bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soil surveillance for monitoring soil-transmitted helminth infections: method development and field testing in three countries
Authors: Manuel Malathi , Amato Heather K. , Pilotte Nils , Chieng Benard , Araka Sylvie B. , Siko Joël Edoux Eric , Harris Michael , Nadimpalli Maya , Janagaraj Venkateshprabhu , Houngbegnon Parfait , Rajendiran Rajeshkumar , Thamburaj Joel , Kaliappan Saravanakumar Puthupalayam , Sirois Allison R. , Walch Gretchen , Oswald William E. , Asbjornsdottir Kristjana H. , Galagan Sean R. , Walson Judd L. , Williams Steven A. , Luty Adrian J. F. , Njenga Sammy M. , Ibikounlé Moudachirou , Ajjampur Sitara S.R. , Pickering Amy J. 
Published: September 2023

AbstractOne-fifth of the global population is infected with soil-transmitted helminths (STH). Mass drug administration (MDA) with deworming medication is widely implemented to control morbidity associated with STH infections. However, surveillance of human infection prevalence by collecting individual stool samples is time-consuming, costly, often stigmatized, and logistically challenging. Current methods of STH detection are poorly sensitive, particularly in low-intensity and low-prevalence populations. Here, we developed a sensitive and specific molecular method for detecting STH DNA in large volumes of soil by conducting laboratory and proof of concept studies across field sites in Kenya, Benin, and India. We collected human stool (n=669) and soil (n= 478) from 322 households across the three study sites. The overall prevalence of STH in soil was 31% forAscaris lumbricoides, 3% forT. trichuris, and 24% for any hookworm species. Detection of an STH species in household soil was strongly associated with increased odds of a household member being infected with that species. Soil surveillance for STH has several benefits over stool-based surveillance, including lower cost and higher success rates for sample collection. Considering that delivery of MDA occurs at the community level, environmental surveillance using molecular methods could be a cost-effective alternate strategy for monitoring STH in these populations.SynopsisLimited data exists on the prevalence and reliability of environmental soil-transmitted helminth (STH) DNA as a marker of human infections in endemic populations. We developed a new molecular detection method for STH DNA in large-volume soil samples and field-tested it across three countries.
Association between Body Mass Index and Risk of Aortic Stenosis in Women
Authors: Kontogeorgos Silvana , Rosengren Annika , Sandström Tatiana Zverkova , Fu Michael , Lindgren Martin , Basic Carmen , Svanvik Maria-Teresia , Djekic Demir , Thunström Erik 
Published: September 2023

AbstractBackgroundOverweight and obesity are increasing globally, as are life expectancy and disorders associated with aging, including calcific aortic stenosis (AS). Studies investigating the correlation between high body mass index (BMI) and AS are contradictory and inconclusive. This study examines a potential association between BMI and early AS in women.MethodsBy linking the Swedish Medical Birth Register (MBR) and the Swedish National Patient Register (NPR), we included women between 18 and 55 years with a first childbirth from 1982 to 2020. Diagnosis of subsequent AS and comorbidities were defined according to the International Classification of Diseases (ICD) 8, 9, and 10 codes. The women were divided into eight groups based on their BMI, with BMI 20 kg/m2-<22.5 kg/m2as reference. Cox proportional hazards regression models were used to investigate the difference in the risk of being diagnosed with AS.ResultsThe mean age at inclusion among 1,722,798 women was 28 years, and the mean BMI was 24 kg/m2. Some 21% were overweight (BMI 30 kg/m2-<35 kg/m2) and 10.7% were obese (BMI≥35 kg/m2). During a median follow-up of 19.5 years, 2,513 women (0.15%) were diagnosed with AS. The age-adjusted risk of being diagnosed with AS, compared to a reference group with BMI 20 -<22.5 kg/m2, increased with higher BMI to 2.8 (95%CI 2.43-3.24) times higher in women with BMI 30 -<35 kg/m2, and to 3.67 (95%CI 2.91-4.64) times higher in those with severe obesity (BMI ≥35 kg/m2). Similar results were found after excluding AS of rheumatic and congenital etiology.ConclusionsHigher BMI correlated with a higher risk of developing AS in women, regardless of etiology, beginning with increased risk even within the upper normal range, reaching a three times higher risk in women with severe obesity.Clinical perspectiveWhat is new?This study investigates a subpopulation seldom included in valvular heart diseases studies, younger women, showing that women with overweight and obesity have approximately three times higher risk to be diagnosed with AS.Even women in the BMI group considered high-normal (BMI 22.5 -<25 kg/m2) had higher risk for AS compared those with BMI 20 -<22.5 kg/m2.What are the clinical implications?The percentage of individuals with overweight and obesity increases and in the same time, AS becomes more prevalent as the population ages. Considering that there is no medical treatment that can ameliorate AS prognosis, prevention by maintaining a low-normal or normal BMI becomes even more important.
Intimate partner violence and its correlates in middle-aged and older adults during the COVID-19 pandemic: A multi-country secondary analysis
Authors: Chang Gwendolyn , Tucker Joseph , Walker Kate , Chu Claire , Miall Naomi , Tan Rayner , Wu Dan 
Published: September 2023

