bluuebunny/crossref_metadata_2025_split huggingface dataset:
Music therapy as a migraine treatment: protocol for a systematic review and meta-analysis
Authors: Sanchez Alessio Alberto Gilardi , Guevara Bartolini Milena Ana Micaela , Acosta Maria Luz Pantoja , Lazo-Porras Maria 
Published: February 2021

ABSTRACTIntroductionHeadache disorders are one of the most common health problems worldwide, they can be classified into primary and secondary disorders. In the primary group, migraine - the second most common type of headache - is the most disabling one and one of the most important reasons why its treatment is mandatory. Migraine treatment involves different steps and kinds of medical therapy and patient education, and in these past years studies have been exploring the effect music therapy can have in reducing the severity and duration of an acute migraine attack. It has been reported that adding music to the pharmacological treatment can help decrease the pain severity, thus, reducing the disability migraine can cause.ObjectiveEvaluate the effectiveness of music therapy as a treatment or coadjuvant of migraine attacks in people who suffer this condition.Methods and analysisThis protocol is consistent with the methodology recommended by the PRISMA-P and the Cochrane handbook for systematic reviews of interventions. This study will be carried out as a systematic review and meta-analysis. In order to do so, electronic searches will be performed in PubMed, Medline and Cochrane (through Ovid) and Embase. The data range parameters used in searching all databases are from the last 20 years. Randomized controlled trials (RCTs) published in English, Spanish, French and Portuguese; with the primary outcomes being reduction of headache intensity, resolution of the migraine and decreased frequency of migraine attacks. Three investigators will screen all retrieved studies titles and abstracts, making a first preliminary list. A second screen will be done by the same three investigators similarly to the first one, but reviewing the full texts and building the final list. Then, the evaluation of the risk of bias and extraction of all data will be performed. The risk of bias of the included RCTs will be evaluated by the Cochrane Collaboration’s tool. A qualitative synthesis will be provided in text and tables, to summarize the main results of the selected publications. The heterogeneity between studies will be assessed through the I2 statistic. If there is sufficient homogeneity across outcomes, a meta-analysis will be conducted.ConclusionsThis systematic review will provide evidence regarding the effectiveness of music therapy as a single or coadjuvant treatment in patients with migraine attacks. Based on this analysis, it will be feasible to know whether this intervention is effective in the reduction of the intensity of the migraine attack, if it can help resolve the migraine attack, or reduce the frequency of migraine attacks.
A meta-analysis of 20 years of data on people who inject drugs in metropolitan Chicago to inform computational modeling
Authors: Boodram Basmattee , Mackesy-Amiti Mary Ellen , Khanna Aditya , Brickman Bryan , Dahari Harel , Ozik Jonathan 
Published: February 2021

AbstractProgress toward hepatitis C virus (HCV) elimination in the United States is not on track to meet targets, as injection drug use continues to drive increasing HCV incidence. Computational models are useful in understanding the complex interplay of individual, social, and structural level factors that might alter HCV incidence, prevalence, transmission, and disease progression. However, these models need to be informed with real socio-behavioral data. We conducted a meta-analysis of research studies spanning 20 years of research and interventions with people who inject drugs in metropolitan Chicago to produce parameters for a synthetic population for a computational model. We then fit an exponential random graph model (ERGM) using the network estimates from the meta-analysis in order to develop the dynamic component of a realistic agent-based model.
Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism
Authors: Pulgar Eduardo , Schwayer Cornelia , Guerrero Néstor , López Loreto , Márquez Susana , Härtel Steffen , Soto Rodrigo , Heisenberg Carl-Philipp , Concha Miguel L. 
Published: February 2021

