bluuebunny/crossref_metadata_2025 huggingface dataset:
Regiospecific synthesis of 2,3-disubstituted indoles from isatins
Authors: Ulikowski Artur , Jaromin Anna , Brancolini Giorgia , Bellucci Luca , Furman Bartłomiej
Published: January 2018

Indoles represent a structural element in a myriad of natural products and biologically active molecules. Of special importance are 2,3-disubstituted indoles. Thus, a number of methods for their synthesis have been described. However, these are often hampered by a number of limitations: they often offer poor regioselectivity and suboptimal functional group tolerance. Also, they can normally be adapted to the procurement of a small subclass of indoles only. We have developed an approach to 2,3-disubstituted indoles overcoming these obstacles. By selectively activating the amide carbonyl in isatin-derived oxindoles, we obtained a number of the title compounds in a regiospecific and functional group-tolerant manner. The methodology is normally characterized by excellent yields. The reaction proceeds by chemoselective partial reduction of the amide moiety to an iminium salt and a subsequent nucleophilic addition followed by dehydration, which furnishes the target indole. A number of nucleophiles, including C- and S-nucleophiles, have been examined. The obtained compounds were studied towards acetylcholinesterase (AChE) inhibitory activity, as the indole skeleton is often seen in the struc-ture of enzyme inhibitors. Cholinesterase inhibitors are used in the treatment of Alzheimer's disease, increasing available acetylcholine by decreasing the AChE activity. For the tested agents, properties like logP, logBBB (Blood-Brain Barier penetration) and Caco2 permeabilities were also calculated. Based on the predicted values, only two of them are able to penetrate into the CNS (central nervous system). Molecular docking was performed on the whole set of the syntesized indole derivatives, resulting in a wide range of AChE inhibitory activity. Molecular docking binding interactions reported the lowest energy conformations of the syntesized compounds and the key amino acid residues at the active binding site of AChE. The current synergy between computations and experiments provided the identification of the indole derivatives exhibiting the highest inhibitory activity. The presented results will provide theoretical guidance for further modification and optimization of the indole derivatives.
Physicochemical characteristics of abiraterone acetate used for the treatment of prostate cancer
Authors: Łaszcz Marta , Trzcińska Kinga , Stolarczyk Elżbieta U.
Published: January 2018

Prostate cancer is the most common cancer among men and often has no early symptoms. The major treatment options that include surgical or medical castration cause ablation of the production of testosterone, dihydrotestosterone and related androgens by the testes. These procedures do not affect adrenal, prostate and other tissues androgen production, therefore they are combined with androgen receptor antagonists to block their action. Recent studies have established that in castration-resistant prostate cancer many androgen-regulated genes become re-expressed and tissue androgen levels increase despite low serum levels. Abiraterone acetate inhibits the key enzyme cytochrome P450 17α-hydroxy/17,20-lyase (CYP17) which catalyzes the biosynthesis of androgens and provides the effective treatment of prostate cancer patients. The aim of this work was abiraterone acetate polymorph diagnostics and physcicochemical characteristics of polymorphs. Polymorphism is the ability of a compound in the solid state to exist in different crystalline forms. Molecules, having the same chemical composition, exhibit different spatial arrangements and/or exist in different conformations. Substances that exist in a non-crystalline solid state are said to be amorphous. The term pseudopolymorphism is used to describe solvates (including hydrates). Different polymorphs of a solid compound exhibit distinct physical properties such as, e.g.: hygroscopicity, solubility, dissolution rate, melting point and stability. All of which play a very important role in the pharmaceutical industry. The undesirable polymorphic form with lower solubility and consequently with a lower absorption rate decreases the concentration of active substance in the blood. The Biopharmaceutics Classification System classifies drugs taking into account their solubility. Because a change in a polymorphic form may influence on a drug product affectivity and its toxic properties the regulations required by the ICH Q6A guideline according to the decision tree no 4 demand the control of solid state behavior. Therefore, the polymorphic behavior of abiraterone acetate has to be carefully investigated and all found polymorphs have to be fully characterized. Abiraterone acetate was characterized by following methods: X-ray powder diffraction, infrared and Raman spectroscopy, differential scanning calorimetry. Polymorph screening was performed and single crystals were obtained by a vapour diffusion crystallisation. The structure of abiraterone acetate was solved by the single crystal X-ray diffraction. Additionally the structure was confirmed by the direct sample injection method (DI).
Accessing biological data in R with semantic web technologies
Authors: Willighagen Egon
Published: January 2018

Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness shows advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows.

Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be used in the statistical environment R. The code is exposed as two R packages available from the Comprehensive R Archive Network (CRAN). The RJava library and a custom convenience class is used to bridge between R and the Jena library.

