bluuebunny/crossref_metadata_2025 huggingface dataset:
Awakening ancient polar Actinobacteria: diversity, evolution and specialized metabolite potential
Authors: Millán-Aguiñaga Natalie , Soldatou Sylvia , Brozio Sarah , Munnoch John T. , Howe John , Hoskisson Paul A. , Duncan Katherine R.
Published: October 2019

Polar and subpolar ecosystems are highly vulnerable to global climate change with consequences for biodiversity and community composition. Bacteria are directly impacted by future environmental change and it is therefore essential to have a better understanding of microbial communities in fluctuating ecosystems. Exploration of Polar environments, specifically sediments, represents an exciting opportunity to uncover bacterial and chemical diversity and link this to ecosystem and evolutionary parameters. In terms of specialized metabolite production, the bacterial order

Actinomycetales

, within the phylum

Actinobacteria

are unsurpassed, producing 10 000 specialized metabolites accounting for over 45 % of all bioactive microbial metabolites. A selective isolation approach focused on spore-forming

Actinobacteria

of 12 sediment cores from the Antarctic and sub-Arctic generated a culture collection of 50 strains. This consisted of 39 strains belonging to rare A
﻿ctinomycetales genera including Microbacterium, Rhodococcus and

Pseudonocardia

. This study used a combination of nanopore sequencing and molecular networking to explore the community composition, culturable bacterial diversity, evolutionary relatedness and specialized metabolite potential of these strains. Metagenomic analyses using MinION sequencing was able to detect the phylum

Actinobacteria

across polar sediment cores at an average of 13 % of the total bacterial reads. The resulting molecular network consisted of 1652 parent ions and the lack of known metabolite identification supports the argument that Polar bacteria are likely to produce previously unreported chemistry.
Problematic Internet Use in Children and Adolescents: Associations with psychiatric disorders and impairment
Authors: Restrepo Anita , Scheininger Tohar , Clucas Jon , Alexander Lindsay , Salum Giovanni A. , Georgiades Kathy , Paksarian Diana , Merikangas Kathleen R. , Milham Michael P.
Published: October 2019

Objective

Here, we leveraged the ongoing, large-scale Child Mind Institute Healthy Brain Network, a transdiagnostic self-referred, community sample of children and adolescents (ages 5-21), to examine the associations between Problematic Internet Use (PIU) and psychopathology, general impairment, physical health and sleep disturbances.

Methods

A total sample of 564 (190 female) participants between the ages of 7-15 (mean = 10.80, SD = 2.16), along with their parents/guardians, completed diagnostic interviews with clinicians, answered a myriad of self-report questionnaires, and underwent physical testing as part of the Healthy Brain Network protocol.

Results

PIU was positively associated with depressive disorders (aOR = 2.34; CI: 1.18-4.56; p = .01), the combined subtype of ADHD (aOR = 1.79; CI: 1.08-2.98; p = .02), greater levels of impairment (Standardized Beta = 4.79; CI: 3.21-6.37; p < .01) and increased sleep disturbances (Standardized Beta = 3.01; CI: 0.58-5.45; p = .02), even when accounting for demographic covariates and psychiatric comorbidity.

Conclusion

The association between PIU and psychopathology, as well as its impact on impairment and sleep disturbances, highlight the urgent need to gain an understanding of mechanisms in order to inform public health recommendations on internet use in U.S. youth.
Is e-cigarette use in non-smoking young adults associated with later smoking? A systematic review and meta-analysis
Authors: Khouja Jasmine N , Suddell Steph F , Peters Sarah , Taylor Amy E , Munafò Marcus R
Published: October 2019

Objective

The aim of this review was to investigate whether e-cigarette use compared to non-use in young non-smokers is associated with subsequent cigarette smoking.

Data sources

PubMed, Embase, Web of Science, Wiley Cochrane Library databases, and the 2018 Society for Research on Nicotine and Tobacco and Society for Behavioural Medicine conference abstracts.

Study selection

All studies of young people (up to age 30 years) with a measure of e-cigarette use prior to smoking and an outcome measure of smoking where an odds ratio could be calculated were included (excluding reviews and animal studies).

Data Extraction

Independent extraction was completed by multiple authors using a pre-prepared extraction form.

Data synthesis

Of 9,199 results, 17 studies were included in the meta-analysis. There was strong evidence for an association between e-cigarette use among non-smokers and later smoking (OR 4.59, 95% CI 3.60 to 5.85) when the results were meta-analysed in a random effects model. However, there was high heterogeneity (I2 = 88%).

Conclusions

Whilst the association between e-cigarette use among non-smokers and subsequent smoking appears strong, the available evidence is limited by the reliance on self-report measures of smoking history without biochemical verification. None of the studies included negative controls which would provide stronger evidence for whether the association may be causal. Much of the evidence also failed to consider the nicotine content of e-liquids used by non-smokers meaning it is difficult to make conclusions about whether nicotine is the mechanism driving this association.
Surgical Intervention for Paediatric Infusion-Related Extravasation Injury: A Systematic Review
Authors: Little MR , Dupré S , Wormald JCR , Gardiner MD , Gale C , Jain A
Published: October 2019

Objectives

This systematic review aims to assess the quality of literature supporting surgical interventions for paediatric extravasation injury and to determine and summarize their outcomes.