AbstractThe developmental strategies used by progenitor cells to endure a safe journey from their induction place towards the site of terminal differentiation are still poorly understood. Here we uncovered a progenitor cell allocation mechanism that stems from an incomplete process of epithelial delamination that allows progenitors to coordinate their movement with adjacent extra-embryonic tissues. Progenitors of the zebrafish laterality organ originate from the surface epithelial enveloping layer by an apical constriction process of cell delamination. During this process, progenitors retain long-term apical contacts that enable the epithelial layer to pull a subset of progenitors along their way towards the vegetal pole. The remaining delaminated progenitors follow apically-attached progenitors’ movement by a co-attraction mechanism, avoiding sequestration by the adjacent endoderm, ensuring their fate and collective allocation at the differentiation site. Thus, we reveal that incomplete delamination serves as a cellular platform for coordinated tissue movements during development.Impact StatementIncomplete delamination serves as a cellular platform for coordinated tissue movements during development, guiding newly formed progenitor cell groups to the differentiation site.
Brain Morphometry and Diminished Physical Growth in Bangladeshi Children Growing up in Extreme Poverty: a Longitudinal Study
Authors: Turesky Ted K. , Shama Talat , Kakon Shahria Hafiz , Haque Rashidul , Islam Nazrul , Someshwar Amala , Petri William A. , Nelson Charles A. , Gaab Nadine 
Published: February 2021

AbstractDiminished physical growth is a common marker of malnutrition and it affects approximately 200 million children worldwide. Despite its importance and prevalence, it is not clear whether diminished growth affects brain development and neurocognitive outcomes. Further, diminished growth is more common in areas of extreme poverty, raising the possibility that it may serve as a mechanism for previously shown links between poverty and brain development. To address these questions, 79 children growing up in an extremely poor, urban area of Bangladesh underwent MRI at 6 years. Structural brain images were submitted to Mindboggle software, a Docker-compliant and highly reproducible tool for tissue segmentation and regional estimations of volume, surface area, cortical thickness, travel depth, and mean curvature. Diminished growth predicted brain morphometry and mediated the link between poverty and brain morphometry most consistently for white matter and subcortical volumes. Meanwhile, brain volume in left pallidum and right ventral diencephalon mediated the relationship between diminished growth and full-scale IQ. These findings offer malnutrition as one possible mechanism by which poverty affects brain development and neurocognitive outcomes in areas of extreme poverty.
Natural selections on both amino acid sequences and expression levels are determinants of ohnolog retention
Authors: Miao Lin , Li Miaoxin 
Published: February 2021

AbstractThe mechanism of ohnolog retention is a subject of concern in evolutionary biology. Natural selections on coding sequences and gene dosages have been proposed to be determinants of ohnolog retention. However, the relationship between the two models is not widely accepted, and the role of regulatory sequences on ohnolog retention has long been neglected. In this study, based on a model of complex traits’ genetic architecture, we compared the natural selection’s strength on corresponding sequences between ohnologs and non-ohnologs by comparing complex traits’ heritability enrichments. We showed that complex traits’ regulatory sequences’ heritability enrichments (p= 1.1 × 10−5in 5 kb flanking regions) and expression-mediated heritability enrichments (p= 2.1 × 10−5) of ohnologs were significantly higher than non-ohnologs. Then, we deduced that regulatory sequences of ohnologs were under substantial natural selection, which was also a determent of ohnolog retention. Meanwhile, we showed that in coding sequences, the complex traits’ heritability enrichments of ohnologs were significantly higher than of non-ohnologs (p= 9.9 × 10−5), supporting the ohnolog retention model of natural selection on coding sequences. We also showed that complex traits’ causal gene expression effect sizes of ohnologs were significantly larger than of non-ohnologs (p= 8.8 × 10−6), supporting the ohnolog retention model of natural selection on gene dosages. In conclusion, we provide the first unified framework to show that both amino acid sequences and expression levels of ohnologs are under substantial selection, which may end the long-standing debate on ohnolog retention models.
Agency rescues competition for credit assignment among predictive cues from adverse learning conditions
Authors: Kang Mihwa , Reverte Ingrid , Volz Stephen , Kaufman Keith , Fevola Salvatore , Matarazzo Anna , Alhazmi Fahd H. , Marquez Inmaculada , Iordanova Mihaela D. , Esber Guillem R. 
Published: February 2021

