bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small supernumerary marker chromosomes derived from human chromosome 11
Authors: Liehr Thomas , Ziegler Monika , Person Luisa , Kankel Stefanie , Padutsch Niklas , Weise Anja , Weimer Jörg Paul , Williams Heather , Ferreira Susana , Melo Joana B. , Carreira Isabel M. 
Published: December 2023

Introduction: With only 39 reported cases in the literature, carriers of a small supernumerary marker chromosome (sSMC) derived from chromosome 11 represent an extremely rare cytogenomic condition.Methods: Herein, we present a review of reported sSMC(11), add 18 previously unpublished cases, and closely review eight cases classified as ‘centromere-near partial trisomy 11’ and a further four suited cases from DECIPHER.Results and discussion: Based on these data, we deduced the borders of the pericentric regions associated with clinical symptoms into a range of 2.63 and 0.96 Mb for chromosome 11 short (p) and long (q) arms, respectively. In addition, the minimal pericentric region of chromosome 11 without triplo-sensitive genes was narrowed to positions 47.68 and 60.52 Mb (GRCh37). Furthermore, there are apparent differences in the presentation of signs and symptoms in carriers of larger sSMCs derived from chromosome 11 when the partial trisomy is derived from different chromosome arms. However, the number of informative sSMC(11) cases remains low, with overlapping presentation between p- and q-arm-imbalances. In addition, uniparental disomy (UPD) of ‘normal’ chromosome 11 needs to be considered in the evaluation of sSMC(11) carriers, as imprinting may be an influencing factor, although no such cases have been reported. Comprehensively, prenatal sSMC(11) cases remain a diagnostic and prognostic challenge.
Clinical application of single nucleotide polymorphism microarray analysis in pregnancy loss in Northwest China
Authors: Xue ShuYuan , Wang LiXia , Wei Jie , Liu YuTong , Ding GuiFeng , Dai PengGao 
Published: December 2023

Background: Spontaneous abortion is the most common complication of early pregnancy. In this study, we aim to investigate the clinical application value of genetic diagnosis using single nucleotide polymorphism (SNP) microarray analysis on the products of conception and to characterize the types of genetic abnormalities and their prevalence in pregnancy loss in Northwest China.Methods: Over 48 months, we selected 652 products of conception, which included chorionic villi, fetal tissues, germ cell samples, amniotic fluid samples, cord blood samples, and a cardiac blood sample. We analyzed the distribution of chromosomal abnormalities leading to fetal arrest or abortion using SNP array. The patients were then categorized divided into groups based on maternal age, gestational age, number of miscarriages, and maternal ethnic background. The incidences of various chromosomal abnormalities in each group were compared.Results: Of the 652 cases, 314 (48.16%) exhibited chromosomal abnormalities. These included 286 cases with numerical chromosomal abnormalities, 24 cases with copy number variation, and four cases with loss of heterozygosity. Among them, there were 203 trisomy cases, 55 monosomy cases, and 28 polyploidy cases. In the subgroup analysis, significant differences were found in the frequency of numerical chromosomal abnormalities and copy number variation between the advanced and younger maternal age group as well as between the early and late abortion groups. Furthermore, we identified significant differences in the frequency of numerical chromosomal abnormalities between the first spontaneous abortion and recurrent miscarriage groups. However, there were no significant differences in the frequency of numerical chromosomal abnormalities between the Han and Uighur groups.Conclusion: Our research highlights chromosomal abnormalities as the primary cause of spontaneous abortion, with a higher incidence in early pregnancy and among women of advanced age. The use of SNP array analysis emerges as an effective and reliable technique for chromosome analysis in aborted fetuses. This method offers a comprehensive and dependable genetic investigation into the etiology of miscarriage, establishing itself as a valuable routine selection for genetic analysis in cases of natural abortions.
DPred_3S: identifying dihydrouridine (D) modification on three species epitranscriptome based on multiple sequence-derived features
Authors: Ren Jinjin , Chen Xiaozhen , Zhang Zhengqian , Shi Haoran , Wu Shuxiang 
Published: December 2023