Methods

We performed a systematic review by searching Ovid MEDLINE and EMBASE as well as AMED, CINAHL, Cochrane Central Register of Controlled Trials (CENTRAL), Cochrane Database of Systematic Reviews andclinicaltrials.govfrom inception to February 2019. All studies other than case reports were eligible for inclusion if the population was younger than 18 years old, there was a surgical intervention aimed at treating extravasation injury and they reported on outcomes. Risk of bias was graded according to the National Institutes of Health (NIH) study quality assessment tools.

Results

26 studies involving 728 children were included – one before-and-after study and 25 case series. Extravasation injuries were mainly confined to skin and subcutaneous tissues but severe complications were also encountered, including amputation (one toe and one below elbow). Of the surgical treatments described, the technique of multiple puncture wounds and instillation of saline and/or hyaluronidase was the most commonly used. However, there were no studies in which its effectiveness was tested against another treatment or a control and details of functional and aesthetic outcomes were generally lacking.

Conclusion

There is a lack of high quality evidence to support treatment of extravasation injury in children. A definitive trial of extravasation injuries, or a centralized extravasation register using a universal grading scheme and core outcome set with adequate follow-up, are required to provide evidence to guide clinician decision-making.

Strengths and Limitations

A systematic review was performed according to PRISMA guidelines and registered on PROSPERO

Two authors used a bespoke inclusion/exclusion form to independently assess study eligibility

Studies were eligible for inclusion if the population was younger than 18 years old, if there was a surgical intervention aimed at treating extravasation injury in any setting and if they reported on short- or long-term outcomes

Two researchers also independently assessed the included studies’ risk of methodological bias using the National Institutes of Health (NIH) study quality assessment tools

18 years old may represent a relatively arbitrary cut-off age to differentiate between ‘paediatric’ and ‘adult’ in terms of extravasation injury
Platinum chemotherapy induces lymphangiogenesis in cancerous and healthy tissues that can be prevented with adjuvant anti-VEGFR3 therapy
Authors: Harris Alexandra R. , Esparza Savieay , Azimi Mohammad S. , Cornelison Robert , Azar Francesca N. , Llaneza Danielle C. , Belanger Maura , Mathew Alexander , Tkachenko Svyatoslav , Perez Matthew J. , Rosean Claire Buchta , Bostic Raegan R. , Cornelison R. Chase , Tate Kinsley M. , Peirce-Cottler Shayn M. , Paquette Cherie , Mills Anne , Landen Charles N. , Saucerman Jeff , Dillon Patrick M. , Pompano Rebecca R. , Rutkowski Melanie A. , Munson Jennifer M.
Published: October 2019

Chemotherapy has been used to inhibit cancer growth for decades, but emerging evidence shows it can affect the tumor stroma unintentionally promoting cancer malignancy. After treatment of primary tumors, remaining drugs drain via lymphatics. Though all drugs interact with the lymphatics, we know little of their impact on them. Here, we show a previously unknown effect of platinums, a widely used class of chemotherapeutics, to directly induce systemic lymphangiogenesis and activation. These changes are dose-dependent, long-lasting, and occur in healthy and cancerous tissue in multiple mouse models of breast cancer. We saw similar effects in human ovarian and breast cancer patients whose treatment regimens included platinums. Carboplatin treatment of healthy mice prior to mammary tumor inoculation increases cancer metastasis as compared to no pre-treatment. These platinum-induced phenomena could be blocked by VEGFR3 inhibition. These findings have implications for cancer patients receiving platinums and may support the inclusion of anti-VEGFR3 therapy into treatment regimens or differential design of treatment regimens to alter these potential effects.

Platinum chemotherapy induces VEGFR3-dependent lymphangiogenesis, priming tissues for metastasis of breast cancer. Inhibition of VEGFR3 via antibody blockade can reverse these effects.
Coexistence of lipid phases stabilizes interstitial water in the outer layer of mammalian skin
Authors: MacDermaid Christopher M. , Hall Kyle Wm. , DeVane Russell H. , Klein Michael L. , Fiorin Giacomo
Published: October 2019

The lipid matrix in the outer layer of mammalian skin, the stratum corneum, has been previously investigated by multiple biophysical techniques, aimed at identifying hydrophilic and lipophilic pathways of permeation. While consensus is developing over the microscopic structure of the lipid matrix, no molecular-resolution model describes the permeability of all chemical species simultaneously. Using molecular dynamics simulations of a model mixture of skin lipids, the self-assembly of the lipid matrix lamellae has been studied. At higher humidity, the resulting lamellar phase is maintained by partitioning excess water into isolated droplets of controlled size and spatial distribution. The droplets may fuse together to form intra-lamellar water channels, thereby providing a pathway for the permeation of hydrophilic species. These results reconcile competing data on the outer skin’s structure and broaden the scope of molecular-based methods to improve the safety of topical products and to advance transdermal drug delivery.
Sensitization of knee-innervating sensory neurons by tumor necrosis factor-α activated fibroblast-like synoviocytes: an in vitro, co-culture model of inflammatory pain
Authors: Chakrabarti Sampurna , Hore Zoe , Pattison Luke A. , Lalnunhlimi Sylvine , Bhebhe Charity N. , Callejo Gerard , Bulmer David C. , Taams Leonie S. , Denk Franziska , Smith Ewan St. John
Published: October 2019

