bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlations between microbiota-derived metabolites and cervical precancerous lesions in women with HPV
Authors: Shen Su , Zhao Shixian , Shan Jinjun , Ren Qingling 
Published: July 2023

Abstract
High-risk human papillomavirus (HR-HPV) causes cervical squamous intraepithelial lesions and cervical cancer; however, only a small group of people infected with HR-HPV will develop cervical precancerous lesions or cervical cancer. Current studies have shown that an imbalance in the cervicovaginal flora may be one of the factors for persistent HR-HPV infection. Cervicovaginal secretions are easily accessible and may be advantageous tools for diagnosing risks for cervical cancer. Thus, in this pilot study we collected 156 cervicovaginal secretions of women with HPV infection with precancerous cervical lesions to determine whether microflora-derived metabolites present in the secretion can be used for assessing the risk of cervical cancer in patients. We performed 16S rRNA sequencing and metabolomic analyses to identify changes in the cervicovaginal flora and its metabolites in patients with HPV infection with different grades of cervical lesions. We detected 164 common known metabolites in the three groups of samples. There are significant differences in the metabolic patterns of cervical lesion groups with different degrees, and multiple metabolites are significantly related to the vaginal flora. Among them, the content of metabolites such as taurine, guanine, and uric acid are significantly different in patients with persistent HR-HPV infection with different degrees of cervical lesions. Taurine is positively correlated with Weissella, and negatively correlated with Corynebacterium. Related. Which may involve 7 related metabolic pathways. Metabolites such as taurine, guanine, and uric acid are closely related to the activation of the human immune system. Cervical vaginal flora can regulate the synthesis and decomposition of amino acids, purines, and uric acid, and may play a major role in activating inflammation and the immune system. These metabolisms It is worthy of further research to assess the risk of HR-HPV infection progressing to cervical cancer.
The clinical characteristics of non-cystic fibrosis bronchiectasis patients with positive serum tumor markers: a retrospective study
Authors: Wang Xiaoyue , Wang Juan , He Siqi , Li Jing , Chen Xiaoting , Ma Tianyuan , Liu Lu , Zhang Lei , Bu Xiao-ning 
Published: July 2023

Abstract
Background
Serum tumor markers (STM), extensively used for the diagnosis, monitoring and prognostic assessment of tumors, can be increased in some non-malignant lung diseases. To date, there is a paucity of studies regarding the clinical characteristics of non-cystic fibrosis bronchiectasis patients with positive STMs.
Objective
To investigate the clinical characteristics and risk factors of bronchiectasis with one and multiple positive STMs.
Methods
The clinical data of 377 bronchiectasis patients was retrospectively collected from January 2017 to December 2019 from Beijing Chaoyang Hospital. Patients were divided into STM positive and STM negative group. According to the number of the positive STMs, the STM positive group was further subdivided into the single STM positive group and the ≥ 2 STMs positive group. The clinical characteristics are described and compared separately and the multivariate logistic regression analysis model was used to investigate the risk factors regarding the positive STMs.
Results
Patients in the STM positive group were older (P = 0.005), had a longer disease duration (P = 0.026), higher mMRC scores (P = 0.019) and developed higher fever (P = 0.027). Additionally, patients with positive STMs also had lower Albumin/Globulin Ratio (A/G), prealbumin (PAB) (P = 0.016, P = 0.043, respectively) and higher CRP, ESR and Fbg (P = 0.001, P = 0.002 and P < 0.001, respectively). ESR (OR 1.824, 95%CI 1.061–3.137; P = 0.030) and the number of affected lobes (OR 1.388, 95%CI 1.184–1.627; P < 0.001) were independently associated with one and two or more positive STMs in bronchiectasis patients.
Conclusion
The positive STM is associated with a higher inflammation status and severer radiologic manifestations in bronchiectasis patients.
Towards establishing a correlate of protection against shigellosis: assessing immunological endpoints across immune responses to the Shigella sonnei 1790GAHB GMMA investigational vaccine
Authors: Nakakana Usman , Conti Valentino , Rossi Omar , Clarkson Kirsten , Mancini Francesca , Sarakinou Eleanna , Callegaro Andrea , Ferruzzi Pietro , Acquaviva Alessandra , Arora Ashwani , Marchetti Elisa , Necchi Francesca , Frenck Robert , Martin Laura , Kaminski Robert , Podda Audino , Micoli Francesca 
Published: July 2023

