bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of the COVID-19 pandemic on pain and psychological functioning in young adults with chronic pain
Authors: Tham See Wan , Murray Caitlin B. , Law Emily F. , Slack Katherine E. , Palermo Tonya M. 
Published: April 2022

Abstract
Data are equivocal on the consequences of COVID-19 pandemic on pain and well-being for individuals with chronic pain. Furthermore, little is known regarding its impact on the health of young adults with chronic pain. We conducted a longitudinal study to compare pain, psychological functioning, and substance use before and during the pandemic of 196 young adults with chronic pain. Participants aged 18 to 24 years (M = 21.1 years; 79.6% females) reported on pain, anxiety, depression, and substance use before (October 2018–August 2019) and during the pandemic (October 2020–November 2020), in addition to the assessment of COVID-19 exposure and its impact. Before the pandemic, young adults experienced mild-to-moderate pain intensity (M = 3.75, SD = 2.33) and pain interference (M = 3.44, SD = 2.69). Findings were that pain intensity, pain interference, and depression symptoms remained stable during the pandemic. In contrast, anxiety symptoms increased significantly (M = 8.21, SD = 5.84 vs M = 8.89, SD = 5.95, P = 0.04). Tobacco, alcohol, and cannabis use were unchanged. Mixed linear models revealed that COVID-19 exposure and impact were not associated with changes in pain intensity or interference, with female sex associated with increased pain intensity (β = 0.86, P = 0.02) and pain interference (β = 0.87, P = 0.02). Our findings indicated relative stability of pain symptoms experienced by young adults with chronic pain. However, the increases in anxiety highlight the need to facilitate treatment access for mental health services to mitigate downstream impact.
Swing phase considerations in prosthetic knee design: Case series to validate simulations
Authors: Sudeesh S. , Shunmugam M. S. , Ojha R. , Moulic S. G. , Sujatha S. 
Published: April 2022

Background:
Previously reported simulations comparing a new polycentric knee (called IPK) and a single-axis knee suggested that polycentricity could lead to improved performance during swing phase and negate the need for an extension assist. They also showed that an anteriorly translated socket adapter for enhanced stance stability compromises foot clearance during swing.

Objectives:
The objectives of this study are to validate those findings using gait trials to enable further improvement in the IPK design before mass production.

Methods:
Three subjects regularly using three different passive knees, single-axis knee without extension assist, single-axis knee with extension assist (SAK-EA), and polycentric knee with extension assist (Mobility India–sourced polycentric knee), participated in this study. Their gait with their regular prosthesis and with IPK (having no extension assist) were analyzed, compared, and broadly correlated with simulation results.

Results:
Extension assist in single-axis knee with extension assist improved swing performance, affected foot clearance in Mobility India–sourced polycentric knee, and was found to be unnecessary in the IPK. With an anteriorly placed socket adapter in the IPK, compensatory strategies were necessary for foot clearance. The IPK was found to provide better knee extension characteristics with lower hip effort (up to 42% reduction) than other knees.

Conclusions:
This case series confirmed previously reported simulation results on the swing phase behavior of passive prosthetic knees. The performance of the IPK during swing obviated the need for an extension assist, thereby simplifying the design. Appropriate design changes in the IPK’s socket adapter location are required to achieve both stance stability and reduce gait compensations for foot clearance.
Asymptomatic SARS-CoV-2 Infection Is Common Among ART-Treated People With HIV
Authors: Overton Edgar T. , Weir Isabelle R. , Zanni Markella V. , Fischinger Stephanie , MacArthur Rodger D. , Aberg Judith A. , Fitch Kathleen V. , Frank Michael , Albrecht Helmut , Goodenough Elliot , Rhame Frank S. , Fichtenbaum Carl J. , Bloomfield Gerald S. , Malvestutto Carlos , Supparatpinyo Khuanchai , McCallum Sara , Douglas Pamela S. , Alter Galit , Ribaudo Heather , Grinspoon Steven K. 
Published: April 2022

Background:
Limited data are available regarding asymptomatic COVID-19 among people with HIV (PWH). Data on a representative subset of PWH enrolled in Randomized Trial to Prevent Vascular Events in HIV, a global clinical trial, are presented here.

Methods:
Randomized Trial to Prevent Vascular Events in HIV is an atherosclerotic cardiovascular disease prevention trial among 7770 PWH on antiretroviral therapy. Beginning April 2020, targeted data on coronavirus disease 2019 (COVID-19) diagnosis and symptoms were collected during routine trial visits. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was defined as either COVID-19 clinical diagnosis or presence of SARS-CoV-2 Immunoglobulin G (IgG) or Immunoglobulin A (IgA) receptor binding domain protein (antispike) antibodies in the absence of prior COVID-19 vaccine.

