bluuebunny/crossref_metadata_2025_split huggingface dataset:
The association between short-term exposure to nitrogen dioxide and hospital admission for schizophrenia: A systematic review and meta-analysis
Authors: Xu Jiating , Lan Zhiyong , Xu Penghao , Zhang Zhihua 
Published: September 2023

Background:
Ambient air pollution has been identified as a primary risk factor for mental disorders. In recent years, the relationship between exposure to ambient nitrogen dioxide (NO2) and the risk of hospital admissions (HAs) for schizophrenia has garnered increasing scientific interest, but evidence from epidemiological studies has been inconsistent. Therefore, a systematic review and meta-analysis were conducted to comprehensively identify potential correlations.

Methods:
A literature search in 3 international databases was conducted before December 31, 2022. Relative risk (RR) and corresponding 95% confidence intervals (CI) were calculated to evaluate the strength of the associations. Summary effect sizes were calculated using a random-effects model due to the expected heterogeneity (I
2 over 50%).

Results:
A total of ten eligible studies were included in the meta-analysis, including 1,412,860 participants. The pooled analysis found that an increased risk of HAs for schizophrenia was associated with exposure to each increase of 10 μg/m3 in NO2 (RR = 1.029, 95% CI = 1.016–1.041, P < .001). However, the heterogeneity was high for the summary estimates, reducing the credibility of the evidence. In 2-pollutant models, results for NO2 increased by 0.3%, 0.2% and 2.3%, respectively, after adjusting for PM2.5, PM10 and SO2.

Conclusions:
This study provides evidence that NO2 exposure significantly increases the risk of hospital admission for schizophrenia. Future studies are required to clarify the potential biological mechanism between schizophrenia and NO2 exposure to provide a more definitive result.
Lennox-Gastaut syndrome characterized by super-refractory status epilepticus treated with high-dose anesthetics: A case report
Authors: Yang Xiaoqian , Xu Guangjun , Chong Zonglei , Liang Yangyang , Du Jingwei , Zhao Lin , Chen Wei 
Published: September 2023

Rationale:
Super-refractory status epilepticus is a serious illness with high morbidity and mortality, which is defined as an SE that continues or recurs 24 hours or more after the onset of anesthesia. Anesthetic agents can be either pro-convulsant or anticonvulsant or both.

Patient concerns:
Epilepsy occurred at the age of 3 years. At the age of 4 years, generalized tonic-clonic seizure occurred for the first time. The patient was hospitalized at the age of 27 and 28 years for treating status epilepticus. At the age of 33 years, antiepileptic drugs were stopped due to poor appetite. In an early morning, the patient was found delirious with reduced speech.

Diagnosis:
Occasionally, the patient blinked his eyelids, or deflected his eyeballs to 1 side. When propofol was lowered to 10 mL/H, the epileptic wave reduced obviously. Afterwards, the patient opened his eyes autonomously and his consciousness gradually recovered. The patient could answer questions, and the limbs had voluntary movements. The patient breathing also gradually recovered, and his urine gradually returned to pale yellow from green. After anesthetic was stopped for 10 days, the patient lost his consciousness again. The patient eyes turned upward frequently, which was relieved in 1 to 2 seconds with an attack once every 2 to 5 minutes.

Interventions:
Clonazepam was gradually reduced to 2 mg qn, and the patient gradually woke up during this process. The patient was also treated with levetiracetam 1.5 g bid, oxcarbazepine 0.6 g bid, topiramate 50 mg bid and valproate 0.4 g tid.

Outcomes:
After 1 month follow-up, status epilepticus did not appear again.

Lessons:
Propofol aggravated the tonic seizures. As tonic seizures occur during natural sleep and after sleep induced by various narcotic drugs, the decrease of consciousness level induced by excessive sedation of narcotic drugs has been suggested as the reason for poor seizure control.
Global trends and future prospects of COVID-19 and physical activity: Bibliometric analysis
Authors: Toktaş Neşe , Köse Elif , Lapa Tennur-Yerlisu , Kaas Evren-Tercan , Serdar Yücel Ali , Derman Süleyman 
Published: September 2023

Background:
Containment measures implemented during the COVID-19 pandemic have led to drastic changes in daily life and effects on health behaviors such as decrease in physical activity (PA) levels. This study aims to present a general framework to researchers on COVID-19 and PA research in relation with changes in studies within years, current trend topics, gaps in the research field and possible future trends.

