affects the substrates for brain plasticity and function, and anxiety and depression-like behavior. Methods: Pregnant rats were fed with omega-3 supplemented diet from their 2nd day of gestation period as well as their male pups for 12 weeks. Afterwards, the animals were randomly assigned to either a group fed on the same diet or a group fed on a high-fat diet (HFD) rich in saturated fats for 3 weeks. Anxiety and depression-like behaviors were assessed by using open field (OF) and elevated plus maze (EPM). Molecular assessments were performed in the frontal cortex and hippocampus as dysfunctions in these brain regions are main contributors towards depression, anxiety-like behavior and stress. Results: We found that the HFD increased vulnerability for anxiety and depression-like behavior, and that these modifications harmonized with changes in the anxiety-related neuropeptide Y (NPY)-1 receptor. The HFD reduced levels of brain-derived neurotrophic factor (BDNF), and the BDNF signaling receptor pTrkB, as well as the cyclic AMP response element binding protein (CREB), in these brain regions. Brain DHA contents were significantly associated with the levels of anxiety and depression-like behavior in these rats. Conclusions: These results suggest that the change in dietary lifestyle leading to alteration of dietary n3/n-6 fatty acids levels imposes a risk factor for anxiety-like behaviors. Dietary DHA might help for building cognitive reserve that can resist psychiatric disorders.

Description: In vivo, half-lives of cytidine analogues such as 5-azacytidine and decitabine, used to treat myelodysplastic syndromes (MDS), are determined largely by cytidine deaminase (CDA), an enzyme that rapidly metabolizes these drugs into inactive uridine counterparts. Genetic factors influence CDA activity, and hence, could impact 5-azacytidine/decitabine levels and efficacy, a possibility requiring evaluation. Using an HPLC assay, plasma CDA activity was confirmed to be decreased in individuals with the CDA SNP A79C. More interestingly, there was an even larger decrease in females. Explaining the decrease in enzyme activity, liver CDA expression was significantly lower in female versus male mice. As expected, decitabine plasma levels, measured by mass-spectrometry, were significantly higher in females. In mathematical modeling, the detrimental effect of shortening half-life of S-phase specific therapy was amplified in low S-phase fraction disease (e.g., MDS). Accordingly, in multivariate analysis of MDS patients treated with 5-azacytidine/decitabine, overall survival was significantly worse in males.

Description: Biological molecules such as proteins and metabolites interact to accomplish a biological function and to respond to environmental stimuli. Pathways capture this information derived through scientific experimentation and data analysis. They contain information about genes that appear in complexes, the interacting genes, the directionality of the interactions (e.g. inhibitors versus activators), the cellular locations where the reactions occur, and the metabolites that are affected by the processes. Using our open-source pathway analysis platform, PathVisio, we will connect pathway analysis to different quantitative approaches already in development for metabolic network modeling, such as flux balance analysis and dynamic simulation. In order to use system-wide measurements to gain insights into this mechanism, we have to integrate large scale data analysis with modeled or measured fluxomics dataresults. For this we will develop a BridgeDb database for reaction identifiers, develop a PathVisio plugin for visualization of modeling results and architect a flexible, standards-based visualization approach (e.g. using MIM and SBGN) that will enable visualization of any conforming model, including visualization of the model output (e.g. flux changes). The focus here is on visualization of the modeling results, which will be critical for understanding how simulated models correlate with experimental measurements On the same lines, we will also find a solution to the problem of annotating metabolites in all pathways. The approach here is to use known Gene Ontology annotations for associated genes. Firstly we will incorporate automatically inferred GO categories into all WikiPathways. Develop GO visualization plugin to show gene categories on pathways and further assign automatically inferred GO categories to all addressable metabolites in WikiPathways. The last step would be to develop basic metabolite ontology analysis tools both with python GUIs and as Bioconductor modules.

Description: The generation of biodiversity is tied to the evolution and re-wiring of gene regulatory networks (GRNs). One component of these GRN are transcription factors and other transcriptional regulators. We have devised a pipeline for the identification of TFs and TRs, exploiting the domain architecture of these proteins. Currently we have a set of rules, representing 138 proteins families, that we have applied to the identification of ~20 different plant species and several species of Stramenopiles, where important plant pathogens are found. Results for plant species are available at http://plntfdb.uniandes.edu.co/; we are now developing a newer interface for Stramenopiles.

Description: Over the last few years, good quality freezable semen was not utilized effectively due to less knowledge about the freezability of semen. One reason is the lack of sufficient antioxidants in the seminal plasma and semen extender. The antioxidant content is reduced during the cryopreservation process and causes premature cryo-capacitation and modification of sperm membrane structure upon thawing. So the study of pre-freezing and post thaw seminal parameters like viability, motility, acrosomal integrity, lipid peroxide assay, vanguard distance traveled by sperm, mitochondrial membrane potential, velocity and motility parameters (CASA) and field fertility trial helped to assess the effectiveness of the additives. The conception rate was better in reduced glutathione than the cysteine hydrochloride treated group. The glutathione has improved the poor freezing and maintained the good freezable semen. Thus the field fertility rate was enhanced and in turn helped to prevent waste of good quality germplasm and repeat breeder syndrome in cows.

Description: We show here the effects of heavy-hydrogen water (2H2O) and heavy-oxygen water (H218O) on the gliding speed of microtubules on kinesin-1 coated surfaces. Increased fractions of isotopic waters used in the motility solution decreased the gliding speed of microtubules by a maximum of 21% for heavy-hydrogen and 5% for heavy-oxygen water. We discuss possible interpretations of these results and the importance for future studies of water effects on kinesin and microtubules. We also discuss the implication for biomolecular devices incorporating molecular motors.

Description: Acute and chronic progression of injury to the kidney leads to the failure of the renal system and has become an increasingly important cause of morbidity and mortality. Present diagnosis detects the condition only after irreversible loss of 70 percent of kidney function. Current research is focused only on the clinical manifestations after the kidney injuries and not towards the exact cause of the condition. Here we propose a new outlook- that there is an involvement of a pathogen in the pathogenesis of kidney injuries. Basis for our proposal is given by the similarity of the pathogenesis events occurring between a classical example of hepatitis and kidney injuries. Furthermore, literature regarding the role of early kidney injury biomarkers in innate immunity indicates the involvement of the pathogen. Research in this theme possesses a strong possibility in the development of therapeutic, preventive and management strategies for the acute and chronic kidney injuries.

Description: Bacteria will experience starvation-free environment if infinite nutrition is supplied continuously for a long period. In this study, an evolutionary experiment was performed for 118 days where bacteria adapted to starvation-free environment and reduced their doubling time. It is anticipated that this finding will help to select bacterial strains that can grow more rapidly in rich media.

Description: : The SBML Reaction Finder (SRF) application leverages the deep semantic annotations in the BioModels database to provide efficient retrieval and extraction of individual reactions from SBML models. We hope that the SRF will be useful to quantitative modelers who seek to accelerate their modeling efforts by reusing previously published representations of specific chemical reactions.Availability and Implementation: The SRF is open source, coded in Java, and distributed under the Mozilla Pubic License Version 1.1. Windows, Macintosh and Linux distributions are available for download at http://sourceforge.net/projects/sbmlrxnfinder.