AbstractA fundamental assumption of learning theories is that the credit assigned to predictive cues is not simply determined by their probability of reinforcement, but by their ability to compete with other cues present during learning. This assumption has guided behavioral and neural science research for decades, and tremendous empirical and theoretical advances have been made identifying the mechanisms of cue competition. However, when learning conditions are not optimal (e.g., when training is massed), credit assignment is no longer competitive. This is a catastrophic failure of the learning system that exposes the individual’s vulnerability to form spurious associations in the real world. Here, we uncover that cue competition can be rescued when conditions are suboptimal provided that the individual has agency over the learning experience. Our findings reveal a new connection between agency over learning and credit assignment to cues, and open new avenues of investigation into the underlying mechanisms.
Dual mechanisms of opioid-induced respiratory depression in the inspiratory rhythm-generating network
Authors: Baertsch Nathan A , Bush Nicholas E , Burgraff Nicholas J , Ramirez Jan-Marino 
Published: February 2021

AbstractThe analgesic utility of opioid-based drugs is limited by the life-threatening risk of respiratory depression. Opioid-induced respiratory depression (OIRD), mediated by the μ-opioid receptor (MOR), is characterized by a pronounced decrease in the frequency and regularity of the inspiratory rhythm, which originates from the medullary preBötzinger Complex (preBӧtC). To unravel the cellular- and network-level consequences of MOR activation in the preBötC, MOR-expressing neurons were optogenetically identified and manipulated in transgenic micein vitroandin vivo. Based on these results, a model of OIRD was developedin silico. We conclude that hyperpolarization of MOR-expressing preBötC neurons alone does not phenocopy OIRD. Instead, the effects of MOR activation are twofold: 1) pre-inspiratory spiking is reduced and 2) excitatory synaptic transmission is suppressed, thereby disrupting network-driven rhythmogenesis. These dual mechanisms of opioid action act together to make the normally robust inspiratory-rhythm-generating network particularly prone to collapse when challenged with exogenous opioids.
A novel morphometric signature of brain alterations in type 2 diabetes: patterns of changed cortical gyrification
Authors: Crisóstomo Joana , Duarte João V. , Moreno Carolina , Gomes Leonor , Castelo-Branco Miguel 
Published: February 2021

AbstractType 2 diabetes is a chronic disease that creates atrophic signatures in the brain, including decreases of total and regional volume of grey matter, white matter, and cortical thickness. However, there is a lack of studies assessing cortical gyrification in type 2 diabetes. Changes in this emerging feature has been associated mainly with genetic legacy, but environmental factors may also play a role. Here, we investigated alterations of the gyrification index and classical morphometric measures in type 2 diabetes, a disease with complex etiology with both underlying genetic and more preponderant environmental factors.In this cross-sectional study we analyzed brain anatomical magnetic resonance images of 86 participants with type 2 diabetes and 40 healthy control participants, to investigate structural alterations in type 2 diabetes, including whole-brain volumetric measures, local alterations of grey matter volume, cortical thickness and the gyrification index.We found concordant significant decrements in total and regional grey matter volume, and cortical thickness. Surprisingly, the cortical gyrification index was found to be mainly increased in cortical sensory areas in type 2 diabetes. Moreover, it correlated with features of metabolic control. Our findings challenge the classical neurodevelopmental association of gyrification mostly with genetic determinants. While we found mainly increased gyrification in more genetically constrained sensory areas in type 2 diabetes, our correlation results concurrently suggest an influence of metabolic control in alterations of gyrification in type 2 diabetes. Further studies should address causal influences of genetic and/or environmental factors in patterns of cortical gyrification in type 2 diabetes.
MtrA regulation of essential peptidoglycan cleavage inMycobacterium tuberculosisduring infection
Authors: Peterson Eliza J. R. , Brooks Aaron N , Reiss David J. , Kaur Amardeep , Wu Wei-Ju , Morrison Robert , Srinivas Vivek , Turkarslan Serdar , Pan Min , Carter Warren , Arrieta-Ortiz Mario L. , Ruiz Rene A. , Bhatt Apoorva , Baliga Nitin S. 
Published: February 2021