Methods:
A total of 1819 articles indexed in the WoS core collection database were analyzed according to publication year, citation, country and institution collaborations, coword, co-citation networks, concept–topic trends and topic clusters using bibliometric analysis.

Results:
The most productive country was the USA(n = 335), and the most productive institution was University of London in UK (n = 38). The most cited publication was the study by Ammar et al, (2020) (n = 188). In 2020, the most popular topics were PA and health meanwhile in 2021 behavior, lifestyle, social media and in 2022 habits, long COVID, sleep quality topics were in the foreground. Studies in 2023 focus on how COVID-19 affects PA habits and the associations between COVID-19-based anxiety and sleep patterns. These studies focused especially on effects of sport participation on life quality, diet, depression, mental health on young athletes, children, adolescent persons, older adult groups.

Conclusions:
An important gap in the study area is research on effect of changing lifestyle due to pandemic on individuals and the society during the Post COVID-19 period. If benefits of PA will not be limited to only physical benefits and psychological emotional, cognitive and social benefits are also taken into consideration, it is important that researchers conduct long-term and widescale observations.
Efficacy of autogenous tooth block for lateral ridge augmentation compared with autogenous bone block: A systematic review and meta-analysis
Authors: Guan Delin , Zhao Ruimin , Guo Yan , Li Jianxue , Ma Na , Gong Jiaming 
Published: September 2023

Background:
Autogenous tooth block (ATB) has been used as an alternative material for bone regeneration, but its efficacy compared with autogenous bone block (ABB) remains uncertain. The aim of this systematic review was to investigate and compare the clinical and histological performance of ATB and ABB grafts in lateral alveolar ridge augmentation (LARA).

Methods:
Electronic retrieval of MEDLINE, Embase, Cochrane Library (CENTRAL), Scopus, Web of Science, China national knowledge infrastructure, Wanfang data, SinoMed, and manual searching until July 2023 were used to identify controlled clinical trials employing ATB grafts in LARA. The identified reports included at least one of the following outcome variables: ridge width gain, graft resorption, postoperative complications, histology, and histomorphometry. Weighted or mean differences (MD), relative risk, and corresponding 95% confidence intervals (CI) were calculated. Descriptive analysis was applied to the qualitative statistics. The protocol followed the preferred reporting items for systematic reviews and meta-analyses statement and was prospectively registered in PROSPERO (CRD42023399611).

Results:
Four controlled clinical trials with 77 participants each using ATB and ABB grafts were included. Meta-analysis indicated that ATB grafts resulted in greater bone width (MD = 1.31, 95% CI [0.92, 1.71], P < .00001) and less graft resorption (MD = −0.71, 95% CI [−1.22, −0.21], P = .005) than ABB grafts on LARA. There was no statistical difference in postoperative complications between ATB and ABB grafts (relative risk = 0.81, 95% CI [0.32, 2.04], P = .66). Furthermore, the ATB grafts exhibited positive replacement resorption with alveolar bone for favorable signs of new bone activity on histology and histomorphometry.

Conclusion:
Within the limitations of this study, ATB grafts could serve as an alternative material for ABB to support LARA. Further research with a longer follow-up period is required to verify these findings.
Identification of differential immune cells and related diagnostic genes in patients with diabetic retinopathy
Authors: Yuan LinHui , Zhang LiJun , Liu Xin , Li Sheng , Zou JiXin 
Published: September 2023

Background:
Diabetic retinopathy (DR) is a frequent microvascular abnormality associated with diabetes mellitus. The loss of retinal immunity is an important underlying mechanism of the DR pathogenesis, including the change in retinal immunosuppressive characteristics and the blood-retinal barrier disturbances. Therefore, this investigation screens immune-associated biomarkers in the retina of DR patients.