Results. We here present three examples showing how the Resource Description Framework (RDF) and SPARQL query standards can be employed in R. The first example takes input on BRCA1 SNPs from a BioMart and converts this into a RDF data set. The second example runs a query on an experimental remote SPARQL end point provided by Uniprot, and searches textual annotations of proteins encoded by the BRCA1 gene. The third example shows how the package can be used to handle RDF returned by OpenTox web services.

Discussion. The two provided library bring basic semantic web technologies to R. This paper only shows examples from the biology domain, but we believe the approaches are generally applicable. It currently only exposes a subset of key Apache Jena, but the rrdf package makes it easy to make more of the library's functionality, such as the shortest path finding. The rrdf libraries are freely available from the CRAN under the Affero GNU Public License version 3: http://cran.r-project.org/web/packages/rrdf/.
Insights into the morphology of symbiotic shrimp eyes (Crustacea, Decapoda, Pontoniinae); the effects of habitat demands
Authors: Dobson Nicola C , Johnson Magnus L , De Grave Sammy
Published: January 2018

Morphometric differences in the optical morphology of symbiotic palaemonid shrimps can be observed among species symbiotic with different host organisms. Discriminant functional analysis revealed three distinct groups within the species examined. Of these, bivalve symbionts appear to have an eye design that is solely unique to this host-symbiont grouping, a design that spans across multiple genera of phylogenetically unrelated animals. Although some taxonomic effects may be evident, this does not explain the difference and similarities in eye morphology that are seen within these shrimps. Therefore evolutionary pressures from their host environments are having an impact on the optical morphology of eyes however, as indicated by host-hopping events there ecological adaptations occur post host invasion.
Depression, anxiety, and stress in partners of Australian combat veterans and military personnel: A comparison with Australian population norms
Authors: MacDonell Gail V , Bhullar Navjot , Thorsteinsson Einar B
Published: January 2018

Partners of Australian combat veterans are at an increased risk of experiencing mental health problems. For a comparative analysis of mental health of partners of veterans with that of their non-military counterparts, the study sample comprised female partners of (a) Australian combat veterans (Sample 1: n = 282, age M = 60.79, SD = 5.05), (b) a random sub-sample of partners of Australian combat veterans from the previous sample (Sample 2: n = 50; M = 60.06, SD = 4.80), (c) partners of Special Air Services Regiment (SASR) personnel (Sample 3: n = 41, age M = 34.39 SD = 7.01), and (d) partners of current serving military (non-SASR) personnel (Sample 4: n = 38, age M = 32.37, SD= 6.20). Respondents completed measures to assess their reported levels of depression, anxiety, and stress. The two samples (Samples 1 and 2) for partners of Australian combat veterans reported significantly poorer symptoms of depression, anxiety, and stress than the comparative population norms. The sample of SASR personnel partners reported significantly greater levels of depression and anxiety, while the sample with non‑SASR personnel partners reported a significantly poorer symptomatology in stress than the comparative norms. Lessons and protective factors can be learnt from groups within the current military as to what may assist partners and families to maintain a better level of psychosocial health. C
BibeR: A Web-based tool for bibliometric analysis in scientific literature
Authors: Liu Yang , Li Meng
Published: January 2018

Bibliometric analysis is a statistical method to summarize the amount of scientific activity in a domain. Insights can be derived from bibliometrics to understand the development trend of the research domain. R is an open sourced programming language specialized for statistical computing and graphic visualization. To benefit from the convenience of R and the outcome of bibliometric analysis, we here introduce BibeR, a web-based application for the visualization of bibliometric analysis. An example of bibliometric analysis on the articles published in journal Scientometrics is used to illustrate the usage of BibeR. The development of BibeR is still in progress, and future possibly improvements on BibeR are discussed.
VERVENet: the viral ecology research and virtual exchange network
Authors: Kindler Lori J , Stoliartchouk Alexei , Gomez Celina , Thornton James , Teytelman Leonid , Hurwitz Bonnie L
Published: January 2018

The advent of metagenomic methods to sequence DNA directly from an environment has revolutionized viral ecology, making it possible to “see” natural viral communities that could not be previously studied through culture. This technological leap has enabled further innovation in: extracting and sequencing limited viral DNA from communities, enriching and sequencing wild viruses through single-cell genomics, and creating new bioinformatics methods for large-scale comparative and functional metagenomics. Yet, the knowledge for specialized techniques in viral ecology remains in a subset of labs. We present a viral ecology community forum called VERVENet that strives to increase connectivity and knowledge dissemination in viral ecology research at all levels from undergraduates to accomplished viral ecologists. Our forum leverages and refines existing software from protocols.io to enhance a researcher’s ability to: discuss and share protocols, connect with fellow community members, and learn about new and innovative research in the field. In delivering these valuable tools, VERVENet is a central resource to connect, collaborate, share and innovate for the viral ecology community. Moreover, these tools are broadly useful to any community or individual lab to promote scientific inquiry, reproduction of results, and dissemination and optimization of both molecular and bioinformatics protocols.
Competitive interactions between corals and turf algae depend on coral colony form
Authors: Swierts Thomas , Vermeij Mark JA
Published: January 2018

