bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depletion of hemoglobin transcripts and long read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus)
Authors: Byrne Ashley , Supple Megan A. , Volden Roger , Laidre Kristin L. , Shapiro Beth , Vollmers Christopher 
Published: January 2019

AbstractTranscriptome studies evaluating whole blood and tissues are often confounded by overrepresentation of highly abundant transcripts. These abundant transcripts are problematic as they compete with and prevent the detection of rare RNA transcripts, obscuring their biological importance. This issue is more pronounced when using long-read sequencing technologies for isoform-level transcriptome analysis, as they have relatively lower throughput compared to short-read sequencers. As a result long-read based transcriptome analysis is prohibitively expensive for non-model organisms. While there are off-the-shelf kits available for select model organisms capable of depleting highly abundant transcripts for alpha (HBA) and beta (HBB) hemoglobin, they are unsuitable for non-model organisms. To address this, we have adapted the recent CRISPR/Cas9 based depletion method (Depletion of Abundant Sequences by Hybridization) for long-read full-length cDNA sequencing approaches that we call Long-DASH. Using a recombinant Cas9 protein with appropriate guide RNAs, full-length hemoglobin transcripts can be depleted in-vitro prior to performing any short- and long-read sequencing library preparations. Using this method, we sequenced depleted full-length cDNA in parallel using both our Oxford Nanopore Technology (ONT) based R2C2 long-read approach, as well as the Illumina short-read based Smart-seq2 approach. To showcase this, we have applied our methods to create an isoform-level transcriptome from whole blood samples derived from three polar bears (Ursus maritimus). Using Long-DASH, we succeeded in depleting hemoglobin transcripts and generated deep Smart-seq2 Illumina datasets and 3.8 million R2C2 full-length cDNA consensus reads. Applying Long-DASH with our isoform identification pipeline, Mandalorion we discovered ~6,000 high-confidence isoforms and a number of novel genes. This indicates there is a high diversity of gene isoforms within Ursus maritimus not yet reported. This reproducible and straightforward approach has not only improved the polar bear transcriptome annotations but will serve as the foundation for future efforts to investigate transcriptional dynamics within the 19 polar bear subpopulations around the Arctic.
Applications of Machine Learning in Decision Analysis for Dose Management for Dofetilide
Authors: Levy Andrew E. , Biswas Minakshi , Weber Rachel , Tarakji Khaldoun , Chung Mina , Noseworthy Peter A. , Newton-Cheh Christopher , Rosenberg Michael A. 
Published: January 2019

AbstractInitiation of the antiarrhythmic medication dofetilide requires an FDA-mandated 3 days of telemetry monitoring due to heightened risk of toxicity within this time period. Although a recommended dose management algorithm for dofetilide exists, there is a range of real-world approaches to dosing the medication. In this multicenter investigation, we examined the decision process for dose adjustment of dofetilide during the observation period using machine-learning approaches, including supervised, unsupervised, and reinforcement learning applications. Logistic regression approaches identified any dose-adjustment as a strong negative predictor of successful loading (i.e., discharged on dofetilide) of the medication (OR 0.19, 95%CI 0.12 – 0.31, p < 0.001 for discharge on dofetilide), indicating that these adjustments are strong determinants of whether patients “tolerate” the medication. Using multiple supervised approaches, including regularized logistic regression, random forest, boosted gradient decision trees, and neural networks, we were unable to identify any model that predicted dose adjustments better than a naïve approach. A reinforcement-learning algorithm, in contrast, predicted which patient characteristics and dosing decisions that resulted in the lowest risk of failure to be discharged on the medication. Future studies could apply this algorithm prospectively to examine improvement over standard approaches.
Flexible pivoting of dynamin PH-domain catalyzes fission: Insights into molecular degrees of freedom
Authors: Baratam K. K. , Jha K. , Srivastava A. 
Published: January 2019