Methods:
In this investigation, the differential expression genes (DEGs) were acquired from Gene Expression Omnibus data GSE102485. The relative expression of 22 immune cell types in each sample was calculated by CIBERSORT analysis based on gene expression profile. The core module closely associated with immune infiltration was also screened by weighted gene co-expression network analysis (WGCNA). The overlapping DEGs and module genes were the differentially expressed immune-related genes (DEIRGs). With the help of the genes/proteins (STRING) database and MCODE plug-in, the protein-protein interaction (PPI) network hub genes were screened. Furthermore, the miRNA—hub genes and transcription factor (TF)—hub gene regulatory network were used to explain the possible signal pathways in DR. The hub genes verification was carried out by Polymerase Chain Reaction. Lastly, select CSF1R and its related pathway factor p-ERK1/2 to verify their expression in RF/6A under normal and high glucose environments.

Results:
A total of 3583 principle DEGs, that enriched immune-related GO terms and infection-related pathways were identified. CIBERSORT analysis showed that naive B cells, M2 macrophages, eosinophils, and neutrophil infiltration were significantly different. After intersecting 3583 DEGs, 168 DEIRGs and 181 module genes were identified. Furthermore, 15 hub genes, TYROBP, FCGR3A, CD163, FCGR2A, PTPRC, TLR2, CD14, VSIG4, HCK, CSF1R, LILRB2, ITGAM, CTSS, CD86, and LY86, were identified via PPI network. The identified hub genes were up-regulated in DR and showed a high DR diagnostic value. Regulatory networks of the miRNA- and TF-hub genes can help understand the etiology of disease at the genetic level and optimize treatment strategy. CD14, VSIG4, HCK, and CSF1R were verified to be highly expressed in the vitreous of patients with DR. n RF/6A, CSF1R, and p-ERK1/2 were significantly overexpressed under high glucose conditions, with a statistically significant difference.

Conclusion:
This investigation identified 15 genes (TYROBP, FCGR3A, CD163, FCGR2A, PTPRC, TLR2, CD14, VSIG4, HCK, CSF1R, LILRB2, ITGAM, CTSS, CD86, and LY86) as hub DR genes, which may serve as a new potential point for the diagnosis and treatment of DR. CSF1R/p-ERK1/2 signaling may promotes the development of retinal neovascularization.
Immunogenicity of tetanus, diphtheria and acellular pertussis vaccination among pregnant women living with and without HIV
Authors: Nunes Marta C. , Tamblyn Amy , Jose Lisa , Ntsimane Mathapelo , Lerotholi Ntoetse , Machimana Charmaine , Taylor Ashleigh , Laher Farzanah , Madhi Shabir A. 
Published: September 2023

Objective:
Vaccination during pregnancy with tetanus–diphtheria–acellular pertussis (Tdap) vaccine is recommended to protect the young infants against pertussis. There is a paucity of data on immune responses to Tdap in pregnant women with HIV (PWWH), and its impact on the protection of their infants has not been described.

Methods:
In an open label phase IV clinical trial in South Africa, we evaluated the immunogenicity and safety of Tdap in PWWH compared with HIV-uninfected women. Antigen-specific immunoglobulin G (IgG) to pertussis toxoid, filamentous haemagglutinin, pertactin, fimbriae, diphtheria and tetanus were measured by electrochemiluminescence-based multiplex assay.

Results:
Overall, 91 PWWH and 136 HIV-uninfected pregnant women were enrolled. All PWWH were on antiretroviral treatment and 94.5% had HIV viral loads <40 copies per millilitre. Antibody levels prevaccination were lower among PWWH compared with HIV-uninfected women for all antigens. At 1 month postvaccination PWWH compared with HIV-uninfected women had lower fold-increase and antibody concentrations for all epitopes. Also, a lower proportion of PWWH achieved ≥4-fold increase from pre to postvaccination for pertussis toxoid and pertactin, or diphtheria IgG levels ≥0.1 IU/ml and ≥1 IU/ml postvaccination. Adverse events postvaccination were similar in PWWH and HIV-uninfected.