Turf algae are becoming more abundant on coral reefs worldwide, but their effects on other benthic organisms remain poorly described. To describe the general characteristics of competitive interactions between corals and turf algae, we determined the occurrence and outcomes of coral – turf algal interactions among different coral growth forms (branching, upright, massive, encrusting, plating, and solitary) on a shallow reef in Vietnam. In total, the amount of turf algal interaction, i.e., the proportion of the coral boundary directly bordering turf algae, was quantified for 1276 coral colonies belonging to 27 genera and the putative outcome of each interaction was noted. The amount of turf algal interaction and the outcome of these interactions differed predictably among the six growth forms. Encrusting corals interacted most often with turf algae, but also competed most successfully against turf algae. The opposite was observed for branching corals, which rarely interacted with turf algae and rarely won these competitive interactions. Including all other growth forms, a positive relationship was found between the amount of competitive interactions with neighboring turf algae and the percentage of such interaction won by the coral. This growth form dependent ability to outcompete turf algae was not only observed among coral species, but also among different growth forms in morphologically plastic coral genera (Acropora, Favia, Favites, Montastrea, Montipora, Porites) illustrating the general nature of this relationship.
libPLS: An Integrated Library for Partial Least Squares Regression and Discriminant Analysis
Authors: Li Hongdong , Xu Qingsong , Liang Yizeng
Published: January 2018

Partial least squares (PLS) have gained wide applications especially in chemometrics, metabolomics/metabonomics as well as bioinformatics. To our knowledge, an integrated PLS library that include not only basic PLS modeling algorithms but also advanced and/or recently developed methods on model assessment, outlier detection and variable selection is in lack. Here we present libPLS which provides an integrated platform for developing PLS regression and/or discriminant analysis (PLS-DA) models. This library is written in MATLAB and freely available at www.libpls.net.
Association between osteoporosis and polymorphisms of the bone estrogen receptor 1, calcitonin receptor genes in Mongolian postmenopausal women
Authors: Lkhagvasuren Unentsatsral , Jav Sarantuya , Batjargal Ochbadrakh , Batsukh Myagmarsuren
Published: January 2018

In this study, we have investigated the association between osteoporosis and estrogen receptor 1 (ER1) 397 T>C, and calcitonin receptor (CALCR) 1340 T>C polymorphisms. Genomic DNA was obtained from 104 persons (52 osteoporotic and 52 healthy controls). Genomic DNA was extracted from EDTA-preserved peripheral venous blood of patients and controls and analyzed by PCR-RFLP. As a result, there was no statistically significant difference in the genotype and allele frequencies of patients and controls for ER1 397 T>C and CALCR 1340 T>C polymorphisms. ER1 CC and TC single nucleotides genotypes compared with TT genotypes was found more significantly women with osteoporosis [p=0.016; p=0.0046, OR=2.66; 0.44, 95% CI 1.185-5.988; 0.199-0.991)]. There was no statistically significant difference in the genotype and allele frequencies of patient and controls for ER1 combined nucleotides [p=0,148, OR=1.051, 95% CI (0.993–1.112)]. Our study showed that CALCR genes single and combined nucleotides genotypes were not significant women with osteoporotic and healthy postmenopausal women.
Saving Waves: BioAcoustica progress report 1
Authors: Baker Edward
Published: January 2018

This report details work on the BioAcoustica project up to the end of March 2016. Functionality and datasets currently available are described and ongoing work is listed. Usage statistics are provided and future plans are presented. Outputs of the project are listed in appendices including a list of peer-reviewed papers generated by the project and peer-reviewed papers that have deposited their bioacoustic data in BioAcoustica. In addition a list of species which are represented in the BioAcoustica database is provided.
A possible link between pyriproxyfen and microcephaly
Authors: Evans Dan , Nijhout Fred , Parens Raphael , Morales Alfredo J , Bar-Yam Yaneer
Published: January 2018

The Zika virus is the primary suspect in the large increase in microcephaly cases in 2015-6 in Brazil, however its role is unconfirmed despite individual cases of viral infections found in neural tissue. Here we consider the alternative that the insecticide pyriproxyfen, used in Brazilian drinking water for mosquito control, may actually be the cause. Pyriproxifen is an analog of juvenile hormone, which corresponds in mammals to regulatory molecules including retinoic acid, a vitamin A metabolite, with which it has cross-reactivity and whose application during development causes microcephaly. Methoprene, another juvenile hormone analog approved as an insecticide has metabolites that bind to the retinoid X receptor, and causes developmental disorders in mammals. Isotretinoin is another example of a retinoid causing microcephaly in human babies via activation of the retinoid X receptor. Moreover, tests of pyriproxyfen by the manufacturer, Sumitomo, widely quoted as giving no evidence for developmental toxicity, actually found some evidence for such an effect, including low brain mass and arhinencephaly--incomplete formation of the anterior cerebral hemispheres--in rat pups. Finally, the pyriproxyfen use in Brazil is unprecedented--it has never before been applied to a water supply on such a scale. Claims that it is not being used in Recife, the epicenter of microcephaly cases, do not distinguish the metropolitan area of Recife, where it is widely used, and the municipality, where it is not. Given this combination of information we strongly recommend that the use of pyriproxyfen in Brazil be suspended pending further investigation.
Species and size diversity in protective services offered by coral guard crabs
Authors: McKeon C. Seabird , Moore Jenna M.
Published: January 2018