Abstract
Shigella spp. are a leading bacterial cause of diarrhea. No widely licensed vaccines are available and there is no generally accepted correlate of protection. We tested a S. sonnei GMMA-based vaccine (1790GAHB) in a phase 2b, placebo-controlled, randomized, controlled human infection model study (NCT03527173) enrolling healthy US adults aged 18–50 years. We report analyses evaluating immune responses to vaccination, with the aim to identify correlates of risk for shigellosis among assessed immunomarkers. We found that 1790GAHB elicited S. sonnei lipopolysaccharide specific α4β7 + IgG and IgA secreting B cells which are likely homing to the gut, indicating the ability to induce a mucosal in addition to a systemic response, despite parenteral delivery. We were unable to establish or confirm threshold levels that predict vaccine efficacy facilitating the evaluation of vaccine candidates. However, serum anti-lipopolysaccharide IgG and bactericidal activity were identified as potential correlates of risk for shigellosis.
Correlation of glomerular mannose-binding lectin deposition with the clinicopathology and prognosis of PLA2R-associated membranous nephropathy
Authors: Pan Yan , Liu Lei , Zhang Jiqiang , Zhao Ruiping , Han Yuzhe , Chen Weidong 
Published: July 2023

Abstract
Mannose-binding lectin (MBL) and autoantibody IgG4 staining against the phospholipase A2 receptor (PLA2R)were correlated. To enquire into the pathogenic effect of MBL in IMN as well as its relevance to clinicopathology and prognosis.Patients with IMN in 2021–2022 at our hospital were divided into positive and negative groups based on glomerular MBL immunofluorescence results and anti-PLA2R antibody characterization, and their clinical, pathological and follow-up data were evaluated.Among 39 patients with IMN, the positive rates of glomerular MBL and IgG4 deposition and serum anti-PLA2R antibodies were 31 (79.5%), 37 (100%) and 26 (70.3%), respectively. There were no notable differences in clinical and pathological features between the MBL-positive and negative groups of patients, but there were differences in IgG4 expression in the renal tissues (p < 0.05). There were no notable differences in MBL deposition between IMN patients grouped qualitatively by blood PLA2R antibodies. Renal tissue MBL was highly expressed (79.5%) and C1q was lowly expressed (15.38%). Kaplan-Meier analysis of clinical remission was similar in both groups. In multivariate COX regression analysis adjusted for sex, age, serum anti-PLA2R antibody concentration and blood pressure, MBL deposition (HR, 0.776; 95% CI, 0.311–1.939; p = 0.587) was not associated with IMN remission in the MBL-negative compared with the positive group.Renal tissue MBL characterization correlates with IgG4 and anti-PLA2R antibodies are involved in the pathogenesis of IMN through the induction of complement activation by the complement agglutinin pathway. No significant clinical, pathological or prognostic differences between patients with positive and negative MBL deposits were found in the study.
Time to Failure Prediction of Rotating Machinery using Dynamic Feature Extraction and Gaussian Process Regression
Authors: Lee Wo Jae , Sutherland John W. 
Published: July 2023

Abstract
Recent advances in sensor technology and computing power allow for the generation/utilization of larger and more diverse sets of data. These developments enable the creation of data-driven models that can support real-time decision making. Such a decision aid can allow for predictive maintenance (PdM) to be undertaken on a much greater scale in manufacturing plants. PdM includes data-driven prognostics and health management (PHM). To enhance the performance of a prognostic model, one key task is to collect high-quality data, and in the past this has often involved using a feature extraction method to get meaningful information from a large noisy dataset. However, such methods may not handle noisy data well or address measurement errors adequately. Consequently, extracted features may not represent a degradation process suitably as a machine approaches a failure or fault. Also, effects of sensor types on the feature extraction and prediction model have not been much explored yet. To overcome this limitation, dynamic feature extraction is proposed to mitigate the effect of noisy statistical features in a monotonic trend by introducing a statistical penalty. Then, the features extracted through the method are used to construct a health indicator (HI). With the available historical HI values, a probabilistic regression model may be used to forecast the time to failure (TTF) of rotating machinery with uncertainty propagation. To validate the proposed method, acceleration data were collected from rotating machinery for several run-to-failure cases. The proposed method is demonstrated to provide excellent forecasts of TTF for both accelerometer types.
Occurrence of Emerging Mycotoxins in Chicken Feed and Eggs from Algeria
Authors: Laouni Chahinez , Hernández-Mesa Maykel , Messai Ahmed , Redouane-Salah Sara , Lara Francisco J. , Gámiz-Gracia Laura , García-Campaña Ana M. 
Published: July 2023

