bluuebunny/crossref_metadata_2025_split huggingface dataset:
The predictive significance of prognostic nutritional index and serum albumin/globulin ratio on the overall survival of penile cancer patients undergoing penectomy
Authors: Song Wei-Jie , Li Ni Chu-Jie , Gao Jun , Xu Zhi-Peng , Liu Jian-Ye , Long Zhi , He Le-Ye 
Published: April 2022

AbstractObjectiveTo assess the value of using the prognostic nutritional index (PNI) and serum albumin/globulin ratio (AGR) in predicting the overall survival (OS) of patients with penile cancer (PC) undergoing penectomy.Materials and methodsA retrospective analysis of 123 patients who were admitted to our hospital due to PC from April 2010 to September 2021 and underwent penectomy were included in the study. The optimal cut-off value of PNI and AGR was determined by receiver operating characteristic curve analysis. Kaplan-Meier analysis and the Cox proportional hazard model were used to evaluate the correlation between PNI, AGR, and OS in patients with PC.ResultsThe best cut-off values of PNI and AGR were set to 49.03 (95% confidence interval 0.705-0.888, Youden index=0.517, sensitivity=57.9%, specificity=93.7%, P<0.001) and 1.28 (95% confidence interval 0.610-0.860, Youden index=0.404, sensitivity=84.1%, specificity=56.2%, P=0.003). Kaplan-Meier analysis showed that the OS of the patients in the high PNI group and the high AGR group was significantly higher than that of the patients in the low PNI group and the low AGR group (P<0.001). Univariate analysis showed that patient age, clinical N stage, pathological stage, PNI, and SII are all predictors of OS in patients with PC (P<0.05). Multivariate analysis showed that pathological stage (P=0.005), PNI (P=0.021), and AGR (P=0.004) are independent prognostic factors for predicting OS in patients with PC undergoing penectomy.ConclusionsBoth PNI score and serum AGR are independent prognostic factors for predicting OS in patients with PC undergoing penectomy.
Dupilumab use is associated with protection from COVID-19 mortality: A retrospective analysis
Authors: Donlan A. , Mallawaarachchi I. , Sasson J. , Preissner R. , Loomba J. , Petri W.A. 
Published: April 2022

AbstractWe previously found that type 2 immunity promotes COVID-19 pathogenesis in a mouse model. To test relevance to human disease we used electronic health record databases and determined that patients on dupilumab (anti-IL-4Rα monoclonal antibody that blocks IL-13 and IL-4 signaling) at the time of COVID-19 infection had lower mortality.
Sleep problems effect on developmental trajectories in children with autism
Authors: Levin Jonah , Khokhlovich Edward , Vyshedskiy Andrey 
Published: April 2022

AbstractThe effect of sleep problems in 2-to 5-year-old children with ASD was investigated in the largest and the longest observational study to-date. Parents assessed the development of 7069 children quarterly for three years on five orthogonal subscales: receptive language, expressive language, sociability, sensory awareness, and health. Moderate and severe sleep problems were reported in 13% of children. Children with no sleep problems developed faster compared to matched children with sleep problems in all subscales. The greatest difference in trajectories was detected in the health subscale. When controlling for the health score (in addition to each subscale score at baseline as well as gender and severity), the effect of sleep problems decreased in all subscales except the combinatorial receptive language subscale (where the effect of sleep problems was increased), suggesting that sleep problems affect combinatorial language acquisition irrespective of the overall health. This study confirms a high prevalence of sleep problems in ASD children and points to the need for more systematic research as an initial step in developing treatment strategies.
Behaviour change interventions improve maternal and child nutrition in sub-Saharan Africa: a systematic review
Authors: Watson Daniella , Mushamiri Patience , Beeri Paula , Rouamba Toussaint , Jenner Sarah , Kehoe Sarah H , Ward Kate A , Barker Mary , Lawrence Wendy ,   the INPreP Study Group
Published: April 2022