ABSTRACTThe neuronal dynamin1 functions in the release of synaptic vesicles by orchestrating the process of GTPase-dependent membrane fission. Dynamin1 associates with the plasma membrane-localized phosphatidylinositol-4,5-bisphosphate (PIP2) with its centrally-located pleckstrin homology domain (PHD). The PHD is dispensable as fission can be managed, albeit at much slower rates, even when the PHD-PIP2 interaction is replaced by a generic polyhistidine- or polylysine-lipid interaction. However, even when the PHD is present, the length of the dynamin scaffold and in turn the membrane remodeling and fission rates are severely restricted with mutations such as I533A on membrane-interacting variable loop 1 (VL1) of PHD. These observations suggest that PIP2-containing membrane interactions of PHD could have evolved to expedite fission to fulfill the requirement of rapid kinetics of synaptic vesicle recycling. Here, we use a suite of multiscale modeling approaches that combine atomistic molecular dynamics simulations, mixed resolution membrane mimetic models, coarse-grained molecular simulations and advanced free-energy sampling methods (metadynamics and umbrella sampling) to explore PHD-membrane interactions. Our results reveal that: (a) the binding of PHD to PIP2-containing membranes modulates the lipids towards fission-favoring conformations and softens the membrane, (b) that PHD engages another loop (VL4) for membrane association, which acts as an auxiliary pivot and modulates the orientation flexibility of PHD on the membrane – a mechanism we believe may be important for high fidelity dynamin collar assembly on the membrane. (c) Through analyses of our trajectories data and free-energy calculations on membrane-bound WT and mutant systems, we also identify key residues on multiple VLs that stabilizes PHD membrane association. And we suggest experiments to explore the ability of PHD to associate with membrane in orientations that favors faster fission. Together, these insights provide a molecular-level understanding of the “catalytic” role of the PHD in dynamin-mediated membrane fission.SIGNIFICANCEDynamin, a large multi-domain GTPase, remodels the membrane by self-assembling onto the neck of a budding vesicle and induces fission by its energy driven conformational changes. In this work, we use multi-scale molecular simulations to probe the role of dynamin’s pleckstrin-homology domain (PHD), which facilitates membrane interactions. Notably, PHD is dispensable for fission as is the case with extant bacterial and mitochondrial dynamins. However, reconstitution experiments suggest that the functional role of PHD in neuronal-membrane goes beyond that of an adaptor domain as it possibly ‘expedites’ the fission reaction during synaptic vesicle recycling. We provide a molecular-dynamics picture of how PHDs make membranes more pliable for fission and suggest new insights into the molecular-level processes driving the expedited fission behavior.
Inhibiting IFT dynein with ciliobrevin in C. elegans chemosensory cilia
Authors: Mijalkovic Jona , Peterman Erwin J.G. 
Published: January 2019

AbstractCytoplasmic dyneins play a role in a myriad of cellular processes, such as retrograde intracellular transport and cell division. Small-molecule cytoplasmic dynein antagonists, ciliobrevins, have recently been developed as tools to acutely probe cytoplasmic dynein function. Although widely used to investigate cytoplasmic dynein 1, far fewer studies explore the effect of ciliobrevin on cytoplasmic dynein 2 or IFT dynein. Here, we use ciliobrevin A to partially disrupt IFT dynein in the chemosensory cilia of living C. elegans. Acute, low-concentration ciliobrevin treatment results in shortening of cilia and reduction of transport velocity in both directions. After longer exposure to ciliobrevin, we find concentration-dependent motor accumulations and axonemal deformations. We propose that maintenance of ciliary length requires a high fraction of active IFT-dynein motors, while structural integrity can be preserved by only a few active motors.
Extinctions in marine plankton preceded by stabilizing selection
Authors: Weinkauf Manuel F. G. , Bonitz Fabian G. W. , Martini Rossana , Kučera Michal 
Published: January 2019