Abstract

Poultry farming has developed into one of Algeria's most productive agricultural indus-tries because of the growing demand for sources of protein among Algerian society. Laying hen feed consists mainly of cereals, which can be contaminated with molds and subsequently with their secondary metabolites known as mycotoxins. These later can pose a serious danger to the produc-tion and quality of eggs in the commercial layer industry. This work focuses on the detection of emerging mycotoxins, mainly enniatins (ENNs) and beauvericin (BEA), in poultry feed and eggs from different locations in Algeria. Two different QuEChERS-based extractions were established to extract ENNs and BEA from chicken feed and eggs. The determination of mycotoxins occurrence was achieved by a UHPLC-MS/MS method using 0.1% (v/v) formic acid in water and MeOH as mobile phase, an ESI interface operating in positive mode and a triple quadrupole mass spectrom-eter operating in MRM for the detection. Matrix-matched calibration curves were carried out for both matrices, obtaining good linearity (R2 > 0.99). The method performance was assessed in terms of extraction recovery (from 87% to 107%), matrix effect (from -47% to -86%), precision (RSD < 15%) and limits of quantitation (≤1.1 µg/kg for feed and ≤ 0.8 µg/kg for eggs). The analysis of 10 chicken feed samples and 35 egg samples showed that ENN B1 was the most common mycotoxin (i.e. found in 9 samples) with contamination levels ranging from 3.6 to 41.5 µg/kg, while BEA was detected only in one sample (12 µg/kg). However, eggs were not found to be contaminated with any my-cotoxin at the detection limit levels. Our findings indicate that the searched mycotoxins are present in traces in feed and absent in eggs. This can be explained by the application of mycotoxins binder. However, this does not put a stop on the conduction of additional research and ultimately setting regulations to prevent the occurrence of emerging mycotoxins.
Identification machine learning-based model of programmed cell-death patterns for investigating the immune microenvironment and prognosis of ovarian cancer patients after surgery and providing therapeutic strategies
Authors: Han Lei , Wang Fei , Chen Weiwei , Zhai Qingliang , Zhang Xianghui , Xu Huishu , Zhang Baolin , Wang Yanlin , An Jiajia , Pan Yitong 
Published: July 2023

AbstractBackground Ovarian cancer (OV) is a highly aggressive and often fatal disease that frequently goes undetected until it has already metastasized. The classic treatment for ovarian cancer involves surgery followed by chemotherapy. However, despite the effectiveness of surgery, relapse is still a common occurrence. Unfortunately, there is currently no ideal predictive model for the progression and drug sensitivity of postoperative ovarian cancer patients. Cell death patterns play an important role in tumor progression and have the potential to be used as indicators of postoperative OV prognosis and drug sensitivity. Materials and methods A total of 12 PCD patterns were employed to construct the model. Bulk transcriptome, single-cell transcriptome, genomics, and clinical information were collected from TCGA-OV, GSE9891, GSE26712, GSE49997 and GSE63885. In addition, single-cell transcriptome data GSE210347 was procured from the Gene Expression Omnibus (GEO) database for subsequent analysis. Results In this study, a programmed cell death index (PCDI) was established using an 8-gene signature with the help of a machine learning algorithm. The PCDI was validated in four independent datasets, and it was found that patients with high-PCDI had a worse prognosis after surgery in OV. The investigation also revealed that PCDI is associated with chemokines, interleukins, interferons, and checkpoint genes, as well as important components of the immune microenvironment, as determined through a comprehensive analysis of bulk and single-cell transcriptomes. In addition, we also found that patients with low-PCDI values may exhibit sensitivity to immunotherapy, while those with high PCDI values may display increased responsiveness to tyrosine kinase inhibitors. Conclusion This study provides new insights into the significance of programmed cell death (PCD) patterns in ovarian cancer patients following surgery. Through a comprehensive analysis of different cell death patterns, we have developed a novel PCD model that can effectively predict the clinical prognosis and drug sensitivity of OV patients post-surgery.
An epidemiological modeling framework to inform institutional-level response to infectious disease outbreaks: A Covid-19 case study
Authors: Rennert Lior , Ma Zichen 
Published: July 2023