Description: For the genome-wide identification of nucleosome depleted regions under carbon deprivation, we analyze an available set of data from an assay of formaldehyde-assisted isolation of regulatory elements followed by sequencing (FAIRE-seq). Mapping to the sequenced nuclear genome of C.reinhardtii, followed by the identification of the enrichment-sequenced fragments was performed. We examined the location of these fragments relative to annotated genes. The related genes were associated to the corresponding Gene-Ontology (GO), for an evaluation of over-representate GO categories. Some genes, link with functions or locations, that have been previous described, indicating the success of the method finding carbon-metabolism related fragments.

Description: Complex Systems Biology models and theories are axiomatically defined in terms of concrete categories and organismic supercategories (OS) to include both complete self-reproduction of logically defined pi-entities founded in Quine’s logic and dynamic system diagrams subject to both algebraic and topological transformations. Mathematical models of complex organisms are expressed in terms of category theory and organismic supercategories (OS). OS theories have applications in: Bioinformatics, Developmental Biology, Genomics and Molecular Cell Biology

Description: Quantitative models of biological systems provide an understanding of chemical and biological phenomena based on their underlying mechanisms. Moreover, they can be used for example, to predict the behaviour of a system under given conditions or direct future experiments. This has made quantitative models the perfect tools to answer a variety of questions in the biological sciences and has lead to a steady growth of the number of published models.To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. BioModels Database(http://www.ebi.ac.uk/biomodels/) has been developed to exactly fulfil those needs. In order to ensure the correctness of the models distributed, their structure and behaviour are thoroughly checked. To ease their understanding, the model elements are annotated with terms from controlled vocabularies as well as linked to relevant data resources. Finally, to allow their reuse, the models are provided encoded in community supported and standardised formats.However, the modelling field is constantly evolving and data providers, like BioModels Database, are faced with new challenges. For example, models are getting more and more complex (with for instance the availability of whole organism metabolic network reconstructions) and this has a direct impact on the performance of hosting infrastructures and annotation procedures. Also, models are now being developed collaboratively: this requires new methodologies and systems, akin to the ones used in software development (with for example versioned repositories of models). Moreover, very different kinds of models are being developed by diverse communities, but ultimately their data management needs are very similar.This talk will introduce the needs which lead to the development of BioModels Database, present the resource and its current infrastructure and finally discuss the challenges that we are facing today and the plans to overcome them.

Description: Cadmium- and lead-based quantum dots are normally coated for biological applications, because their degradation may result in the release of toxic heavy metal ions. Here, we synthesize silicon quantum dots that are expected to biodegrade to non-toxic products. A chitosan coating is used to render the silicon quantum dots stable in storage conditions and biodegradable at physiological conditions. The applications of these particles are demonstrated in cellular imaging with single and two-photon excitation. These results open the door for a new generation of silicon quantum dots that may have a wide variety of applications derived from the flexibility of chitosan.

Description: Protein kinases are essential effectors of cellular signaling. Surprisingly, using bioinformatics tools, we predicted protein kinase structure and function for proteins of unknown function (FAM69 family) coded by five related human genes and their Metazoan homologues. Analysis of three-dimensional structure models and conservation of the classic catalytic motifs of protein kinases in four of human FAM69 proteins suggests they might have retained catalytic phosphotransferase activity. The FAM69 genes, FAM69A, FAM69B, FAM69C, C3ORF58 and CXORF36, are by large uncharacterized molecularly, yet linked to several neurological disorders in genetics studies. An EF-hand Ca2+-binding domain in FAM69A and FAM69B proteins, inserted within the structure of the kinase domain, suggests they function as Ca2+-dependent kinases.

Description: The activity of cortical neurons in sensory areas covaries with perceptual decisions, a relationship often quantified by choice probabilities. While choice probabilities have been measured extensively, their interpretation has remained fraught with difficulty. Here, we derive the mathematical relationship between choice probabilities, read-out weights and noise correlations within the standard neural decision making model. Our solution allows us to prove and generalize earlier observations based on numerical simulations, and to derive novel predictions. Importantly, we show how the read-out weight profile, or decoding strategy, can be inferred from experimentally measurable quantities. Furthermore, we present a test to decide whether the decoding weights of individual neurons are optimal, even without knowing the underlying noise correlations. We confirm the practical feasibility of our approach using simulated data from a realistic population model. Our work thus provides the theoretical foundation for a growing body of experimental results on choice probabilities and correlations.

Description: The aim of our work was to develop a tool integrated into Quantum GIS (QGIS) that can helpthe user estimate and visualize the possible infective areas around an outbreak based on HYbrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model.

Description: Computational and statistical analysis has formed a large component of the biophysical efforts put forth to understand protein structure and function, due to the diversity and complexity of their structure. Outer membrane proteins form a diverse and complex set of proteins. Of these, porins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective. The objective of this study is to analyze the structural organization of porins using atomic temperature factor as a parameter. Generally atomic temperature factors of molecules from crystal structures indicate the degree of mobility or disorder seen in the crystal structure. As good crystal structures have fewer possibilities of errors so there is less chance that errors are playing roles in temperature factors. Structures of six porins (four 16 stranded beta barrel porins and two 8 stranded beta barrel porins) were taken from the PDB for the analysis based on resolution and R-factor. Programs and scripts were written for extracting the temperature factors for the beta strands, loops and turns so that the analysis could be done for different atom-types and residue-types. The residue distribution and mobility distribution was found to be characteristic of each of the porins. The mobility and residue distribution amongst the secondary structural elements were found to follow the level of homology at the sequence and structural level. The loops that had defined functional roles in structural terms were found to have lower temperature factors than the other loops. The turn regions that are thought to face the periplasmic region in the cell, showed higher temperature factors. For both the 16 stranded and the 8 stranded barrels it was found one part of the barrel (the lower wall or ‘inner’ wall comprising the trimer interface in the case of the 16 stranded barrels) was more rigid and the other half of the barrel (the higher or ‘outer’ wall) showed more mobility as seen from the temperature factors. This seems to be an intrinsic structural component of the beta barrels.

Description: The theories on obesity genesis shifted during the past years from the simple conception of “just overeating” to data supporting the diencephalic origin of the disease. Summarized findings on this issue are displayed.

Description: Gene transduction and expression efficiencies among several type cell lines were compared by using vesicular stomatitis virus-glycoprotein (VSV-G) pseudotyped human immunodeficiency virus type-1 (HIV-1) based lentivirus vector. Large discrepancies of the efficiencies were shown among them. B lymphocytes showed high susceptibility of gene transduction and expression, while other cell lines marked lower potential. Variable gene transduction strategies have been assessed to apply immunological therapies. This study showed that B lymphocytes had facilities enough to support the gene transduction and expression by lentivirus vector. Our result suggested that the lentivirus vector would be a powerful tool to express exogenous genes in B lymphocytes.

Description: The genomes of nine isolates of Hemileia vastatrix, the causal agent of coffee leaf rust were sequenced by Illumina and 454. Quality control, cleaning and de novo assemblies of data were performed. Since isolates were obtained from the field and it is not possible to produce axenic cultures of H. vastatrix, MEGAN software was used to evaluate contamination levels and to select contigs with fungal similarities. Mitochondrial contigs were identified and annotated by comparing this assembly against the Puccinia genome. Furthermore, two transcriptomes from isolates of H. vastatrix were assembled to complement the genomic data.

