bluuebunny/crossref_metadata_2025_split huggingface dataset:
MAGNITUDE AND DETERMINANTS OF DELAYED BREASTFEEDING INITIATION AMONG MOTHERS WHO DELIVER BY CESAREAN SECTION IN A RURAL GENERAL HOSPITAL IN EAST AFRICA
Authors: Ogah Adenike Oluwakemi , Kapasa Monica 
Published: June 2023

AbstractBackgroundThe BFHI program and timely breastfeeding initiation may be threatened by the worldwide rise in cesarean section deliveries, and this might promote prelacteal feeding. What is the current burden and determinants of delayed breastfeeding initiation among mothers, who gave birth via cesarean section?Subject and methodsThis was the baseline data of a prospective cohort study, where 529 healthy, singleton mother-newborn pairs were recruited consecutively at birth, from Gitwe district hospital in Rwanda.ResultsOverall, the burden of cesarean section delivery, delayed initiation of breastfeeding and prelacteal feeding were 38.8%, 17.0% and 6.0%, respectively. Rate of delayed breastfeeding initiation among mothers, who delivered by cesarean section was 37.6%, compared to 4.0% among those that delivered vaginally, p<0.001. Prelacteal feeds were given to 12.7% of the babies that were delivered by cesarean section, compared to 1.9% among those delivered vaginally, p<0.001. Use of probably ‘unsafe’ water sources located in the household yards was strongly linked to both cesarean section delivery (p<0.000; OR=5.71; 95%CI=2.43, 13.41) and delayed breastfeeding initiation (p<0.000; OR=44.40; 95% CI 7.97, 247.32). Mothers delivered by c-section, who were prenatally exposed to potentially harmful substances, were more likely to delay breastfeeding initiation compared to unexposed mothers (p=0.001; OR=3.14; 95% CI 1.56, 6.31). Cesarean section delivery was more likely with HIV positive mothers (p=0.010; OR=7.14; 95% CI:1.61, 33.33), teenage and entrepreneur mothers. Rate of cesarean section delivery amongst HIV positive mothers was 88.9%, compared to 36.1% among HIV negative mothers.Conclusion and RecommendationsHIV positivity and non-medical causes still drive the over-use of cesarean section for delivery in this rural community, and this impacted negatively on breastfeeding initiation, thereby promoting prelacteal feeding. The uncertain safety of the water sources and prenatal exposures to harmful social habits also need to be addressed.
SHaploseek: A sequencing-only high-resolution implementation of comprehensive preimplantation genetic testing
Authors: Backenroth Daniel , Altarescu Gheona , Zahdeh Fouad , Mann Tzvia , Murik Omer , Renbaum Paul , Segel Reeval , Zeligson Sharon , Hakam-Spector Elinor , Carmi Shai , Zeevi David A. 
Published: June 2023

AbstractPurposeWe previously developed Haploseek, a clinically-validated, variant-agnostic comprehensive preimplantation genetic testing (PGT) solution. Haploseek is based on microarray genotyping of the embryo’s parents and relatives, combined with low-pass sequencing of the embryos. Here, to increase throughput and versatility, we aimed to develop a sequencing-only implementation of Haploseek.MethodsWe developed SHaploseek, a universal PGT method to determine genome-wide haplotypes of each embryo based on low-pass (≤5x) sequencing of the parents and relative(s) along with ultra-low pass (0.2-0.4x) sequencing of the embryos. We used SHaploseek to analyze five single lymphoblast cells and 31 embryos from 14 families. We validated the genome-wide haplotype predictions against either bulk DNA, Haploseek, or, at focal genomic sites, PCR-based PGT results.ResultsSHaploseek achieved >99% concordance with bulk DNA in two families from which single cells were derived from grown-up children. In embryos from 12 PGT families, all of SHaploseek’s focal site haplotype predictions were concordant with clinical PCR-based PGT results. Genome-wide, there was >99% median concordance between Haploseek and SHaploseek’s haplotype predictions. Concordance remained high at all assayed sequencing depths ≥2x, as well as with only 1ng of parental DNA input. In subtelomeric regions, significantly more haplotype predictions were high-confidence in SHaploseek compared to Haploseek.ConclusionAs a single-platform comprehensive PGT solution with higher sensitivity in subtelomeric regions, SHaploseek constitutes a significantly improved, accurate, and cost-effective re-embodiment of Haploseek.
A Deep Learning Approach for Transgender and Gender Diverse Patient Identification in Electronic Health Records
Authors: Hua Yining , Wang Liqin , Nguyen Vi , Rieu-Werden Meghan , McDowell Alex , Bates David W. , Foer Dinah , Zhou Li 
Published: June 2023

ABSTRACTBackgroundAlthough accurate identification of gender identity in the electronic health record (EHR) is crucial for providing equitable health care, particularly for transgender and gender diverse (TGD) populations, it remains a challenging task due to incomplete gender information in structured EHR fields.ObjectiveTo develop a deep learning classifier to accurately identify patient gender identity using patient-level EHR data, including free-text notes.MethodsThis study included adult patients in a large healthcare system in Boston, MA, between 4/1/2017 to 4/1/2022. To identify relevant information from massive clinical notes and to denoise, we compiled a list of gender-related keywords through expert curation, literature review, and expansion via a fine-tuned BioWordVec model. This keyword list was used to pre-screen potential TGD individuals and create two datasets for model training, testing, and validation. Dataset I was a balanced dataset that contained clinician-confirmed TGD patients and cases without keywords. Dataset II contained cases with keywords. The performance of the deep learning model was compared to traditional machine learning and rule-based algorithms.ResultsThe final keyword list consists of 109 keywords, of which 58 (53.2%) were expanded by the BioWordVec model. Dataset I contained 3,150 patients (50% TGD) while Dataset II contained 200 patients (90% TGD). On Dataset I the deep learning model achieved a F1 score of 0.917, sensitivity of 0.854, and a precision of 0.980; and on Dataset II a F1 score of 0.969, sensitivity of 0.967, and precision of 0.972. The deep learning model significantly outperformed rule-based algorithms.ConclusionThis is the first study to show that deep learning algorithms can accurately identify gender identity using EHR data. Future work should leverage and evaluate additional diverse data sources to generate more generalizable algorithms.Graphical abstract
Brain morphometry is not associated with non-motor outcomes after deep brain stimulation in Parkinson’s disease
Authors: Loehrer Philipp Alexander , Schumacher Wibke , Jost Stefanie T. , Silverdale Monty , Petry-Schmelzer Jan Niklas , Sauerbier Anna , Gronostay Alexandra , Visser-Vandewalle Veerle , Fink Gereon R. , Evans Julian , Krause Max , Rizos Alexandra , Antonini Angelo , Ashkan Keyoumars , Martinez-Martin Pablo , Gaser Christian , Chaudhuri K. Ray , Timmermann Lars , Baldermann Carlos , Dafsari Haidar S. 
Published: June 2023

AbstractDeep brain stimulation of the subthalamic nucleus (STN-DBS) is an established therapy in advanced Parkinson’s disease (PD). Motor and non-motor outcomes, however, show considerable inter-individual variability. Morphometry-based metrics have recently received increasing attention to predict treatment effects. As evidence for the prediction of non-motor outcomes is limited, we sought to investigate the association between metrics of voxel-based morphometry and short-term non-motor outcomes following STN-DBS in this prospective open-label study. 49 PD patients underwent structural MRI and a comprehensive clinical assessment at preoperative baseline and 6-month follow-up. Voxel-based morphometry was used to assess associations between cerebral volume and non-motor outcomes corrected for multiple comparisons using a permutation-based approach. We replicated existing results associating atrophy of the superior frontal cortex with subpar motor outcomes. Non-motor outcomes, however, were not associated with morphometric features, limiting its use as a marker to inform patient selection and holistic preoperative counselling.
Enhanced Recovery After Cesarean from the Patient Perspective: A Prospective Study of the ERAC Questionnaire (ERAC-Q)
Authors: Meyer Jessica A , Alton Suzanne , Seung Hyunuk , Pahlavan Autusa , Trilling Ariel R , Coghlan Martha , Goetzinger Katherine R , Cojocaru Liviu 
Published: June 2023

ABSTRACTOBJECTIVETo evaluate the impact of an Enhanced Recovery After Cesarean (ERAC) protocol on the post-cesarean recovery experience using a validated ten-item questionnaire (ERAC-Q).METHODSThis is a prospective cohort study of patients completing ERAC quality-of-life questionnaires (ERAC-Q) during inpatient recovery after cesarean delivery (CD) between October 2019 and September 2020, before and after the implementation of our ERAC protocol. Patients with non-Pfannenstiel incision, ICU admission, massive transfusion, bowel injury, existing chronic pain disorders, acute postpartum depression, or neonatal demise were excluded. The ERAC-Q was administered on postoperative day one and day of discharge to the pre– and post-ERAC implementation cohorts, rating aspects of their recovery experience on a scale of 0 (best) to 10 (worst). The primary outcome was ERAC-Q scores. Statistical analysis was performed with SAS software.RESULTSThere were 196 and 112 patients in the pre– and post-ERAC cohorts, respectively. The post-ERAC group reported significantly lower total ERAC-Q scores compared to the pre-ERAC group, reflecting fewer adverse symptoms and greater perceived recovery on postoperative day one (1.6 [0.7, 2.8] vs. 2.7 [1.6, 4.3]) and day of discharge (0.8 [0.3, 1.5] vs. 1.4 [0.7, 2.2]) (p<0.001). ERAC-Q responses did not predict the time to achieve objective postoperative milestones. However, worse ERAC-Q pain and total scores were associated with higher inpatient opiate use.CONCLUSIONSERAC implementation positively impacts patient recovery experience. The administration of ERAC-Q can provide real-time feedback on patient-perceived recovery quality and how healthcare protocol changes may impact their experience.
Discrete projections from MCH neurons mediate anti-parkinsonian effects of acupuncture
Authors: Oh Ju-Young , Lee Hyowon , Jang Sun-Young , Kim Hyunjin , Park Geunhong , Serikov Almas , Jang Jae-Hwan , Kim Junyeop , Yang Seulkee , Sa Moonsun , Lee Sung Eun , Han Young-Eun , Hwang Tae-Yeon , Kim Hee Young , Lee Seung Eun , Oh Soo-Jin , Kim Jeongjin , Kim Jongpil , Lee C. Justin , Nam Min-Ho , Park Hi-Joon 
Published: June 2023

AbstractParkinson’s disease (PD) presents with typical motor dysfunction and non-motor symptoms, including memory loss. Although acupuncture is suggested as an alternative therapy for PD, its neuroanatomical mechanisms remain unclear. We demonstrate that acupuncture ameliorates both motor and memory deficits in PD mice through activation of melanin-concentrating hormone (MCH) neurons in the lateral hypothalamus and zona incerta (LH/ZI)—MCHLH/ZI— via nerve conduction. We identify two distinct subpopulations of MCHLH/ZIprojecting to the substantia nigra and hippocampus, each of which is responsible for controlling motor and memory function. This effect can be attributed to MCH-mediated recovery from dopaminergic neurodegeneration, reactive gliosis, and impaired hippocampal synaptic plasticity. Collectively, MCHLH/ZIconstitutes not only the neuroanatomical basis of acupuncture but also a potential cellular target for treating both motor and non-motor PD symptoms.One-Sentence SummaryAcupuncture alleviates both motor and non-motor symptoms in Parkinson’s disease by activating two distinct MCH projections.
CViewer: A Java-based statistical framework for integration of shotgun metagenomics with other omics datasets
Authors: Koci Orges , Russell Richard K. , Shaikh M. Guftar , Edwards Christine , Gerasimidis Konstantinos , Ijaz Umer Zeeshan 
Published: June 2023

AbstractWe have developed CViewer, a java-based framework to consolidate, visualize, and explore enormous amount of information recovered from shotgun sequencing experiments. This information includes and integrates all levels of gene products, mRNA, protein, metabolites, as well as their interactions in a single platform. The software provides a single platform to give statistical inference, and employs algorithms, some borrowed from numerical ecology literature to allow exploratory as well as hypothesis driven analyses. The end product is a highly interactive toolkit with multiple document interface, that makes it easier for a person without specialized knowledge to perform analysis of multiomics datasets and unravel biologically relevant hypotheses. As a proof-of-concept, we have used CViewer to explore two distinct metagenomics datasets: a dietary intervention study to understand Crohn’s disease changes during a dietary treatment to include remission, as well as a gut microbiome profile for an obesity dataset comparing subjects who suffer from obesity of different aetiologies and against controls who were lean.
Cross-reactivity of antibodies against T cell markers in the Bank vole (Myodes glareolus)
Authors: Magdalena Migalska , Kazimierz Weglarczyk , Renata Mezyk-Kopec , Katarzyna Baliga-Klimczyk , Joanna Homa 
Published: June 2023

AbstractThe bank vole is a common Cricetidae rodent that is a reservoir of several zoonotic pathogens and an emerging model in eco-immunology. Here, we add to a developing immunological toolkit for this species by testing the cross-reactivity of commercially available monoclonal antibodies (mAbs) to the bank vole lymphocyte differentiation molecules and a transcription factor. We show that a combination of mAbs against CD4, CD3, and Foxp3 allows flow cytometric distinction of the main subsets of T cells: putative helper CD4+, cytotoxic CD8+ (as CD3+CD4-) and regulatory CD4+Foxp3+. We also provide a comparative analysis of amino acid sequences of CD4, CD8αβ, CD3εγδ and Fopx3 molecules for a number of commonly studied Cricetidae rodents and discuss mAb cross-reactivity patterns reported so far in this rodent family.
METABOLIC MODELLING AS A POWERFUL TOOL TO IDENTIFY CRITICAL COMPONENTS OFPNEUMOCYSTISGROWTH MEDIUM
Authors: Nev Olga A. , Zamaraeva Elena , De Oliveira Romain , Duvenage Lucian , Abou-Jaoudé Wassim , Ouattara Djomangan Adama , Hoving Jennifer Claire , Gudelj Ivana , Brown Alistair J. P. 
Published: June 2023