Results:
The group (N = 2464) had a median age 53 years, 35% female sex, 47% Black or African American race, median CD4 count 649 c/mm3, and 97% with HIV VL <400 cp/m. SARS-CoV-2 infection occurred in 318 persons (13%): 58 with clinical diagnosis and 260 with detectable antibodies. Of these PWH, 304 completed symptom questionnaires: 121 (40%) reported symptoms, but 183 (60%) were asymptomatic. PWH with asymptomatic SARS-CoV-2 infection were more likely to be from low-income or middle-income regions, of Black or African American race, older in age, and with higher atherosclerotic cardiovascular disease risk score. Symptomatic COVID was more common with obesity, metabolic syndrome, and low HDL levels. CD4 counts and HIV viral suppression rates were similar among PWH with symptomatic vs. asymptomatic COVID.

Conclusions:
Asymptomatic SARS-CoV-2 infection is common among antiretroviral therapy–treated PWH globally. We determined that 60% of infections in PWH were asymptomatic. HIV clinicians must remain vigilant about COVID-19 testing among PWH to identify asymptomatic cases.
Barcoding and its application for visualizing ecological dynamics
Authors: Agarwal Vitul , Mouw Colleen B. 
Published: April 2022

AbstractTime is perceived to be unidirectional and continuous in the philosophy of science. This continuity can play a crucial role in time series analysis as events are generally seen as an outcome of the past, or subject to events that occurred previously in time. In this study, we describe an ordinal approach to perceiving ecological time series – one that relies on pattern formation with both antecedent and future events. Our approach defines a limited set of structural shapes that can occur for past, present, and future time points. Such a library of all possible shapes can then be used for novel approaches to data visualization and time series analysis. We applied this method to simple ecological models and then to natural time series data for measles cases in London and the phytoplankter Pseudo-nitzschia spp. in Narragansett Bay, Rhode Island. Alternative perspectives on time series representation can strengthen our ability to identify important patterns in dynamics and effectively discriminate between similar time series. When used in conjunction with conventional line-plots, barcodes can be tailored to demonstrate the presence or absence of specific structural patterns or features. Our results show that data exploration without the assumption of time series continuity can yield important and novel insight into the behavior of ecological systems.
Plant growers’ environmental consciousness may not be enough to mitigate pollinator declines: a questionnaire-based case study in Hungary
Authors: Varga-Szilay Zsófia , Pozsgai Gábor 
Published: April 2022

ABSTRACTBACKGROUNDPesticides are one of the most important anthropogenic-related stressors. In times of global pollinator decline, the role of integrated farming and that of urban gardens in supporting wild pollinators is becoming increasingly important. We circulated an online questionnaire to survey the plant protection practices among Hungarian farmers and garden owners with a particular emphasis on pollinator protection.RESULTSWe found that plant growers heavily rely on pesticide use, and pesticides are widely used in otherwise pollinator-friendly gardens. Whether pesticide use practices were driven by expert opinion and the respondents’ gender were the best predictors of pesticide use. Although most respondents supported pollinators, pesticides are also widely used among home garden owners, which can pose a non-evident ecological trap for pollinator populations in the gardens.CONCLUSIONSpecial attention should be paid to implementing measures to reduce pesticide, use not only in farmlands but also in home gardens. Environmental education and financial support through agroecological schemes could efficiently promote the transition. However, whereas farmers can be encouraged to reduce pesticide use mostly by expert advice, garden owners are likely to rely on more conventional information channels. The attitude of Hungarian plant growers can provide an insight into pesticide use practices of Central and Eastern European countries, but similar surveys are needed across Europe for a complete understanding of broad-scale processes. This work lays the foundations for similar studies which can inform and facilitate the transformation processes to pesticide-free farming and gardening.
Subtyping of major SARS-CoV-2 variants reveals different transmission dynamics
Authors: Yang Hsin-Chou , Wang Jen-Hung , Yang Chih-Ting , Lin Yin-Chun , Hsieh Han-Ni , Chen Po-Wen , Liao Hsiao-Chi , Chen Chun-houh , Liao James C. 
Published: April 2022