Pain is a principal contributor to the global burden of arthritis with peripheral sensitization being a major cause of arthritis-related pain. Within the knee joint, distal endings of dorsal root ganglion neurons (knee neurons) interact with fibroblast-like synoviocytes (FLS) and the inflammatory mediators they secrete, which are thought to promote peripheral sensitization. Correspondingly, RNA-sequencing has demonstrated detectable levels of pro-inflammatory genes in FLS derived from arthritic patients. This study confirms that stimulation with tumor necrosis factor (TNF-α), results in expression of pro-inflammatory genes in mouse and human FLS (derived from OA and RA patients), as well as increased secretion of cytokines from mouse TNF-α stimulated FLS (TNF-FLS). Electrophysiological recordings from retrograde labelled knee neurons co-cultured with TNF-FLS, or supernatant derived from TNF-FLS, revealed a depolarized resting membrane potential, increased spontaneous action potential firing and enhanced TRPV1 function, all consistent with a role for FLS in mediating the sensitization of pain-sensing nerves in arthritis. Therefore, data from this study demonstrate the ability of FLS activated by TNF-α to promote neuronal sensitization, results that highlight the importance of both non-neuronal and neuronal cells to the development of pain in arthritis.
Transcriptome Analysis of Desquamative Interstitial Pneumonia (DIP)
Authors: Saito Shigeki , Kolls Jay K. , Liu Yaozhong , Higashi Yusuke , Ohkochi Shinya , Kondoh Yasuhiro , Lasky Joseph A. , Suzuki Takuji
Published: October 2019

Desquamative interstitial pneumonia (DIP) is a rare diffuse parenchymal lung disease of unclear etiology. A recent study showed that mice overexpressing granulocyte macrophage colony-stimulating factor (GM-CSF) in lungs develop DIP-like disease, suggesting that pulmonary GM-CSF may be involved in the pathogenesis of DIP. To determine if GM-CSF is involved in human DIP lungs, we performed transcriptome analysis on human DIP lung tissue. We also extended transcriptome analysis to respiratory bronchiolitis-associated interstitial lung disease (RB-ILD), which has been thought to be in the same spectrum of disease. The analysis revealed that DIP has a distinct transcriptome profile compared to both RB-ILD and non-diseased lung controls. It also suggested that GM-CSF was a key upstream regulator in the DIP transcriptome and that the GM-CSF signaling pathway was highly activated in DIP tissue. Further bioinformatics analysis using xCell, a novel computational method that assesses enrichments of individual cell types based on gene expression, suggested that DIP is enriched for gene signatures of macrophages and other immune cells such as dendritic cells and B cells. In conclusion, our analysis shows that DIP is characterized by a GM-CSF signature, and thus GM-CSF is likely to be involved in the pathogenesis of DIP. Our analysis also suggests that immune cells other than alveolar macrophages, such as B cells, may also be involved in the pathogenesis of DIP.
The usage of human IGHJ genes follows a particular nonrandom selection: The recombination signal sequence affects the usage of human IGHJ genes
Authors: Shi Bin , Dong Xiaoheng , Ma Qingqing , Sun Suhong , Ma Long , Yu Jiang , Wang Xiaomei , Pan Juan , He Xiaoyan , Su Danhua , Yao Xinsheng
Published: October 2019

The formation of the B cell receptor (BCR) heavy chain variable region is derived from the germline V(D)J gene rearrangement according to the “12/23” rule and the “beyond 12/23” rule. The usage frequency of each V(D)J gene in the peripheral BCR repertoires is related to the initial recombination, self-tolerance selection, and the clonal proliferative response. However, their specific differences and possible mechanisms are still unknown. We analyzed in-frame and out-of-frame BCR-H repertoires from human samples with physiological and various pathological conditions by high-throughput sequencing. Our results showed that IGHJ gene frequency follows a similar pattern where IGHJ4 is used at high frequency (>40%), IGHJ6/IGHJ3/IGHJ5 is used at medium frequencies (10%∼20%), and IGH2/IGHJ1 is used at low frequency (<4%) under whether physiological or various pathological conditions. Furthermore, analysis of the recombination signal sequences suggested that the conserved nonamer and heptamer and certain 23 bp spacer length may affect the initial IGHD-IGHJ recombination, which results in different frequencies of IGHJ genes among the initial BCR-H repertoire. Based on this “background repertoire”, we recommend that re-evaluation and further investigation are needed when analyzing the significance and mechanism of IGHJ gene frequency in self-tolerance selection and the clonal proliferative response.
High admixture between forest an cultivated chestnut (Castanea sativaMill.) in France
Authors: Bouffartigue Cathy , Debille Sandrine , Fabreguette Olivier , Ramos Cabrer Ana , Pereira-Lorenzo Santiago , Flutre Timothée , Harvengt Luc
Published: October 2019

Context

Renewed interest in European chestnut in France is focused on finding locally adapted populations partially resistant to ink disease and identifying local landraces.

Aims

We genotyped trees to assess (i) the genetic diversity of wild and cultivated chestnut across most of its range in France, (ii) their genetic structure, notably in relation with the sampled regions, and (iii) relations with its neighbors in Spain and Italy.

Methods

A total of 693 trees in 16 sampling regions in France were genotyped at 24 SSRs, and 1,401 trees in 17 sampling regions at 13 SSRs.