AbstractBackgroundEvidence that nutrition-specific and nutrition-sensitive interventions can improve maternal and child nutrition status in sub-Saharan Africa is inconclusive. Using behaviour change theory and techniques in intervention design may increase effectiveness and make outcomes more predictable. This systematic review aimed to determine whether interventions that included behaviour change functions were effective.MethodsSix databases were searched systematically, using MeSH and free-text terms, for articles describing nutrition-specific and nutrition-sensitive behaviour change interventions published in English until January 2022. Titles, abstracts and full-text papers were double-screened. Data extraction and quality assessments followed Centre for Reviews and Dissemination guidelines. Behaviour change functions of interventions were mapped onto the COM-B model and Behaviour Change Wheel. PROSPERO registered (135054).FindingsThe search yielded 1149 articles: 71 articles met inclusion criteria, ranging from low (n=30) to high (n=11) risk of bias. Many that applied behaviour change theory, communication or counselling resulted in significant improvements in infant stunting and wasting, household dietary intake and maternal psychosocial measures. Interventions with >2 behaviour change functions (including persuasion, incentivisation, environmental restructuring) were the most effective.InterpretationWe recommend incorporating behaviour change functions in nutrition interventions to improve maternal and child outcomes, specifically drawing on the Behaviour Change Wheel, COM-B model. To enhance the designs of these interventions, and ultimately improve the nutritional and psychosocial outcomes for mothers and infants in sub-Saharan Africa, collaborations are recommended between behaviour change and nutrition experts, intervention designers, policy makers and commissioners to fund and roll-out multicomponent behaviour change interventions.
COVID-19 in people with neurofibromatosis 1, neurofibromatosis 2, or schwannomatosis
Authors: Banerjee Jineta , Friedman Jan M. , Klesse Laura J. , Yohay Kaleb ,   Children’s Tumor Foundation Clinical Care Advisory Board, Jordan Justin T , Plotkin Scott , Allaway Robert J , Blakeley Jaishri 
Published: April 2022

ABSTRACTPurposePeople with pre-existing conditions may be more susceptible to severe Coronavirus disease 2019 (COVID-19) when infected by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The relative risk and severity of SARS-CoV-2 infection in people with rare diseases like neurofibromatosis (NF) type 1 (NF1), neurofibromatosis type 2 (NF2), or schwannomatosis (SWN) is unknown.MethodsWe investigated the proportions of SARS-CoV-2 positive or COVID-19 patients in people with NF1, NF2, or SWN in the National COVID Collaborative Cohort (N3C) electronic health record dataset.ResultsThe cohort sizes in N3C were 2,501 (NF1), 665 (NF2), and 762 (SWN). We compared these to N3C cohorts of other rare disease patients (98 - 9844 individuals) and the general non-NF population of 5.6 million. The site- and age-adjusted proportion of people with NF1, NF2, or SWN who tested positive for SARS-CoV-2 or were COVID-19 patients (collectively termed positive cases) was not significantly higher than in individuals without NF or other selected rare diseases. There were no severe outcomes reported in the NF2 or SWN cohorts. The proportion of patients experiencing severe outcomes was no greater for people with NF1 than in cohorts with other rare diseases or the general population.ConclusionHaving NF1, NF2, or SWN does not appear to increase the risk of being SARS-CoV-2 positive or of being a COVID-19 patient, or of developing severe complications from SARS-CoV-2.
Emulation of epidemics via Bluetooth-based virtual safe virus spread: experimental setup, software, and data
Authors: Asanjarani Azam , Shausan Aminath , Chew Keng , Graham Thomas , Henderson Shane G. , Jansen Hermanus M. , Short Kirsty R. , Taylor Peter G. , Vuorinen Aapeli , Yadav Yuvraj , Ziedins Ilze , Nazarathy Yoni 
Published: April 2022