Description: One of the authors (AL) presented a poster on 34 pregnancies of maternal Lyme borreliosis (Lb) in 1995. It was striking that untreated Lb associated with higher probability of adverse outcome but the number of patients were small and the statistical power was low. We have recently published a paper on 95 maternal Lb and the outcome of their pregnancies. Since the closure of the database for that manuscript the number of the pregnant women with Borrelia infection observed in our Centre increased to 124, and the statistical analysis strengthened our previous doubtful observations and reached significant results in important aspects by now. This series is the largest study to date on this topic. Treatment was administered parenterally to 87 (70%) women and orally to 25 (20.0%). Infection remained untreated in 12 (10%) pregnancies. Adverse outcomes were seen in 7/87 (8%), 9/25 (36%), 8/12 (67%), of the parenterally, orally treated and untreated women, respectively. In comparison to patients treated with antibiotics, untreated women had a significantly higher risk of adverse pregnancy outcomes (OR: 11.62, ps triad in syphilis is unlikely.

Description: The epidermal depigmentary trigger in humans at post-natal level may occur with the toxification of skin organ with the endogenously produced melanocytotoxic hydrogen peroxide and subsequent formation of hydrogen peroxide- melanolipoprotein conjugate involving the hydrogen bonding of complementary hydroxyl and carbonyl molecular surfaces of these biosignitures respectively. The condition is multifactorial but reversible. The structural and functional degeneration of melanocytes under the acquired condition never occur. The molecular conjugation theory on the aetiology and line of treatment of the epidermal depigmentary disorder (recoined as hepato-epidermal syndrome HES) has been proposed. The inherent sulfoxides of Allium cepa have been found as the renaturant of HES condition with the capacity to dislodge the denaturant hydrogen peroxide forming stronger hydrogen bonding with hydrogen peroxide than that of carbonyl molecular surface of melanolipoprotein, the epidermal colour determinant. The orally and topically defined plant based combined therapy advances the recovery time of HES condition.

Description: We report the twining handedness of Codonopsis pilosula, which has either a left- or right-handed helix among different plants, among different tillers within a single plant, and among different branches within a single tiller. The handedness was randomly distributed among different plants, among the tillers within the same plants, but not among the branches within the same tillers. Moreover, the handedness of the stems can be strongly influenced by external forces, i.e. the compulsory left and right forming inclined to produce more left- and right-handed twining stems, respectively, and the reversing could make a left-handed stem to be right-handed and vice versa. We also discuss the probable mechanisms these curious cases happen.

Description: Intravenous drug self-administration is the most valid animal model of human addiction because it allows volitional titration of the drug in the blood based on an individual’s motivational state together with the pharmacokinetic properties of the drug. Here we describe a reliable low-cost mouse self-administration catheter assembly and protocol that that can be used to assess a variety of drugs of abuse with a variety of protocols. We describe a method for intravenous catheter fabrication that allows for efficient and long-lasting intravenous drug delivery. The intravenous catheters remained intact and patent for several weeks allowing us to establish stable maintenance of cocaine acquisition. This was followed by a dose response study in the same mice. For collaborators interested in premade catheters for research please make a request at www.neuro-cloud.net/nature-precedings/pomerenze.

Description: We researched the ecology of the third rarest crane species, Siberian crane, which breeds in northern-eastern Siberian tundra. Nesting in places near great lakes, this crane appears to be an indicator of the global warming processes that affect lake growth as a result of the permafrost situation close to the surface in tundra. Research has shown that these birds are presumably fish-eating during their incubation period, coinciding with the flooding season when fish come to areas around great lakes. Such a diet may be explained by the necessity of high-energy food during the incubating period as well as the particularity of this species for leaving plant resources around the nest point for the period of the first days after chick hatching. This situation emphasizes tight connections in the vulnerable northern ecosystems. If the water level in tundra lakes starts to be higher due to global warming, all these links may be destroyed.

Description: One of the most influential observations in molecular evolution has been a strong association between regional recombination rate and amount of nucleotide polymorphism in those genomic regions, interpreted as evidence for ubiquitous natural selection. The alternative explanation, that recombination is mutagenic, has been rejected by the absence of a similar association between regional recombination rate and nucleotide divergence between species. However, many recent studies show that recombination rates are often very different even in closely related species, questioning whether an association between recombination rate and divergence between species has been tested satisfactorily. To circumvent this problem, we directly surveyed recombination across approximately 43% of the D. pseudoobscura physical genome in two separate recombination maps, and 31.3% of the D. miranda physical genome, and we identified both global and local differences in recombination rate between these two closely related species. Using only regions with conserved recombination rates between and within species and accounting for multiple covariates, our data support the conclusion that recombination is positively related to diversity because recombination modulates hitchhiking in the genome. Finally, our data show that diversity around nonsynonymous substitutions is recovered at closer distances in areas of higher recombination than in areas of lower recombination — empirically demonstrating that recombination rate can limit the size and severity of potential selective sweeps.

Description: The present study was aimed to assess the effect of pre-freeze addition of cysteine hydrochloride and glutathione (GSH) on post-thaw sperm functional parameters and field fertility. The experimental bulls aged 4 to 6 years were used for the present study. A total of 36 ejaculates, 6 ejaculates from each bull (n=6) were collected and divided in to three groups, group I (control), group II (5mM cysteine hydrochloride) and group III (5mM GSH). The extended semen samples were added with @5mM additives, filled in mini straw using automatic filling and sealing machine (IMV, France) and cryopreserved in liquid nitrogen. Post-freeze seminal traits were also recorded after thawing at 37oC for 30 seconds. Post thaw livability was significantly (p 〈 0.01) higher in GSH group as compared to cysteine and control groups. The loss of acrosomal integrity was significantly (p 〈 0.01) lower in GSH group than cysteine and control groups. Analysis of variance for post thaw motility parameters (Forward progressive and Total motility) has revealed that significant difference (p 〈 0.05) between the good and poor freezer in the group II and there was no difference in the group I and III under study at 0 and 1 hr incubation period and at 2 hrs the group III and at 4 hrs group I has revealed significance difference (p 〈 0.05).The curvilinear velocity (VCL) and amplitude of lateral head displacement (ALH) values were significantly (P0.05) higher than cysteine (58) and control (49) groups. The post-thaw sperm progressive forward motility (r=0.4) had moderate but, no significant correlation with conception rate. However post-thaw VSL (r=0.7), loss of acrosomal integrity (r=-0.8) and mitochondrial membrane potential (r=0.9) had significant (p 〈 0.05) correlation with field fertility. The present study indicates that the use of glutathione as semen additives may be recommended for improving semen quality and overall augmentation of pregnancy in cows. The present study suggests that pre-freeze addition of glutathione was found to be better than cysteine in improving sperm fertility.

Description: Scientific literature is the primary resource for relevant and innovative information. The integration of the literature with other data resources in the biomedical research community generates overhead that can be avoided through the used of Semantic Web Technology generating openly accessible data. Projects such as SESL and CALBC have producted significant amount of data that that are ready for exploitation.The tutorial will teach different approaches on how to integrate the scientific literature with the content from biomedical databases, and will discuss the inferences that can be achieved. Furthermore, the tutorial will point to the resources that are ready for use and enable integration of the literature at your discretion. A good understanding of Semantic Web technology, ontologies, OWL and the existing biomedical data resources is advantageous to easily follow the tutorial.