Results

Genetic diversity was high in most sampling regions, with redundancy between them. No significant differentiation was found between wild and cultivated chestnut. A genetic structure analysis with noa prioriinformation found a low, yet significant structure, and identified two clusters. One cluster gathers trees from south-east France and Corsica (RPP1) and another cluster gathers trees from all other sampled regions (RPP2). A substructure was detected at 13 SSRs suggesting differentiation within both RPP1 and RPP2. RPP1 was split between south-east France and Corsica. RPP2 was split between north-west France, Aveyron, Pyrenees and a last cluster gathering individuals from several other regions.

Conclusion

The genetic structure within and between our sampling regions is likely the result of natural events (recolonization after the last glaciation) and human activities (migration and exchanges). Notably, we provide evidence for a common origin of most French and Iberian chestnut trees, except those from south-east France that were associated with the Italian gene pool. This advances our knowledge of chestnut genetic diversity and structure, will benefit conservation and help our local partners’ valorization efforts.
Determinants of telomere length across human tissues
Authors: Demanelis Kathryn , Jasmine Farzana , Chen Lin S. , Chernoff Meytal , Tong Lin , Shinkle Justin , Sabarinathan Mekala , Lin Hannah , Ramirez Eduardo , Oliva Meritxell , Kim-Hellmuth Sarah , Stranger Barbara E. , Ardlie Kristin G. , Aguet François , Ahsan Habibul ,   GTEx Consortium, Doherty Jennifer , Kibriya Muhammad G. , Pierce Brandon L.
Published: October 2019

Telomere shortening is a hallmark of aging. Telomere length (TL) in blood cells has been studied extensively as a biomarker of human aging and disease; however, little is known regarding variability in TL in non-blood, disease-relevant tissue types. Here we characterize variability in TL measurements for 6,391 tissue samples, representing >20 tissue types and 952 individuals from the Genotype-Tissue Expression (GTEx) Project. We describe differences across tissue types, positive correlation among tissue types, and associations with age and ancestry. We show that genetic variation impacts TL in multiple tissue types, and that TL can mediate the effect of age on gene expression. Our results provide the foundational knowledge regarding TL in healthy tissues that is needed to interpret epidemiological studies of TL and human health.

ONE SENTENCE SUMMARY

Telomere length varies by tissue type but is generally correlated among tissue types (positively) and with age (negatively).
Physical fitness in community dwelling older adults is linked to dietary intake, gut microbiota and metabolomic signatures
Authors: Castro-Mejía Josué L. , Khakimov Bekzod , Krych Łukasz , Bülow Jacob , Bechshøft Rasmus L. , Højfeldt Grith , Mertz Kenneth H. , Garne Eva Stahl , Schacht Simon R. , Ahmad Hajar F. , Kot Witold , Hansen Lars H. , Perez-Cueto Federico J. A. , Lind Mads V. , Lassen Aske J. , Tetens Inge , Jensen Tenna , Reitelseder Søren , Jespersen Astrid P. , Holm Lars , Engelsen Søren B. , Nielsen Dennis S.
Published: October 2019

When humans age, changes in body composition arise along with lifestyle-associated disorders influencing fitness and physical decline. Here we provide a comprehensive view of dietary intake, physical activity, gut microbiota (GM) and host metabolome in relation to physical fitness of 207 community dwelling subjects aged +65 years. Stratification on anthropometric/body-composition/physical-performance measurements (ABPm) variables identified two phenotypes (high/low-fitness) clearly linked to dietary intake, physical activity, GM and host metabolome patterns. Strikingly, despite a higher energy intake high-fitness subjects were characterized by leaner bodies and lower fasting proinsulin-C-peptide/blood glucose levels in a mechanism likely driven by higher dietary-fiber intake, physical activity and increased abundance of Bifidobacteriales and Clostridiales species in GM and associated metabolites (i.e. enterolactone). These factors explained 50.1% of the individual variation in physical fitness. We propose that targeting dietary strategies for modulation of GM and host metabolome interactions may allow establishing therapeutic approaches to delay and possibly revert comorbidities of aging.
Representation of Task Structure in Human Hippocampus and Orbitofrontal Cortex
Authors: Mizrak Eda , Bouffard Nichole R. , Libby Laura A. , Boorman Erie , Ranganath Charan
Published: October 2019

The hippocampus is thought to support episodic memory, or memory for specific events, but recent work also suggests that it may be involved in extracting structure from the world to guide future decisions and predictions. Recent evidence in rodents suggests that the hippocampus supports decision-making in cooperation with orbitofrontal cortex (OFC), possibly based on representation of task structure. Here, we used functional magnetic resonance imaging (fMRI) to test how the human hippocampus and OFC represents decision-relevant information extracted from previous experiences. Participants performed a task in which they learned values of different foods in grocery store contexts. The task was structured such that we could examine the degree to which neural representations could reflect generalized information about different task structures. Specifically, we manipulated whether a food’s desirability varied with store context or not. Some foods were desirable in some store contexts and not in others; some foods were always desirable or undesirable. Participants needed to extract these two task sub-structures (i.e., context-determined vs. context-invariant) from the task structure. We examined hippocampal and OFC activity patterns during a decision-making task after participants were trained with the task structure. Our results showed that both hippocampus and OFC carried task structure information that was relevant to the decision outcomes. Hippocampal and lateral OFC representations differentiated between context-determined (deterministic) and context-invariant (probabilistic) task structures. The degree of this differentiation, an index of task structure representation, was highly correlated between hippocampus and lateral OFC. These results add to a mounting evidence suggesting that the hippocampus and OFC support decision-making by representing task relevant information to the decision outcomes after the task structure is learned.
Venlafaxine stimulates an MMP-9-dependent increase in excitatory/inhibitory balance in a stress model of depression
Authors: Alaiyed Seham , McCann Mondona , Mahajan Gouri , Rajkowska Grazyna , Stockmeier Craig A. , Kellar Kenneth J. , Wu Jian Young , Conant Katherine
Published: October 2019