AbstractWe describe an experimental setup and a currently running experiment for evaluating how physical interactions over time and between individuals affect the spread of epidemics. Our experiment involves the voluntary use of the Safe Blues Android app by participants at The University of Auckland (UoA) City Campus in New Zealand. The app spreads multiple virtual safe virus strands via Bluetooth depending on the social and physical proximity of the subjects. The evolution of the virtual epidemics is recorded as they spread through the population. The data is presented as a real-time (and historical) dashboard. A simulation model is applied to calibrate strand parameters. Participants’ locations are not recorded, but participants are rewarded based on the duration of participation within a geofenced area, and aggregate participation numbers serve as part of the data. Once the experiment is complete, the data will be made available as an open-source anonymized dataset.This paper outlines the experimental setup, software, subject-recruitment practices, ethical considerations, and dataset description. The paper also highlights current experimental results in view of the lockdown that started in New Zealand at 23:59 on August 17, 2021. The experiment was initially planned in the New Zealand environment, expected to be free of COVID and lockdowns after 2020. However, a COVID Delta strain lockdown shuffled the cards and the experiment is currently extended into 2022.Author summaryIn this paper, we describe the Safe Blues Android app experimental setup and a currently running experiment at the University of Auckland City Campus. This experiment is designed to evaluate how physical interactions over time and between individuals affect the spread of epidemics.The Safe Blues app spreads multiple virtual safe virus strands via Bluetooth based on the subjects’ unobserved social and physical proximity. The app does not record the participants’ locations, but participants are rewarded based on the duration of participation within a geofenced area, and aggregate participation numbers serve as part of the data. When the experiment is finished, the data will be released as an open-source anonymized dataset.The experimental setup, software, subject recruitment practices, ethical considerations, and dataset description are all described in this paper. In addition, we present our current experimental results in view of the lockdown that started in New Zealand at 23:59 on August 17, 2021. The information we provide here may be useful to other teams planning similar experiments in the future.
Effect of vaccination rates on the prevalence and mortality of COVID-19
Authors: Westerhout Jacob , Khataee Hamid , Neufeld Zoltan 
Published: April 2022

AbstractBy looking at trends in global epidemic data, we evaluate the effectiveness of vaccines on the incidence and mortality from the delta variant of COVID-19. By comparing countries of varying vaccination levels, we find that more vaccinated countries have lower deaths while not having lower cases. This cannot be explained by testing rates or restrictions, but can be partly explained by the most susceptible countries also being the highest vaccinated countries. We also find that during the period when many countries have high vaccination rates, cases and deaths are both increasing in time. This seems to be caused by the waning of the protection vaccines grant against infection.
Cervicovaginal immune mediators increase when young women begin to have sexual intercourse: a prospective study and meta-analysis
Authors: Hughes Sean M. , Levy Claire N. , Calienes Fernanda L. , Martinez Katie A. , Selke Stacy , Tapia Kenneth , Chohan Bhavna H. , Oluoch Lynda , Kiptinness Catherine , Wald Anna , Ghosh Mimi , Hardy Liselotte , Ngure Kenneth , Mugo Nelly R. , Hladik Florian , Roxby Alison C. 
Published: April 2022

AbstractBackgroundAdolescent girls and young women (AGYW) are at high risk of sexually transmitted infections (STIs). It is unknown whether beginning to have sexual intercourse causes changes to immune mediators in the cervicovaginal tract that contribute to this risk.MethodsWe collected cervicovaginal lavages from Kenyan AGYW in the months before and after first penile-vaginal sexual intercourse and measured the concentrations of 20 immune mediators. We compared concentrations pre- and post-first sex using mixed effects models. Secondary analyses included adjustment for possible confounding factors. We additionally performed a systematic review to identify similar studies and combined them with our results by meta-analysis of individual participant data.ResultsWe included 180 samples from 95 AGYW, with 44% providing only pre-first sex samples, 35% matched pre and post, and 21% only post. We consistently detected 19/20 immune mediators, all of which increased post-first sex (median increase 54%; p<0.05 for 13/19; Holm-Bonferroni-adjusted p<0.05 for IL-1β, IL-2 and CXCL8). Effects remained similar after adjusting for confounding factors including STIs and Nugent score.Our systematic review identified two eligible studies, one of 93 Belgian participants and the other of 18 American participants. Nine immune mediators were measured in at least 2/3 studies. Meta-analysis confirmed higher levels post-first sex for 8/9 immune mediators (median increase 47%; p<0.05 for six mediators, most prominently IL-1α, IL-1β and CXCL8).ConclusionsCervicovaginal immune mediator concentrations increased after the beginning of sexual activity independently of confounding factors including STIs. Results were consistent across three studies conducted on three different continents.
Late maturation of semantic control promotes conceptual development
Authors: Jackson Rebecca L. , Lambon Ralph Matthew A. , Rogers Timothy T. 
Published: April 2022

