bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hernia surgical treatment; multi-options and paucity of statistical conformation for the preferred surgical option
Authors: Marzoog Basheer Abdullah , Vladimirovich Kostin Sergey 
Published: December 2022

AbstractBackgroundHernia is a common pathology in the globe and reported more frequently, particularly, inguinal hernia.AimsTo identify the surgery of choice for the treatment of hernias by evaluating the required postoperative hospitalization time, as no other complications have been reported according to data from Mordovian Republic hospital.Material and methodsA retrospective cohort study involved 790 patients for the period 2017-2022 treated surgically for various types of hernia; inguinal hernia, umbilical hernia, spontaneously reduced strangulated post-operative ventral hernia, incarcerated post-operative ventral hernia, and hernia of the Lina Alba. For statistical analysis, used T test, one way ANOVA test, and Pearson correlation test by using Statistica program.ResultsThe hospitalization period after Lichtenstein surgery is statistically less than Postemsky surgery (mean 6.88 days, 7.43 days, respectively, t value -2.29593, p<0.02) and laparoscopic surgery (mean 6.88 days, 8.19072 days, respectively, t value 4,206817, p<0,000031). Whereas, Postemsky surgery has shorter post-operative hospitalization period in compare to laparoscopic surgery (mean 7.43 days, 8.19072 days, respectively, t value -2.19326, p<0.02). According to the used surgical approach, the patient’s post-operative hospitalization days differs (mean days: min. days; max. days, 7.50192: 0.00; 30.00). According to Postemsky (M ± m; 7.43262, ±0.167012), according to Martynov (M ± m; 8.37500, ±0.113440), according to Lichtenstein (M ± m; 6.88153, ±0.146845), according to Mayo (M ± m; 7.51282, ±0.280156), according to Bassini (M ± m; 8.77778, ± 2.379179), laparoscopically (M ± m; 8.19072, ± 0.268434), according to Sapezhko (M ± m; 8.25000, ± 1.380074), and another type of surgery (M ± m; 11.40000, ± 2.501999). Women (mean 8.525114 days) hospitalized longer than men (mean 7.065371 days), t value 5.871044, p< 0.001. A statistically significant correlation has been found between age and post-operative hospitalization time (Pearson Rank Order Correlations r=0.215561, p <0.05).ConclusionsThe study shows that the Lichtenstein surgery is the surgery of choice in terms of hospitalization time after the surgery. Straight association between sex and age with postoperative hospitalization days.
Altitude, not potential larval habitat availability, explains pronounced variation inPlasmodium falciparuminfection prevalence in the western Kenya highlands
Authors: Oduma Colins O. , Ombok Maurice , Zhao Xingyuan , Huwe Tiffany , Ondigo Bartholomew N. , Kazura James W. , Grieco John , Achee Nicole , Liu Fang , Ochomo Eric , Koepfli Cristian 
Published: December 2022

ABSTRACTBackgroundProgress in malaria control has stalled over the recent years. Knowledge on main drivers of transmission explaining small-scale variation in prevalence can inform targeted control measures.MethodsWe collected finger-prick blood samples from 3061 individuals irrespective of clinical symptoms in 20 clusters in Busia in western Kenya and screened forPlasmodium falciparumparasites using qPCR and microscopy. Clusters spanned an altitude range of 207 meters (1077-1284 m). We mapped potential mosquito larval habitats and determined their number within 250 m of a household and distances to households using ArcMap.ResultsAcross all clusters,P. falciparumparasites were detected in 49.8% (1524/3061) of individuals by qPCR and 19.5% (596/3061) by microscopy. Across the clusters, prevalence ranged from 26% to 70% by qPCR. Three to 34 larval habitats per cluster and 0-17 habitats within a 250m radius around households were observed. Using a generalized linear mixed effect model (GLMM), a 5% decrease in the odds of getting infected per each 10m increase in altitude was observed, while the number of larval habitats and their proximity to households were not statistically significant predictors for prevalence. Kitchen located indoors, open eaves, a lower level of education of the household head, older age, and being male were significantly associated with higher prevalence.ConclusionPronounced variation in prevalence at small scales was observed and needs to be taken into account for malaria surveillance and control. Potential larval habitat frequency had no direct impact on prevalence.
SARS-CoV-2 seroprevalence and longitudinal antibody response following natural infection in pregnancy: a prospective cohort study
Authors: Drake Alison L. , Escudero Jaclyn N. , Aurelio Morgan C. , Ellington Sascha R. , Zapata Lauren B. , Galang Romeo R. , Snead Margaret C. , Yamamoto Krissy , Salerno Carol , Richardson Barbra A. , Greninger Alexander L. , Kachikis Alisa B. , Englund Janet A. , LaCourse Sylvia M. 
Published: December 2022