Coral guard crabs in the genus Trapezia are well-documented defenders of their pocilloporid coral hosts against coral predators such as the Crown-of-Thorns seastar (Acanthaster planci complex). The objectives of this study were to examine the protective services of six species of Trapezia against corallivory, and the extent of functional diversity among these Trapezia species. Studies conducted in Mo'orea, French Polynesia showed the Trapezia – coral mutualism protected the host corals from multiple predators through functional diversity in the assemblage of crab symbionts. Species differed in their defensive efficacy, but species within similar size classes shared similar abilities. Smaller Trapezia species, which were previously thought to be ineffective guards, play important defensive roles against small corallivores. We also measured the benefits of this mutualism to nearby coral species in the midst of an Acanthaster outbreak that reduced the live coral cover on the fore reef to less than 4%. The mutualism positively affects the reef coral demography and potential for recovery during adverse predation events through shelter of multiple species of small corals near the host coral. Our results show that some Trapezia species may be functionally equivalent within the same size class, decreasing the threat of gaps in coral protection caused by absence or replacement of any single Trapezia species.
Protein-RNA linkage and posttranslational modifications of feline calicivirus and murine norovirus VPg proteins
Authors: Olspert Allan , Hosmillo Myra , Chaudhry Yasmin , Peil Lauri , Truve Erkki , Goodfellow Ian
Published: January 2018

Members of the Caliciviridae family of positive sense RNA viruses cause a wide range of diseases in both humans and animals. The detailed characterization of the calicivirus life cycle had been hampered due to the lack of robust cell culture systems and experimental tools for many of the members of the family. However a number of caliciviruses replicate efficiently in cell culture and have robust reverse genetics systems available, most notable feline calicivirus (FCV) and murine norovirus (MNV). These are therefore widely used as representative members with which to examine the mechanistic details of calicivirus genome translation and replication. The replication of the calicivirus RNA genome occurs via a double stranded RNA intermediate in the cytoplasm of the infected cell which is then used as a template for the production of new positive sense viral RNA, which is covalently linked to the virus-encoded protein VPg. The covalent linkage to VPg occurs during genome replication via the nucleotidylylation activity of the viral RNA-dependent RNA polymerase. Using FCV and MNV, we used mass spectrometry-based approach to identify the specific amino acid linked to the 5’ end of the viral nucleic acid. We observed that both VPg proteins are covalently linked to GDP moieties via tyrosine positions 24 and 26 for FCV and MNV respectively. These data fit with previous observations indicating that mutations introduced into these specific amino acids are deleterious for viral replication and fail to produce infectious virus. In addition, we also detected serine phosphorylation sites within the FCV VPg protein with positions 80 and 107 found consistently phosphorylated on VPg-linked viral RNA isolated from infected cells. This work provides the first direct experimental characterisation of the linkage of infectious calicivirus viral RNA to the VPg protein and highlights that post-translational modifications of VPg may also occur during the viral life cycle.
MOST: A modified MLST typing tool based on short read sequencing
Authors: Tewolde Rediat , Dallman Timothy , Schaefer Ulf , Sheppard Carmen L , Ashton Philip , Pichon Bruno , Ellington Matthew , Swift Craig , Green Jonathan , Underwood Anthony
Published: January 2018

Multilocus sequence typing (MLST) is an effective method to describe bacterial populations. Conventionally, MLST involves Polymerase Chain Reaction (PCR)amplification of housekeeping genes followed by Sanger DNA sequencing. Public Health England (PHE) is in the process of replacing the conventional MLST methodology with a method based on short read sequence data derived from Whole Genome Sequencing (WGS). This paper reports the comparison of the reliability of MLST results derived from WGS data, comparing mapping and assembly-based approaches to conventional methods using 325 bacterial genomes of diverse species. The sensitivity of the two WGS based methods were further investigated with 26 mixed and 29 low coverage genomic data sets from Salmonella enteridis and Streptococcus pneumoniae. Of the 325 samples, 92.9% (n=302), 97.2% (n=316) and 99.7% (n=324) full MLST profiles were derived by the conventional method, assembly- and mapping-based approaches, respectively. The concordance between samples that were typed by conventional (92.9%) and both WGS methods was 100%. From the 55 mixed and low coverage genomes, 90.9% (n=50) and 67.3% (n=37) full MLST profiles were derived from the mapping and assembly based approaches, respectively. In conclusion, deriving MLST from WGS data is more sensitive than the conventional method. When comparing WGS based methods, the mapping based approach was the most sensitive. In addition, the mapping based approach described here derives quality metrics, which are difficult to determine quantitatively using conventional and WGS-assembly based approaches.
Do plant secondary metabolites help drive avian granivore seed selection?
Authors: Whelan Christopher J , Majumdar Diya , Brown Joel S , Hank Amy E , Iorgovan Andrea
Published: January 2018