AbstractUnless they adapt, populations facing persistent stress are threatened by extinction. Theoretically, populations facing stress can react by either disruption, increasing trait variation, or stabilisation, decreasing trait variation. In the short term, the more economical response is stabilisation, because it quickly transfers a large part of the population closer to a new ecological optimum. However, canalisation is deleterious in the face of persistently increasing stress because it reduces variability and thus decreases the ability to react to further change in stress. Understanding how natural populations react to intensifying stress reaching terminal levels is key to assessing their resilience to environmental change such as that caused by global warming. Because extinctions are hard to predict, observational data on the adaptive reaction of populations facing extinction are rare. In this study, we make use of the glacial salinity rise in the Red Sea as a natural experiment allowing us to analyse the reaction of planktonic Foraminifera to stress escalation in the geological past. We analyse morphological trait state and variance in two species across a salinity rise leading to their local extinction. One species reacted by stabilisation in shape and size, detectable several thousand years prior to extinction. The second species reacted by trait divergence, but each of the two divergent populations remains stable or reacted by further stabilisation. These observations indicate that the default reaction of the studied Foraminifera is stabilisation and that stress escalation did not lead to the local emergence of adapted forms. Inability to breach the global adaptive threshold would explain why communities of Foraminifera, and many other groups of marine plankton, reacted to Quaternary climate change by faithfully tracking their zonally shifting environments. It also means that populations of marine species adapted to response by migration, when exposed to stress outside of the adaptive range, will be at risk of extinction.
The fitness cost of a congenital heart defect shapes its genetic architecture
Authors: Akhirome Ehiole , Regmi Suk D. , Magnan Rachel A. , Ugwu Nelson , Qin Yidan , Schulkey Claire E. , Cheverud James M. , Jay Patrick Y. 
Published: January 2019

ABSTRACTBackgroundIn newborns, severe congenital heart defects are rarer than mild ones. The reason why is unknown, but presumably related to a liability threshold that rises with the severity of a defect. Because the same genetic mutation can cause different defects, other variables may contribute to pushing an individual past a defect-specific liability threshold. We consider here how variables in the genetic architecture of a heart defect depend upon its fitness cost, as defined by the likelihood of survival to reproductive age in natural history studies.MethodsWe phenotyped ~10,000Nkx2-5+/-newborn mice, a model of human congenital heart disease, from two inbred strain crosses. Genome-wide association analyses detected loci that modify the risk of an atrial septal defect, membranous or muscular ventricular septal defect, or atrioventricular septal defect. The number of loci, heritability and quantitative effects on risk of pairwise (G×GNkx) and higher-order (G×G×GNkx) epistasis between the loci andNkx2-5mutation were examined as a function of the fitness cost of a defect.ResultsNkx2-5+/-mice have pleiotropic heart defects; about 70% have normal hearts. The model recapitulates the epidemiological relationship between the severity and incidence of a heart defect. Neither the number of modifier loci nor heritability depends upon the severity of a defect, but G×GNkxand G×G×GNkxeffects on risk do. Interestingly, G×G×GNkxeffects are three times more likely to suppress risk when the genotypes at the first two loci are homozygous and from the same, rather than opposite strains in a cross. Syn- and anti-homozygous genotypes at G×G×GNkxinteractions can have an especially large impact on the risk of an atrioventricular septal defect.ConclusionsGiven a modestly penetrant mutation, epistasis contributes more to the risk of severe than mild congenital heart defect. Conversely, genetic compatibility between interacting genes, as indicated by the protective effects of syn-homozygosity at G×G×GNkxinteractions, plays a newfound role in the robustness of cardiac development. The experimental model offers practical insights into the nature of genetic risk in congenital heart disease. The results more fundamentally address a longstanding question regarding how mutational robustness could arise from natural selection.
Exosome labeling by lipophilic dye PKH26 results in significant increase in vesicle size
Authors: Dehghani Mehdi , Gulvin Shannon M. , Flax Jonathan , Gaborski Thomas R. 
Published: January 2019

