bluuebunny/crossref_metadata_2025_split huggingface dataset:
The gut microbiome influences host diet selection behavior
Authors: Trevelline Brian K. , Kohl Kevin D. 
Published: July 2020

ABSTRACTDiet selection is a fundamental aspect of animal behavior with numerous ecological and evolutionary implications. While the underlying mechanisms are complex, the availability of essential dietary nutrients can strongly influence diet selection behavior. The gut microbiome has been shown to metabolize many of these same nutrients, leading to the untested hypothesis that intestinal microbiota may influence diet selection. Here we show that germ-free mice colonized by gut microbiota from three rodent species with distinct foraging strategies differentially selected diets that varied in macronutrient composition. Specifically, we found that herbivore-conventionalized mice voluntarily selected a higher protein:carbohydrate ratio diet, while omnivore- and carnivore-conventionalized mice selected a lower P:C ratio diet. In support of the long-standing hypothesis that tryptophan – the essential amino acid precursor of serotonin – serves as a peripheral signal regulating diet selection, bacterial genes involved in tryptophan metabolism and plasma tryptophan availability prior to the selection trial were significantly correlated with subsequent voluntary carbohydrate intake. Finally, herbivore-conventionalized mice exhibited larger intestinal compartments associated with microbial fermentation, broadly reflecting the intestinal morphology of their donor species. Together, these results demonstrate that gut microbiome can influence host diet selection behavior, perhaps by mediating the availability of essential amino acids, thereby revealing a novel mechanism by which the gut microbiota can influence host foraging behavior.SIGNIFICANCEThe behavior of diet choice or diet selection can have wide-reaching implications, scaling from individual animals to ecological and evolutionary processes. Previous work in this area has largely ignored the potential for intestinal microbiota to modulate these signals. This notion has been highly speculated for years but has not yet been explicitly tested. Here we show that germ-free mice colonized by differential microbiomes (from wild rodents with varying natural feeding strategies) exhibited significant differences in their voluntary dietary selection. Specifically, differences in voluntary carbohydrate selection were associated with plasma amino acid levels and bacterial genes involved in the metabolism of tryptophan. Together, these results demonstrate a role for the microbiome in host nutritional physiology and behavior.
Image-based pooled whole genome CRISPR screening for Parkin and TFEB subcellular localization
Authors: Kanfer Gil , Sarraf Shireen A. , Maman Yaakov , Baldwin Heather , Johnson Kory R. , Ward Michael E. , Kampmann Martin , Lippincott-Schwartz Jennifer , Youle Richard J. 
Published: July 2020

AbstractGenome-wide CRISPR screens have transformed our ability to systematically interrogate human gene function, but are currently limited to a subset of cellular phenotypes. We report a novel pooled screening approach for a wider range of cellular and subtle subcellular phenotypes. Machine learning and convolutional neural network models are trained on the subcellular phenotype to be queried. Genome-wide screening then utilizes cells stably expressing dCas9 (CRISPRi), photoactivatable fluorescent protein (PA-mCherry), and a lentiviral guide RNA (gRNA) pool. Cells are screened by microscopy and classified by artificial intelligence (AI) algorithms, which precisely identify the genetically altered phenotype. Cells with the phenotype of interest are photoactivated, isolated via flow cytometry, and the gRNAs are identified by sequencing. A proof-of-concept screen accurately identified PINK1 as essential for Parkin recruitment to mitochondria. A genome-wide screen identified factors mediating TFEB relocation from the nucleus to the cytosol upon prolonged starvation. Twenty of the sixty-four hits called by the neural network model were independently validated, revealing new effectors of TFEB subcellular localization. This approach, AI-Photoswitchable Screening (AI-PS) offers a novel screening platform capable of classifying a broad range of mammalian subcellular morphologies, an approach largely unattainable with current methodologies at genome-wide scale.
A clinically-relevant polymorphism in the Na+/taurocholate cotransporting polypeptide (NTCP) occurs at a rheostat position
Authors: Ruggiero Melissa J. , Malhotra Shipra , Fenton Aron W. , Swint-Kruse Liskin , Karanicolas John , Hagenbuch Bruno 
Published: July 2020