AbstractSARS-CoV-2 continues to evolve, causing waves of the pandemic. Up to March 2022, eight million genome sequences have accumulated, which are classified into five major variants of concern. With the growing number of sequenced genomes, analysis of the big dataset has become increasingly challenging. Here we developed systematic approaches for comprehensive subtyping and pattern recognition for transmission dynamics. By analyzing the first two million viral genomes as of July 2021, we found that different subtypes of the same variant exhibited distinct temporal trajectories. For example, some Delta subtypes did not spread rapidly, while others did. We identified sets of characteristic single nucleotide variations (SNVs) that appeared to enhance transmission or decrease efficacy of antibodies for some subtypes of the Delta and Alpha variants. We also identified a set of SNVs that appeared to suppress transmission or increase viral sensitivity to antibodies. These findings are later confirmed in an analysis of six million genomes as of December 2021. For the Omicron variant, the dominant type in the world, we identified the subtypes with enhanced and suppressed transmission in an analysis of seven million genomes as of January 2022 and further confirmed the findings in a later analysis of eight million genomes as of March 2022. While the “enhancer” SNVs exhibited an enriched presence on the spike protein, the “suppressor” SNVs are mainly elsewhere. Disruption of the SNV correlation largely destroyed the enhancer-suppressor phenomena. These results suggest the importance of fine subtyping of variants, and point to potential complex interactions among SNVs.
Super-Resolution NMR Spectroscopy using the Intersection of Non-Redundant Information on Resonance Groups
Authors: Lorieau Justin L , Malooley Alexander , Banerjee Indrani 
Published: April 2022

AbstractThe resolution of spectra is a major limitation in the application of Nuclear Magnetic Resonance (NMR) spectroscopy to large and complex molecular systems. In this report, we introduce a technique to enhance the resolution of NMR spectra beyond the intrinsic limitations of a spectrometer for a single spectrum by using the Intersection of Non-Redundant Information on Resonance Groups (INIR). With INIR, we reconstruct 900-MHz (21.1T) spectra from a 500-MHz (11.7T) NMR spectrometer, which compare favorably to experimental 900-MHz spectra. INIR holds promise in significantly enhancing the resolution of NMR spectra and in extending the size and complexity of molecules studied by NMR.
Multimodal single cell data integration challenge: results and lessons learned
Authors: Lance Christopher , Luecken Malte D. , Burkhardt Daniel B. , Cannoodt Robrecht , Rautenstrauch Pia , Laddach Anna , Ubingazhibov Aidyn , Cao Zhi-Jie , Deng Kaiwen , Khan Sumeer , Liu Qiao , Russkikh Nikolay , Ryazantsev Gleb , Ohler Uwe ,   NeurIPS 2021 Multimodal data integration competition participants, Pisco Angela Oliveira , Bloom Jonathan , Krishnaswamy Smita , Theis Fabian J. 
Published: April 2022

AbstractBiology has become a data-intensive science. Recent technological advances in single-cell genomics have enabled the measurement of multiple facets of cellular state, producing datasets with millions of single-cell observations. While these data hold great promise for understanding molecular mechanisms in health and disease, analysis challenges arising from sparsity, technical and biological variability, and high dimensionality of the data hinder the derivation of such mechanistic insights. To promote the innovation of algorithms for analysis of multimodal single-cell data, we organized a competition at NeurIPS 2021 applying the Common Task Framework to multimodal single-cell data integration. For this competition we generated the first multimodal benchmarking dataset for single-cell biology and defined three tasks in this domain: prediction of missing modalities, aligning modalities, and learning a joint representation across modalities. We further specified evaluation metrics and developed a cloud-based algorithm evaluation pipeline. Using this setup, 280 competitors submitted over 2600 proposed solutions within a 3 month period, showcasing substantial innovation especially in the modality alignment task. Here, we present the results, describe trends of well performing approaches, and discuss challenges associated with running the competition.
Two-photon microscopy in vivo reveals brain vessel type-specific loss of glycocalyx caused by apoM/S1P signaling impairment
Authors: Kucharz Krzysztof , Mathiesen Janiurek Mette , Christoffersen Christina , Lauritzen Martin 
Published: April 2022

ABSTRACTIncreases in adsorptive mediated transcytosis (AMT) at the blood-brain barrier (BBB) are linked to many brain disorders. In a healthy brain, AMT is suppressed by sphingosine-1-phosphate (S1P) receptor 1 (S1PR1) signaling. Low levels of S1P lead to a rise in AMT, but the mechanisms are incompletely understood. Here, we explored whether the rises in AMT are caused by the loss of the endothelial glycocalyx (gcx). We used two-photon microscopy in mice with low S1P plasma levels (Apom-/-) and developed a novel photobleaching approach to measure gcx in vivo at distinct classes of cerebral microvessels, i.e., arterioles, capillaries and venules. We show that S1P signaling impairment reduced gcx in arterioles but not in other vessel segments. The location of gcx loss corresponded to the vascular topology of AMT increases. The S1PR1 agonist SEW2871 restores low levels of AMT in Apom-/- mice but did not restore the gcx within the same time window. We propose that while the gcx loss may contribute to AMT increase, restoring gcx is not necessary for AMT to return to normal. These data establish a new imaging method to study gcx in the living mouse brain, demonstrate zonation of gcx in cerebral microvessels, and suggest differences in vascular susceptibility to gcx loss in disease states.
Identification of a novel AP2 transcription factor in zygotes with an essential role in Plasmodium ookinete development
Authors: Nishi Tsubasa , Kaneko Izumi , Iwanaga Shiroh , Yuda Masao 
Published: April 2022