AbstractControl processes underpinned by the prefrontal cortex are critical for generating task-appropriate behaviour across cognitive domains, yet this region develops extremely late. Traditionally, this developmental pattern is considered negative but necessary. However, an alternative (yet perhaps complementary) view suggests that a developmental period without control could support learning, particularly in the semantic domain. Here, we exploit a recent computational model to test formally whether late development of the context-sensitive use of conceptual knowledge, or ‘semantic control’, would promote concept acquisition. Simulations show that late maturation of semantic control and anatomical connectivity conspire to promote conceptual learning. Delayed control speeds conceptual learning without compromising conceptual representations, particularly when control connects to intermediate layers. To assess whether semantic control also develops late in human children, we conducted a meta-analysis of the classic triadic matching task where participants decide which of two options best matches a third. Matching can be based on taxonomic or thematic relations. When these conflict, participants must exert semantic control to determine which relation is task appropriate. Context-sensitivity develops later than conceptual knowledge with large increases between 3 and 6 years. Thus, the protracted PFC development leads to a delay in acquiring semantic control processes, benefiting conceptual learning.
Informational Masking Constrains Vocal Communication in Nonhuman Animals
Authors: Gupta Saumya , Kalra Lata , Rose Gary J. , Bee Mark A. 
Published: April 2022

AbstractNoisy social environments constrain human speech communication in two important ways: spectrotemporal overlap between signals and noise can reduce speech audibility (“energetic masking”) and noise can interfere with processing informative features of otherwise audible speech (“informational masking”). Whether and how informational masking impacts vocal communication in nonhuman animals remains unknown. In this study of a treefrog, in which females choose mates in noisy breeding choruses, we investigated whether informational masking disrupts the recognition of vocal signals that guide mating decisions. We observed significantly reduced rates of responding to the vocalizations of a potential mate when target signals were broadcast concurrently with other biologically relevant sounds that obscured signal information in the absence of energetic masking. These informational masking effects were evident across a broad range of signal levels and were more pronounced when competing sounds fell in a particularly salient frequency range for processing vocalizations. Our results confirm informational masking is a general communication problem among humans and other animals and identify a crucial yet understudied source of selection on animal communication systems.
Beneficial and Detrimental Effects of Nonspecific Binding During DNA Hybridization
Authors: Phan Tam T. M. , Phan Tien M. , Schmit Jeremy D. 
Published: April 2022

AbstractDNA strands have to sample numerous states to find the alignment that maximizes Watson-Crick-Franklin base pairing. This process depends strongly on sequence, which affects the stability of the native duplex as well as the prevalence of non-native inter- and intra-molecular helices. We present a theory which describes DNA hybridization as a three stage process: diffusion, registry search, and zipping. We find that non-specific binding affects each of these stages in different ways. Mis-registered intermolecular binding in the registry search stage helps DNA strands sample different alignments and accelerates the hybridization rate. Non-native intramolecular structure affects all three stages by rendering portions of the molecule inert to intermolecular association, limiting mis-registered alignments to be sampled, and impeding the zipping process. Once inregister base-pairs are formed, the stability of the native structure is important to hold the molecules together long enough for non-native contacts to break.
Decision Tree Ensembles Utilizing Multivariate Splits Are Effective at Investigating Beta-Diversity in Medically Relevant 16S Amplicon Sequencing Data
Authors: Rudar Josip , Golding G. Brian , Kremer Stefan C. , Hajibabaei Mehrdad 
Published: April 2022