Description: Muscle-derived nitric oxide (NO) mediates fundamental physiological actions on skeletal muscle including glucose uptake into muscle cells. Recently, we have shown that the altered glucose metabolism in skeletal muscle of patients with type 2 diabetes (T2D) is associated with changes in the metabolic profile of individual muscle fibres, but fibre-type specific changes in NO synthase (NOS) expression in skeletal muscle of T2D patients remain to be elucidated. Here we investigated fibre-type related NOS expression in vastus lateralis muscle of T2D patients compared with healthy individuals with normal glucose tolerance (NGT). Cytophotometrical assay and Western blotting did not reveal any quantitative differences between NOS expression in muscles from NGT and T2D subjects. Positive NOS immunoreactivity in vastus lateralis of T2D patients was found to be associated with fast-oxidative glycolytic (FOG) muscle phenotype. This indicates that NOS expression in T2D patients correlates both with skeletal muscle fibre type distribution and the activity of oxidative and glycolytic enzymes.

Description: A critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several recent clinical studies have shown that gene expression data for cancer cells can be employed to distinguish between tumor types as well as to predict outcomes. Potentially important applications of such results are individualized human cancer therapies or, in general,’personalized medicine’ that will have to be validated through optimally designed clinical trials in cancer. A Human Cancer Genomes and Epigenetics Project is proposed that can provide the essential data required for the optimal design of clinical trials with the goal of achieving significant improvements of the survival rates of cancer patients participating in clinical trials for advanced cancer stages. The results of such a six-year Human Cancer Genomes and Epigenetics Project should also greatly aid with the accelerated, rational development of effective anti-cancer medicines and the chemoprevention of cancers.

Description: Life is an inordinately complex unsolved puzzle. Despite significant theoretical progress, experimental anomalies, paradoxes, and enigmas have revealed paradigmatic limitations. Thus, the advancement of scientific understanding requires new models that resolve fundamental problems. Here, I present a theoretical framework that economically fits evidence accumulated from examinations of life. This theory is based upon a straightforward and non-mathematical core model and proposes unique yet empirically consistent explanations for major phenomena including, but not limited to quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and amino acids, homeoviscous adaptation, the triplet code, and DNA mutations. The theoretical framework proves the unity of macrocosmic and microcosmic realms, validates predicted laws of nature, and solves the puzzle of the origin and evolution of cellular life in the universe.

Description: Soybean isoflavones are of considerable interest in relation to their possible health effects in human diets. The rapid and economical determination of soybean isoflavone concentrations is essential for the investigation and development of soybean health foods as well as the selection of soybean seeds with optimal isoflavone levels for such foods. Fourier transforms near infrared reflectance spectroscopy (FT-NIRS) calibrations were developed for the rapid and cost-effective analysis of isoflavones in soybean seeds. FT-NIRS measurements were carried out in quadruplicate for 50 soybean lines selected from the USDA Soybean Germplasm Collection. The selected soybean seeds provided a wide range of isoflavone concentrations (from 0.3 to 6.0 mg/g) that is necessary for development of high-quality calibrations. Laboratory reference values of isoflavone composition were obtained by HPLC analysis of extracted soybean powders. Single soybean seeds were selected for each standard sample and were cut in half in order to avoid screening of the isoflavones NIR absorption bands by the seed coat. For comparison purposes, measurements were also made on soybean powders of the same samples. FT -NIR spectra were collected with a spectral range from 4000 to 12000 cm-1 at a resolution of 8 cm-1 on a Perkin-Elmer Spectrum one NTS spectrometer model. This spectrometer is optimized for high sensitivity analysis of single seed composition, being equipped with an NIRA, integrating sphere accessory and an extended range InGaAs detector.

Description: We have developed a methodology for recording a robust P300 event related potential (ERP) in rats. In these experiments a contingency shaped model of the human “oddball’ paradigm was employed in which rats were shaped to press a lever for food reinforcement signaled by the click of the pellet dispenser. A target tone cued the insertion of the lever that retracted after 1­sec or immediately following a single reinforced response, while a non­target tone was randomly presented. Brain activity was recorded through stainless steel electrodes implanted 1mm below the skull. Here, we compared the amplitude of the P300 response to the click of the pellet dispenser to the amplitude of the P300 response to the target and non­target tones. We found that the amplitude to food click was significantly greater that the amplitude to the target tone that cued lever insertion. Since the food click is more proximal to the primary reinforcer than the lever tone, it is a stronger conditioned reinforcer than the lever tone that sets the occasion for the food click. Accordingly we suggest that the P300 in rats is a correlate of conditioned reinforcement.

Description: The manuscript advances a hypothesis that there are few fundamental principles of neural organization of cognition, which explain several wide areas of the cognitive functioning. We summarize the fundamental principles, experimental, theoretical, and modeling evidence for these principles, relate them to hypothetical neural mechanisms, and made a number of predictions. We consider cognitive functioning including concepts, emotions, drives-instincts, learning, “higher” cognitive functions of language, interaction of language and cognition, role of emotions in this interaction, the beautiful, sublime, and music. Among mechanisms of behavior we concentrate on internal actions in the brain, learning and decision making. A number of predictions are made, some of which have been previously formulated and experimentally confirmed, and a number of new predictions are made that can be experimentally tested. Is it possible to explain a significant part of workings of the mind from a few basic principles, similar to how Newton explained motions of planets? This manuscript summarizes a part of contemporary knowledge toward this goal.

Description: The main objective of this review is to highlight and explore the inter-relationship and the functioning of the intellectual property right in the pharmaceutical and biotechnology industry. The rising tide of patent applications can be witnessed globally in this industry as the need for such protection and licensing has become imperative so as to safeguard the rights of the inventor and also to encourage and promote new talents, inventions and innovations which can be a boon for the economy. The field of biotechnology is an upcoming science which is still at the initial stage of establishing a foundation but it promises a revolution in the fields of medicine, agriculture, pharmaceuticals and industrial sector amongst other sectors of the economy along with contribution to the GDP growth.

Description: Hepatitis is deadly, and the fifth leading cause of death after heart disease, stroke, chest disease and cancer. Worldwide, 1.5 million deaths per year have been estimated. Detection of hepatitis is a big problem for general practitioners. An expert doctor commonly makes decisions by evaluating the current test results of a patient or by comparing the patient with others with the same condition with reference to the previous decisions. Many machine learning and data mining techniques have been designed for the automatic diagnosis of hepatitis. However, no one tool is available to the general population for the diagnosis of Hepatitis. Hence, a graphical user interface-enabled tool needs to be developed, through which medical practitioners can feed patient data easily and find hepatitis diagnoses instantly and accurately. Methods: In this study a hepatitis dataset was taken from the UCI machine repository database with a total of 20 attributes of two classes, Affected and Not Affected. Results and Conclusion: The models have been generated with a mixture of experts as a classification method for the diagnosis of hepatitis. Very good accuracy has been observed in the generated models. Finally, the model having the least minimum square error was selected. This model was then linked with GUI for the design of tools for hepatitis prediction.

Description: Systems biology is a multi-disciplinary field that deals with mechanisms involved in complex biological processes by considering them as integrated systems of multiple interacting components. The huge amount of data involved in this study necessitates the use of computational tools.

Description: A salient feature of prefrontal cortex organization is the vast diversity of cell types that support the temporal integration of events required for sculpting future responses. A major obstacle in understanding the routing of information among prefrontal neuronal subtypes is the inability to manipulate the electrical activity of genetically defined cell types over behaviorally relevant timescales and activity patterns. To address these constraints, we present here a simple approach for selective activation of prefrontal excitatory neurons in both in vitro and in vivo preparations. Rat prelimbic pyramidal neurons were genetically targeted to express a light-­activated nonselective cation channel, channelrhodopsin-­2, or a light-­driven inward chloride pump, halorhodopsin, which enabled them to be rapidly and reversibly activated or inhibited by pulses of light. These light responsive tools provide a spatially and temporally precise means of studying how different cell types contribute to information processing in cortical circuits. Our customized optrodes and optical commutators for in vivo recording allow for efficient light delivery and recording and can be requested at www.neuro-­cloud.net/nature-precedings/baratta.