Emerging evidence suggests that there is a reduction in overall cortical excitatory to inhibitory balance in major depressive disorder (MDD), which afflicts approximately 14-20% of individuals. Reduced pyramidal cell arborization occurs with stress and MDD, and may diminish excitatory neurotransmission. Enhanced deposition of perineuronal net (PNN) components also occurs with stress. Since parvalbumin-expressing interneurons are the predominant cell population that is enveloped by PNNs, which enhance their ability to release GABA, excess PNN deposition likely increases pyramidal cell inhibition. In the present study we investigate the potential for matrix metalloprotease-9 (MMP-9), an endopeptidase secreted in response to neuronal activity, to contribute to the antidepressant efficacy of venlafaxine, a serotonin/norepinephrine reuptake inhibitor. Chronic venlafaxine increases MMP-9 levels in murine cortex, and increases both pyramidal cell arborization and PSD-95 expression in the cortex of wild-type but not MMP-9 null mice. We have previously shown that venlafaxine reduces PNN deposition and increases the power ofex vivogamma oscillations in conventionally-housed mice. Gamma power is increased with pyramidal cell disinhibition and with remission from MDD. Herein we observe that PNN expression is increased in a corticosterone-induced stress model of disease and reduced by venlafaxine. As compared to mice that receive concurrent venlafaxine, corticosterone treated mice also display reducedex vivogamma power and impaired working memory. Autopsy-derived prefrontal cortex samples show elevated MMP-9 levels in anti-depressant treated MDD patients as compared to controls. These preclinical and postmortem findings highlight a link between extracellular matrix regulation and MDD.
Senescence and entrenchment in evolution of amino acid sites
Authors: Stolyarova A. V. , Nabieva E. , Ptushenko V. V. , Favorov A. V. , Popova A. V. , Neverov A. D. , Bazykin G. A.
Published: October 2019

Amino acid propensities at a site change in the course of protein evolution. This may happen for two reasons. Changes may be triggered by substitutions at epistatically interacting sites elsewhere in the genome; alternatively, they may arise due to environmental changes that are external to the genome. Here, we design a framework for distinguishing between these alternatives. Using analytical modelling and simulations, we show that they cause opposite dynamics of the fitness of the allele currently occupying the site: its fitness tends to increase with the time since its origin due to epistasis (“entrenchment”), but to decrease due to random environmental fluctuations (“senescence”). We analyse the phylogenetic distribution of substitutions in nuclear genomes, and show that among the amino acids originating at negatively selected sites of vertebrates, nearly all experience strong entrenchment. By contrast, among the amino acids originating at positively selected sites, 18% experience senescence. A similar pattern is observed in phylogenies of insects. We propose that senescence of the current allele is a cause of adaptive evolution.
Orbitofrontal control of visual cortex gain promotes visual associative learning
Authors: Liu Dechen , Deng Juan , Zhang Zhewei , Zhang Zhi-Yu , Sun Yan-Gang , Yang Tianming , Yao Haishan
Published: October 2019

The orbitofrontal cortex (OFC) encodes expected outcomes and plays a critical role in flexible, outcome-guided behavior. The OFC projects to primary visual cortex (V1), yet the function of this top-down projection is unclear. We find that optogenetic activation of OFC projection to V1 reduces the amplitude of V1 visual responses via the recruitment of local somatostatin-expressing (SST) interneurons. Using mice performing a Go/No-Go visual task, we show that the OFC projection to V1 mediates the outcome-expectancy modulation of V1 responses to the reward-irrelevant No-Go stimulus. Furthermore, V1-projecting OFC neurons reduce firing during expectation of reward. In addition, chronic optogenetic inactivation of OFC projection to V1 impairs, whereas chronic activation of SST interneurons in V1 improves the learning of Go/No-Go visual task, without affecting the immediate performance. Thus, OFC top-down projection to V1 is crucial to drive visual associative learning by modulating the response gain of V1 neurons to non-relevant stimulus.
Introducing ExHiBITT – Exploring Host microbiome inTeractions in Twins-, a colon multiomic cohort study
Authors: Mora-Ortiz Marina , Ibraheim Hajir , Kottoor Sherine Hermangild , Bowyer Ruth C. E. , Metrustry Sarah , Sanderson Jeremy , Powell Nicholas , Spector Tim D. , Small Kerrin S. , Steves Claire J.
Published: October 2019

The colon is populated by approximately 1012 microorganisms, but the relationships between this microbiome and the host health status are still not completely understood. Participants from the TwinsUK cohort were recruited to study the interactions between the microbiome and host adaptive immunity. In total, 205 monozygotic twins were recruited from the wider TwinsUK cohort. They completed health questionnaires, and provided saliva, blood, colon biopsies from three different locations, caecal fluid, and two faecal-samples.