AbstractThe sexual phase of Plasmodium represents a crucial step in malaria transmission, during which these parasites fertilize and form ookinetes to infect mosquitoes. Plasmodium development after fertilization is thought to proceed with female-stored mRNAs until the formation of a retort-form ookinete; thus, transcriptional activity in zygotes has previously been considered quiescent. In this study, we reveal the essential role of transcriptional activity in zygotes by investigating the function of a newly identified AP2 transcription factor, AP2-Z. ap2-z was previously reported as a female transcriptional regulator gene whose disruption resulted in developmental arrest at the retort stage of ookinetes. In this study, although ap2-z was transcribed in females, we show that it was translationally repressed by the DOZI complex and translated after fertilization with peak expression at the zygote stage. ChIP-seq analysis of AP2-Z shows that it binds on specific DNA motifs, targeting the majority of genes known as an essential component of ookinetes, which largely overlap with the AP2-O targets, as well as genes that are unique among the targets of other sexual transcription factors. The results of this study also indicate the existence of a cascade of transcription factors, beginning with AP2-G, that proceeds from gametocytogenesis to ookinete formation.Author summarySexual development in Plasmodium parasites, a causative agent of malaria, is essential for their transmission from vertebrate hosts to mosquitoes. This important developmental process proceeds as follows: formation of a gametocyte/gamete, fertilization and conversion of the zygote into the mosquito midgut invasive stage, called the ookinete. As a target of transmission blocking strategies, it is important to understand the mechanisms regulating Plasmodium sexual development. In this study, we assessed transcriptional regulation after fertilization by investigating the function of a novel transcription factor, AP2-Z. The results revealed the essential role of de novo transcription activated by AP2-Z in zygotes for promoting ookinete development. As transcriptional activity during the zygote stage has previously been considered silent in Plasmodium, novel genes important for ookinete formation can now be explored in the target genes of AP2-Z. Investigating the functions of these genes can help us understand the mechanisms of Plasmodium zygote/ookinete development and identify new targets for transmission blocking vaccines.
A phenotypic screen of Marfan syndrome iPSC-derived vascular smooth muscle cells uncovers GSK3β as a new target
Authors: Davaapil Hongorzul , McNamara Madeline , Granata Alessandra , Macrae Robyn G.C. , Hirano Mei , Fitzek Martina , Aragon-Martin Jose Antonio , Child Anne , Smith David M. , Sinha Sanjay 
Published: April 2022

AbstractMarfan syndrome (MFS) is a rare connective tissue disorder caused by mutations in FBN1. Patients with MFS notably suffer from aortic aneurysm and dissection. Despite considerable effort, animal models have proven to be poorly predictive for therapeutic intervention in human aortic disease. Using a “humanised” model system may be more appropriate in identifying new therapeutic targets. Patient-derived induced pluripotent stem cells can be differentiated into vascular smooth muscle cells (VSMCs) and recapitulate major features of MFS. We have screened 1,022 small molecules in our in vitro model, exploiting the highly-proteolytic nature of MFS-VSMCs, and identified 36 effective compounds. Further analysis identified GSK3β as a recurring target in the compound screen. GSK3β inhibition/knockdown did not ameliorate the proliferation defect in MFS-VSMCs but improved MFS-VSMC apoptosis and proteolysis. To conclude, we have identified GSK3β as a novel target for MFS, forming the foundation for future work in MFS and other aortic diseases.
The conservation of human functional variants and their effects across mammals
Authors: Zhao R. , Talenti A. , Fang L. , Liu S. , Liu G. , Hong N.P. Chue , Tenesa A. , Hassan M. A. , Prendergast J.G.D. 
Published: April 2022

AbstractDespite the clear potential of livestock models of human functional variants to provide important insights into the biological mechanisms driving human diseases and traits, their use to date has been limited. Generating such models via genome editing is costly and time consuming, and it is unclear which variants will have conserved effects across species. In this study we address these issues by studying naturally occurring livestock models of human functional variants. We show that orthologues of over 1.6 million human variants are already segregating in domesticated mammalian species, including several hundred previously directly linked to human traits and diseases. Models of variants linked to particular phenotypes, including metabolomic disorders and height, have been preferentially maintained across species, meaning studying the genetic basis of these phenotypes is particularly tractable in livestock. Using machine learning we demonstrate it is possible to identify human variants that are more likely to have an existing livestock orthologue, and, importantly, we show that the effects of functional variants are often conserved in livestock, acting on orthologous genes with the same direction of effect. Consequently, this work demonstrates the substantial potential of naturally occurring livestock carriers of orthologues of human functional variants to disentangle their functional impacts.