Plant secondary metabolites (PSMs), found virtually universally throughout the plant kingdom, function in myriad ways, including defense against enemies, attraction of pollinators, communication between plants, and protection against various abiotic stressors. Extensive research has examined how PSMs mediate interactions between plants and herbivores and plant and frugivores. In contrast, little research has investigated their potential role in defense against granivores. In two seed selection experiments, we quantified seed preference of house sparrows and native granivores, respectively, when offered each of 10 native seeds and proso millet, a commercial bird seed. House sparrows and native granivores greatly preferred millet over all offered native seeds. House sparrows largely rejected seeds of all five wildflower species, but native granivores preferred three of the five wildflowers. House sparrows readily consumed seeds of all five native grass species, but native granivores rejected Canada rye. House sparrows and native granivores both rejected seeds of Illinois bundle flower. Although seed preferences in the non-native house sparrow and native granivores differed significantly, we have found no consistent relationship between seed selection and presence or absence of classes of plant secondary metabolites.
Detection of methylation, acetylation and glycosylation of protein residues by monitoring 13C chemical-shift changes
Authors: Garay Pablo G. , Martin Osvaldo A. , Scheraga Harold A. , Vila Jorge A.
Published: January 2018

Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here, as a proof-of-concept, the feasibility of using 13C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the 13C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a validation test of this approach, we compare our theoretical computations of the 13Ce chemical-shift values against experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ~1 ppm. Then, further use of this approach to select the most suitable 13C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results.
Oops, my tests broke the build: An analysis of Travis CI builds with GitHub
Authors: Beller Moritz , Gousios Georgios , Zaidman Andy
Published: January 2018

Continuous Integration (CI) has become a best practice of modern software development. At present, we have a shortfall of insight into the testing practices that are common in CI-based software development. In particular, we seek quantifiable evidence on how central testing really is in CI, how strongly the project language influences testing, whether different integration environments are valuable and if testing on the CI can serve as a surrogate to local testing in the IDE. In an analysis of 2,640,825 Java and Ruby builds on Travis CI, we find that testing is the single most important reason why builds fail. Moreover, the programming language has a strong influence on both the number of executed tests, their test run time and proneness to fail. The use of multiple integration environments leads to 10% more failures being caught at build time. However, testing in the CI does not seem to be a good surrogate for running tests in the IDE. To facilitate further research on Travis CI with GitHub, we introduce TravisTorrent.
Social isolation increased ADAR1 expressions leading to cognitive deficits of mice
Authors: Chen Wei , An Dong , Xu Hong , Cheng Xiaoxin , Wang Shiwei , Yu Weizhi , Yu Deqin , Zhao Dan , Sun Yiping , Deng Wuguo , Tang Yiyuan , Yin Shengming
Published: January 2018

A lot of literature show that social isolation stress could be a key reason that leads to cognitive deficits for both humans and rodent models; however, the detailed mechanisms are still not clear completely. ADAR1 (Adenosine deaminase acting on RNA) is an enzyme involved in RNA editing that has a close relation to cognitive function. We hypothesize that social isolation stress may impact the expression of ADAR1, leading to cognitive deficits. To prove our hypothesis, we evaluated the cognition ability of the mice isolated for different durations (2, 4, and 8 weeks) using object recognition and object location tests; we also measured ADAR1 expressions in hippocampus and cortex using immunohistochemistry and western blot. Our study showed that social isolation stress significantly induced spatial and non-spatial cognition deficits. In addition, social isolation significantly increased both the immuno reactivity and protein expressions of ADAR1 in the hippocampus and frontal cortex. Furthermore, we found that adolescent re-socialization recovered not only the cognition deficits but also the increased ADAR1 protein expression in hippocampus and the increased number of ADAR1 positive cells in frontal cortex of the isolated mice. In conclusion, social isolation stress significantly increased ADAR1 expressions in the hippocampus and cortex, leading to cognitive deficits.
Is visceral fat a better predictor of the incidence of impaired glucose tolerance or type 2 diabetes mellitus than subcutaneous abdominal fat: a systematic review and meta-analysis of cohort studies.
Authors: Castro Ana Valeria B , Nunes Vania S , Ionut Viorica , Bergman Richard N , El Dib Regina
Published: January 2018