AbstractBackgroundIntimate partner violence (IPV) may have been exacerbated during the COVID-19 pandemic. Middle-aged and older adults, ages 45 years or older, are at higher risk of COVID-19 mortality and social isolation. However, most studies on IPV during the pandemic do not focus on this important subpopulation. Informed by the social-ecological theory, this study examines individual, household, community, and country-level correlates of IPV among middle-aged and older adults in multiple countries using a cross-sectional online survey.MethodsData from 2867 participants aged over 45 in the International Sexual Health and Reproductive Health (I-SHARE) survey from July 2020 to February 2021 were described using univariate analysis. IPV was defined using four validated WHO measures. Individual characteristics included self-isolation and food security. At the country-level, we examined social distancing stringency. Logistic regression models with a random intercept for country were conducted to explore IPV correlates among 1730 eligible individuals from 20 countries with complete data.ResultsMost participants were heterosexual (2469/2867), cisgender (2531/2867) females (1589/2867) between the ages of 45-54 (1539/2867). 12.1% (346/2867) of participants experienced IPV during social distancing measures. After adjustment, participants who self-isolated experienced 1.4 (95% CI 1.0, 2.0, p=0.04) times the odds of IPV compared to those who had not isolated. Those who reported an increase in food insecurity compared to pre-pandemic experienced 2.2 times the odds (95% CI 1.6, 3.0, p<0.0001) of IPV compared to those who did not report increased food insecurity. People in countries with more stringent social distancing policies were less likely to experience IPV compared to people in countries with lower levels of stringency (aOR=0.6, 95% CI 0.4, 0.9, p=0.04).ConclusionsIPV was common among middle-aged and older adults during the COVID-19 pandemic. Our data suggest the need for further crisis management and social protection measures for middle-aged and older adults who have intersecting vulnerabilities to IPV to mitigate COVID-19 impact.
Wild sulphur-crested cockatoos match human activity rhythms to access food in the urban environment
Authors: Fehlmann G. , Martin J. M. , Safi K. , Aplin L. M. 
Published: September 2023

AbstractUrban areas are growing rapidly across the globe, and wild species are occupying this new environment. Despite offering potential resources, disparities in the urban matrix can lead to specific challenges, with pathways and resources fragmented in space and time. Urban-dwelling species would therefore benefit from learning when and where to exploit human derived food. Here, we investigate whether birds synchronize the exploitation of the most urbanized areas to match food-provisioning patterns, using the example of the popular hand-feeding of sulphur-crested cockatoos (Cacatua galerita) in Sydney, Australia. We monitored the provisioning behaviour of people via a large-scale citizen science program, and tested for synchrony with the spatial behaviour of eight birds equipped with GPS loggers. Our data show that sulphur-crested cockatoos exploited the urban environment, relying on the green areas of the city; importantly, they also visited buildings within more urbanized areas. Sulphur-crested cockatoos used urban space with specific time patterns particularly matching human recreational feeding routines, suggestive of time-place learning. We show that urban environments provide daily temporal foraging resources for which species adjust behaviorally. Thus, our data support the general claim that retaining green spaces in cities is essential to sustainable urban planning, and key to allow species to exploit the urban environment, particularly in areas of high human density. This study builds on the literature investigating human-animal interactions, expanding our understanding of animals’ exploitation of human behavior. Further research should include the impact of such interactions on urban wildlife’s fitness according to their cognitive and behavioral traits.
Quantifying brain connectivity signatures by means of polyconnectomic scoring
Authors: Libedinsky Ilan , Helwegen Koen , Guerrero Simón Laura , Gruber Marius , Repple Jonathan , Kircher Tilo , Dannlowski Udo , van den Heuvel Martijn P. 
Published: September 2023