Description: Human childhood and adolescence is the period in which adult cognitive competences (including those that create the unique cooperativeness of humans) are acquired. It is also a period when neural development puts a juvenile’s survival at risk due to the high vulnerability of their brain to energy shortage. The brain of a 4 year-old human uses ≈50% of its total energy expenditure (TEE) (cf. adult ≈12%). This brain expensiveness is due to (1) the brain making up ≈6% of a 4 year-old body compared to 2% in an adult, and (2) increased energy metabolism that is ≈100% greater in the gray matter of a child than in an adult (a result of the extra costs of synaptic neuromaturation). The high absolute number of neurons in the human brain requires as part of learning a prolonged neurodevelopment. This refines inter- and intraarea neural networks so they become structured with economical “small world” connectivity attributes (such as hub organization and high cross-brain differentiation/integration). Once acquired, this connectivity enables highly complex adult cognitive capacities. Humans evolved as hunter-gatherers. Contemporary hunter-gatherers (and it is also likely Middle Paleolithic ones) pool high energy foods in an egalitarian manner that reliably supported mothers and juveniles with high energy intake. This type of sharing unique to humans protects against energy shortage happening to the immature brain. This cooperation that protects neuromaturation arises from adults having the capacity to communicate and evaluate social reputation, cognitive skills that exist as a result of extended neuromaturation. Human biology is therefore characterized by a presently overlooked bioenergetic-cognition loop (called here the “HEBE ring”) by which extended neuromaturation creates the cooperative abilities in adults that support juveniles through the potentially vulnerable period of the neurodevelopment needed to become such adults.

Description: The ejaculated semen consists of two major components viz. sperm cells (spermatozoa) and the fluid part obtained after centrifugation called seminal plasma. The spermatozoa originate from the semniferous tubule and are suspended in the seminal plasma. The seminal plasma is composed of secretions contributed by the testis, epididymis, seminal vesicles, ampullae, prostate and bulbourethral glands. About 60-80 % of the ejaculated semen of the bull originates from these sources. Seminal plasma is a highly complex biological fluid containing proteins, amino acids, enzymes, fructose and other carbohydrates, lipids, major minerals and trace elements. Seminal plasma proteins partly originates from the blood plasma by exudation through the lumen of the male genital tract and partly are synthesized and secreted by various reproductive organs and are known as seminal plasma specific proteins. Several seminal plasma proteins of blood origin viz. prealbumin, albumin, globulin, transferring, α-antitrypsin, β-lipoprotein, β-glycoprotein, orsomucoid, kininogen, Peptide hormones, IgG, IgA and IgM have been identified and characterized. These proteins are involved in regulation of osmotic pressure and pH of seminal plasma, transport of ions, lipid and hormones. A major part of seminal plasma proteins originate from the testis, epididymis, vas deference, prostate, seminal vesicle and bulbourethral glands. The biosynthesis and secretion of these proteins is regulated by testosterone levels in the blood.

Description: In this study we identify, and classify into families, transcription factors (TFs) and other transcriptional regulators (TRs) in genome sequences available from the Stramenopile group. For this we exploit the presence of protein domains and their combinations to build rules in the form of boolean rules, that are specific for each family of TFs and TRs. We found a correlation between the family size and some traits that has been described to be involved in the complexity of organisms. Furthermore, we found specific gains, losses and families that shows higher abundance in different lineages, which may be involved in the regulation of specific traits for some Stramenopile species.

Description: Foraging bees use colour cues to help identify rewarding from unrewarding flowers, but as conditions change, bees may require behavioural flexibility to reverse their learnt preferences. Perceptually similar colours are learnt slowly by honeybees and thus potentially pose a difficult task to reverse-learn. Free-flying honeybees (N = 32) were trained to learn a fine colour discrimination task that could be resolved at ca. 70% accuracy following extended differential conditioning, and were then tested for their ability to reverse-learn this visual problem multiple times. Subsequent analyses identified three different strategies: ‘Deliberative-decisive’ bees that could, after several flower visits, decisively make a large change to learnt preferences; ‘Fickle- circumspect’ bees that changed their preferences by a small amount every time they encountered evidence in their environment; and ‘Stay’ bees that did not change from their initially learnt preference. The next aim was to determine if there was any advantage to a colony in maintaining bees with a variety of decision-making strategies. To understand the potential benefits of the observed behavioural diversity agent-based computer simulations were conducted by systematically varying parameters for flower reward switch oscillation frequency, flower handling time, and fraction of defective ‘target’ stimuli. These simulations revealed that when there is a relatively high frequency of reward reversals, fickle-circumspect bees are more efficient at nectar collection. However, as the reward reversal frequency decreases the performance of deliberative-decisive bees becomes most efficient. These findings show there to be an evolutionary benefit for honeybee colonies with individuals exhibiting these different strategies for managing resource change. The strategies have similarities to some complex decision-making processes observed in humans, and algorithms implemented in artificial intelligence systems.

Description: Pigeonpea is one of the most popular legume grains in the world, especially in the Indian sub-continent. Keeping in view the importance of the crop, an efficient protocol for rapid in vitro plant regeneration from cotyledon of redgram has been reported in this paper. The concentraion of the hormones played an important role in shoot and root regeneration.

Description: The nature of competition and biodiversity are open basic questions since Darwin. To investigate mechanisms of interspecific competition and their contribution in biodiversity as closely as possible we offer a white-box modelling method based on physically interpreted ecological axioms. These models are implemented as deterministic individual-based cellular automata and able to give a direct physico-mechanistic insight into studied phenomena. Competition of two trophically identical but fitness different species, competing for one limiting resource in one stable uniform habitat (which is closed for immigration, emigration, predation, herbivory and parasitism) has been investigated in conditions, which are the most unfavourable for their coexistence. The species are per capita identical in fecundity, ontogeny, regeneration features of microhabitats, and in habitat requirements. We have modelled following 8 mechanistic mechanisms of interspecific competition: 1. A case of the competitive exclusion when competing species differ only in fitness. 2. Coexistence based on periodic dominance changeovers as a consequence of environmental changes. Competing species differ only in fitness. 3. A strong violation of the competitive exclusion principle due to the lowered fecundity of both competitors. Competing species differ only in fitness.4. Coexistence based on the competition–colonisation trade-off when greater fitness is compensated by r-strategy.5. A competition–colonisation trade-off based on differences in ontogeny. 6. Competitive exclusion when recessive species drives out the dominant one having four times greater fecundity than the dominant one in stable environment (the greater fitness cannot compensate r-strategy). 7. An inverted competitive exclusion when recessive species drives out the dominant one by strategy of anticipatory deprivation of resources for competitor’s offsprings propagation. Recessive species drives out the dominant one in stable environment and both competing species have identical fecundity (tripod neighbourhood). Paradoxically, but the greater fitness cannot save the dominant species when the all other parameters of the species are equal.8. Both competing species die because the regeneration of a limiting environmental resource takes too much time and they cannot propagate. The revealed mechanisms of competition can be useful not only in conservation biology, but also in economics and politics. Additionally, we speculate that the simplest way to maintain biodiversity is a controlled reduction of human fertility as the decrease in biodiversity occurs largely due to humankind overloading of biosphere resources.