ABSTRACTEstablishing suitablein vitroculture conditions for microorganisms is crucial for dissecting their biology and empowering potential applications. However, a significant number of bacterial and fungal species, includingPneumocystis jirovecii, remain unculturable, hampering research efforts.P. jiroveciiis a deadly pathogen of humans that causes life-threatening pneumonia in immunocompromised individuals and transplant patients. Despite the major impact ofPneumocystison human health, we remain ignorant about the pathobiology of this fungus. This is largely due to the fact that its experimental dissection has been constrained by the inability to culture the organismin vitro. We present a comprehensivein silicogenome-scale metabolic model ofPneumocystisgrowth and metabolism, with a view to identifying metabolic requirements and imbalances that hinder growthin vitro. We utilise recently published genome data and available information in the literature as well as bioinformatics and software tools to develop and validate the model. In addition, we employ Flux Balance Analysis and Reinforcement Learning approaches to make predictions regarding metabolic fluxes and to identify critical components of thePneumocystisgrowth medium. Our findings offer insights into the biology ofPneumocystisand provide a novel strategy to overcome the longstanding challenge of culturing this pathogenin vitro.
Enteric glial hub cells coordinate intestinal motility
Authors: Scavuzzo Marissa A. , Letai Katherine C. , Maeno-Hikichi Yuka , Wulftange William J. , Shah Isha K. , Rameshbabu Jeyashri S. , Tomar Alka , Shick H. Elizabeth , Shah Aakash K. , Xiong Ying , Cohn Erin F. , Allan Kevin C. , Tesar Paul J. 
Published: June 2023

AbstractEnteric glia are the predominant cell type in the enteric nervous system yet their identities and roles in gastrointestinal function are not well classified. Using our optimized single nucleus RNA-sequencing method, we identified distinct molecular classes of enteric glia and defined their morphological and spatial diversity. Our findings revealed a functionally specialized biosensor subtype of enteric glia that we call “hub cells.” Deletion of the mechanosensory ion channel PIEZO2 from adult enteric glial hub cells, but not other subtypes of enteric glia, led to defects in intestinal motility and gastric emptying in mice. These results provide insight into the multifaceted functions of different enteric glial cell subtypes in gut health and emphasize that therapies targeting enteric glia could advance the treatment of gastrointestinal diseases.
Intraspecific encounters can induce home-range shifts
Authors: Fagan William F. , Krishnan Ananke , Liao Qianru , Fleming Christen H. , Liao Daisy , Lamb Clayton , Patterson Brent , Wheeldon Tyler , Martinez-Garcia Ricardo , Menezes Jorge F. S. , Noonan Michael J. , Gurarie Eliezer , Calabrese Justin M. 
Published: June 2023

AbstractDirect encounters, in which two or more individuals are physically close to one another, are a topic of increasing interest as more and better movement data become available. Recent progress, including the development of statistical tools for estimating robust measures of changes in animals’ space use over time, facilitates opportunities to link direct encounters between individuals with the long-term consequences of those encounters. Working with movement data for coyotes (Canis latrans) and grizzly bears (Ursus arctos horribilis), we investigate whether close intraspecific encounters were associated with spatial shifts in the animals’ range distributions, as might be expected if one or both of the individuals involved in an encounter were seeking to reduce or avoid conflict over space. We analyze the movement data of a pair of coyotes in detail, identifying how a shift in home range location resulting from altered movement behavior was apparently a consequence of a close intraspecific encounter. With grizzly bear movement data, we approach the problem from the perspective of a set of encounter pairs within a population. We find support for the hypotheses that 1) close intraspecific encounters between bears are, on average, associated with subsequent shifts in range distributions and 2) encounters defined at finer spatial scales are followed by greater changes in space use. Our results suggest that animals can undertake long-term, large-scale spatial shifts in response to close intraspecific encounters that have the potential for conflict. These results lend support for existing theory on the evolution of territories and space use (e.g., Maynard-Smith’s bourgeois strategy regarding low-conflict coexistence). Overall, we find that analyses of movement data in a pairwise context can 1) identify distances at which individuals’ proximity to one another may alter behavior and 2) facilitate testing of population-level hypotheses concerning the potential for direct encounters to alter individuals’ space use.Open Research StatementMovement data for the coyotes and grizzly bears are posted onMovebank.orgas datasets 1614661371 and 1044288582, respectively. Statistical tools for estimating, manipulating, and comparing home ranges from movement data are implemented in the open-source R packagectmm. R scripts used to carry out specific analyses for this study are openly available on GitHub athttps://github.com/anagkrish/encounter_homerangeshift.
Sleep disruption precedes forebrain synaptic Tau burden and contributes to cognitive decline in a sex-dependent manner in the P301S Tau transgenic mouse model
Authors: Martin Shenee C. , Joyce Kathryn K. , Harper Kathryn M. , Nikolova Viktoriya D. , Cohen Todd J. , Moy Sheryl S. , Diering Graham H. 
Published: June 2023