AbstractThe success ofMycobacterium tuberculosis(Mtb) is largely due to its ability to withstand multiple stresses encountered in the host. Here, we present a data-driven model that captures the dynamic interplay of environmental cues and genome-encoded regulatory programs in Mtb. The model captures the genome-wide distribution ofcis-acting gene regulatory elements and the conditional influences of transcription factors at those elements to elicit environment-specific responses. Analysis of transcriptional responses that may be essential for Mtb to survive acidic stress within the maturing macrophage, identified regulatory control by the MtrAB two-component signal system. Using genome-wide transcriptomics as well as imaging studies, we have characterized the MtrAB circuit by tunable CRISPRi knockdown in both Mtb and the non-pathogenic organism,M. smegmatis(Msm). These experiments validated the essentiality of MtrA in Mtb, but not Msm. We identified that MtrA regulates multiple enzymes that cleave cell wall peptidoglycan and is required for efficient cell division. Moreover, our results suggest that peptidoglycan cleavage, regulated by MtrA, is necessary for Mtb to survive intracellular stress. Further, we present MtrA as an attractive drug target, as even weak repression ofmtrAresults in loss of Mtb viability and completely clears the bacteria with low-dose isoniazid or rifampicin treatment.
Visual object categorization in infancy
Authors: Spriet Céline , Abassi Etienne , Hochmann Jean-Rémy , Papeo Liuba 
Published: February 2021

AbstractHumans make sense of the world by organizing things into categories. When and how does this process begin? We investigated whether real-world object categories that spontaneously emerge in the first months of life match categorical representations of objects in the human visual cortex. Taking infants’ looking times as a measure of similarity, we defined a representational space where each object was defined in relation to others of the same or different categories. This space was compared with hypothesis-based and fMRI-based models of visual-object categorization in the adults’ visual cortex. Analyses across different age groups revealed an incremental process with two milestones. Between 4 and 10 months, visual exploration guided by saliency gives way to an organization according to the animate-inanimate distinction. Between 10 and 19 months, a category spurt leads towards a mature organization. We propose that these changes underlie the coupling betweenseeingandthinkingin the developing mind.
A crosswalk to align the GSS and NIH grants databases based on university names
Authors: Pickett Christopher L. 
Published: February 2021

AbstractNotable reports over the past dozen years have recommended the federal government and others improve data collection on the research workforce in the United States. The federal government already collects a wealth of data, but important datapoints, like the number of biomedical postdocs working in the U.S., for example, are still not well defined. Furthermore, of the data that are collected, differences in collection method and data naming conventions, like inconsistent naming of universities, hinders our ability to merge information across different datasets. Here I describe the creation of three macros meant to align the National Center for Science and Engineering Statistics’ Survey of Graduate Students and Postdoctorates in Science and Engineering (GSS) with NIH grants databases based on consolidating university names under a single name common to both databases. Aligning these databases will allow for a deeper understanding of how various federal and university policies affect the number trainees, grants, and funding at individual institutions.
Pathogenic tau accelerates aging-associated activation of transposable elements in the mouse central nervous system
Authors: Ramirez Paulino , Sun Wenyan , Zuniga Gabrielle , Thomas Elizabeth Ochoa , DeVos Sarah L. , Hyman Bradley , Chiu Gabriel , Roy Ethan R. , Cao Wei , Orr Miranda , Buggia-Prevot Virginie , Ray William J. , Frost Bess 
Published: February 2021

ABSTRACTTransposable elements comprise almost half of the mammalian genome. A growing body of evidence suggests that transposable element dysregulation accompanies brain aging and neurodegenerative disorders, and that transposable element activation is neurotoxic. Recent studies have identified links between pathogenic forms of tau, a protein that accumulates in Alzheimer disease and related tauopathies, and transposable element-induced neurotoxicity. Starting with transcriptomic analyses, we find that age- and tau-induced transposable element activation occurs in the mouse brain. Among transposable elements that are activated at the RNA level in the context of brain aging and tauopathy, we find that the endogenous retrovirus (ERV) class of retrotransposons is particularly enriched. We show that protein encoded byIntracisternal A-particle, a highly active mouse ERV, is elevated in brains of tau transgenic mice. We further demonstrate that brains of tau transgenic mice contain increased DNA copy number of transposable elements, raising the possibility that these elements actively retrotranspose in the context of tauopathy. Taken together, our study lays the groundwork for future mechanistic studies focused on transposable element regulation in the aging mouse brain and in mouse models of tauopathy, while providing support for therapeutic approaches targeting transposable element activation for Alzheimer disease and related tauopathies.
Self-contained and modular structured illumination microscope
Authors: Van den Eynde Robin , Vandenberg Wim , Hugelier Siewert , Bouwens Arno , Hofkens Johan , Müller Marcel , Dedecker Peter 
Published: February 2021

AbstractWe present a modular implementation of structured illumination microscopy (SIM) that is fast, largely self-contained and that can be added onto existing fluorescence microscopes. Our instrument, which we call HIT-SIM, can theoretically deliver well over 50 super-resolved images per second and is readily compatible with existing acquisition software packages. We provide a full technical package consisting of schematics, a list of components and an alignment scheme that provides detailed specifications and assembly instructions. We illustrate the performance of the instrument by imaging optically large samples containing sequence-specifically stained DNA fragments.
The type 2 asthma mediator IL-13 inhibits SARS-CoV-2 infection of bronchial epithelium
Authors: Bonser Luke R. , Eckalbar Walter L. , Rodriguez Lauren , Shen Jiangshan , Koh Kyung Duk , Zlock Lorna T. , Christenson Stephanie , Woodruff Prescott G. , Finkbeiner Walter E. , Erle David J. 
Published: February 2021

AbstractRationaleAsthma is associated with chronic changes in the airway epithelium, a key target of SARS-CoV-2. Many epithelial changes are driven by the type 2 cytokine IL-13, but the effects of IL-13 on SARS-CoV-2 infection are unknown.ObjectivesWe sought to discover how IL-13 and other cytokines affect expression of genes encoding SARS-CoV-2-associated host proteins in human bronchial epithelial cells (HBECs) and determine whether IL-13 stimulation alters susceptibility to SARS-CoV-2 infection.MethodsWe used bulk and single cell RNA-seq to identify cytokine-induced changes in SARS-CoV-2-associated gene expression in HBECs. We related these to gene expression changes in airway epithelium from individuals with mild-moderate asthma and chronic obstructive pulmonary disease (COPD). We analyzed effects of IL-13 on SARS-CoV-2 infection of HBECs.Measurements and Main ResultsTranscripts encoding 332 of 342 (97%) SARS-CoV-2-associated proteins were detected in HBECs (≥1 RPM in 50% samples). 41 (12%) of these mRNAs were regulated by IL-13 (>1.5-fold change, FDR < 0.05). Many IL-13-regulated SARS-CoV-2-associated genes were also altered in type 2 high asthma and COPD. IL-13 pretreatment reduced viral RNA recovered from SARS-CoV-2 infected cells and decreased dsRNA, a marker of viral replication, to below the limit of detection in our assay. Mucus also inhibited viral infection.ConclusionsIL-13 markedly reduces susceptibility of HBECs to SARS-CoV-2 infection through mechanisms that likely differ from those activated by type I interferons. Our findings may help explain reports of relatively low prevalence of asthma in patients diagnosed with COVID-19 and could lead to new strategies for reducing SARS-CoV-2 infection.
Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
Authors: Liu Bin-Bin , Ma Zhi-Yao , Ren Chen , Hodel Richard G.J. , Sun Miao , Liu Xiu-Qun , Liu Guang-Ning , Hong De-Yuan , Zimmer Elizabeth A. , Wen Jun 
Published: February 2021

AbstractWith the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 datasets with different sequencing coveragein silico. We tested the performance of the four datasets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of theVitisclade at the genus-level and Vitaceae at the family-level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10× coverage. Without the steps of synthesizing baits and enrichment experiments, we showcase that deep genome skimming (DGS) is effective for capturing large datasets of SCNs, in addition to plastomes, mtDNA, and entire nrDNA repeats, and may serve as an economical alternative to the widely used target enrichment Hyb-Seq approach.