Description: A four year old child devotes half their total energy expenditure (TEE) to their brains. Even by 10 years-of-age it is still 30% (compared to an adult’s ≈12%). This extreme energy use results from a high brain/body size ratio – combined with a doubling of cerebral gray matter energy utilization (due to synaptic exuberance during cognitive neuromaturation). With extreme energy expenditure goes extreme vulnerability to hypoglycemia: (1) children become hypoglycemic after 24-36 hours of fast (compared to 60-72 hours in adults), and (2) their brains suffer neurological impairment (shown in disrupted P300 potentials) at a lower decrease in plasma glucose: 3.6 – 4.2 mmol L-1 in children rather than 〈 3.0 mmol L-1 in adults (against a normal level in both of 4.6-4.8 mmol L-1). Human biology has selected adaptations that buffer and protect children from this energy lability. A physiological one is that energy metabolism in skeletal muscles is biased towards using fatty acids, and this minimizes uptake competition of plasma glucose between muscles and the brain. Behavioral adaptations (in human hunter-gatherers) include adults cooperatively pooling high energy foods with juveniles for ≈15 years, this provides juveniles with a reliable ≈3.5-7 MJ per day. Hunter-gatherers share food with juveniles due to gossip enforced indirect reciprocity. This reciprocity depends for its existence upon adult cognitions that require prolonged energy- expensive neuromaturation. This raises the possibility that human adult cognitions are both a cause of children having extreme energy lability (by requiring prolonged energy expensive neuromaturation), and a means (by enabling indirect reciprocity) by which the risks of such lability are mitigated.

Description: A new approach to the modular, complex systems analysis of nonlinear dynamics of arrested neural cell Differentiation—induced cell proliferation during organismic development and the analogous cell cycling network transformations involved in carcinogenesis is proposed. Neural tissue arrested differentiation that induces cell proliferation during perturbed development and Carcinogenesis are complex processes that involve dynamically inter-connected biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments. Such ‘dynamically inter-connected’ biomolecules form numerous inter-related pathways referred to as ‘molecular networks’. One such family of signaling pathways contains the cell cyclins. Cyclins are proteins that link several critical pro-apoptotic and other cell cycling/division components, including the tumor suppressor gene TP53 and its product, the Thomsen-Friedenreich antigen (T antigen), Rb, mdm2, c-Myc, p21, p27, Bax, Bad and Bcl-2, which play major roles in various neoplastic transformations of many tissues. The novel theoretical analysis presented here is based on recently published studies of arrested cell differentiation that normally leads to neural system formation during early developmental stages; the perturbed development may involve cyclin signaling and cell cycling responsible for rapidly induced cell proliferation without differentiation into neural cells in such experimental studies.

Description: This study is a meta-analysis of 367 mice from a collection of behaviour neuroscience and behaviour genetic studies run in the same lab in Zurich, Switzerland. We employed correlation-based statistics to confirm and quantify consistencies in behaviour across the testing environments. All 367 mice ran exactly the same behavioural arenas: the light/dark box, the null maze, the open field arena, an emergence task and finally an object exploration task. We analysed consistency of three movement types across those arenas (resting, scanning, progressing), and their relative preference for three zones of the arenas (home, transition, exploration). Results were that 5/6 measures showed strong individual-differences consistency across the tests. Mean inter-arena correlations for these five measures ranged from +.12 to +.53. Unrotated principal component factor analysis (UPCFA) and Cronbach’s alpha measures showed these traits to be reliable and substantial (32-63% of variance across the five arenas). UPCFA loadings then indicate which tasks give the best information about these cross-task traits. One measure (that of time spent in “intermediate” zones) was not reliable across arenas. Conclusions centre on the use of individual differences research and behavioural batteries to revise understandings of what measures in one task predict for behaviour in others. Developing better behaviour measures also makes sound scientific and ethical sense.

Description: There has been a substantial amount of research on the relationship between hippocampal neurogenesis and behaviour over the past fifteen years, but the causal role that new neurons have on cognitive and affective behavioural tasks is still far from clear. This is partly due to the difficulty of manipulating levels of neurogenesis without inducing off-target effects, which might also influence behaviour. In addition, the analytical methods typically used do not directly test whether neurogenesis mediates the effect of an intervention on behaviour. Previous studies may have incorrectly attributed changes in behavioural performance to neurogenesis because the role of known (or unknown) neurogenesis-independent mechanisms were not formally taken into consideration during the analysis. Causal models can tease apart complex causal relationships and were used to demonstrate that the effect of exercise on pattern separation is via neurogenesis-independent mechanisms. Many studies in the neurogenesis literature would benefit from the use of statistical methods that can separate neurogenesis-dependent from neurogenesis-independent effects on behaviour.

Description: Historical trends in streamflow and climate were investigated for the Coldwater River watershed in south-central British Columbia, Canada. Temporal increases in rainfall and total precipitation during the spring, summer, and autumn periods, as well as on an annual basis, at the city of Merritt near the mouth of the watershed, and year-round temperature increases at this site, compare with declining summertime and annual streamflows at the nearby Merritt hydrometric station on the Coldwater River. Declining summer flows at this site could reflect the dominance of temporally increasing evaporation that is offsetting increased precipitation over the same periods of the hydrologic year. Alternatively, increased water abstractions, altered regulation regimes, and/or land use changes in the watershed may also play significant/dominant roles. The relative absence of any coherent hydrological temporal patterns at the upstream Brookmere hydrometric station on the Coldwater River suggests that the net effects of warming temperatures, increasing precipitation, and any anthropogenic drivers over the past four decades are in approximate balance.

Description: In the background of facing up to the global climate change, it is becoming the inevitable demand to add forest biomass estimation to national forest resource monitoring. The biomass equations to be developed for forest biomass estimation should be compatible with volume equations. Based on the tree volume and aboveground biomass data of Masson pine (Pinus Massoniana Lamb.) in south China, the one, two and three-variable aboveground biomass equations and biomass conversion functions compatible with tree volume equations were constructed using the error-in-variable simultaneous equations in this paper. The results showed: (i) the prediction precision of aboveground biomass estimates from one variable equation was more than 95%; (ii) the regressions of aboveground biomass equations improved slightly when tree height and crown width were used together with diameter on breast height, although the contributions to regressions were statistically significant; (iii) for biomass conversion function on one variable, the conversion factor was decreased with growing diameter, but for conversion function on two variables, the factor was increased with growing diameter while decreased with growing tree height.

Description: Once cognition is recognized as having a ‘dual’ information source, the information theory chain rule implies that isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to the rapid, shifting global neural broadcasts of consciousness. The argument is quite analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in neurons and neuronal subsystems. Astrobiological implications are obvious.

Description: The unpalatable and warning-patterned butterflies Heliconius erato and Heliconius melpomene provide the best studied example of mutualistic Müllerian mimicry, thought – but rarely demonstrated – to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of H. erato and H. melpomene, and this was initially hailed as the most striking known case of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence) that argued against codivergence. We present the first explicit cophylogenetic test of codivergence between mimetic populations of H. erato and H. melpomene, and re-examine the timing of these radiations. We find statistically significant topological congruence between multilocus coalescent population phylogenies of H. erato and H. melpomene, supporting repeated codivergence of mimetic populations. Divergence time estimates, based on a Bayesian coalescent model, suggest that the evolutionary radiations of H. erato and H. melpomene occurred over the same time period, and are compatible with a series of temporally congruent codivergence events. This evidence supports a history of reciprocal coevolution between Müllerian co-mimics characterised by phylogenetic codivergence and parallel phenotypic change.