Conclusion:
Tdap vaccination was safe and immunogenic. PWHW had, however, attenuated humoral immune responses, which could affect the effectiveness of protecting their infants against pertussis compared with those born to women without HIV.
ClinicalTrials.gov identifier: NCT05264662
Mapping the anatomical and transcriptional landscape of early human fetal ovary development
Authors: McGlacken-Byrne Sinead M , del Valle Ignacio , Xenakis Theodoros , Simcock Ian C , Suntharalingham Jenifer P , Buonocore Federica , Crespo Berta , Moreno Nadjeda , Liptrot Danielle , Niola Paola , Brooks Tony , Conway Gerard S , Dattani Mehul T , Arthurs Owen J , Solanky Nita , Achermann John C 
Published: September 2023

AbstractThe complex genetic mechanisms underlying human ovary development can give rise to clinical phenotypes if disrupted, such as Primary Ovarian Insufficiency and Differences of Sex Development. Through a clinically-focused lens, we combine single-nuclei RNA sequencing, bulk RNA sequencing, and micro-focus computed tomography to elucidate the anatomy and transcriptional landscape of the human fetal ovary across key developmental timepoints (Carnegie Stage 22 until 20 weeks post conception). We show the marked growth and distinct morphological changes within the fetal ovary at the critical timepoint of germ cell expansion, and demonstrate that the fetal ovary becomes more transcriptomically distinct from the testis with age. We describe novel ovary developmental pathways, relating to neuroendocrine signalling, energy homeostasis, mitochondrial networks, piRNA processes, and inflammasome regulation. We define transcriptional regulators and candidate genes for meiosis within the developing ovary. Together, this work advances our fundamental understanding of human ovary development and clinical ovarian insufficiency phenotypes.
A simple method to genetically differentiate invasive F1Typhahybrids (T. ×glauca) and advanced-generation/backcrossed hybrids from parent species (T. latifoliaandT. angustifolia) in eastern Canada and northeastern USA
Authors: Chambers Avery , Chambers Braidy , Bhargava Deven , Aleman Alberto , Dorken Marcel , Freeland Joanna 
Published: September 2023

AbstractA widespreadTypha(cattail) hybrid zone in southeastern Canada and northeastern USA comprisesT. latifolia, T. angustifolia, and their hybridT. ×glauca. In this region the hybrid is considered invasive because of its detrimental impacts on wetlands and biodiversity. Researchers and managers are increasingly interested in tracking and controlling the spread of the invasive hybrid, but this can be hampered by challenges in differentiating taxa: while the parent species and F1 hybrids can often be identified from morphological characteristics, advanced-generation and backcrossed hybrids can be common, and these have obscured morphological distinctions among taxa. Here we present five species-specific genetic markers that differentiateT. latifolia, T. angustifolia, F1hybrids, and advanced-generation/backcrossed hybrids. Unlike the pre-existing species-specific microsatellite markers, these markers require only PCR or PCR followed by a restriction enzyme digest, and can be visualized on an agarose gel. As a result, they require less specialized equipment than existing species-specific markers, and should therefore be useful for a larger group of practitioners. Future use of these markers could include monitoring range expansions, assessing the outcomes of restoration programs, and avoiding the unnecessary elimination of nativeTypha.
SCancerRNA: Expression at the Single Cell Level and Interaction Resource of Non-coding RNA Biomarkers for Cancers
Authors: Guo Hongzhe , Zhang Liyuan , Cui Xinran , Cheng Liang , Zhao Tianyi , Wang Yadong 
Published: September 2023

AbstractNon-coding RNAs (ncRNAs) participate in multiple biological processes associated with cancer as tumor suppressors or oncogenic drivers. Due to their high stability in plasma, urine, and many other fluids, ncRNAs have the potential to serve as key biomarkers for early diagnosis and screening of cancers. During cancer progression, tumor heterogeneity plays a crucial role, and it is particularly important to understand the gene expression patterns of individual cells. With the development of single-cell RNA sequencing (scRNA-seq) technologies, uncovering gene expression in different cell types for human cancers has become feasible by profiling transcriptomes at the cellular level. However, a well-organized and comprehensive online resource that provides access to the expression of genes corresponding to ncRNA biomarkers in different cell types at the single cell level is not available yet. Therefore, we developed the SCancerRNA database to summarize experimentally supported data on long ncRNA (lncRNA), microRNA (miRNA), piwi-interacting RNA (piRNA), small nucleolar RNA (snoRNA), and circular RNA (circRNA) biomarkers, as well as data on their differential expression at the cellular level. Furthermore, we collected biological functions and clinical applications of biomarkers to facilitate the application of ncRNA biomarkers to cancer diagnosis, as well as monitoring of progression and targeted therapies. SCancerRNA also allows users to explore interaction networks of different types of ncRNAs, and build computational models in the future. SCancerRNA is freely accessible athttp://www.scancerrna.com/BioMarker.
Deep Variational Autoencoders for Population Genetics
Authors: Geleta Margarita , Montserrat Daniel Mas , Giro-i-Nieto Xavier , Ioannidis Alexander G. 
Published: September 2023