AbstractExosomes are membrane vesicles secreted by cells and distributed widely in all biofluids. Exosomes can modulate the biological activities of cells in a paracrine or endocrine manner, in part by transferring their content, such as miRNA, following uptake in recipient cells. Fluorescent labelling of exosomes is a commonly used technique for understanding their cellular targeting and biodistribution. Lipophilic fluorescent dyes such as those in the PKH family have been widely used for exosome labelling. One concern with the use of lipophilic dyes is an increase in the exosome size due to membrane fusion or intercalation. This size shift alone may undermine the validity of exosomes tracing studies as small changes in the size of inorganic nanoparticles are known to affect their cellular uptake and biodistribution. Here, the possibility of minimizing the size shift of PKH labelled exosomes was systematically studied by changing the labelling condition. Unfortunately, the size shift towards larger particles was observed in all the PKH labelling conditions, including those where the labelled exosomes were below the fluorescent detection limit. As opposed to lipophilic dyes, no significant shift in the size of labelled exosomes was detected with protein binding dyes. Since the size shifts identified in all the PKH labelling conditions are likely to affect the cellular uptake and biodistribution, PKH may not be a reliable technique for exosomes tracking.
Draft genome sequence of the Solanum aethiopicum provides insights into disease resistance, drought tolerance and the evolution of the genome
Authors: Song Bo , Song Yue , Fu Yuan , Kizito Elizabeth Balyejusa , Kabod Pamela Nahamya , Liu Huan , Kamenya Sandra Ndagire , Muthemba Samuel , Kariba Robert , Li Xiuli , Wang Sibo , Cheng Shifeng , Muchugi Alice , Jamnadass Ramni , Shapiro Howard-Yana , Deynze Allen Van , Yang Huanming , Wang Jian , Xu Xun , Odeny Damaris Achieng , Liu Xin 
Published: January 2019

AbstractBackgroundS. aethiopicum is a close relative to S. melongena and has been routinely used to improve disease resistance in S. melongena. However, these efforts have been greatly limited by the lack of a reference genome and the clear understanding of the genes involved during biotic and abiotic stress response.ResultsWe present here a draft genome assembly of S. aethiopicum of 1.02 Gb in size, which is predominantly occupied by repetitive sequences (76.2%), particularly long terminal repeat elements. We annotated 37,681 gene models including 34,905 protein-coding genes. We observed an expansion of resistance genes through two rounds of amplification of LTR-Rs, occurred around 1.25 and 3.5 million years ago, respectively. The expansion also occurred in gene families related to drought tolerance. A number of 14,995,740 SNPs are identified by re-sequencing 65 S. aethiopicum genotypes including “Gilo” and “Shum” accessions, 41,046 of which are closely linked to resistance genes. The domestication and demographic history analysis reveals selection of genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum with a total of 36,250 protein-coding genes was assembled, of which 1,345 genes are missing in the reference genome.ConclusionsOverall, the genome sequence of S. aethiopicum increases our understanding of the genomic mechanisms of its extraordinary disease resistance and drought tolerance. The SNPs identified are available for potential use by breeders. The information provided here will greatly accelerate the selection and breeding of the African eggplant as well as other crops within the Solanaceae family.
The molecular clock of Mycobacterium tuberculosis
Authors: Menardo F. , Duchêne S. , Brites D. , Gagneux S. 
Published: January 2019

AbstractThe molecular clock and its phylogenetic applications to genomic data have changed how we study and understand one of the major human pathogens, Mycobacterium tuberculosis (MTB), the causal agent of tuberculosis. Genome sequences of MTB strains sampled at different times are increasingly used to infer when a particular outbreak begun, when a drug resistant clone appeared and expanded, or when a strain was introduced into a specific region. Despite the growing importance of the molecular clock in tuberculosis research, there is a lack of consensus as to whether MTB displays a clocklike behavior and about its rate of evolution. Here we performed a systematic study of the MTB molecular clock on a large genomic data set (6,285 strains), covering most of the global MTB diversity and representing different epidemiological settings. We found wide variation in the degree of clocklike structure among data sets, indicating that sampling times are sometimes insufficient to calibrate the clock of MTB. For data sets with temporal structure, we found that MTB genomes accumulate between 1×10−8 and 5×10−7 nucleotide changes per-site-per-year, which corresponds to 0.04 – 2.2 SNPs per-genome-per-year. Contrary to what expected, these estimates were not dependent on the time of the calibration points as they did not change significantly when we used epidemiological isolates (sampled in the last 40 years) or ancient DNA samples (about 1,000 years old) to calibrate the tree. Additionally, the uncertainty and the discrepancies in the results of different methods were often large, highlighting the importance of using different methods, and of considering carefully their assumptions and limitations.Significance StatementOne of the major recent advancement in evolutionary biology is the development of statistical methods to infer the past evolutionary history of species and populations with genomic data. In the last five years, many researchers have used the molecular clock to study the evolution of Mycobacterium tuberculosis, a bacterial pathogen that causes tuberculosis and is responsible for millions of human deaths every year. The application of the molecular clock to tuberculosis is extremely useful to understand the evolution of drug resistance, the spread of different strains and the origin of the disease. Since some of these studies found contrasting results, we performed a systematic analysis of the molecular clock of MTB. This study will provide an important guideline for future analyses of tuberculosis and other organisms.
Self-efficacy and workplace well-being: moderating role of sustainability practices
Authors: Singh Sanjay Kumar , Pradhan Rabindra Kumar , Panigrahy Nrusingh Prasad , Jena Lalatendu Kesari 
Published: January 2019