AbstractA broad range of neuropsychiatric disorders are associated with alterations in macroscale brain circuitry and connectivity. Identifying consistent brain patterns underlying these disorders by means of structural and functional MRI has proven challenging, partly due to the vast number of tests required to examine the entire brain, which can lead to an increase in missed findings. In this study, we propose polyconnectomic score (PCS) as a metric designed to quantify the presence of disease-related brain connectivity signatures in connectomes. PCS summarizes evidence of brain patterns related to a phenotype across the entire landscape of brain connectivity into a subject-level score. We evaluated PCS across four brain disorders (autism spectrum disorder, schizophrenia, attention deficit hyperactivity disorder, and Alzheimer’s disease) and 14 studies encompassing ∼35,000 individuals. Our findings consistently show that patients exhibit significantly higher PCS compared to controls, with effect sizes that go beyond other single MRI metrics ([min, max]: Cohen’sd= [0.30, 0.87],AUC= [0.58, 0.73]). We further demonstrate that PCS serves as a valuable tool for stratifying individuals, for example within the psychosis continuum, distinguishing patients with schizophrenia from their first-degree relatives (d= 0.42,p= 4 x 10−3, FDR-corrected), and first-degree relatives from healthy controls (d= 0.34,p= 0.034, FDR-corrected). We also show that PCS is useful to uncover associations between brain connectivity patterns related to neuropsychiatric disorders and mental health, psychosocial factors, and body measurements.
A simple theory for finding related sequences by adding probabilities of alternative alignments
Authors: Frith Martin C. 
Published: September 2023

SummaryThe main way of analyzing genetic sequences is by finding sequence regions that are related to each other. There are many methods to do that, usually based on this idea: find an alignment of two sequence regions, which would be unlikely to exist between unrelated sequences. Unfortunately, it is hard to tell if an alignment is likely to exist by chance. Also, the precise alignment of related regions is uncertain. One alignment does not hold all evidence that they are related. We should consider alternative alignments too. This is rarely done, because we lack a simple and fast method that fits easily into practical sequence-search software. Here is described a simplest-possible change to standard sequence alignment, which sums probabilities of alternative alignments. Remarkably, this makes it easier to tell if a similarity is likely to occur by chance. This approach is better than standard alignment at finding distant relationships, at least in a few tests. It can be used in practical sequence-search software, with minimal increase in implementation difficulty or run time. It generalizes to different kinds of alignment, e.g. DNA-versus-protein with frameshifts. Thus, it can widely contribute to finding subtle relationships between sequences.
Endometrial zinc transporterSlc39a10/Zip10is indispensable for progesterone responsiveness and successful pregnancy in mice
Authors: Kawata Yui , Terakawa Jumpei , Takeshita Ayuu , Namiki Takafumi , Kageyama Atsuko , Noguchi Michiko , Murakami Hironobu , Fukada Toshiyuki , Ito Junya , Kashiwazaki Naomi 
Published: September 2023