AbstractMotivationModern biobanks provide numerous high-resolution genomic sequences of diverse populations. These datasets enable a better understanding of genotype-phenotype interactions with genome-wide association studies (GWAS) and power a new personalized precision medicine with polygenic risk scores (PRS). In order to account for diverse and admixed populations, new algorithmic tools are needed in order to properly capture the genetic composition of populations. Here we explore deep learning techniques, namely variational autoencoders (VAEs), to process genomic data from a population perspective. We hope this work will encourage the adoption of deep neural networks in the population genetics community.ResultsIn this paper, we show the power of VAEs for a variety of tasks relating to the interpretation, classification, simulation, and compression of genomic data with several worldwide whole genome datasets from both humans and canids and evaluate the performance of the proposed applications with and without ancestry conditioning. The unsupervised setting of autoencoders allows for the detection and learning of granular population structure and inferring of informative latent factors. The learned latent spaces of VAEs are able to capture and represent differentiated Gaussian-like clusters of samples with similar genetic composition on a fine-scale from single nucleotide polymorphisms (SNPs), enabling applications in dimensionality reduction, data simulation, and imputation. These individual genotype sequences can then be decomposed into latent representations and reconstruction errors (residuals) which provide a sparse representation useful for lossless compression. We show that different population groups have differentiated compression ratios and classification accuracies. Additionally, we analyze the entropy of the SNP data, its effect on compression across populations, its relation to historical migrations, and we show how to introduce autoencoders into existing compression pipelines.
Structure-based humanization of a therapeutic antibody for Multiple Myeloma
Authors: Marino Stephen F. , Daumke Oliver 
Published: September 2023

AbstractThe optimal efficacy of xenogeneically generated proteins intended for application in humans requires that their own antigenicity be minimized. This necessary adaptation of antibodies to a humanized version poses challenges since modifications even distant from the binding sites can greatly influence antigen recognition and this is the primary feature that must be maintained during all modifications. Current strategies often rely on grafting and/or randomization/selection to arrive at a humanized variant retaining the binding properties of the original molecule. However, in terms of speed and efficiency, rationally directed approaches can be superior, provided the requisite structural information is available. We present here a humanization procedure based on the high-resolution X-ray structure of a chimeric IgG against a marker for Multiple Myeloma. Based onin silicomodelling of humanizing amino acid substitutions identified from sequence alignments, we devised a straightforward cloning procedure to rapidly evaluate the proposed sequence changes. Careful inspection of the structure allowed identification of a potentially problematic amino acid change that indeed disrupted antigen binding. Subsequent optimization of the antigen binding loop sequences resulted in substantial recovery of binding affinity lost in the completely humanized antibody. X-ray structures of the humanized and optimized variants demonstrate that the antigen binding mode is preserved, with surprisingly few direct contacts to antibody atoms. These results underline the importance of structural information for the efficient optimization of protein therapeutics.
skDER: microbial genome dereplication approaches for comparative and metagenomic applications
Authors: Salamzade Rauf , Kalan Lindsay R. 
Published: September 2023

AbstractskDER (https://github.com/raufs/skDER) combines recent advances to efficiently estimate average nucleotide identity (ANI) between thousands of microbial genomes by skani1with two low-memory methods for genomic dereplication. The first method implements a dynamic algorithm to determine a concise set of representative genomes. This approach is well-suited for selecting reference genomes to align metagenomic reads onto for tracking strain presence across related microbiome samples. This is because fewer representative genomes should alleviate the concern that reads belonging to the same strain get falsely partitioned across closely related genomes. The other method, which uses a greedy approach, is better suited for use in comparative genomics, where users might be overwhelmed with the high number of genomes available for certain taxa and aim to reduce redundancy and, therefore, computational requirements for downstream analytics. This method selects a larger number of representative genomes to comprehensively sample the pangenome space for the taxon of interest. To further aid usage for comparative genomics studies, skDER also features an option to automatically download genomes classified as a particular species or genus in the Genome Taxonomy Database2–4and we provide precomputed representative genomes for commonly studied bacterial taxa5.