BACKGROUND: Several lines of evidence show that abdominal fat is strongly associated with insulin resistance and dysglycemia (impaired glucose tolerance - IGT or type 2 diabetes mellitus - T2DM). However, which component of abdominal fat, subcutaneous or intra-abdominal, has a major impact on the development of insulin resistance and dysglycemia is still a matter of debate. The aim of this review is to summarize the best available evidence on the contribution of subcutaneous and/or intra-abdominal adipose tissues to the incidence of impaired glucose tolerance and/or type 2 diabetes mellitus, in adults as well as to determine which type of abdominal fat is a better predictor of these metabolic disorders. METHODS: A search of published articles on PUBMED (1966 to June 2013), EMBASE (1980 to June 2013), LILACS (1982 to June 2013) and Central Cochrane databases was conducted to identify studies evaluating the relationship between intra-abdominal and/or subcutaneous adipose tissue and the incident IGT or T2DM). Cohort studies examining the association between intra-abdominal and/or subcutaneous adipose tissue values and the prospective development of impaired glucose tolerance or type 2 diabetes mellitus (estimated risk) were included in this review. Data extraction and risk of bias assessments were performed in duplicate by 2 reviewers. Random-effects meta-analyses were performed to pool OR estimates from individual studies to assess the association between intra-abdominal and/or subcutaneous adipose tissue values at baseline and the risk of development of impaired glucose tolerance or type 2 diabetes mellitus. Statistical heterogeneity was assessed using the I2 statistics. The risk of bias was assessed by examining the sample selected, recruitment method, completeness of follow up and blinding according to the guidelines for assessing quality in prognostic studies proposed by Hayden (29) and the MOOSE (30) statement, and adapted by us. RESULTS: Five relevant studies were suitable for this review. The analysis showed that both VAT and abdominal SAT measurements at baseline were strong predictors of incident impaired glucose tolerance or type 2 diabetes mellitus, in minimally adjusted models. However, when other confounding variables besides age, sex and ethnicity were taken into account, VAT, but not SAT, measurements pose a high risk of the incident IGT or T2DM in a wide range of age and ethnic backgrounds (Japanese-, Hispanic-, African-Americans and Canadians). CONCLUSIONS: In conclusion, the present results provide some evidence that VAT imposes more risk to the development of IGT and T2DM than abdominal SAT. However, more studies are necessary to confirm these results and to address the issue of changes in VAT and abdominal SAT and their predictive value regarding IGT and type 2 diabetes developments.
Quick tips to perform a metabolomics study
Authors: Misra Biswapriya B
Published: January 2018

Nascent, burgeoning, youngest, ‘connecting link between genotype and phenotype’ are just some of the phrases associated with this ‘omics’ where small molecules (metabolites with molecular weight < 2000 Daltons) are studied in biological systems, i.e., metabolomics. Currently, due to recent advances in the field, metabolomics has demanded large attention from scientists as it has shown tremendous potential in basic research such as the study interaction of ‘omes’ and the discovery of new biochemical pathways. Other areas of impact include metabolic regulation, disease biomarker identification, personalized medicine, clinical trials, toxicology, nutrigenomics, medicine diagnosis, and agriculture. Also included are industrial applications such as metabolic engineering in strain improvement in microbes. Here, the attempt is to get the scientific community interested and excited about the potential use of metabolomics in their existing research areas, by widening its dimensions to another level of data-oriented science leading to better interpretation and understanding of the function and behavior of organisms. Nonetheless, while excellent pioneering reviews and extremely successful studies exist in metabolomics, a summary and/or overview of this area is lacking at this moment. Thus, the target audience are not only researchers who are venturing into metabolomics, but also early career researchers, investigators, students, and individuals interested in implementing metabolomics in their current research and field. Typically, study design to publication can span from months to years in some cases, but without a general grasp of how beneficial and easy to implement metabolomics can be, further inquiry into the field may be mistakenly overlooked. I attempt to summarize and encapsulate the ‘usual’ trends in such efforts, identifying the critical steps to make the trends all fit into these quick tips. The objective of this article is to provide a bird’s eye view of metabolomics research that can be enjoyed over a mug of coffee while simultaneously providing an outline for a variety of audiences interested in incorporating this fascinating field in their work.
Geometric morphometric analysis of intratrackway variability: A case study on theropod and ornithopod dinosaur trackways from Münchehagen (Lower Cretaceous, Germany)
Authors: Lallensack Jens N , van Heteren Anneke H , Wings Oliver
Published: January 2018