AbstractDeveloping an understanding of how microbial communities vary across conditions is an important analytical step. We used 16S rRNA data isolated from human stool to investigate if learned dissimilarities, such as those produced using unsupervised decision tree ensembles, can be used to improve the analysis of the composition of bacterial communities in patients suffering from Crohn’s Disease and adenomas/colorectal cancers. We also introduce a workflow capable of learning dissimilarities, projecting them into a lower dimensional space, and identifying features that impact the location of samples in the projections. For example, when used with the centered log-ratio transformation, our new workflow (TreeOrdination) could identify differences in the microbial communities of Crohn’s Disease patients and healthy controls. Further investigation of our models elucidated the global impact ASVs had on the location of samples in the projected space and how each ASV impacted individual samples in this space. Furthermore, this approach can be used to integrate patient data easily into the model and results in models that generalize well to unseen data. Models employing multivariate splits can improve the analysis of complex high-throughput sequencing datasets since they are better able to learn about the underlying structure of the dataset.Author SummaryThere is an ever-increasing level of interest in accurately modeling and understanding the role that commensal organisms play in human health and disease. We show that learned representations can be used to create informative ordinations. We also demonstrate that the application of modern model introspection algorithms can be used to investigate and quantify the impact of taxa in these ordinations and that the taxa identified by these approaches have been associated with immune-mediated inflammatory diseases and colorectal cancer.
What factors converged to create a COVID-19 hot-spot? Lessons from the South Asian community in Ontario
Authors: Anand Sonia S , Arnold Corey , Bangdiwala Shrikant , Bolotin Shelly , Bowdish Dawn , Chanchlani Rahul , de Souza Russell , Desai Dipika , Kandasamy Sujane , Khan Farah , Khan Zainab , Langlois Marc-André , Limbachia Jayneel , Lear Scott , Loeb Mark , Loh Lawrence , Manoharan Baanu , Nakka Kiran , Pelchat Martin , Punthakee Zubin , Schulze Karleen , Williams Natalie , Wahi Gita 
Published: April 2022

AbstractBackgroundSouth Asians represent the largest non-white ethnic group in Canada. The Greater Toronto Area (GTA), home to a high proportion of South Asians, emerged as a COVID-19 hot spot. Early in the pandemic, the South Asian community was identified as having risk factors for exposure and specific barriers to accessing testing and reliable health information, rendering them uniquely vulnerable to SARS-CoV-2 infection.ObjectivesTo investigate the burden of SARS-CoV-2 infection among South Asians in the GTA, and to determine which demographic characteristics were most closely aligned with seropositivity, in this cross-sectional analysis of a prospective cohort study.MethodsParticipants from the GTA were enrolled between April and July 2021. Seropositivity for anti-spike and anti-nucleocapsid antibodies was determined from dried blood spots, and age and sex standardized to the Ontario South Asian population. Demographics, risk perceptions, and sources of COVID-19 information were collected via questionnaire in a subset.ResultsAmong the 916 South Asians enrolled, mean age 41 years, the age and sex standardized seropositivity was 23.6% (95% CI: 20.8%-26.4%). Approximately one-third identified as essential workers, and 19% reported living in a multi-generational household. Over half perceived high COVID-19 risk due to their geographic location, and 36% due to their type of employment. The top three most trusted sources of COVID-related information included healthcare providers/public health, traditional media sources, and social media.ConclusionBy the third wave of the COVID-19 pandemic, approximately one-quarter of a sample of South Asians in Ontario had serologic evidence of prior SARS-CoV-2 infection. Insight into factors that render certain populations at risk can help future pandemic planning and disease control efforts.