Description: The interconversion of carbon in organic, inorganic and refractory carbon is still beyond the grasp of present environmentalists. The bacteria and their phages, being the most abundant constituents of the aquatic environment, represent an ideal model for studing carbon regulation in the aquatic system. The refractory dissolved organic carbon (DOC), a recently coined terminology from the microbe-driven conversion of bioavailable organic carbon into difficult-to-digest refractory DOC by microbial carbon pump (MCP), is suggested to have the potential to revolutionize our view of carbon sequestration. It is estimated that about 95% of organic carbon is in the form of refractory DOC, which is the largest pool of organic matter in the ocean. The refractory DOC is supposed to be the major factor in the global carbon cycle whose source is not yet well understood. A key element of the carbon cycle is the microbial conversion of dissolved organic carbon into inedible forms. The time studies of phage-host interaction under control conditions reveal their impact on the total carbon content of the source and their interconversion among organic, inorganic and other forms of carbon with respect to control source. The TOC- analysis statistics stipulate an increase in inorganic carbon content by 15-25 percent in the sample with phage as compared to the sample without phage. The results signify a 60-70 fold increase in inorganic carbon content in sample with phage, whereas, 50-55 fold in the case of sample without phages as compared with control. This increase in inorganic carbon content may be due to lysis of the host cell releasing its cellular constituents and utilization of carbon constituent for phage assembly and development. It also proves the role of phages in regulating the carbon flow in aquatic systems like oceans, where their concentration outnumbered other species.

Description: The interconversion of carbon in organic, inorganic and refractory carbon is still beyond the grasp of present environmentalists. The bacteria and their phages, being the most abundant constituents of the aquatic environment, represent an ideal model for studing carbon regulation in the aquatic system. The refractory dissolved organic carbon (DOC), a recently coined terminology from the microbe-driven conversion of bioavailable organic carbon into difficult-to-digest refractory DOC by microbial carbon pump (MCP), is suggested to have the potential to revolutionize our view of carbon sequestration. It is estimated that about 95% of organic carbon is in the form of refractory DOC, which is the largest pool of organic matter in the ocean. The refractory DOC is supposed to be the major factor in the global carbon cycle whose source is not yet well understood. A key element of the carbon cycle is the microbial conversion of dissolved organic carbon into inedible forms. The time studies of phage-host interaction under control conditions reveal their impact on the total carbon content of the source and their interconversion among organic, inorganic and other forms of carbon with respect to control source. The TOC- analysis statistics stipulate an increase in inorganic carbon content by 15-25 percent in the sample with phage as compared to the sample without phage. The results signify a 60-70 fold increase in inorganic carbon content in sample with phage, whereas, 50-55 fold in the case of sample without phages as compared with control. This increase in inorganic carbon content may be due to lysis of the host cell releasing its cellular constituents and utilization of carbon constituent for phage assembly and development. It also proves the role of phages in regulating the carbon flow in aquatic systems like oceans, where their concentration outnumbered other species.

Description: Ions are commonly believed to impose their effects on proteins by unspecific electrostatic screening. Here, by NMR we reveal that in water sulfate, chloride and thiocyanate are able to bind a well-folded WW domain at distinctive residues and affinities, which is surprisingly masked by the pre-existing buffer. Our study reveals that the specific anion binding is so ubiquitous and consequently no longer negligible in establishing "postreductionist framework" for protein biochemistry.

Description: Many bats of the Rhinolophidae family are currently threatened all over the world. In Algeria they are represented by six species listed in the IUCN red list and whose hunting habits and diet are, at best, poorly known. This paper describes the diet composition of four of these species (Rhinolophus ferrumequinum, R. hipposideros, R. euryale and R. blasii) in the Bejaia and Jijel districts, and in Kabylia of the Babors region, in northern Algeria. Between March 2007 and January 2008 guano was sampled every fortnight in the different sites used by the species and preys remains identified under microscope. Results show that these Algerian Rhinolophidae prey on three groups of Arthropodes (Insects, Chilopodes and Spiders) whose frequencies vary from one species to another.

Description: A time trend study of groundwater monitoring well levels was conducted in British Columbia, Canada. Trend data was available for a total of 210 groundwater monitoring well stations throughout the province with end-of-month water levels over the period of record. Significant temporal trends in groundwater levels were found at 67 stations (40.4% of all stations amenable to statistical examination, and 31.9% of all available stations). Of these 67 stations, 10 had increasing groundwater level trends and the remaining 57 had declining groundwater level trends. Thus, 34.3% of stations with a sufficiently long time series for analysis displayed declining groundwater level trends, while 6.0% have increasing trends, and 59.6% of these stations appear to have no significant temporal variation in groundwater levels. Geographic distinctions in groundwater level time trends are difficult to make owing to the unbalanced distribution of monitoring sites throughout the province. Based on percentages of total stations with a sufficiently long monitoring record for statistical analysis, it appears that the semi-arid Thompson/Nicola and Okanagan zones of British Columbia are most likely to have declining groundwater levels. Overall, a substantial proportion of groundwater monitoring wells in British Columbia – which have been operated with varying record lengths dating from recent installations to sites with records back to the 1950s – are exhibiting declining levels. At a significant number of other sites in the monitoring network, records are too short and/or poorly populated to facilitate statistical analysis.

Description: Background/Question/MethodsThe recog­ni­tion that ecosys­tems can undergo sud­den shifts to alter­nate, less desir­able sta­ble states has led to the desire to iden­tify early warn­ing signs of these impend­ing col­lapses. This search has been moti­vated by the math­e­mat­ics of bifur­ca­tions, in which sud­den shifts result not from direct per­tur­ba­tions to the state (i.e. the pop­u­la­tion abun­dance, through mech­a­nisms such as over-harvesting) but to a slowly chang­ing para­me­ter that impacts the sys­tem sta­bil­ity. While these col­lapses can­not be antic­i­pated by observ­ing only the mean dynam­ics (as described by a deter­min­is­tic model), signs of the impend­ing col­lapse are expressed in the ran­dom per­tur­ba­tions, or noise, inher­ent in real sys­tems. The math­e­mat­i­cal the­ory of early warn­ing signs exploits this fact by seek­ing to detect pat­terns such as “crit­i­cal slow­ing down” of these per­tur­ba­tions due to the grad­ual loss of sta­bil­ity which leads to a bifurcation.While much atten­tion has been given to empha­siz­ing the exis­tence both of sud­den col­lapses and of signs of crit­i­cal slow­ing down, lit­tle atten­tion has been paid to its detec­tion. Faced with only finite data, any method risks both false alarms and failed detec­tion events. We believe that weigh­ing these risks must be the bur­den of man­age­ment pol­icy, while research must first pro­vide a reli­able way to quan­tify the rel­a­tive risks of each. We present a method which quan­ti­fies this risk and show how to decrease the uncer­tainty inher­ent in com­mon summary-statistic approaches through the use of a like­li­hood based mod­el­ing approach.Results/ConclusionsWe demon­strate that com­monly used cor­re­la­tion tests applied to sum­mary sta­tis­tics such as auto­cor­re­la­tion and vari­ance are both inap­pro­pri­ate and insuf­fi­cient tests of early warn­ing signals.Our method esti­mates directly the para­me­ters of a gen­er­al­ized model of the bifur­ca­tion pos­tu­lated by early warn­ing sig­nals the­ory, with and with­out the pres­ence of a grad­ual change lead­ing towards col­lapse. Using Monte Carlo sim­u­la­tion we gen­er­ate the dis­tri­b­u­tion of warning-signal sta­tis­tics expected under each model. From this we can quan­tify the risk of false alarms and missed detec­tion. We then show how apply­ing this approach to the data directly rather than the sum­mary sta­tis­tic increases the power of detec­tion. We illus­trate the approach in both sim­u­lated and empir­i­cal data of sud­den eco­log­i­cal shifts.