Introduction: Dihydrouridine (D) is a conserved modification of tRNA among all three life domains. D modification enhances the flexibility of a single nucleotide base in the spatial structure and is disease- and evolution-associated. Recent studies have also suggested the presence of dihydrouridine on mRNA.Methods: To identify D in epitranscriptome, we provided a prediction framework named “DPred_3S” based on the machine learning approach for three species D epitranscriptome, which used epitranscriptome sequencing data as training data for the first time.Results: The optimal features were evaluated by the F-score and integration of different features; our model achieved area under the receiver operating characteristic curve (AUROC) scores 0.955, 0.946, and 0.905 for Saccharomyces cerevisiae, Escherichia coli, and Schizosaccharomyces pombe, respectively. The performances of different machine learning algorithms were also compared in this study.Discussion: The high performances of our model suggest the D sites can be distinguished based on their surrounding sequence, but the lower performance of cross-species prediction may be limited by technique preferences.
New insights from integrated bioinformatics analysis: the role of circadian rhythm disruption and immune infiltration in obstructive sleep apnea disease
Authors: Zhang Xinyue , Wang Yixuan , Pan Zhou , Hu Ke 
Published: December 2023

BackgroundCircadian rhythm disruption and immune infiltration are both closely associated with the development of Obstructive sleep apnea (OSA) disease and a variety of cardiovascular and neurological complications, but their interactions with OSA disease are not clear. In this study, we used bioinformatics to investigate the roles of circadian rhythm disruption and immune microenvironments in OSA.MethodsWe analyzed differential genes and their associated functional pathways in the circadian rhythm-associated OSA dataset, then regrouped OSA samples using the differential genes and explored differences in immune cell infiltration between the two different subgroups. Meanwhile, we used two machine learning algorithms to further define circadian rhythm-related signature genes and to explore the relationship between key genes and immune cell infiltration. Finally, we searched for the transcription factors of the key differential gene JUN.ResultsWe screened 15 circadian rhythm-related differential genes in the OSA-related dataset and further defined 3 signature genes by machine learning algorithms. Immunoassays showed a significant increase in resting mast cell infiltration and a decrease in monocyte infiltration in the OSA group. The results of our animal experiments also confirmed that the expression of these 3 key genes, as well as the immune cell infiltration, showed a trend consistent with the results of the bioinformatics analysis.ConclusionsIn conclusion, this study reveals the interaction between circadian rhythm disruption and immune infiltration in OSA, providing new insights into the potential pathogenesis of OSA.
Oncolytic virotherapy in cancer treatment: challenges and optimization prospects
Authors: Chen Lingjuan , Zuo Mengsi , Zhou Qin , Wang Yang 
Published: December 2023

Oncolytic viruses (OVs) are emerging cancer therapeutics that offer a multifaceted therapeutic platform for the benefits of replicating and lysing tumor cells, being engineered to express transgenes, modulating the tumor microenvironment (TME), and having a tolerable safety profile that does not overlap with other cancer therapeutics. The mechanism of OVs combined with other antitumor agents is based on immune-mediated attack resistance and might benefit patients who fail to achieve durable responses after immune checkpoint inhibitor (ICI) treatment. In this Review, we summarize data on the OV mechanism and limitations of monotherapy, which are currently in the process of combination partner development, especially with ICIs. We discuss some of the hurdles that have limited the preclinical and clinical development of OVs. We also describe the available data and provide guidance for optimizing OVs in clinical practice, as well as a summary of approved and promising novel OVs with clinical indications.
Advancing acceptance: assessing acceptance of the ESR iGuide clinical decision support system for improved computed tomography test justification
Authors: Singer Clara , Luxenburg Osnat , Rosen Shani , Vaknin Sharona , Saban Mor 
Published: December 2023

BackgroundA clinical decision support system (CDSS), the European Society of Radiologists (ESR) iGuide, was developed to address gaps in the availability and use of effective imaging referral guidelines.AimThis study aimed to assess the appropriateness of computed tomography (CT) exams with and without ESR iGuide use, as well as the usability and acceptance of the physician systems.MethodsA retrospective single-center study was conducted in which data from 278 consecutive CT tests referred by physicians were collected in the first phase (T1), and physicians used the ESR iGuide system for imaging referrals in the second phase (T2; n = 85). The appropriateness of imaging referrals in each phase was assessed by two experts, and physicians completed the System Usability Scale.ResultsThe mean appropriateness level on a scale of 0–9 was 6.62 ± 2.69 at T1 and 7.88 ± 1.4 at T2. When using a binary variable (0–6 = non-appropriate; 7–9 = appropriate), 70.14% of cases were found appropriate at T1 and 96.47% at T2. Surgery physician specialty and post-intervention phase showed a higher likelihood of ordering an appropriate test (p = 0.0045 and p = 0.0003, respectively). However, the questionnaire results indicated low system trust and minimal clinical value, with all physicians indicating they would not recommend collegial use (100%).ConclusionThe study suggests that ESR iGuide can effectively guide the selection of appropriate imaging tests. However, physicians showed low system trust and use, indicating a need for further understanding of CDSS acceptance properties. Maximizing CDSS potential could result in crucial decision-support compliance and promotion of appropriate imaging.
Rumen and fecal microbiomes are related to diet and production traits in Bos indicus beef cattle
Authors: Conteville Liliane Costa , da Silva Juliana Virginio , Andrade Bruno Gabriel Nascimento , Cardoso Tainã Figueiredo , Bruscadin Jennifer Jessica , de Oliveira Priscila Silva Neubern , Mourão Gerson Barreto , Coutinho Luiz Lehmann , Palhares Julio Cesar Pascale , Berndt Alexandre , de Medeiros Sergio Raposo , Regitano Luciana Correia de Almeida 
Published: December 2023

BackgroundRuminants harbor a complex microbial community within their gastrointestinal tract, which plays major roles in their health and physiology. Brazil is one of the largest producers of beef in the world and more than 90% of the beef cattle herds are composed of pure and crossbred Nelore (Bos indicus). Despite its importance to the Brazilian economy and human feeding, few studies have characterized the Nelore microbiome. Therefore, using shotgun metagenomics, we investigated the impact of diet on the composition and functionality of the Nelore microbiome, and explored the associations between specific microbial taxa and their functionality with feed efficiency and methane emission.ResultsThe ruminal microbiome exhibited significantly higher microbial diversity, distinctive taxonomic profile and variations in microbial functionality compared to the fecal microbiome, highlighting the distinct contributions of the microbiomes of these environments. Animals subjected to different dietary treatments exhibited significant differences in their microbiomes’ archaeal diversity and in the abundance of 89 genera, as well as in the functions associated with the metabolism of components of each diet. Moreover, depending on the diet, feed-efficient animals and low methane emitters displayed higher microbial diversity in their fecal microbiome. Multiple genera were associated with an increase or decrease of the phenotypes. Upon analyzing the functions attributed to these taxa, we observed significant differences on the ruminal taxa associated with feed efficient and inefficient cattle. The ruminal taxa that characterized feed efficient cattle stood out for having significantly more functions related to carbohydrate metabolism, such as monosaccharides, di−/oligosaccharides and amino acids. The taxa associated with methane emission had functions associated with methanogenesis and the production of substrates that may influence methane production, such as hydrogen and formate.ConclusionOur findings highlight the significant role of diet in shaping Nelore microbiomes and how its composition and functionality may affect production traits such as feed efficiency and methane emission. These insights provide valuable support for the implementation of novel feeding and biotechnological strategies.
Linking ecological niches to bacterial community structure and assembly in polluted urban aquatic ecosystems
Authors: Sun Yuming , Ye Fei , Huang Qianhao , Du Fengfeng , Song Tao , Yuan Haiyan , Liu Xiaojing , Yao Dongrui 
Published: December 2023

IntroductionBacterial communities play crucial roles in the functioning and resilience of aquatic ecosystems, and their responses to water pollution may be assessed from ecological niches. However, our understanding of such response patterns and the underlying ecological mechanisms remains limited.MethodsIn this study, we comprehensively investigated the effects of water pollution on the bacterial structure and assembly within different ecological niches, including water, sediment, submerged plant leaf surfaces, and leaf surfaces, using a 16S high-throughput sequencing approach.ResultsEcological niches had a greater impact on bacterial community diversity than pollution, with a distinct enrichment of unique dominant phyla in different niches. This disparity in diversity extends to the bacterial responses to water pollution, with a general reduction in α-diversity observed in the niches, excluding leaf surfaces. Additionally, the distinct changes in bacterial composition in response to pollution should be correlated with their predicted functions, given the enrichment of functions related to biogeochemical cycling in plant surface niches. Moreover, our study revealed diverse interaction patterns among bacterial communities in different niches, characterized by relatively simply associations in sediments and intricate or interconnected networks in water and plant surfaces. Furthermore, stochastic processes dominated bacterial community assembly in the water column, whereas selective screening of roots and pollution events increased the impact of deterministic processes.DiscussionOverall, our study emphasizes the importance of ecological niches in shaping bacterial responses to water pollution. These findings improve our understanding of the complicated microbial response patterns to water pollution and have ecological implications for aquatic ecosystem health.
Reaction of the endogenous regulatory mechanisms to early weekday wakeups: a review of its popular explanations in light of model-based simulations
Authors: Putilov Arcady A. 
Published: December 2023

Introduction: Several widely held explanations of the mechanisms underlying the responses of endogenous sleep–wake-regulating processes to early weekday wakeups have been proposed. Here, they were briefly reviewed and validated against simulations based on the rhythmostatic version of a two-process model of sleep–wake regulation.Methods: Simulated sleep times on weekdays and weekends were compared with the times averaged over 1,048 samples with either earlier or later weekday risetimes. In total, 74 paired samples were collected before and during lockdown, and 93 paired samples were collected during early and later school start times.Results: The counterintuitive predictions of the simulations included the following: 1) only one night of ad lib sleep is sufficient to restore the endogenously determined sleep times after 1 day/5 days of larger/smaller reduction/extension of the sleep/wake phase of the circadian sleep–wake cycle; 2) sleep loss on weekdays is irrecoverable; 3) irrespective of the amount of such deadweight loss, sleep on weekends is not prolonged; and 4) the control of the circadian clocks over the sleep–wake cyclicity is not disrupted throughout the week.Discussion: The following popular explanations of the gaps between weekends and weekdays in sleep timing and duration were not supported by these simulations: 1) early weekday wakeups cause “social jetlag,” viewed as the weekend and weekday (back and forth) shifts of the sleep phase relative to the unchanged phase of the circadian clocks, and 2) early weekday wakeups cause an accumulation of “sleep debt paid back” on weekends, or, in other terms, people can “catch-up” or “compensate” sleep on weekends.
Weak nystagmus in the dark persists for months after acute unilateral vestibular loss
Authors: Chen Chih-Chung , Bery Anand K. , Chang Tzu-Pu 
Published: December 2023

BackgroundWeak nystagmus with fixation removed can be seen both in normal individuals and in recovery from a unilateral vestibular insult, thus its clinical significance is unclear in patients with dizziness. We thus sought to compare features of nystagmus at various stages following unilateral vestibular loss (UVL).MethodsWe enrolled thirty consecutive patients after acute UVL with impaired vestibulo-ocular reflex (VOR) gain. The patients were allocated into three groups according to time from onset of symptoms: acute (1–7 days), subacute (8–30 days), and chronic (&gt;30 days). Patients underwent video-oculography (with and without fixation) and video head impulse testing (vHIT) to determine VOR gain. We examined the relationships amongst SPV, VOR gain, and time from symptom onset across groups.ResultsThere were 11, 10, and 9 patients in the acute, subacute, and chronic stages of UVL, respectively. With visual fixation, only 8 patients (26.7%) demonstrated nystagmus, all from the acute group. With fixation removed, 26 patients (86.7%) exhibited spontaneous nystagmus, including 90.9%, 90%, and 77.8% of the patients from the acute, subacute, and chronic groups, respectively. Horizontal nystagmus was paralytic (i.e., fast phase contralesional) in 25 (96.7%) cases. Horizontal SPV was negatively correlated with logarithm of time from onset to examination (r = −0.48, p = 0.007) and weakly negatively correlated with ipsilesional VOR gain (r = −0.325, p = 0.08).ConclusionIn the subacute or chronic stages of UVL, paralytic nystagmus with fixation removed persisted at a low intensity. Therefore, weak nystagmus in the dark may have diagnostic value in chronic dizziness.
Association between dietary intake and risk of Parkinson’s disease: cross-sectional analysis of survey data from NHANES 2007–2016
Authors: Liu Ling , Shen Qiuyan , Bao Yi , Xu Fang , Zhang Dan , Huang Hongyan , Tu Liangdan , Xu Yanming 
Published: December 2023

BackgroundWhile dietary factors have shown an association with Parkinson’s disease (PD), the available data remains a subject of ongoing debate and controversy.AimWe sought to evaluate potential relationships between dietary consumption of nutrients and micronutrients and risk of PD in a large sample.MethodsCross-sectional data were retrospectively analyzed for 10,651 adults aged 40–80 years that had been collected in the US between 2007 and 2016 as a component of the nationwide National Health and Nutrition Examination Survey. Aspects of dietary intake were compared between those who reported having specific PD medication regimens or not when they completed the survey, and potential associations between diet and risk of PD were explored using binomial logistic regression. We employed Propensity Score Matching (PSM) to minimize the impact of potential confounding factors, thus enhancing the reliability of the results. Additionally, subgroup analysis based on gender and age was conducted to investigate these relationships.ResultsHigher dietary intake of iron was linked to greater PD risk [odds ratio (OR) 1.065, 95% confidence interval (CI) 1.019–1.114, p = 0.006], whereas risk decreased with higher intake of vitamin K (OR 0.999, 95% CI 0.998–1.000, p = 0.024) or vitamin C (OR 0.998, 95% CI 0.996–0.999, p = 0.039). Even after applying PSM, the connection between dietary iron intake and dietary vitamin C intake with PD risk remained substantial. Subgroup analysis results revealed a significant positive association between dietary intake of iron from food and the PD risk, which was evident among individuals under 60 years of age and among males.ConclusionThe intake of micronutrients can influence risk of PD, which should be verified and explored further in prospective samples with other dietary habits and ethnic backgrounds.
The effectiveness and safety of palbociclib and ribociclib in stage IV HR+/HER-2 negative breast cancer: a nationwide real world comparative retrospective cohort study
Authors: Al-Ziftawi Nour Hisham , Elazzazy Shereen , Alam Mohammed Fasihul , Shafie Asrul , Hamad Anas , Bbujassoum Salha , Mohamed Ibrahim Mohamed Izham 
Published: December 2023

IntroductionPalbociclib and ribociclib are indicated in the first-line treatment of hormonal receptor-positive HER-2 negative (HR+/HER2- negative) advanced breast cancer. Although randomized-controlled trials (RCTs) proved their clinical efficacy, there are no observational studies yet to validate the clinical findings in the real-world. Therefore, this study aimed to evaluate and compare the clinical effectiveness and safety profiles of palbociclib and ribociclib in Qatar.Materials and methodsA retrospective observational study was conducted on HR+/HER-2-negative stage-IV breast cancer patients receiving palbociclib or ribociclib in the state of Qatar. Clinical data were collected from the National Center for Cancer Care and Research (NCCCR) in Qatar using Cerner®. Primary outcomes were progression-free-survival (PFS) and overall-survival (OS) generated by Kaplan-Meier curves. Moreover, safety profiles of both two treatments were evaluated.ResultsThe data from 108 patients were included in the final analysis. There was no statistically significant difference in PFS between the palbociclib and ribociclib groups; PFS was 17.85 versus 13.55 months, respectively(p&gt; 0.05). Similarly, there was no statistically significant difference in OS between the two medications, 29.82 versus 31.72 months, respectively(p&gt;0.05). Adverse events were similar between the two groups. Neutropenia was the most common side effect in the study population accounting for 59.3% of the patients.ConclusionsTherefore, both treatments have similar efficacy and safety profiles. Further research on a larger-scale population and longer follow-up period is recommeneded.