Here, our objective is to present the cohort characteristics of ExHiBITT including i) biomedical phenotypes, ii) environmental factors and ii) colonoscopic findings. A significant proportion of this apparently normal cohort had colonic polyps (28%), which are of interest as potential precursors of colorectal cancer, and as expected, the number of polyps found was significantly correlated with BMI and age. Hitherto undiagnosed diverticulosis was also not infrequently found during colonoscopy (26%) and was associated in changes in Hybrid Th1-17 cells in the colon. Twin proband cooccurrence rate for diverticulosis (82%), was much higher than for polyps (42%). Familial factors affecting morphology or tolerance may contribute to the ease of endoscopy, as both the time to reach the caecum, and pain perceived were highly concordant (proband concordance: 85% and 56% respectively). We found the expected positive relationship between BMI and colonoscopic anomalies such as diverticular disease and polyps in the whole population, but within twin pairs this association was reversed. This suggests that familial factors confound these associations. Host and microbial Next Generation Sequencing and metabolomics of the samples collected are planned in this cohort.
GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations
Authors: Manchanda Nancy , Portwood John L. , Woodhouse Margaret R. , Seetharam Arun S. , Lawrence-Dill Carolyn J. , Andorf Carson M. , Hufford Matthew B.
Published: October 2019

Background

Genome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, genomic diversity and differences in gene expression across individuals and tissue types. Quality metrics for genome assemblies gauge both the completeness and contiguity of an assembly and help provide confidence in downstream biological insights. To compare quality across multiple assemblies, a set of common metrics are typically calculated and then compared to one or more gold standard reference genomes. While several tools exist for calculating individual metrics, applications providing comprehensive evaluations of multiple assembly features are, perhaps surprisingly, lacking. Here, we describe a new toolkit that integrates multiple metrics to characterize both assembly and gene annotation quality in a way that enables comparison across multiple assemblies and assembly types.

Findings

Our application, named GenomeQC, is an easy-to-use and interactive web framework that integrates various quantitative measures to characterize genome assemblies and annotations. GenomeQC provides researchers with a comprehensive summary of these statistics and allows for benchmarking against gold standard reference assemblies.

Conclusions

The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license.

All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.
Architectural analyses of tree forking habit with single-image photogrammetry: a case study of post-mature temperate oaks
Authors: Kędra Kamil
Published: October 2019

Tree forking is both ecologically and economically relevant, but remains much understudied. Here, thirty post-mature temperate oaks (Quercus robur or Q. petraea) forking habit was both qualitatively and quantitatively analysed with the single-image photogrammetry (SIP), in a north-exposed mixed, deciduous forest remnant (near Krakow; Poland). A new classification of mature oak architectures was proposed, based on the original Hallé-Oldeman model, with modified locations of the main branches and presence or absence of bifurcation in the main stem. Two of the new classes were most clearly represented by the studied oaks. It was found that the trees tended to either keep branches at varying heights, with no forks, or to iterate forking, with no major (non-fork) branches below the first fork. The quantitative analysis confirmed the applicability of the branch to parent stem diameter ratio to define a fork. Branching ratio was positively correlated with both tree diameter and height of a branch above the ground, which is consistent with a previous study, based on much younger trees. It is concluded, that most probably the tree-level factors and phenomena, such as water supplies and posture control, played the key role in the studied oaks forking habit. The SIP method enabled valuable insights into the large oaks’ forking, both at the tree and branch levels, and may be further employed to study mature trees’ bifurcation patterns. Based on this study, some possible improvements to the methodology were discussed.
Multi Epitope Vaccine Prediction Against Aichi Virus using Immunoinformatic Approach
Authors: Hassan Ali Asma Ali , Abdalla Mohamed Sahar Abdeen , Omer Musa Marwa Abdulrahman , Bushra ELtahier Amani Faisal , Abdelrahman Ali Walaa Mohammed Alsamani , Ali Ibrahim Elaf Ahmed Mohammed , Hamdi Ahmed , Hassan Mohamed A.
Published: October 2019

Aichi virus, AiV is single stranded negative sense RNA genome belonging to the genusKobuviru, a family ofPicornaviridaethat causes severe gastroenteritis. There is no treatment or vaccine for it, thus the aim of this study is to design a peptide vaccine using immunoinformatic approaches to analyze the viral Protein VP1 of AiV-1 strain, to determine the conserved region which is further studied to predict all possible epitopes that can be used as a peptide vaccine. A total of 38 Aichi virus VP1 retrieved from NCBI database were aligned to determine the conservancy and to predict the epitopes using IEDB analysis resource. Three epitopes predicted as a peptide vaccine for B cell was (PLPPDT, PPLPTP, and LPPLPTP). For T cell, two epitopes showed high affinity to MHC class I (FSIPYTSPL and TMVSFSIPY) and high coverage against the whole world population. Also, in MHC class II, three epitopes that interact with most frequent MHC class II alleles (FTYIAADLR and YMAEVPVSA) with high coverage in the whole world population. For both MHCI and MHCII the T-cell peptide with the strongest affinity to the worldwide population was FSIPYTSPL.