A profound understanding of the influence of trackmaker anatomy, foot movements and substrate properties is crucial for any interpretation of fossil tracks. In this case study we analyze variability of footprint shape within one large theropod (T3), one medium-sized theropod (T2) and one ornithopod (I1) trackway from the Lower Cretaceous of Münchehagen (Lower Saxony, Germany) in order to determine the informativeness of individual features and measurements for ichnotaxonomy, trackmaker identification, and the discrimination between left and right footprints. Landmark analysis is employed based on interpretative outline drawings derived from photogrammetric data, allowing for the location of variability within the footprint and the assessment of covariation of separate footprint parts. Objective methods to define the margins of a footprint are tested and shown to be sufficiently accurate to reproduce the most important results. The lateral hypex and the heel are the most variable regions in the two theropod trackways. As indicated by principal component analysis, a posterior shift of the lateral hypex is correlated with an anterior shift of the margin of the heel. This pattern is less pronounced in the ornithopod trackway, indicating that variation patterns can differ in separate trackways. In all trackways, hypices vary independently from each other, rendering their relative position a questionable feature for ichnotaxonomic purposes. Most criteria commonly employed to differentiate between left and right footprints assigned to theropods are found to be reasonably reliable. The described ornithopod footprints are asymmetrical, again allowing for a left-right differentiation. Strikingly, 12 out of 19 measured footprints of the T2 trackway are stepped over the trackway midline, rendering the trackway pattern a misleading left-right criterion for this trackway. Traditional measurements were unable to differentiate between the theropod and the ornithopod trackways. Geometric morphometric analysis reveals potential for improvement of existing discriminant methods.
Pleistocene phylogeography of tiger beetle, Calomera littoralis, in North-Eastern Mediterranean and Pontic regions inferred from mitochondrial COI gene sequence
Authors: Jaskuła Radomir , Rewicz Tomasz , Płóciennik Mateusz , Grabowski Michał
Published: January 2018

Background. Calomera littoralis is a Palearctic species, widely distributed in Europe; inhabiting predominantly its Atlantic, Mediterranean and Black Sea coastlines. Methods. Its phylogeography on the Balkan Peninsula and on the north-western Black Sea coast was inferred using a 697 bp long portion of the mitochondrial COI gene, amplified from 169 individuals collected on 43 localities. Results. The results revealed two genetically divergent groups/lineages, the southern one inhabiting both the Balkan Peninsula and the Pontic Region and the northern one found exclusively in the Pontic Region. Species delimitation based on DNA barcoding gap suggested an interspecific level of divergence between these groups. Multivariate analysis of eight male and female morphometric traits detected no difference between the groups, implying they may represent cryptic species. The Bayesian time-calibrated reconstruction of phylogeny suggested that the lineages diverged ca. 2.3 Ma, in early Pleistocene. Discussion. This might result from contemporary isolation of the Pontic basin from the Mediterranean that broke the continuous strip of coastal habitats inhabited by C. littoralis. Demographic analyses indicated that both lineages have been in demographic and spatial expansion since ca. 0.15 Ma. It coincides with the terminal stage of MIS-6, i.e. Wartanian/Saalian glaciation, and beginning of MIS-5e, i.e. Eemian interglacial, during which, due to eustatic sea level rise, a wide connection between Mediterranean and the Pontic basin was re-established. This, along with re-appearance of coastal habitats could initiate north-east expansion of the southern lineage and its secondary contact with the northern one. Isolation of Pontic basin from Mediterranean during the Weichselian glaciation did not have probably any effect on their phylogeography.
Hypo- and hyper-connectivity in default mode network related to social impairment in tweens with autism spectrum disorder
Authors: Matthysen Wilma , Marinazzo Daniele , Siugzdaite Roma
Published: January 2018

Background. Autism spectrum disorder is a neurodevelopmental disorder, marked by impairment in social communication and restricted, repetitive patterns of behavior, interests, or activities. Accumulating data suggests that alterations in functional connectivity might contribute to these deficits. Whereas functional connectivity in resting state fMRI is expressed by several resting-state networks, for this study we examined several of them, but our particular interest was in the default mode network (DMN), given its age dependent alteration of functional connectivity and its relation to social communication. Methods. Since the studies investigating young children (6-8 years) with autism have found hypo-connectivity in DMN and studies on adolescents (12-16 years old) with autism have found hyper-connectivity in the DMN, we were interested in connectivity pattern during the age of 8 to 12, so we investigated the role of altered intrinsic connectivity in 16 children (mean age 9.75 ±1.6 years) with autism spectrum disorder compared to 16 typically developing controls in the DMN and other resting-state networks. Results. Results show that, compared to controls, the group with autism spectrum disorder showed signs of both hypo- and hyper-connectivity in different regions of the resting-state networks related to social communication. Conclusion. That suggests that transition period from childhood to adolescence carries the complexity of functional connectivity from both age groups. Regions that showed differences in functional connectivity were discussed in relation to social communication difficulties.
The GRIM test: A simple technique detects numerous anomalies in the reporting of results in psychology
Authors: Brown Nicholas J L , Heathers James A J
Published: January 2018