Description: Background/Question/MethodsThe recog­ni­tion that ecosys­tems can undergo sud­den shifts to alter­nate, less desir­able sta­ble states has led to the desire to iden­tify early warn­ing signs of these impend­ing col­lapses. This search has been moti­vated by the math­e­mat­ics of bifur­ca­tions, in which sud­den shifts result not from direct per­tur­ba­tions to the state (i.e. the pop­u­la­tion abun­dance, through mech­a­nisms such as over-harvesting) but to a slowly chang­ing para­me­ter that impacts the sys­tem sta­bil­ity. While these col­lapses can­not be antic­i­pated by observ­ing only the mean dynam­ics (as described by a deter­min­is­tic model), signs of the impend­ing col­lapse are expressed in the ran­dom per­tur­ba­tions, or noise, inher­ent in real sys­tems. The math­e­mat­i­cal the­ory of early warn­ing signs exploits this fact by seek­ing to detect pat­terns such as “crit­i­cal slow­ing down” of these per­tur­ba­tions due to the grad­ual loss of sta­bil­ity which leads to a bifurcation.While much atten­tion has been given to empha­siz­ing the exis­tence both of sud­den col­lapses and of signs of crit­i­cal slow­ing down, lit­tle atten­tion has been paid to its detec­tion. Faced with only finite data, any method risks both false alarms and failed detec­tion events. We believe that weigh­ing these risks must be the bur­den of man­age­ment pol­icy, while research must first pro­vide a reli­able way to quan­tify the rel­a­tive risks of each. We present a method which quan­ti­fies this risk and show how to decrease the uncer­tainty inher­ent in com­mon summary-statistic approaches through the use of a like­li­hood based mod­el­ing approach.Results/ConclusionsWe demon­strate that com­monly used cor­re­la­tion tests applied to sum­mary sta­tis­tics such as auto­cor­re­la­tion and vari­ance are both inap­pro­pri­ate and insuf­fi­cient tests of early warn­ing signals.Our method esti­mates directly the para­me­ters of a gen­er­al­ized model of the bifur­ca­tion pos­tu­lated by early warn­ing sig­nals the­ory, with and with­out the pres­ence of a grad­ual change lead­ing towards col­lapse. Using Monte Carlo sim­u­la­tion we gen­er­ate the dis­tri­b­u­tion of warning-signal sta­tis­tics expected under each model. From this we can quan­tify the risk of false alarms and missed detec­tion. We then show how apply­ing this approach to the data directly rather than the sum­mary sta­tis­tic increases the power of detec­tion. We illus­trate the approach in both sim­u­lated and empir­i­cal data of sud­den eco­log­i­cal shifts.

Description: The subsidy on phosphate fertilizers rose to an unacceptable level while alternate cost effective technologies are available. Fertilizer industry needs to develop innovative products using the recent advances in the agricultural sciences. Manure producing industries to be supplied rock phosphate mineral (at subsidized costs) as being supplied to chemical fertilizers industries suitable to produce PROM Khad (Phosphate Rich Organic Manure).

Description: Attempts to quantitatively reconstruct the range of motion of sauropod necks are intrinsically flawed because of ubiquitous distortion in preserved cervical vertebrae. This is true even for specimens that are usually considered particularly well preserved, such as the Carnegie Diplodocus and the Berlin Giraffatitan.

Description: Natural agricultural production functions in open system, where energy and matter are exchanged freely between geosphere (especially pedosphere), biosphere, and atmosphere. The self regulation of biophysical processes in these spheres is crucial for global sustainability. However, modern farming practices have stressed the system to the extent that damaged C, N, and P cycles are threatening catastrophic consequences. High food-wastage coupled with high food price, high soil fertility zones but low crop productivity, and highly productive irrigated farming marred with ecological disasters are examples of global paradoxes associated with modern farming. High incidence of pesticide residues in soil and water bodies, low use efficiency of agricultural inputs, vulnerability to climate, and low conversion of energy by crops leaving high amount of residues and their subsequent burden on environment, and hunger and malnutrition in many parts of the world are threatening civilizations to crumble. Nanotechnology promises to break these vicious cycles, because technology is based on applying exact amounts of inputs for use by the crops, and only when they are required. Some of the examples are: nanofabricating nutrient ions to improve nutrient use efficiency, targeted use of nano-pesticides, holding of water and then releasing it at the time of crop need by nps, forecasting and elimination of diseases, packaging of food to improve shelf-life, protecting food during storage, DNA nanotechnology, smart treatment delivery systems, bioanalytical nanosensors, bioselective surfaces, nanobioprocessing, protection of the environment by the reduction and conversion of agricultural materials into valuable products, design and development of new nanocatalysts to convert vegetable oils into biobased fuels and biodegradable industrial solvents, and controlled ecological life support system.

Description: Calorific values of plants are important indices for evaluating and reflecting material cycle and energy conversion in forest ecosystems. Based on the data of Masson Pine (Pinus massoniana) in southern China, the calorific values (CVs) and ash contents (ACs) of different plant organs were analyzed systematically using hypothesis test and regression analysis in this paper. The results show: (i) the CVs and ACs of different plant organs are almost significantly different, and the order by AFCV (ash-free calorific value) from the largest to the smallest is foliage (23.55 kJ/g), branches (22.25 kJ/g), stem bark (21.71 kJ/g), root (21.52 kJ/g) and stem wood (21.35 kJ/g); and the order by AC is foliage (2.35%), stem bark (1.44%), root (1.42%), branches (1.08%) and stem wood (0.33%); (ii) the CVs and ACs of stem woods on top, middle and lower sections are significantly different, and the CVs are increasing from top to lower sections of trunk while the ACs are decreasing; (iii) the mean GCV (gross calorific value) and AFCV of aboveground part are larger than those of belowground part (roots), and the differences are also statistically significant; (iv) the CVs and ACs of different organs are related, to some extent, to diameter, height and origin of the tree, but the influence degrees of the factors on CVs and ACs are not the same.

Description: Albeit several studies examined the association between cardiac resynchronization therapy (CRT) and atrial fibrillation (AF) in heart failure (HF), results are still unclear and quite conflicting. We thereby designed a single-center prospective study to determine whether CRT has a favorable effect on the incidence of new-onset AF in a homogeneous population of patients with non-ischemic idiopathic dilated cardiomyopathy and severe heart failure HF. We enrolled 58 patients, AF naïve when received CRT. After 1 year of follow-up our population was subdivided into responders (72.4%) and non (27.6%), so to compare the incidence of AF after 1, 2 and 3 years of follow-up in these two groups. Already after 1 year, there is a significant (p

Description: A categorical and Łukasiewicz-Topos framework for Łukasiewicz LM-Algebraic Logic models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes is proposed. Łukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks.