bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness of targeted antenatal family planning information provision on early postpartum family planning uptake in Kisumu county: Study protocol for a Simple Randomized Control Trial
Authors: Shisanya Morris Senghor , Ouma Collins , Mary Kipmerewo 
Published: February 2022

AbstractOverlooking the contraceptive needs of postpartum women constitutes missed opportunities in health system. Inter-birth interval of at least three years can prevent poor maternal, perinatal and neonatal outcomes and afford women socioeconomic benefits of family planning (FP). The unmet need for FP in the postpartum period remains unacceptably high and far exceeds the FP unmet need of other women. The Kenya Demographic and Health Survey (KDHS) estimate the unmet need for postpartum FP to be 74%. Maternal and Child Health (MCH) continuum provides a great opportunity for postpartum FP (PPFP) interventions integration especially Antenatal targeted FP information giving and gauging fertility intentions. However, there is no protocol for structured, targeted Antenatal FP information giving and behavioural contracting to influence postpartum fertility intentions of mothers before delivery. Knowledge gap regarding fertility intentions and best antenatal strategies for postpartum FP still exists. The available evidence differs across settings and demography. Equally, there has been inadequate exploration of operationally-feasible ways to integrate FP counselling into existing ANC services with limited number of methodologically rigorous trials. This study will therefore examine the effectiveness of antenatal family planning information provision on early postpartum FP uptake using a randomized control trial in Kisumu. The researcher will; assess socio-cultural beliefs towards of PPFP and perceived individual control of PPFP choice, analyze knowledge and intention for PPFP, compare and examine the determinants of PPFP uptake between study groups. A group of 246 antenatal mothers will be randomly assigned to control, community and facility intervention groups as per eligibility criteria in the study facilities that will be cluster sampled. After at least 3 months of intervention and 3 months of postpartum follow-up, clinical superiority will be used to gauge which invention was effective and the model superiority. Questionnaire and Case Report Forms will be the main source of data. The participant will form the unit of analysis which will be by intention to treat. Bivariate analysis will be done as the selection criteria for inclusion of predictors of intention and uptake with a P≤ 0.05 in the final logistic regression model. P-values, ≤0.05, Odds Ratios and 95% confidence interval (CI) will be used to demonstrate significance and the strength of association between selected variables. Dissemination will be through conference presentations and peer reviewed journals. The trial has been registered with the Pan African Clinical Trials Registry PACTR202109586388973 on the 28th September 2021.
Alteration of plasma von Willebrand factor in the treatment of retinal vein occlusion with cystoid macular edema
Authors: Hirai Hiromasa , Yamashita Mariko , Matsumoto Masanori , Nishiyama Takeyuki , Wada Daishi , Okabe Naoko , Mizusawa Yutaro , Jimura Hironobu , Ueda Tetsuo , Ogata Nahoko 
Published: February 2022

AbstractRetinal vein occlusion (RVO) is a major retinal disease accompanied by venous thrombosis. Although several studies have proposed an association between venous thrombosis and von Willebrand factor (VWF), the association between RVO and VWF remains unclear. We aimed to investigate the association between RVO and VWF and the alteration of VWF levels under the anti-vascular endothelial growth factor (VEGF) treatment. We enrolled 55 patients with RVO involved cystoid macular edema. They received intravitreal injection of anti-VEGF drugs, either ranibizumab or aflibercept. We examined the clinical data, measured plasma VWF: antigen (VWF: Ag) and plasma a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13 (ADAMTS13) activity (ADAMTS13: AC) and analyzed them to identify variabilities during the treatment. At the baseline there was no significant difference between the RVO group and age-matched controls in both VWF: Ag and ADAMTS13: AC levels but ADAMTS13:AC was significantly lower in central RVO (CRVO) than in branch RVO (BRVO) (P = 0.015). In BRVO, the negative correlation was found between VWF: Ag and central choroidal thickness (CCT) (r = −0.51, P < 0.001). In BRVO after the anti-VEGF treatment, VWF: Ag decreased significantly from 134% at the baseline to 109% at 1 day after (P = 0.002) and to 107% at 1 month after (P = 0.030). In contrast, ADAMTS13: AC showed no significant difference during this period. In BRVO at 1 month after treatment, we found a negative correlation between VWF: Ag and CCT (r = −0.47, P = 0.001). Our findings suggest an association between VWF and CCT in patients with BRVO, thus the measurement of VWF may be useful for evaluating the disease activity and prognosis.
The Effect of Genome Graph Expressiveness on the Discrepancy Between Genome Graph Distance and String Set Distance
Authors: Qiu Yutong , Kingsford Carl 
Published: February 2022

AbstractMotivationIntra-sample heterogeneity describes the phenomenon where a genomic sample contains a diverse set of genomic sequences. In practice, the true string sets in a sample are often unknown due to limitations in sequencing technology. In order to compare heterogeneous samples, genome graphs can be used to represent such sets of strings. However, a genome graph is generally able to represent a string set universe that contains multiple sets of strings in addition to the true string set. This difference between genome graphs and string sets is not well characterized. As a result, a distance metric between genome graphs may not match the distance between true string sets.ResultsWe extend a genome graph distance metric, Graph Traversal Edit Distance (GTED) proposed by Ebrahimpour Boroojeny et al., to FGTED to model the distance between heterogeneous string sets and show that GTED and FGTED always underestimate the Earth Mover’s Edit Distance (EMED) between string sets. We introduce the notion of string set universe diameter of a genome graph. Using the diameter, we are able to upper-bound the deviation of FGTED from EMED and to improve FGTED so that it reduces the average error in empirically estimating the similarity between true string sets. On simulated TCR sequences and Hepatitis B virus genomes, we show that the diameter-corrected FGTED reduces the average deviation of the estimated distance from the true string set distances by more than 250%.AvailabilityData and source code for reproducing the experiments are available at:https://github.com/Kingsford-Group/gtedemedtest/Contactcarlk@cs.cmu.edu
Tensor decomposition- and principal component analysis-based unsupervised feature extraction to select more reasonable differentially expressed genes: Optimization of standard deviation versus state-of-art methods
Authors: Taguchi Y-h. , Turki Turki 
Published: February 2022

AbstractBackgroundTensor decomposition- and principal component analysis-based unsupervised feature extraction were proposed almost 5 and 10 years ago, respectively; although these methods have been successfully applied to a wide range of genome analyses, including drug repositioning, biomarker identification, and disease-causing genes’ identification, some fundamental problems have been identified: the number of genes identified was too small to assume that there were no false negatives, and the histogram of P-values derived was not fully coincident with the null hypothesis that principal component and singular value vectors follow the Gaussian distribution.ResultsOptimizing the standard deviation such that the histogram of P-values is as much as possible coincident with the null hypothesis results in an increase in the number and biological reliability of the selected genes.ConclusionsTensor decomposition- and principal component analysis-based unsupervised feature extraction are perhaps better than state-of-art methods in regard to predicting differentially expressed genes because they achieve the desired property that the less expressed differentially expressed genes should be less likely selected or even associated with the same amount of logarithmic fold change, although they assume neither negative binomial distribution nor dispersion relation, which is usually assumed in state-of-art methods.
Occurrence and significance of Omicron BA.1 infection followed by BA.2 reinfection
Authors: Stegger Marc , Edslev Sofie Marie , Sieber Raphael Niklaus , Cäcilia Ingham Anna , Ng Kim Lee , Tang Man-Hung Eric , Alexandersen Soren , Fonager Jannik , Legarth Rebecca , Utko Magdalena , Wilkowski Bartlomiej , Gunalan Vithiagaran , Bennedbæk Marc , Byberg-Grauholm Jonas , Møller Camilla Holten , Christiansen Lasse Engbo , Svarrer Christina Wiid , Ellegaard Kirsten , Baig Sharmin , Johannesen Thor Bech , Espenhain Laura , Skov Robert , Cohen Arieh Sierra , Larsen Nicolai Balle , Sørensen Karina Meden , White Emily Dibba , Lillebaek Troels , Ullum Henrik , Krause Tyra Grove , Fomsgaard Anders , Ethelberg Steen , Rasmussen Morten 
Published: February 2022

AbstractThe newly found Omicron SARS-CoV-2 variant of concern has rapidly spread worldwide. Omicron carries numerous mutations in key regions and is associated with increased transmissibility and immune escape. The variant has recently been divided into four subvariants with substantial genomic differences, in particular between Omicron BA.1 and BA.2. With the surge of Omicron subvariants BA.1 and BA.2, a large number of reinfections from earlier cases has been observed, raising the question of whether BA.2 specifically can escape the natural immunity acquired shortly after a BA.1 infection.To investigate this, we selected a subset of samples from more than 1,8 million cases of infections in the period from November 22, 2021, until February 11, 2022. Here, individuals with two positive samples, more than 20 and less than 60 days apart, were selected. From a total of 187 reinfection cases, we identified 47 instances of BA.2 reinfections shortly after a BA.1 infection, mostly in young unvaccinated individuals with mild disease not resulting in hospitalization or death.In conclusion, we provide evidence that Omicron BA.2 reinfections do occur shortly after BA.1 infections but are rare.
Voxel-wise Intermodal Coupling Analysis of Two or More Modalities using Local Covariance Decomposition
Authors: Hu Fengling , Weinstein Sarah M. , Baller Erica B. , Valcarcel Alessandra M. , Adebimpe Azeez , Raznahan Armin , Roalf David R. , Robert-Fitzgerald Timothy E. , Gonzenbach Virgilio , Gur Ruben C. , Gur Raquel E. , Vandekar Simon , Detre John A. , Linn Kristin A. , Alexander-Bloch Aaron , Satterthwaite Theodore D. , Shinohara Russell T. 
Published: February 2022

AbstractWhen individual subjects are imaged with multiple modalities, biological information is present not only within each modality, but also between modalities – that is, in how modalities covary at the voxel level. Previous studies have shown that local covariance structures between modalities, or intermodal coupling (IMCo), can be summarized for two modalities, and that two-modality IMCo reveals otherwise undiscovered patterns in neurodevelopment and certain diseases. However, previous IMCo methods are based on the slopes of local weighted linear regression lines, which are inherently asymmetric and limited to the two-modality setting. Here, we present a generalization of IMCo estimation which uses local covariance decompositions to define a symmetric, voxel-wise coupling coefficient that is valid for two or more modalities. We use this method to study coupling between cerebral blood flow, amplitude of low frequency fluctuations, and local connectivity in 803 subjects ages 8 through 22. We demonstrate that coupling is spatially heterogeneous, varies with respect to age and sex in neurodevelopment, and reveals patterns that are not present in individual modalities. As availability of multi-modal data continues to increase, principal-component-based IMCo (pIMCo) offers a powerful approach for summarizing relationships between multiple aspects of brain structure and function. An R package for estimating pIMCo is available at: https://github.com/hufengling/pIMCo.
Assessing evidence accumulation and rule learning in humans with an online game
Authors: Do Quan , Kane Gary A. , McGuire Joseph T. , Scott Benjamin B. 
Published: February 2022

AbstractEvidence accumulation, how the brain integrates sensory information over time, is an essential component of perception and decision making. In humans, evidence accumulation is commonly modeled as a diffusion process in which noise accumulates linearly with the incoming evidence. However, recent studies in rodents have shown that during perceptual decision making, noise scales non-linearly with the strength of accumulated evidence. The question of whether nonlinear noise scaling also holds for humans has been clouded by differences in the methodologies typically used to collect and analyze human and rodent data. For example, whereas humans are typically given explicit instructions in these tasks, rodents are trained using feedback. Therefore, to evaluate how perceptual noise scales with accumulated evidence, we developed an online evidence accumulation game and nonverbal training pipeline for humans inspired by pulse-based evidence accumulation tasks for rodents. Using this game, we collected and analyzed behavioral data from hundreds of participants trained either with an explicit description of the relevant decision rule or merely with experiential feedback. Across all participants, performance was well described by an accumulation process, in which stimuli were integrated equally across time. Participants trained using feedback alone learned the game rules rapidly and used similar strategies to those who received explicit instructions. Decisions in both groups were influenced in similar ways by biases and perceptual noise, suggesting that explicit instructions did not reduce bias or noise in pulse-based accumulation tasks. Finally, by leveraging data across all participants, we show that perceptual noise during evidence accumulation was best described by a non-linear model of noise scaling, consistent with previous animal studies, but inconsistent with diffusion models widely used in human studies. These results challenge the conventional description of humans’ accumulation process and suggest that online games inspired by evidence accumulation tasks provide a valuable large-scale behavioral assessment platform to examine perceptual decision making and learning in humans. In addition, the feedback-based training pipeline developed for this game may be useful for evaluating perceptual decision making in human populations with difficulty following verbal instructions.HighlightsDevelopment and validation of an online video game to measure perceptual decision making.Humans trained using a feedback-based pipeline exhibit similar strategies and performance compared with those receiving instructions.Perceptual noise increases superlinearly with sensory evidence.
Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection
Authors: Guarnieri Joseph W. , Dybas Joseph M. , Fazelinia Hossein , Kim Man S. , Frere Justin , Zhang Yuanchao , Albrecht Yentli Soto , Murdock Deborah G. , Angelin Alessia , Singh Larry N. , Weiss Scott L. , Best Sonja M. , Lott Marie T. , Cope Henry , Zaksas Viktorija , Saravia-Butler Amanda , Meydan Cem , Foox Jonathan , Mozsary Christopher , Kidane Yared H. , Priebe Waldemar , Emmett Mark R. , Meller Robert , Singh Urminder , Bram Yaron , tenOever Benjamin R. , Heise Mark T. , Moorman Nathaniel J. , Madden Emily A. , Taft-Benz Sharon A. , Anderson Elizabeth J. , Sanders Wes A. , Dickmander Rebekah J. , Baxter Victoria K. , Baylin Stephen B. , Wurtele Eve Syrkin , Moraes-Vieira Pedro M. , Taylor Deanne , Mason Christopher E. , Schisler Jonathan C. , Schwartz Robert E. , Beheshti Afshin , Wallace Douglas C. 
Published: February 2022

AbstractDefects in mitochondrial oxidative phosphorylation (OXPHOS) have been reported in COVID-19 patients, but the timing and organs affected vary among reports. Here, we reveal the dynamics of COVID-19 through transcription profiles in nasopharyngeal and autopsy samples from patients and infected rodent models. While mitochondrial bioenergetics is repressed in the viral nasopharyngeal portal of entry, it is up regulated in autopsy lung tissues from deceased patients. In most disease stages and organs, discrete OXPHOS functions are blocked by the virus, and this is countered by the host broadly up regulating unblocked OXPHOS functions. No such rebound is seen in autopsy heart, results in severe repression of genes across all OXPHOS modules. Hence, targeted enhancement of mitochondrial gene expression may mitigate the pathogenesis of COVID-19.One-Sentence SummaryCovid-19 is associated with targeted inhibition of mitochondrial gene transcription.
Omicron booster in ancestral strain vaccinated mice augments protective immunities against both the Delta and Omicron variants
Authors: Jia Liqiu , Zhou Yang , Li Shaoshuai , Zhang Yifan , Yan Dongmei , Wang Wanhai , Zhang Wenhong , Wan Yanmin , Qiu Chao 
Published: February 2022

AbstractA booster vaccination is called for constraining the evolving epidemic of SARS-CoV-2. However, the necessity of a new COVID-19 vaccine is currently unclear. To compare the effect of an Omicron-matched S DNA vaccine and an ancestral S DNA vaccine in boosting cross-reactive immunities, we firstly immunized mice with two-dose of a DNA vaccine encoding the spike protein of the ancestral Wuhan strain. Then the mice were boosted with DNA vaccines encoding spike proteins of either the Wuhan strain or the Omicron variant. Specific antibody and T cell responses were measured at 4 weeks post boost. Our data showed that the Omicron-matched vaccine efficiently boosted RBD binding antibody and neutralizing antibody responses against both the Delta and the Omicron variants. Of note, antibody responses against the Omicron variant elicited by the Omicron-matched vaccine were much stronger than those induced by the ancestral S DNA vaccine. Meanwhile, CD8+ T cell responses against both the ancestral Wuhan strain and the Omicron strain also tended to be higher in mice boosted by the Omicron-matched vaccine than those in mice boosted with the ancestral S DNA vaccine, albeit no significant difference was observed. Our findings suggest that an Omicron-matched vaccine is preferred for boosting cross-reactive immunities.
Single-cell Gene Regulation Network Inference by Large-scale Data Integration
Authors: Dong Xin , Tang Ke , Xu Yunfan , Wei Hailin , Han Tong , Wang Chenfei 
Published: February 2022

AbstractSingle-cell ATAC-seq (scATAC-seq) has proven to be a state-of-art approach to investigating gene regulation at the single-cell level. However, existing methods cannot precisely uncover cell-type-specific binding of transcription regulators (TRs) and construct gene regulation networks (GRNs) in single-cell. ChIP-seq has been widely used to profile TR binding sites in the past decades. Here, we developed SCRIP, an integrative method to infer single-cell TR activity and targets based on the integration of scATAC-seq and a large-scale TR ChIP-seq reference. Our method showed improved performance in evaluating TR binding activity compared to the existing motif-based methods and reached a higher consistency with matched TR expressions. Besides, our method enables identifying TR target genes as well as building GRNs at the single-cell resolution based on a regulatory potential model. We demonstrate SCRIP’s utility in accurate cell-type clustering, lineage tracing, and inferring cell-type-specific GRNs in multiple biological systems. SCRIP is freely available at https://github.com/wanglabtongji/SCRIP.
Multi-pulse transcranial magnetic stimulation of human motor cortex produces short-latency corticomotor facilitation via two distinct mechanisms
Authors: Kesselheim Janine , Takemi Mitsuaki , Christiansen Lasse , Karabanov Anke Ninija , Siebner Hartwig Roman 
Published: February 2022

AbstractBackgroundSingle-pulse transcranial magnetic stimulation of the precentral hand representation (M1HAND) can elicit indirect waves in the corticospinal tract at a periodicity of ~660 Hz, called indirect or I-waves. These synchronized descending volleys are produced by transsynaptic excitation of fastconducting monosynaptic corticospinal axons in M1-HAND. Paired-pulse TMS can induce short-interval intracortical facilitation (SICF) of motor evoked potentials (MEPs) at inter-pulse intervals that match I-wave periodicity.ObjectiveTo examine whether short-latency corticospinal facilitation engages additional mechanisms independently of I-wave periodicity.MethodsIn 19 volunteers, one to four biphasic TMS pulses were applied to left M1-HAND with interpulse interval was adjusted to the first peak or first trough of the individual SICF curve. TMS was applied at different intensities to probe the intensity-response relationship.ResultsPairs, triplets, or quadruplets at individual peak-latency facilitated MEP amplitudes across a wide range of TMS intensities compared to single pulses. Multi-pulse TMSHAND at individual troughlatency also produced a consistent facilitation of MEP amplitude. Short-latency facilitation at trough-latency was less pronounced than short-latency facilitation at peak-latency, but the relative difference in facilitation decreased with increasing stimulus intensity. Increasing the number of pulses from two to four pulses had only a modest effect on MEP facilitation.ConclusionTwo mechanisms underly short-latency corticomotor facilitation caused by biphasic multi-pulse TMS. An intracortical mechanism is related to I-wave periodicity and engages fast-conducting direct projections to spinal motoneurons. A second corticospinal mechanism does not rely on I-wave rhythmicity and may be mediated by slower conducting indirect pyramidal tract projections from M1-HAND to spinal interneurons. The latter mechanism deserves more attention in TMS studies of the corticomotor system.
Effects of Experimental Design, Genetic Architecture and Threshold on Power and False Positive Rate of Genome-Wide Association Studies
Authors: Loh Zhi , Clark Sam , van der Werf Julius H. J. 
Published: February 2022

AbstractGenome-Wide Association Studies are an important tool for identifying genetic markers associated with a trait, but it has been plagued by the multiple testing problem, which necessitates a multiple testing correction method. While many multiple testing methods have been suggested, e.g. Bonferroni and Benjamini-Hochberg’s False Discovery Rate, the quality of the adjusted threshold based on these methods is not as well investigated. The aim of this study was to evaluate the balance between power and false positive rate of a Genome-Wide Association Studies experiment with Bonferroni and Benjamini-Hochberg’s False Discovery Rate multiple testing correction methods and to test the effects of various experimental design and genetic architecture parameters on this balance. Our results suggest that when the markers are independent the threshold from Benjamini-Hochberg’s False Discovery Rate provides a better balance between power and false positive rate in an experiment. However, with correlations between markers the threshold of Benjamini-Hochberg’s False Discovery Rate becomes too lenient with an excessive number of false positives. Experimental design parameters such as sample size and number of markers used, as well as genetic architecture of a trait affect the balance between power and false positive rate. This experiment provided guidance in selecting an appropriate experimental design and multiple testing correction method when conducting an experiment.