Peptide vaccine against AiV is powerfully displace the normal produced vaccines based on the experimental biochemistry tools, as it designed to handle with a wide range of mutated strains, which will effectively minimize the frequent outbreaks and their massive economical wastage consequences.
Observations on the interactions of mammals and birds with badger (Meles meles) dung pits at a site used by a single social group in an urban area
Authors: Hughes Morgan , Brown Scott
Published: October 2019

During a monitoring study of a single social group of badger (Meles meles) at an urban site, incidental observations were noted of mammalian and avian species feeding within and removing material fromM. melesdung pits. In response to these observations, infra-red cameras were deployed at dung pits for a 10-week period to document the nature, timing and frequency of these behaviours. Cameras were triggered a total of 954 times by a total of nine mammal and 12 bird species. Harvesting of material accounted for 28 % of latrine-associated behaviours. Results may have implications for disease transmission and the efficacy of badger surveys, particularly in areas where brown rats are prevalent.
Long-range interhemispheric projection neurons show biased response properties and fine-scale local subnetworks in mouse visual cortex
Authors: Hagihara Kenta M. , Ishikawa Ayako W. , Yoshimura Yumiko , Tagawa Yoshiaki , Ohki Kenichi
Published: October 2019

Integration of information processed separately in distributed brain regions is essential for brain functions. This integration is enabled by long-range projection neurons, and further, concerted interactions between long-range projections and local microcircuits are crucial. It is not well known, however, how this interaction is implemented in cortical circuits. Here, to decipher this logic, using callosal projection neurons (CPNs) as a model of long-range projections, we found that CPNs exhibited distinct response properties and fine-scale local connectivity patterns. In vivo 2-photon calcium imaging revealed that CPNs showed a higher ipsilateral eye (with respect to their somata) preference, and that CPN pairs showed stronger signal/noise correlation than random pairs. Slice recordings showed CPNs were preferentially connected to CPNs, demonstrating the existence of projection target-dependent fine-scale subnetworks. Collectively, our results suggest that long-range projection target predicts response properties and local connectivity of cortical projection neurons.
Mechanism of interaction of an endofungal bacterium Serratia marcescens D1 with its host and non-host fungi
Authors: Hazarika Dibya Jyoti , Gautom Trishnamoni , Parveen Assma , Goswami Gunajit , Barooah Madhumita , Modi Mahendra Kumar , Boro Robin Chandra
Published: October 2019

Association of bacteria with fungi is a major area of research in infection biology, however, very few strains of bacteria have been reported that can invade and reside within fungal hyphae. Here, we report the characterization of an endofungal bacterium Serratia marcescens D1 from Mucor irregularis SS7 hyphae. Upon re-inoculation, colonization of the endobacterium S. marcescens D1 in the hyphae of Mucor irregularis SS7 was demonstrated using stereo microscopy. However, S. marcescens D1 failed to invade into the hyphae of the tested Ascomycetes (except Fusarium oxysporum) and Basidiomycetes. Remarkably, Serratia marcescens D1 could invade and spread over the culture of F. oxysporum that resulted in mycelial death. Prodigiosin, the red pigment produced by the Serratia marcescens D1, helps the bacterium to invade fungal hyphae as revealed by the increasing permeability in fungal cell membrane. On the other hand, genes encoding the type VI secretion system (T6SS) assembly protein TssJ and an outer membrane associated murein lipoprotein also showed significant up-regulation during the interaction process, suggesting the involvement of T6SS in the invasion process.
Relationship of sociodemographic and lifestyle factors and diet habits with metabolic syndrome (MetS) in a multi-ethnic Asian population
Authors: Iqbal Saleem Perwaiz , Ramadas Amutha , Fatt Quek Kia , Shin Ho Loon , Onn Wong Yin , Kadir Khalid Abdul
Published: October 2019

Objectives

Literature shows a high prevalence of MetS among Malaysians, varying across major ethnicities. As sociodemographic characteristics, lifestyle factors and diet habits of such communities have been reported to be diverse, the study objective was to investigate the association of various sociodemographic characteristics, lifestyle factors and diet habits on MetS overall and among the three major ethnic communities in Malaysia.

Materials and Methods

We conducted a cross-sectional study among 481 Malaysians of age 18 years and above living in Johor, Malaysia. Information on demographics, lifestyle and diet habits was collected using a structured questionnaire. MetS was diagnosed among the subjects using the Harmonized criteria. Multiple logistic regression was used to analyse associations between sociodemographic and lifestyle factors and dietary behaviours with MetS.

Results

MetS was found among 32.2% of the respondents, more prevalent among the Indians (51.9%), followed by Malays (36.7%) and Chinese (20.2%). Overall, increasing age (AOR=2.44[95%CI=1.27-4.70] at 40-49 years vs. AOR=4.14[95%CI=1.97-8.69] at 60 years and above) and Indian ethnicity (AOR=1.95[95%CI=1.12-3.38)] increased, while higher education (AOR = 0.44[95%CI = 0.20-0.94] reduced the odds of MetS in this population. Quick finishing of meals (AOR=2.17[95%CI=1.02-4.60]) and low physical activity (AOR=4.76[95%CI=1.49-15.26]) was associated with an increased odds of MetS among the Malays and Chinese, respectively.