AbstractConventionally, most amino acid substitutions at important protein positions are expected to abolish function. However, in several soluble-globular proteins, we identified a class of non-conserved positions for which various substitutions produced progressive functional changes; we consider these evolutionary “rheostats”. Here, we report a strong rheostat position in the integral membrane protein, Na+/taurocholate cotransporting polypeptide (NTCP), at the site of a pharmacologically-relevant polymorphism (S267F). Functional studies were performed for all 20 substitutions (“S267X”) with three substrates (taurocholate, estrone-3-sulfate and rosuvastatin). The S267X set showed strong rheostatic effects on overall transport, and individual substitutions showed varied effects on transport kinetics (Kmand Vmax). However, the outcomes were substrate dependent, indicating altered specificity. To assess protein stability, we measured surface expression and used the Rosetta software suite to model structure and stability changes of S267X. Although buried near the substrate binding site, S267X substitutions were easily accommodated in the NTCP structure model. Across the modest range of changes, calculated stabilities correlated with surface-expression differences, but neither parameter correlated with altered transport. Thus, substitutions at rheostat position 267 had wide-ranging effects on the phenotype of this integral membrane protein. We further propose that polymorphic positions in other proteins might be locations of rheostat positions.
Evolution of sex hormone binding globulins reveals early gene duplication at the root of vertebrates
Authors: Guiguen Yann , Pasquier Jeremy , Fostier Alexis , Bobe Julien 
Published: July 2020

AbstractSex hormone-binding globulin (Shbg) is an important vertebrate blood carrier protein synthetized in the liver and involved in the transport and local regulation of sex steroids in target tissues. A novelshbg gene (shbgb)with a predominant ovarian expression was recently characterized. Being initially found only in salmonids, thisshbgbwas originally thought to result from the Salmonid-specific whole genome duplication. Using updated transcriptomic and genomic resources we identifiedShbgborthologs in non-salmonid teleosts (European eel, arowana), holosteans (spotted gar, bowfin), polypteriformes (reedfish), agnatha (sea lamprey) and in amphibians, and found that the classicalShbggene (Shbga) displays a predominant hepatic expression whereasShbgbhas a predominant gonadal expression. Together, these results indicate that these twoShgbgenes most likely originate from a whole genome duplication event at the root of vertebrate evolution, followed by numerous and independent losses and by tissue expression specialization ofShbgaandShbgbparalogs.HighlightsPhylogeny, synteny and expression analyses shed new light on Shbg evolution in vertebrates.Shbg diversity originates from a duplication event at the root of vertebrate evolution.This duplication was followed by many independent losses ofShbgparalogs in vertebrates.Shbgparalogs have acquired different tissue expression patterns.
Neuronal non-CG methylation is an essential target for MeCP2 function
Authors: Tillotson Rebekah , Cholewa-Waclaw Justyna , Chhatbar Kashyap , Connelly John , Kirschner Sophie A. , Webb Shaun , Koerner Martha V. , Selfridge Jim , Kelly David , De Sousa Dina , Brown Kyla , Lyst Matthew J. , Kriaucionis Skirmantas , Bird Adrian 
Published: July 2020

SUMMARYDNA methylation is implicated in neuronal biology via the protein MeCP2, mutation of which causes Rett syndrome. MeCP2 recruits the NCOR1/2 corepressor complexes to methylated cytosine in the CG dinucleotide, but also to non-CG methylation, which is abundant specifically in neuronal genomes. To test the biological significance of its dual binding specificity, we replaced the MeCP2 DNA binding domain with an orthologous domain whose specificity is restricted to mCG motifs. Knock-in mice expressing the domain-swap protein displayed severe Rett syndrome-like phenotypes, demonstrating that interaction with sites of non-CG methylation, specifically the mCAC trinucleotide, is critical for normal brain function. The results support the notion that the delayed onset of Rett syndrome is due to the late accumulation of both mCAC and its reader MeCP2. Intriguingly, genes dysregulated in bothMecp2-null and domain-swap mice are implicated in other neurological disorders, potentially highlighting targets of particular relevance to the Rett syndrome phenotype.
Identification of antibiotics for use in selection of the chytrid fungi Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans
Authors: Robinson Kristyn A. , Dunn Mallory , Hussey Shane P. , Fritz-Laylin Lillian K. 
Published: July 2020