We present a simple mathematical technique that we call GRIM (Granularity-Related Inconsistency of Means) for verifying the summary statistics of published research reports in psychology. This technique evaluates whether the reported means of integer data such as Likert-type scales are consistent with the given sample size and number of items. We tested this technique with a sample of 260 recent articles in leading journals within empirical psychology. Of the subset of articles that were amenable to testing with the GRIM technique (N = 71), around half (N = 36; 50.7%) appeared to contain at least one reported mean inconsistent with the reported sample sizes and scale characteristics, and more than 20% (N = 16) contained multiple such inconsistencies. We requested the data sets corresponding to 21 of these articles, receiving positive responses in 9 cases. We were able to confirm the presence of at least one reporting error in all cases, with 2 articles requiring extensive corrections. The implications for the reliability and replicability of empirical psychology are discussed.
West Indian manatee movements reveal novel occupancy and distribution patterns in the northern Gulf of Mexico
Authors: Aven Allen , Carmichael Ruth H. , Hieb Elizabeth E , Ross Monica
Published: January 2018

Since the 1980s, West Indian manatees (Trichechus manatus) have been reported more frequently along the northern Gulf of Mexico (GOM) coast in areas that were recently considered to be outside the species' normal areas of occupancy. The ecological importance of the northern GOM region to manatees is currently unclear, but knowledge of the spatial ecology, population linkages, and habitat associations of individuals occupying the fringes of their known range is vital to bring context and improve understanding of demographic trends and potential threats to the species, rangewide. We tracked regional-scale movements of 13 manatees documented in Mobile Bay, AL using satellite telemetry and mark-recapture methods. We determined movement and occupancy patterns including origins, seasonal dispersal and site fidelity, and functional movement modes of those individuals during the tracking period. Focal manatees moved along the GOM coast between Tampa Bay, FL and Lake Pontchartrain, LA, and consistently returned to discrete locations in both the northern GOM and within the species' core range in peninsular FL. Functional movement model fits confirmed that most relatively long-range seasonal movements were migratory in nature, suggesting that consistently occupied migratory endpoints contain relatively important seasonal habitat for manatees and diminishing the possibility that tracked manatees were nomads or transient within the study area. These results provide evidence of shifting seasonal manatee distribution in the US, and highlight repeatedly used locations that may increase in importance to the species if manatee abundance in the northern GOM increases.
Haplotype based genetic risk estimation for complex diseases
Authors: Balazard Félix
Published: January 2018

Genome-wide association studies (GWAS) have uncovered thousands of associations between genetic variants and diseases. Using the same datasets, prediction of disease risk can be attempted. Phase information is an important biological structure that has seldom been used in that setting. We propose here a multi-step machine learning method that aims at using this information. Our method captures local interactions in short haplotypes and combines the results linearly. We show that it outperforms standard linear models on some GWAS datasets. However, a variation of our method that does not use phase information obtains similar performance. Regarding the missing heritability problem, we remark that interactions in short haplotypes contribute to additive heritability. Source code is available on github at https://github.com/FelBalazard/Prediction-with-Haplotypes.
Characterisation of genomic alterations in proximal and distal colorectal cancer patients
Authors: Mohd Yunos Ryia-Illani , Ab Mutalib Nurul-Syakima , Khor Sheau Sean , Saidin Sazuita , Mahamad Nadzir Norshahidah , Abd. Razak Zuraini , Md. Rose Isa , Sagap Ismail , Mazlan Luqman , Mokhtar Norfilza M , Jamal Rahman
Published: January 2018

Background: Colorectal cancer (CRC) is one of the commonest cancers in Malaysia and majority of the patients will present with advanced disease at diagnosis particularly in cases of proximal CRCs. Little is known about the relationship between the genetic landscape and the anatomical location of the tumour as well as the prognostication in CRC patients. Objectives: The objectives of this study were to determine the somatic single nucleotide variants (SNV) and the cellular pathways between the proximal and distal CRCs. Methods: Whole exome sequencing was performed using the Ion Proton platform on 10 pairs of normal and CRC samples. The sequencing results were analysed using the Torrent Suite Software and the variants were annotated using ANNOVAR followed by validation with Sanger sequencing. Results: The commonly altered genes in CRCs are KRAS, APC, TP53 and ATM. APC is the most frequently altered gene in both proximal and distal CRCs. KRAS and ATM genes were exclusively altered in the proximal CRCs with a frequency of 60% and 40%, respectively. On the other hand, TP53 mutations did not show any CRC anatomical predominance. There were five recurrent novel variants in proximal CRCs and one recurrent novel variant in distal CRC. Wnt signalling pathway was the most frequently altered pathway in both proximal and distal CRCs whereas TGF-β and PI3K signalling pathways were predominantly altered in the proximal CRCs. Conclusion: We found that proximal CRCs presented with more variants and altered pathways as compared to distal CRCs. We also discovered that the TGF-Beta signalling (four mutations) and PI3K signalling (two mutations) pathways were exclusively altered in proximal CRCs. However, further study in larger series of samples coupled with functional studies will be needed to confirm the identified variants and determine their role in the genesis of proximal and distal CRCs.