AbstractZinc is a critical trace element that is important for various biological functions including male and female reproductive systems, but the molecular mechanisms that underlie fertility have been unclear. We show here for the first time that zinc signaling in the endometrial tissue is indispensable for successful embryo implantation in mice. We observed that a uterine-specific genetic deletion ofSlc39a10/Zip10, which encodes one of the zinc transporters to elevate the cytoplasmic level of zinc, results in severe female infertility due to failure of embryo invasion into the endometrium.Zip10mRNA is expressed in uterine tissues, especially in the decidualizing stromal cells during embryo implantation. Absence ofZip10results in the suppression of zinc ion influx in the uterine stromal cells and an attenuation of progesterone – progesterone receptor signals between the epithelium and the stroma, leading to failure of embryo invasion due to sustained epithelial integrity and subsequent embryonic loss. Our findings (i) highlight a biological relevance of ZIP10-mediated zinc homeostatic regulation in the establishment of a successful pregnancy and (ii) will help to prevent infertility in humans.
Adaptive Group Behavior of Fragile X Mice in Unfamiliar Environments
Authors: Giua Gabriele , Strauss Benjamin , Lassalle Olivier , Chavis Pascale , Manzoni Olivier J. 
Published: September 2023

AbstractFragile X Syndrome (FXS) stands out as a prominent cause of inherited intellectual disability and a prevalent disorder closely linked to autism. FXS is characterized by substantial alterations in social behavior, encompassing social withdrawal, avoidance of eye contact, heightened social anxiety, increased arousal levels, language deficits, and challenges in regulating emotions. Conventional behavioral assessments primarily focus on short-term interactions within controlled settings. In this study, we conducted a comprehensive examination of the adaptive group behavior of FXS mice over a three-day period, without introducing experimental interventions or task-based evaluations. The data unveiled intricate behavioral anomalies, with the most significant changes manifesting during the initial adaptation to unfamiliar environments. Notably, certain behaviors exhibited a gradual return to typical patterns over time. This dynamic FXS phenotype exhibited heightened activity, featuring increased exploration, amplified social interest, and an unconventional approach to social interactions characterized by a higher frequency of shorter engagements. These findings contribute to the growing understanding of social behavior in individuals with FXS and underscore the significance of comprehending their adaptive responses in various environmental contexts.
Emergence of a somatosensory tonotopic map for substrate vibration in the brainstem
Authors: Lee Kuo-Sheng , Wagner Dominica de Thomas , Sanders Mark , Huber Daniel 
Published: September 2023

ABSTRACTPerceiving substrate vibrations is a fundamental component of tactile perception. The wide frequency spectrum of vibrations is covered by integrating responses of multiple mechanoreceptors that innervate various subtypes of mechanosensitive end organs, each preferring a specific range: Merkel cells (0.5-10Hz), Meissner corpuscles (10-150Hz) and Pacinian corpuscles (150-1000Hz) in primates. As the density of different end organs greatly varies across the body, each body part potentially has a specific frequency preference. How location (somatotopy) and frequency tuning (tonotopy) are processed along the ascending neuraxis and how they converge to drive responses of individual neurons is poorly understood. In this study, we address this question by combiningin vivoperipheral electrophysiology and two-photon calcium imaging along the entire dorsal column-medial lemniscal pathway, including the dorsal root ganglia, dorsal column nuclei (DCN), the thalamus and the cortex. Surprisingly, we found that both frequency, as well as location, are organised into structured maps in the DCN. Furthermore, both maps are intimately related at the fine spatial scale with parallel map gradients that are consistent across the depth of the DCN and preserved along the ascending pathway. Additional sensory mapping experiments based on peripheral characterisation revealed that the tonotopic map only partially reflects the distribution of end organs in the skin and deep tissue. Instead, we show that the emergence of the finescale tonotopy is probably due to the selective dendritic sampling from axonal afferents, right at the first synaptic relay. Taken together, we conclude DCN neural circuits are key to the emergence of these two fine-scale topological organisations in early somatosensory pathways. The underlying computational principle is intriguingly similar to the integration of multiple functional maps along the ascending visual pathways, suggesting a universal law governing the optimization of sensory systems.
An amphioxus neurula stage cell atlas supports a complex scenario for the emergence of vertebrate head mesoderm
Authors: Grau-Bové Xavier , Subirana Lucie , Meister Lydvina , Soubigou Anaël , Neto Ana , Elek Anamaria , Fornas Oscar , Gomez-Skarmeta Jose Luis , Tena Juan J. , Irimia Manuel , Bertrand Stéphanie , Sebé-Pedrós Arnau , Escriva Hector 
Published: September 2023