ABSTRACTGlobal amphibian populations are being decimated by chytridiomycosis, a deadly skin infection caused by the fungal pathogens Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal). Although ongoing efforts are attempting to limit the spread of these infections, targeted treatments are necessary to manage the disease. Currently, no tools for genetic manipulation are available to identify and test specific drug targets in these fungi. To facilitate the development of genetic tools in Bd and Bsal, we have tested five commonly used antibiotics with available resistance genes: Hygromycin, Blasticidin, Puromycin, Zeocin, and Neomycin. We have identified effective concentrations of each for selection in both liquid culture and on solid media. These concentrations are within the range of concentrations used for selecting genetically modified cells from a variety of other eukaryotic species.
A new long-read dog assembly uncovers thousands of exons and functional elements missing in the previous reference
Authors: Wang Chao , Wallerman Ola , Arendt Maja-Louise , Sundström Elisabeth , Karlsson Åsa , Nordin Jessika , Mäkeläinen Suvi , Pielberg Gerli Rosengren , Hanson Jeanette , Ohlsson Åsa , Saellström Sara , Rönnberg Henrik , Ljungvall Ingrid , Häggström Jens , Bergström Tomas F. , Hedhammar Åke , Meadows Jennifer R. S. , Lindblad-Toh Kerstin 
Published: July 2020

AbstractHere we present a new high-quality canine reference genome with gap number reduced 41-fold, from 23,836 to 585. Analysis of existing and novel data, RNA-seq, miRNA-seq and ATAC-seq, revealed a large proportion of these harboured previously hidden elements, including genes, promoters and miRNAs. Short-read dark regions were detected, and genomic regions completed, including the DLA, TCR and 366 cancer genes. 10x sequencing of 27 dogs uncovered a total of 22.1 million SNPs, Indels and larger structural variants (SVs). 1.4% overlap with protein coding genes and could provide a source of normal or aberrant phenotypic modifications.
Rapid, robust plasmid verification byde novoassembly of short sequencing reads
Authors: Gallegos Jenna. E. , Rogers Mark F. , Cialek Charlotte , Peccoud Jean 
Published: July 2020

AbstractPlasmids are a foundational tool for basic and applied research across all subfields of biology. Increasingly, researchers in synthetic biology are relying on and developing massive libraries of plasmids as vectors for directed evolution, combinatorial gene circuit tests, and for CRISPR multiplexing. Verification of plasmid sequences following synthesis is a crucial quality control step that creates a bottleneck in plasmid fabrication workflows. Crucially, researchers often elect to forego the cumbersome verification step, potentially leading to reproducibility and— depending on the application—security issues. In order to facilitate plasmid verification to improve the quality and reproducibility of life science research, we developed a fast, simple, and open source pipeline for assembly and verification of plasmid sequences from Illumina reads. We demonstrate that our pipeline, which relies onde novoassembly, can also be used to detect contaminating sequences in plasmid samples. In addition to presenting our pipeline, we discuss the role for verification and quality control in the increasingly complex life science workflows ushered in by synthetic biology.
Comparison of Multimorbidity in COVID-19 infected and general population in Portugal
Authors: Froes Miguel , Neves Bernardo , Martins Bruno , Silva Mário J. 
Published: July 2020

AbstractUnderstanding COVID-19 and its risk factors in the Portuguese population is critical to combat this condition. To study the impact of multimorbidity in the population with COVID-19 infection, we performed a descriptive analysis of a dataset extracted from all reported confirmed cases of COVID-19 in Portugal until June 30, 2020. We observed a prevalence of multimorbidity in 6.77% of the 36,244 infected patients. Patients showed an increased risk of hospitalization, ICU admission and mortality with OR 2.22 (CI 95%: 2.13-2.32) for every additional morbidity. Further studies should confirm these findings and special attention should be made on data collection to ensure proper recording of patient comorbidities.
Methodological Rigor in COVID-19 Clinical Research – A Systematic Review and Case-Control Analysis
Authors: Jung Richard G. , Di Santo Pietro , Clifford Cole , Prosperi-Porta Graeme , Skanes Stephanie , Hung Annie , Parlow Simon , Visintini Sarah , Ramirez F. Daniel , Simard Trevor , Hibbert Benjamin 
Published: July 2020