Abstract
Institutions have an enhanced ability to implement tailored mitigation measures during infectious disease outbreaks. However, macro-level predictive models are inefficient for guiding institutional decision-making due to uncertainty in local-level model input parameters. We present an institutional-level modeling toolkit used to inform prediction, resource procurement and allocation, and policy implementation at Clemson University throughout the Covid-19 pandemic. Through incorporating real-time estimation of disease surveillance and epidemiological measures based on institutional data, we argue this approach helps minimize uncertainties in input parameters presented in the broader literature and increases prediction accuracy. We demonstrate this through case studies at Clemson and other university settings during the Omicron BA.1 and BA.4/BA.5 variant surges. The input parameters of our toolkit are easily adaptable to other institutional settings during future health emergencies. This methodological approach has potential to improve public health response through increasing the capability of institutions to make data-informed decisions that better prioritize the health and safety of their communities while minimizing operational disruptions.
Sensitivity of DNA double-strand break loci is coupled with spatial interaction density of chromatin
Authors: Chen Hebing , Xu Kang , Chen Bijia , Xie Qiu , Sun Yu , Xu Xiang , Wang Junting , Li Yaru , Hu Pengzhen , Yue Shutong , Yu Guoxian , Wang Jun , Li Hao , Bo Xiaochen 
Published: July 2023

Abstract
Background: DNA double-strand breaks, one of the most serious types of damage to the genome, are closely related to chromatin rearrangement and oncogene activation. However, the mechanisms of DSB formation and repair upon the genome are still unclear. Recent advances in chromatin conformation capture technology Hi-C enable clear identification of the relationship between chromatin 3D structure and DSBs. Nonetheless, how to interpret this relationship, especially the contribution to DSB formation at the level of TAD, remains poorly understood.
Results: Here, we classify the collected DSB data for systematic identification and annotation of these DSB loci from a multi-omics perspective, and construct a systematic framework for studying DSBs. In addition, we propose a model for TAD Density. TAD Density can well characterize the relationship between different TAD internal interaction densities and DSB occurrence. The dynamic changes of TAD Density tend to be associated with the enrichment of fragile regions of the genome or even essential genes. This relationship was explained by the ancient Chinese mythology “Journey to the West”. Furthermore, with TAD Density, we screened for genes associated with prognosis of tumor patients.
Conclusions: In conclusion, our study systematically compared and annotated DSB loci in terms of sequence features, epigenetic modifications, and the three-dimensional structure of chromatin. While validating the general pattern of DSBs, we propose a mechanism for chromatin interaction density within TAD to protect the genome from DSB damage.
The effect of weight-bearing conditions on toe joint angles in healthy volunteers using weight-bearing CT
Authors: Mens M. A. , Bouman C. M. B. , Dobbe J. G. G. , Bus S. A. , Nieuwdorp M. , Maas M. , Wellenberg R. H. H. , Streekstra G. J. 
Published: July 2023

Abstract
Purpose: To determine the effect of weight-bearing (WB) conditions on toe joint angles in healthy volunteers using WB and non-WB (nWB) CT images and to evaluate left and right foot differences.
Methods: In twenty healthy volunteers WB and nWB CT images of both feet were acquired. Bones of the forefoot were segmented and the respective bone models were used to calculate angles for the metatarsophalangeal and interphalangeal joints.
Results: Metatarsophalangeal joint (MTPJ) angles ranged between 6˚ and 40˚, proximal interphalangeal joint (PIPJ) angles between 0.5˚ and 54˚and distal interphalangeal joint (DIPJ) angles between 1˚ and 46˚.MTPJ angles were significantly smaller in WB compared to nWB conditions in the first four digits. The interphalangeal joint angles of the first digit was in WB conditions significantly larger. No left-right foot differences were found for toe joint angles.
Conclusion: Toe joint angles show a wide variety between healthy volunteers although the bilateral symmetry is high. MTPJ angles of the first to fourth toe are smaller under WB conditions, but do not change PIPJ and DIPJ angles compared to nWB conditions.
Does the Law Make Sense in Advancing Women’s Rights to Sexual and Reproductive Health in Uganda? Experiences from Eastern Uganda
Authors: Kagaha Alexander 
Published: July 2023