AbstractImportanceAntenatal care provides unique opportunities to assess SARS-CoV-2 seroprevalence and antibody response duration after natural infection detected during pregnancy; transplacental antibody transfer may inform peripartum and neonatal protection.ObjectiveEstimate seroprevalence and durability of antibodies from natural infection (anti-nucleocapsid (anti-N) IgG) among pregnant people, and evaluate transplacental transfer efficiency.DesignSeroprevalence study: cross-sectional SARS-CoV-2 antibody screening among pregnant people December 9, 2020-June 19, 2021. Cohort study: Pregnant people screened anti-N IgG+ by Abbott Architect chemiluminescent immunoassay in seroprevalence study or identified through medical records with RT-PCR+ or antigen positive results enrolled in a prospective cohort December 9, 2020-June 30, 2022 to longitudinally measure anti-N IgG responses. We collected cord blood and assessed transplacental transfer of maternally-derived anti-N antibodies.SettingThree hospitals and 14 affiliated clinics providing antenatal and delivery care, Seattle, Washington metropolitan area.ParticipantsSeroprevalence study: pregnant people were screened for SAR-CoV-2 anti-N IgG during routine care. Cohort study: Pregnant people with evidence of prior SARS-CoV-2 infection (screened anti-N IgG+ from seroprevalence study or identified with a RT-PCR+ or antigen positive result from medical records) were enrolled in a cohort study to longitudinally measure anti-N IgG responses.Exposure(s) (for observational studies)COVID-19 diagnosis, symptoms, and disease severity.Main Outcome(s) and Measure(s)Presence and durability of SARS-CoV-2 anti-N IgG, transplacental transfer of maternally-derived anti-N IgG.ResultsOf 1289 pregnant people screened in the seroprevalence study, 5% (65) tested SARS-CoV-2 anti-N IgG+, including 39 (60%) without prior RT-PCR+ or antigen positive results and 53 (82%) without symptoms. Among 89 participants enrolled in the cohort study, 73 (82%) had anti-N IgG+ results during pregnancy. Among 49 participants with delivery samples 33 (67%) were anti-N IgG negative by delivery. Of 24 remaining anti-N IgG+ at delivery with paired cord blood samples, 12 (50%) had efficient transplacental anti-N IgG antibody transfer. Median time from first anti-N IgG to below positive antibody threshold was 17 weeks and did not differ by prior RT-PCR+ or antigen positive status.Conclusions and RelevanceMaternally-derived SARS-CoV-2 antibodies to natural infection may wane before delivery. Vaccines are recommended for pregnant persons to reduce severe illness and confer protection to infants.
Agricultural paraquat dichloride use and Parkinson’s disease in California Central Valley
Authors: Paul Kimberly C , Cockburn Myles , Gong Yufan , Bronstein Jeff , Ritz Beate 
Published: December 2022

AbstractBackgroundParaquat dichloride is currently among the most widely used commercial herbicides in the United States. Exposure has been broadly linked to Parkinson’s disease (PD) through experimental and epidemiologic research. In the current study, we provide further epidemiologic assessment of ambient paraquat exposure and Parkinson’s risk in a large population-based study of PD in agricultural regions of Central California.MethodsBased on 829 PD patients and 824 community controls, we assessed associations between ambient paraquat dichloride exposure and PD. We estimated residential and workplace proximity to commercial agricultural applications in three California counties since 1974 using the CA pesticide use reporting (PUR) data and land use maps. We evaluated any, duration, and average intensity (pounds per acre per year) of exposure to paraquat in four time-windows prior to PD diagnosis or interview for controls.ResultsAmbient paraquat exposure assessed at both residence and workplace was associated with PD based on all three exposure measures, indicating that PD patients lived and worked near agricultural facilities that applied greater amounts of the herbicide than community controls. For workplace proximity to commercial applications since 1974, any exposure (yes/no, OR=1.25, 95% CI=1.00, 1.57), duration of exposure (per SD, OR=1.26, 95% CI=1.10, 1.44), and long-term average intensity of exposure (per SD, OR=1.30, 95% CI=1.10, 1.53) increased the odds of PD. Similar associations were observed for residential proximity (duration of exposure: OR=1.23 per SD, 95% CI=1.07,1.40; long-term average exposure: OR=1.22 per SD, 95% CI=1.03, 1.46). Risk estimates were comparable for men and women and the strongest odds were observed for those diagnosed ≤60 years of age.ConclusionThis study provides further evidence that paraquat dichloride exposure increases the risk of Parkinson’s disease.
Metaproteogenomic Analysis of Saliva Samples from Parkinson’s Disease Patients Across the Spectrum of Cognitive Impairment
Authors: Arıkan Muzaffer , Demir Tuğçe Kahraman , Yıldız Zeynep , Nalbantoğlu Özkan Ufuk , Korkmaz Nur Damla , Yılmaz Nesrin H. , Şen Aysu , Özcan Mutlu , Muth Thilo , Hanoğlu Lütfü , Yıldırım Süleyman 
Published: December 2022