AbstractObjectiveTo systematically evaluate the quality of reporting of currently available COVID-19 studies compared to historical controls.DesignA systematic review and case-control analysisData sourcesMEDLINE, Embase, and Cochrane Central Register of Controlled Trials until May 14, 2020Study selectionAll original clinical literature evaluating COVID-19 or SARS-CoV2 were identified and 1:1 historical control of the same study type in the same published journal was matched from the previous yearData extractionTwo independent reviewers screened titles, abstracts, and full-texts and independently assessed methodological quality using Cochrane Risk of Bias Tool, Newcastle- Ottawa Scale, QUADAS-2 Score, or case series checklist.Results9895 titles and abstracts were screened and 686 COVID-19 articles were included in the final analysis in which 380 (55.4%) were case series, 199 (29.0%) were cohort, 63 (9.2%) were diagnostic, 38 (5.5%) were case-control, and 6 (0.9%) were randomized controlled trials. Overall, high quality/low-bias studies represented less than half of COVID-19 articles - 49.0% of case series, 43.9% of cohort, 31.6% of case-control, and 6.4% of diagnostic studies. We matched 539 control articles to COVID-19 articles from the same journal in the previous year for a final analysis of 1078 articles. The median time to acceptance was 13.0 (IQR, 5.0-25.0) days in COVID-19 articles vs. 110.0 (IQR, 71.0-156.0) days in control articles (p<0.0001). Overall, methodological quality was lower in COVID-19 articles with 220 COVID-19 articles of high quality (41.0%) vs. 392 control articles (73.3%, p<0.0001) with similar results when stratified by study design. In both unadjusted and adjusted logistic regression, COVID-19 articles were associated with lower methodological quality (odds ratio, 0.25; 95% CI, 0.20 to 0.33, p<0.0001).ConclusionCurrently published COVID-19 studies were accepted more quickly and were found to be of lower methodological quality than comparative studies published in the same journal. Given the implications of these studies to medical decision making and government policy, greater effort to appropriately weigh the existing evidence in the context of emerging high-quality research is needed.Study registrationPROSPERO: CRD42020187318
Recovery and noise cancelling of the fetal heart signal using a combination of NLMS algorithm and S-G filter
Authors: Ghasemi Ali , Shama Farzin , Karimi Gholamreza , Khosravi Farshad 
Published: July 2020

Purpose
The purpose of this paper is to provide appropriate methods for reducing the abnormalities on the extracted fetal heart signal from the maternal electrocardiogram (ECG).

Design/methodology/approach
In this regard, the extracted signal of the fetal heart from the mother, improved using an active noise cancelation (ANC) system. It uses commonly adaptive algorithms of normalized least mean squares (NLMS). In the present paper, fetal extraction and denoising methodology are proposed. This methodology uses a combination of the NLMS algorithm with Savitzky–Golay (S-G) filter.

Findings
The obtained results show that a combination of NLMS algorithm with filter coefficient of 15 and µ = 0.02 and S-G filter has a better qSNR (qSNR = 3.6727) and good performance for fetal ECG extraction in comparison with the other works for average fmSNR in the range of −30 to −15 dB. Also, with considering the SNR value of −24.7 dB before filtering and SNR = 3.1861 dB after filtering; the SNR improvement of 27.8861 dB has been obtained.

Originality/value
A new method in the extract and noise reduction of fetal ECG from maternal ECG by the combination of NLMS algorithm and S-G filter is proposed.
Is diversity debate farfetched? Psychological contract expectations, performance and intention to stay
Authors: Pant Jyoti Joshi , Venkateswaran Vijaya 
Published: July 2020