Abstract
This paper is based on an ethnographic investigation of experiences of abortion care delivery in eastern Uganda between August 2018- March 201 Advances on liberalization of the law on abortion as an avenue for advancement of women’s freedom and rights to sexual and reproductive health. However, findings from both public and private profit-making health facilities, indicate that: (i) Inside liberalized contexts, all aspects of life (including care practice, and the restrictive law on abortion), was evaluated in the image of the economy. The boundary between right and wrong, legal and illegal is replaced with instrumental viability based on the level of economic value. (ii) Abortion care delivery can no longer be universally interpreted. In profit making health facilities, provision of abortion care service was motivated by the desire for pecuniary interests and so, care was interpreted as a means towards financial goals. Healthcare delivery practice that can be considered to be inherently good without any qualification-were largely observed within publicly owned health facilities. The tension between the duty to serve and the desire to make profits undermine the ethic of duty to care. (iii) Abortion care involved use both allowed and prohibited medical technologies, whose choice and application were mediated through the desire for money. Use of medical technologies in panic triggered fear, resulting in increased risks injuries to patients and this also introduced maladaptive practices in care. Therefore, restrictive boundaries and regulation create dark zones in healthcare, which are difficult to monitor and regulate. Removal of legal restrictions is necessary to bring abortion care under full control and regulation health regulatory bodies.
Prenatal polycyclic aromatic hydrocarbon exposure and asthma at age 8-9 years in a multi-site longitudinal study
Authors: Sherris Allison R. , Loftus Christine T. , Szpiro Adam A. , Dearborn Logan , Hazlehurst Marnie F. , Carroll Kecia N. , Moore Paul E. , Adgent Margaret A. , Barrett Emily S. , Bush Nicole R. , Day Drew B. , Kannan Kurunthachalam , LeWinn Kaja Z. , Nguyen Ruby H.N. , Ni Yu , Riederer Anne M. , Robinson Morgan , Sathyanarayana Sheela , Zhao Qi , Karr Catherine J. 
Published: July 2023

Abstract
Background and aim: Studies suggest prenatal exposure to polycyclic aromatic hydrocarbons (PAHs) may influence wheezing or asthma in preschool-aged children. However, the impact of prenatal PAH exposure on asthma and wheeze in middle childhood remain unclear. We investigated these associations in diverse participants from the ECHO PATHWAYS multi-cohort consortium.Methods We included 1,081 birth parent-child dyads across five U.S. cities. Maternal urinary mono-hydroxylated PAH metabolite concentrations (OH-PAH) were measured during mid-pregnancy. Asthma at age 8–9 years and wheezing trajectory across childhood were characterized by caregiver reported asthma diagnosis and asthma/wheeze symptoms. We used logistic and multinomial regression to estimate odds ratios of asthma and childhood wheezing trajectories associated with five individual OH-PAHs, adjusting for urine specific gravity, various maternal and child characteristics, study site, prenatal and postnatal smoke exposure, and birth year and season in single metabolite and mutually adjusted models. We used multiplicative interaction terms to evaluate effect modification by child sex and explored OH-PAH mixture effects through Weighted Quantile Sum regression.Results The prevalence of asthma in the study population was 10%. We found limited evidence of adverse associations between pregnancy OH-PAH concentrations and asthma or wheezing trajectories. We observed adverse associations between 1/9-hydroxyphenanthrene and asthma and persistent wheeze among girls, and evidence of inverse associations with asthma for 1-hydroxynathpthalene, which was stronger among boys, though tests for effect modification by child sex were not statistically.Conclusions In a large, multi-site cohort, we did not find strong evidence of an association between prenatal exposure to PAHs and child asthma at age 8–9 years, though some adverse associations were observed among girls.