AbstractCognitive impairment (CI) is very common in patients with Parkinson’s Disease (PD) and progressively develops on a spectrum from mild cognitive impairment (PD-MCI) to full dementia (PDD). Identification of PD patients at risk of developing cognitive decline, therefore, is unmet need in the clinic to manage the disease. Previous studies reported that oral microbiota of PD patients was altered even at early stages and poor oral hygiene is associated with dementia. However, data from single modalities often unable to explain complex chronic diseases in the brain and cannot reliably predict the risk of disease progression. Here, we performed integrative metaproteogenomic characterization of salivary microbiota and tested the hypothesis that biological molecules of saliva and saliva microbiota dynamically shift in association with the progression of cognitive decline and harbor discriminatory key signatures across the spectrum of CI in PD. We recruited a cohort of 115 participants in a multi-center study and employed multi-omics factor analysis (MOFA) to integrate amplicon sequencing and metaproteomic analysis to identify signature taxa and proteins in saliva. Our baseline analyses revealed contrasting interplay between the genusNeisseriaandLactobacillusandLigilactobacillusgenera across the spectrum of CI. The group specific signature profiles enabled us to identify candidate biomarkers including 7 bacterial genera (Neisseria, Lactobacillus, Rothia, Ligilactobacillus, Alloprevotella, TM7xandCorynebacteirum) and 4 protein groups (40S ribosomal protein SA, 40S ribosomal protein S15, pyruvate, phosphate dikinase and bactericidal permeability-increasing protein) discriminating CI stages in PD (AUC 0.74-0.86). Our study describes compositional dynamics of saliva across the spectrum of CI in PD and paves the way for developing novel, non-invasive biomarker strategies to predict the risk of CI progression in PD.
MULTIMODAL-MULTITASK-SELFSUPERVISED XDEEP-MSI: EXPLAINABLE BIAS-REJECTING MICROSATELLITE INSTABILITY DEEP LEARNING SYSTEM IN COLORECTAL CANCER
Authors: Bustos Aurelia , Payá Artemio , Torrubia Andres , Alenda Cristina 
Published: December 2022

AbstractThe prediction of microsatellite instability (MSI) in colorectal cancer (CRC) using deep learning (DL) techniques directly from hematoxylin and eosin stained slides (H&E) has been shown feasible by independent works. Nonetheless, when available, relevant information from clinical, oncological and family history could be used to further inform DL predictions. The present work analyzes the effects from leveraging multimodal inputs and multitask supervision in a previously published DL system for the prediction of MSI in CRC (xDEEP-MSI). xDEEP-MSI was a multiple bias rejecting DL system based on adversarial networks trained and validated in 1788 patients from a total of 25 participating centers from EPICOLON and HGUA projects. In the present work, xDEEP-MSI is further enriched with weakly supervised learning in multiple molecular alterations (MSI status, K-RAS and BRAF mutations and Lynch Syndrome confirmed by germline mutations), adapted to multimodal inputs with variable degree of completeness (image, age, gender, localization of CRC, revised Bethesda criteria, Amsterdam II criteria and additional oncological history) and a self-supervised multiple instance learning that integrates multiple image-tiles, to obtain patient-level predictions. The AUC, including all three selected tissues (tumor epithelium, mucin and lymphocytic regions) and 5 magnifications, increases from 0.9 ± 0.03, to 0.94 ± 0.02. The sensibility and specificity reaches 92.5% 95%CI(79.6-98.4%) and 93.4% 95%CI(90.0-95.8%) respectively. To the best of our knowledge this is the first work that jointly uses multimodal inputs, multiple instance learning and multiple molecular supervision for the prediction of MSI in CRC from H&E, demonstrating their gains in performance. Prospective validation in an external independent dataset is still required.
High Sensitivity Top-down Proteomics Captures Single Muscle Cell Heterogeneity in Large Proteoforms
Authors: Melby Jake A. , Brown Kyle A. , Gregorich Zachery R. , Roberts David S. , Chapman Emily A. , Ehlers Lauren E. , Gao Zhan , Larson Eli J. , Jin Yutong , Lopez Justin , Hartung Jared , Zhu Yanlong , Wang Daojing , Guo Wei , Diffee Gary M. , Ge Ying 
Published: December 2022