PurposeThe purpose of the study is to understand whether psychological contract (PC) expectations manifest differently for diversity clusters of gender, physical disability and region in relation to job performance and intention to stay.Design/methodology/approachIt is a survey-based study. Data from 1,065 information technology and business process management professionals were analysed using partial least square based structural equation model (PLS-SEM) and multigroup analysis.FindingsThe met PC expectations related to career growth and development impact performance and are influenced by regional diversity. The met PC expectations related to job and work environment impact the intention to stay. Gender and physical disability do not influence any relationship.Research limitations/implicationsThe findings related to physical disability are based on a small sample of 60 employees. This could be reflective of their actual participation in the workplace.Practical implicationsNo significant differences were found between men and women employees with/without physically disability. However, regional diversity creates significant differences. Diversity policies should reckon these similarities/differences while viewing requirements of job performance and determinants of intention to stay.Social implicationsOne needs to be careful while assuming diversity as a heterogeneous phenomenon. The reality could reflect both differences and similarities. Diverse employee groups having a common set of expectations is a socially positive evolution connoting better social integration.Originality/valueThis article is one of the first to research the influence of gender, physical disability and regional diversity on PC and its outcomes in India. Regional diversity has not been studied based on this framework and this adds to the body of knowledge.
Baromeeter: the funding conundrum
Authors: Ghosh Dastidar Surajit 
Published: July 2020

Learning outcomes
The learning outcomes are as follows: to understand the different options available for funding; to illustrate the growth of the food services industry in India; and to understand a business model canvas.

Case overview/synopsis
Baromeeter (BOM), was a Delhi-based startup founded in the year 2016 by Rishabh Vyas, a 26-year-old MBA graduate. Currently, BOM has operations in Delhi-NCR with 50,000 monthly website visitors and 200-plus partner restaurants and cafes in Delhi-NCR with brands such as Imperfecto, Junkyard Café, Garam Dharam, Out of the Box, Boombox, Jungle Jamboree and many more. BOM also receives over 1,000 deal bookings and 200 plus party bookings monthly. Going forward, Rishabh has plans to expand to other cities such as Mumbai, Hyderabad, Pune and Bangalore. However, there are certain challenges. So far, the startup has raised funds from friends and families. He was confident that he had a compelling product. However, he knew he had to look for fresh investments to scale up. The existing funds may sustain the operations of the company for another six months. Rishabh was considering a number of options. However, whom to approach? Would banks be interested in lending money? How about participating in angel investor’s meet?

Complexity academic level
The case is suitable for a course in graduate and an undergraduate course in entrepreneurship. The case can be used to understand the business model canvas and to understand the funding options available for startups.

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS 3: Entrepreneurship.
MHD hybrid nanofluid flow over a permeable stretching/shrinking sheet with thermal radiation effect
Authors: Yashkun Ubaidullah , Zaimi Khairy , Abu Bakar Nor Ashikin , Ishak Anuar , Pop Ioan 
Published: July 2020

Purpose
This study aims to investigate the heat transfer characteristic of the magnetohydrodynamic (MHD) hybrid nanofluid over the linear stretching and shrinking surface in the presence of suction and thermal radiation effects.

Design/methodology/approach
Mathematical equations are transformed into pairs of self-similarity equations using similarity transformation. Boundary value problem solver (bvp4c) in MATLAB was adopted to solve the system of reduced similarity equations. In this study, the authors particularly examine the flow and heat transfer properties for different values of suction and thermal radiation parameters using single-phase nanofluid model. A comparison of the present results shows a good agreement with the published results.

Findings
It is noticed that the efficiency of heat transfer of hybrid nanofluid (Cu-Al2O3/H2O) is greater than the nanofluid (Cu/H2O). Furthermore, it is also found that dual solutions exist for a specific range of the stretching/shrinking parameter with different values of suction and radiation parameters. The results indicate that the skin friction coefficient and the local Nusselt number increase with suction effect. The values of the skin friction coefficient increases, but the local Nusselt number decreases for the first solution with the increasing of thermal radiation parameter. It is also observed that suction and thermal radiation widen the range of the stretching/shrinking parameter for which the solution exists.

Practical implications
In practice, the investigation on the flow and heat transfer of MHD hybrid nanofluid through a stretching/shrinking sheet with suction and thermal radiation effects is very important and useful. The problems related to hybrid nanofluid has numerous real-life and industrial applications, for example microfluidics, manufacturing, transportation, military and biomedical, etc.

Originality/value
In specific, this study focused on increasing thermal conductivity using a hybrid nanofluid mathematical model. This paper is able to obtain the dual solutions. To the best of author’s knowledge, this study is new and there is no previous published work similar to present study.