AbstractBackgroundSleep is an essential process that supports brain health and cognitive function in part through the modification of neuronal synapses. Sleep disruption, and impaired synaptic processes, are common features in neurodegenerative diseases, including Alzheimer’s disease (AD). However, the casual role of sleep disruption in disease progression is not clear. Neurofibrillary tangles, made from hyperphosphorylated and aggregated Tau protein, form one of the major hallmark pathologies seen in AD and contribute to cognitive decline, synapse loss and neuronal death.Tau has been shown to aggregate in synapses which may impair restorative synapse processes occurring during sleep. However, it remains unclear how sleep disruption and synaptic Tau pathology interact to drive cognitive decline. It is also unclear whether the sexes show differential vulnerability to the effects of sleep loss in the context of neurodegeneration.MethodsWe used a piezoelectric home-cage monitoring system to measure sleep behavior in 3-11month-old transgenic hTau P301S Tauopathy model mice (PS19) and littermate controls of both sexes. Subcellular fractionation and Western blot was used to examine Tau pathology in mouse forebrain synapse fractions. To examine the role of sleep disruption in disease progression, mice were exposed to acute or chronic sleep disruption. The Morris water maze test was used to measure spatial learning and memory performance.ResultsPS19 mice exhibited a selective loss of sleep during the dark phase, referred to as hyperarousal, as an early symptom with an onset of 3months in females and 6months in males. At 6months, forebrain synaptic Tau burden did not correlate with sleep measures and was not affected by acute or chronic sleep disruption. Chronic sleep disruption accelerated the onset of decline of hippocampal spatial memory in PS19 males, but not females.ConclusionsDark phase hyperarousal is an early symptom in PS19 mice that precedes robust Tau aggregation. We find no evidence that sleep disruption is a direct driver of Tau pathology in the forebrain synapse. However, sleep disruption synergized with Tau pathology to accelerate the onset of cognitive decline in males. Despite the finding that hyperarousal appears earlier in females, female cognition was resilient to the effects of sleep disruption.
Successful placentation in human pregnancy is regulated by reciprocal interactions between maternal uterine NK cells and fetal placental trophoblast
Authors: Li Qian , Sharkey Andrew , Sheridan Megan , Magistrati Elisa , Arutyunyan Anna , Huhn Oisin , Sancho-Serra Carmen , Anderson Holly , McGovern Naomi , Esposito Laura , Fernando Ridma , Gardner Lucy , Vento-Tormo Roser , Turco Margherita Yayoi , Moffett Ashley 
Published: June 2023

SummaryFetal growth and development during human pregnancy depends on delivery of adequate maternal oxygen and nutrients to the fetus via the placenta. In humans, the balanced invasion of fetal placental trophoblast cells into the maternal uterine lining, where they interact with uterine natural killer cells (uNK), is thought to be critical for a successful pregnancy but exactly how this influences reproductive outcomes remains undefined. Here, we used our trophoblast organoid model and primary tissue samples to determine how uNK affect placentation. By locating potential interaction axes between primary trophoblast cells and uNK using single cell transcriptomics, andin vitromodelling of these interactions in trophoblast organoids, we identify a uNK-derived cytokine signal that promotes trophoblast differentiation by enhancing epithelial-mesenchymal transition and increasing trophoblast cells at the late stage of the invasive pathway. Moreover, it affects transcriptional programs involved in increasing blood flow, placental access to nutrients, and dampening inflammatory and adaptive immune responses, as well as gene signatures associated with disorders of pregnancy such as pre-eclampsia. Our findings shed new light on how optimal immunological interactions between maternal uNK cells and fetal trophoblast enhance reproductive success.