AbstractThe emergence of new structures can often be linked to the evolution of novel cell types that follows the rewiring of developmental gene regulatory subnetworks. Vertebrates are characterized by a complex body plan compared to the other chordate clades and the question remains of whether and how the emergence of vertebrate morphological innovations can be related to the appearance of new embryonic cell populations. We already proposed, by studying mesoderm development in the cephalochordate amphioxus, a scenario for the evolution of the vertebrate head mesoderm. To further test this scenario at the cell population level, we used scRNA-seq to construct a cell atlas of the amphioxus neurula, stage at which the main mesodermal compartments are specified. Our data allowed us to confirm the presence of a prechordal-plate like territory in amphioxus, and shows that cell populations of the anteriormost somites and of the ventral part of the somites present a transcriptomic profile supporting the homology with vertebrate cranial/pharyngeal and lateral plate mesoderm. Finally, our work provides evidence that the appearance of the specific mesodermal structures of the vertebrate head was associated to both segregation of pre-existing cell populations, and co-option of new genes for the control of myogenesis.
A multiplexed, single-cell sequencing screen identifies compounds that increase neurogenic reprogramming of murine Muller glia
Authors: Tresenrider Amy , Hooper Marcus , Todd Levi , Kierney Faith , Blasdel Nicolai , Trapnell Cole , Reh Thomas A. 
Published: September 2023

AbstractRetinal degeneration in mammals causes permanent loss of vision, due to an inability to regenerate naturally. Some non-mammalian vertebrates show robust regeneration, via Muller glia (MG). We have recently made significant progress in stimulating adult mouse MG to regenerate functional neurons by transgenic expression of the proneural transcription factor Ascl1. While these results showed that MG can serve as an endogenous source of neuronal replacement, the efficacy of this process is limited. With the goal of improving this in mammals, we designed a small molecule screen using sci-Plex, a method to multiplex up to thousands of single nucleus RNA-seq conditions into a single experiment. We used this technology to screen a library of 92 compounds, identified, and validated two that promote neurogenesisin vivo. Our results demonstrate that high-throughput single-cell molecular profiling can substantially improve the discovery process for molecules and pathways that can stimulate neural regeneration and further demonstrate the potential for this approach to restore vision in patients with retinal disease.
Differential Patterns of Associations within Audiovisual Integration Networks in Children with ADHD
Authors: Zamanzadeh Mohammad , Pourhedayat Abbas , Bakouie Fatemeh , Hadaeghi Fatemeh 
Published: September 2023

AbstractAttention deficit hyperactivity disorder (ADHD) is a neurodevelopmental condition characterized by symptoms of inattention and impulsivity and has been linked to disruptions in functional brain connectivity and structural alterations in large-scale brain networks. While anomalies in sensory pathways have also been implicated in the pathogenesis of ADHD, exploration of sensory integration regions remains limited. In this study, we adopted an exploratory approach to investigate the connectivity profile of auditory-visual integration networks (AVIN) in children with ADHD and neurotypical controls, utilizing the ADHD-200 rs-fMRI dataset. In addition to network-based statistics (NBS) analysis, we expanded our exploration by extracting a diverse range of graph theoretical features. These features served as the foundation for our application of machine learning (ML) techniques, aiming to discern distinguishing patterns between the control group and children with ADHD. Given the significant class imbalance in the dataset, ensemble learning models like balanced random forest (BRF), XGBoost, and EasyEnsemble classifier (EEC) were employed, designed to cope with unbalanced class observations. Our findings revealed significant AVIN differences between ADHD individuals and neurotypical controls, enabling automated diagnosis with moderate accuracy. Notably, the XGBoost model demonstrated balanced sensitivity and specificity metrics, critical for diagnostic applications, providing valuable insights for potential clinical use.These findings offer further insights into ADHD’s neural underpinnings and high-light the potential diagnostic utility of AVIN measures, but the exploratory nature of the study underscores the need for future research to confirm and refine these findings with specific hypotheses and rigorous statistical controls.