AbstractSingle-cell proteomics has emerged as a powerful method to characterize cellular phenotypic heterogeneity and the cell-specific functional networks underlying biological processes. However, significant challenges remain in single-cell proteomics for the analysis of proteoforms arising from genetic mutations, alternative splicing, and post-translational modifications. Herein, we have developed a highly sensitive functionally integrated top-down proteomics method for the comprehensive analysis of proteoforms from single cells. We applied this method to single muscle fibers (SMFs) to resolve their heterogeneous functional and proteomic properties at the single cell level. Notably, we have detected single-cell heterogeneity in large proteoforms (>200 kDa) from the SMFs. Using SMFs obtained from three functionally distinct muscles, we found fiber-to-fiber heterogeneity among the sarcomeric proteoforms which can be related to the functional heterogeneity. Importantly, we reproducibly detected multiple isoforms of myosin heavy chain (~223 kDa), a motor protein that drives muscle contraction, with high mass accuracy to enable the classification of individual fiber types. This study represents the first “single-cell” top-down proteomics analysis that captures single muscle cell heterogeneity in large proteoforms and establishes a direct relationship between sarcomeric proteoforms and muscle fiber types, highlighting the potential of top-down proteomics for uncovering the molecular underpinnings of cell-to-cell variation in complex systems.Significance StatementSingle-cell technologies are revolutionizing biology and molecular medicine by allowing direct investigation of the biological variability among individual cells. Top-down proteomics is uniquely capable of dissecting biological heterogeneity at the intact protein level. Herein, we develop a highly sensitive single-cell top-down proteomics method to reveal diverse molecular variations in large proteins (>200 kDa) among individual single muscle cells. Our results both reveal and characterize the differences in protein post-translational modifications and isoform expression possible between individual muscle cells. We further integrate functional properties with proteomics and accurately measure myosin isoforms for individual muscle fiber type classification. Our study highlights the potential of top-down proteomics for understanding how single-cell protein heterogeneity contributes to cellular functions.
nucMACC: A MNase-seq pipeline to identify structurally altered nucleosomes in the genome
Authors: Sara Wernig-Zorc , Fabian Kugler , Leo Schmutterer , Patrick Räß , Clemens Hausmann , Simon Holzinger , Gernot Längst , Uwe Schwartz 
Published: December 2022

ABSTRACTMicrococcal nuclease sequencing (MNase-seq) is the state-of-the-art method for determining chromatin structure and nucleosome positioning. Data analysis is complex due to the AT-dependent sequence bias of the endonuclease, and the requirement for high sequencing depth. Here, we present the newly developed nucleosome-based MNase accessibility (nucMACC) pipeline unveiling the regulatory chromatin landscape by measuring nucleosome accessibility and stability. nucMACC represents the first systematic, and genome-wide approach for detecting unstable (“fragile”) nucleosomes.We characterized the regulatory nucleosomal landscape inD. melanogasterandS. cerevisiae. Two functionally distinct sets of promoters were identified, one associated with an unstable nucleosome and the other being nucleosome depleted. Chromatin structure analysis shows that unstable nucleosomes present intermediate states of nucleosome remodeling, preparing inducible genes for transcriptional activation in response to stimuli or stress. The presence of unstable nucleosomes correlates with RNA polymerase II proximal pausing. The nucMACC pipeline offers unparalleled precision and depth in nucleosome research and is a valuable tool for future nucleosome studies.TeaserThe nucMACC pipeline quantifies the local and global functional alterations of chromatin structure.
Starvation sensing by mycobacterial RelA/SpoT homologue through constitutive surveillance of translation
Authors: Li Yunlong , Majumdar Soneya , Treen Ryan , Sharma Manjuli R. , Corro Jamie , Gamper Howard B. , Manjari Swati R. , Prusa Jerome , Banavali Nilesh K. , Stallings Christina L. , Hou Ya-Ming , Agrawal Rajendra K. , Ojha Anil K. 
Published: December 2022

AbstractThe stringent response, which leads to persistence of nutrient-starved mycobacteria, is induced by activation of the RelA/SpoT homologue (Rsh) upon entry of a deacylated-tRNA in a translating ribosome. However, the mechanism by which Rsh identifies such ribosomesin vivoremains unclear. Here, we show that conditions inducing ribosome hibernation result in loss of intracellular Rsh in a Clp protease-dependent manner. This loss is also observed in non-starved cells using mutations in Rsh that block its interaction with the ribosome, indicating that Rsh association with the ribosome is important for Rsh stability. The cryo-EM structure of the Rsh-bound 70S ribosome in a translation initiation complex reveals unknown interactions between the ACT domain of Rsh and components of the ribosomal L7/L12-stalk base, suggesting that the aminoacylation status of A-site tRNA is surveyed during the first cycle of elongation. Altogether, we propose a surveillance model of Rsh activation that originates from its constitutive interaction with the ribosomes entering the translation cycle.SignificanceBacteria persist under nutrient starvation by activating RelA/SpoT homologue (Rsh), which synthesizes a growth regulating alarmone, ppGpp. Rsh is activated specifically upon recognizing a translation elongation complex with deacylated tRNA at the A-site. It is however unclear how Rsh identifies such a complex in vivo. We show here that conditions inducing ribosome hibernation in mycobacteria cause loss of intracellular Rsh, implying that association with translating ribosomes is necessary for intracellular stability of Rsh. Using structural analysis of Rsh-bound 70S translation initiation complex, we propose here that mycobacterial Rsh identifies a Rsh-activating ribosomal complex by constitutively surveying the ribosome entering the translation cycle at the early elongation stage.
Yttrium-iron garnet film magnetometer for magnetic microparticles in vivo registration studies
Authors: Koshev N. , Kapralov P. , Evstigneeva S. , Lutsenko O. , Shilina P. , Zharkov M. , Pyataev N. , Darwish A. , Timin A. , Ostras M. , Radchenko I. , Sukhorukov G. , Vetoshko P. 
Published: December 2022

AbstractIn the current article, we present a new kind of magnetometer for quantitative determination of magnetic objects in biological fluids and tissues. The sensor is based on yttrium-iron garnet film with optical signal registration system. Inheriting the working principle of a fluxgate magnetometers, the sensor works at a room-temperature, its wide dynamic range allows the measurements in an unshielded environment. A small size of sensitive element combined with a short recovery time after the excitation coils are off provide us with a potentially high spatial and temporal resolution of measurements. We show the feasibility of the sensor by sensing the remanent magnetization of Magnetic Nanoparticles (MNPs) both in vitro (test tubes, dry MNPs) and in vivo (local injection of the MNPs into mice).
Ongoing rapid evolution of a post-Y region revealed by chromosome-scale genome assembly of a hexaploid monoecious persimmon (Diospyros kaki)
Authors: Horiuchi Ayano , Masuda Kanae , Shirasawa Kenta , Onoue Noriyuki , Fujita Naoko , Ushijima Koichiro , Akagi Takashi 
Published: December 2022

AbstractSex chromosomes have evolved independently in many plant lineages. They have often undergone rapid structural degeneration and extension of non-recombining regions, which is conventionally considered to be strongly associated with the expression of sexually dimorphic traits. In this study, we assembled a monoecious hexaploid persimmon (Diospyros kaki) in which the Y chromosome had lost its function in male determination. Comparative genomic analysis amongD. kakiand its dioecious relatives revealed that the non-functional Y chromosome (Ym) via silencing of the sex-determining gene,OGI, arose approximately two million years ago. Comparative analyses of the whole X and Ymchromosomes suggested that the non-functional male-specific region of the Y-chromosome (MSY), or post-MSY, retained certain conserved characteristics of the original functional MSY. Specifically, comparison of the functional MSY inD. lotusand the non-functional post-MSY inD. kakiindicated that the post-MSY had been rapidly rearranged mainly via ongoing transposable element bursts, as well as in the functional MSY. These results suggest a novel interpretation that the rapid evolution of the post-MSY (and possibly also MSYs in dioeciousDiospyrosspecies) might reflect the ancestral genomic properties of these regions, rather than the evolution of male-determining functions and/or sexually dimorphic traits.