PurposeHow psychological variables especially self-efficacy plays significant role to attain workplace well-being is yet to be explained. The extant literature calls for further research works in the field of sustainability practices to bridge the gap between self-efficacy and workplace well-being. The purpose of this paper is to extend the literature of workplace well-being while scientifically examining the moderating role of sustainability practices.Design/methodology/approachThe study collected data from 527 full-time executives of Indian public and private manufacturing industries. The authors performed moderated regression analysis through a series of hierarchical models to test the hypotheses of the study.FindingsThe result indicates positive relationship between self-efficacy and workplace well-being. Furthermore, the result suggests that the relationship between self-efficacy and workplace well-being was stronger among executives with high level of sustainability practices and vice versa.Research limitations/implicationsThe cross-sectional sample of executives employed in Indian manufacturing organizations limits the generalizability of the findings.Practical implicationsHR functionaries and senior management may benefit by closely examining their sustainability practices along with their employees perceived ability to address workplace well-being.Originality/valueThe study contributes to extend the literature on self-efficacy and workplace well-being. This research work is one of the first few studies to examine the moderating effect of sustainability practices.
Modelling and analysis of barriers affecting the implementation of lean green agile manufacturing system (LGAMS)
Authors: Sindhwani Rahul , Mittal Varinder Kumar , Singh Punj Lata , Aggarwal Ankur , Gautam Nishant 
Published: January 2019

Purpose
Many types of research have already investigated the lean, green or agile manufacturing systems in a discrete manner or as combinations of two of them. In today’s competitive scenario, if industry wants to perpetuate its name in the market, then it has to supervene proper thinking and smart approach. Therefore, the combination of lean, green and agile manufacturing systems can provide better and beneficial results. The purpose of this paper is to discern the barriers to the combined lean green agile manufacturing system (LGAMS), understand their interdependence and develop a framework to enhance LGAMS by using total interpretive structural modeling (TISM) and MICMAC (Matriced’ Impacts Croise’s Multiplication Appliquée a UN Classement) Analysis.

Design/methodology/approach
This paper uses TISM methodology and MICMAC analysis to deduce the interrelationships between the barriers and rank them accordingly. A total of 13 barriers have been identified through extensive literature review and discussion with experts.

Findings
An integrated LGAMS has been presented that balances the lean, green and agile paradigms and can help supply chains become more efficient, streamlined and sustainable. Barriers are identified while referring to all three strategies to showcase the clear relevance. TISM models the barriers in different levels showcasing direct and important transitive relations. Further, MICMAC analysis distributes the barriers in four clusters in accordance with their driving and dependence power.

Research limitations/implications
The inferences have been drawn from a model developed on the basis of inputs from a small fraction of the industry and academia and may show variations when considering the whole industry.

Practical implications
The outcome of this research can contribute to bringing the change to the manufacturing systems used in most developing nations. Also, top managers considering adoption of LGAMS can be cautious of the most influential barriers.

Originality/value
A TISM-based model of the barriers to an integrated LGAMS has been proposed with evaluation of the influence of the barriers.