Conclusion

The population in Johor is diverse in these factors, and some of these are associated with MetS in certain ethnicities. In light of such differences, ethnic specific measures are needed to reduce the prevalence of MetS in this population.
The fodder grass resources for ruminants: A indigenous treasure of local communities of Thal desert Punjab, Pakistan
Authors: Shaheen Humaira , Qureshi Rahmatuallah , Qaseem Mirza Faisal , Bruschi Piero
Published: October 2019

Indigenous people have been using their regional grasses for rearing their animals for centuries. The present study is the first recorded traditional knowledge of grasses and feeding system for livestock from the Thal desert in Pakistan. Snowball method was used to identify key informants. Information was collected from 232 informants from six districts of Thal Desert through semi-structural questionnaire and site visits. The data was analyzed through Smith’s salience index and Composite Salience using ANTHROPAC package in R software. On the whole 61 grasses were recorded from the study area and most of the species belongs to the Poaceae family (52 species). Based on palatability grasses were categorized into three major groups i.e. (A) High priority, (B) Medium priority and (C) Low priority. Species in Group A, abundantly present in the study area, highly palatable forage for all ruminants. 232(141M +91W) local informants were interviewed. Informants were grouped into three major age categories: 20–35 (48 informants), 36–50 (116 informants) and 51–67 years (68 informants). ANTHROPAC frequency analysis conformed the Smith’s salience index and Composite Salience; Cynodon dactylon was the favorite species (6.46 SI, 0.6460 CS) followed by Cymbopogon jwarancusa (5.133 SI, 0.5133 CS) and Sorghum sp. was the third most salient species (5.121 SI, 0.5121 CS). Grasses were mostly available during the season of August and October and had also ethnoveterinary importance. This document about the traditional feeding of livestock from Thal Desert can strengthen the value of conserving our traditional knowledge, which was poorly documented before.
Nanopatterned Thermoresponsive Functionalization of Substrates via Nanosphere Lithography
Authors: Mireles Marcela , Soule Cody W. , Delgadillo Luis F. , Gaborski Thomas R.
Published: October 2019

1

Self-assembled monolayers (SAMs) have been widely utilized as a way of tailoring surface chemistry through the adsorption of organic molecules to different materials. SAMs are easy to prepare and offer a wide variety of organic molecules that afford additional or improved properties to the coated material. Spatial control of SAM placement has been achieved over many length-scales, even at the nanoscale. However, nanopatterned SAMs are usually prepared through serial processes utilizing atomic scanning probes or soft-lithography utilizing elastomeric masters. These techniques are expensive or not repeatable. Here we present the use of nanospheres for the creation of nanopatterned Au:Cu films which spatially control the grafting of a thermoresponsive SAM made from poly(N-isopropyl acrylamide) (PNIPAM). Chemical characterization validates the presence of PNIPAM and environmental atomic force microscopy showed its response to temperature which was evidenced by a change in stiffness. Our approach represents an affordable large area methodology for repeatable spatial control of SAMs at the nanoscale.
Atypical processing of uncertainty in individuals at risk for psychosis
Authors: Cole David M. , Diaconescu Andreea O. , Pfeiffer Ulrich J. , Brodersen Kay H. , Mathys Christoph D. , Julkowski Dominika , Ruhrmann Stephan , Schilbach Leonhard , Tittgemeyer Marc , Vogeley Kai , Stephan Klaas E.
Published: October 2019

Background

Current theories of psychosis highlight the role of abnormal learning signals, i.e., prediction errors (PEs) and uncertainty, in the formation of delusional beliefs. We employed computational analyses of behaviour and functional magnetic resonance imaging (fMRI) to examine whether such abnormalities are evident in at-risk mental state (ARMS) individuals.

Methods

Non-medicated ARMS individuals (n=13) and control participants (n=13) performed a probabilistic learning paradigm during fMRI data acquisition. We used a hierarchical Bayesian model to infer subject-specific computations from behaviour – with a focus on PEs and uncertainty (or its inverse, precision) at different levels, including environmental ‘volatility’ – and used these computational quantities for analyses of fMRI data.

Results

Computational modelling of ARMS individuals’ behaviour indicated volatility estimates converged to significantly higher levels than in controls. Model-based fMRI demonstrated increased activity in prefrontal and insular regions of ARMS individuals in response to precision-weighted low-level outcome PEs, while activations of prefrontal, orbitofrontal and anterior insula cortex by higher-level PEs (that serve to update volatility estimates) were reduced. Additionally, prefrontal cortical activity in response to outcome PEs in ARMS was negatively associated with clinical measures of global functioning.

Conclusions

Our results suggest a multi-faceted learning abnormality in ARMS individuals under conditions of environmental uncertainty, comprising higher levels of volatility estimates combined with reduced cortical activation, and abnormally high activations in prefrontal and insular areas by precision-weighted outcome PEs. This atypical representation of high- and low-level learning signals might reflect a predisposition to delusion formation.
Stable task information from an unstable neural population
Authors: Rule Michael E. , Loback Adrianna R. , Raman Dhruva V. , Driscoll Laura , Harvey Christopher D. , O’Leary Timothy
Published: October 2019

Over days and weeks, neural activity representing an animal’s position and movement in sensorimotor cortex has been found to continually reconfigure or ‘drift’ during repeated trials of learned tasks, with no obvious change in behavior. This challenges classical theories which assume stable engrams underlie stable behavior. However, it is not known whether this drift occurs systematically, allowing downstream circuits to extract consistent information. We show that drift is systematically constrained far above chance, facilitating a linear weighted readout of behavioural variables. However, a significant component of drift continually degrades a fixed readout, implying that drift is not confined to a null coding space. We calculate the amount of plasticity required to compensate drift independently of any learning rule, and find that this is within physiologically achievable bounds. We demonstrate that a simple, biologically plausible local learning rule can achieve these bounds, accurately decoding behavior over many days.