bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes
Authors: Tan Asako , Murugapiran Senthil , Mikalauskas Alaya , Koble Jeff , Kennedy Drew , Hyde Fred , Ruotti Victor , Law Emily , Jensen Jordan , Schroth Gary P. , Macklaim Jean M. , Kuersten Scott , LeFrançois Brice , Gohl Daryl M. 
Published: October 2023

AbstractThe microbiota that colonize the human gut and other tissues are dynamic, varying both in composition and functional state between individuals and over time. Gene expression measurements can provide insights into microbiome composition and function. However, efficient and unbiased removal of microbial ribosomal RNA (rRNA) presents a barrier to acquiring metatranscriptomic data. Here we describe a probe set that achieves efficient enzymatic rRNA removal of complex human-associated microbial communities. We demonstrate that the custom probe set can be further refined through an iterative design process to efficiently deplete rRNA from a range of human microbiome samples. Using synthetic nucleic acid spike-ins, we show that the rRNA depletion process does not introduce substantial quantitative error in gene expression profiles. Successful rRNA depletion allows for efficient characterization of taxonomic and functional profiles, including during the development of the human gut microbiome. The pan-human microbiome enzymatic rRNA depletion probes described here provide a powerful tool for studying the transcriptional dynamics and function of the human microbiome.
Non-targeted metabolomics analysis of metabolite changes in two quinoa genotypes under drought stress
Authors: Zhu Xiaolin , Zhang Mingjun , Wang Baoqiang , Song Xinrong , Wang Xian , Wei Xiaohong 
Published: October 2023

Abstract
Background
Quinoa is an important economic crop, drought is one of the key factors affecting quinoa yield. Clarifying the adaptation strategy of quinoa to drought is conducive to cultivating drought-tolerant varieties. At present, the study of quinoa on drought stress-related metabolism and the identification of related metabolites are still unknown. As a direct feature of biochemical functions, metabolites can reveal the biochemical pathways involved in drought response.

Result
Here, we studied the physiological and metabolic responses of drought-tolerant genotype L1 and sensitive genotype HZ1. Under drought conditions, L1 had higher osmotic adjustment ability and stronger root activity than HZ1, and the relative water content of L1 was also higher than that of HZ1. In addition, the barrier-to- sea ratio of L1 is significantly higher than that of HZ1. Using untargeted metabolic analysis, a total of 523, 406, 301 and 272 differential metabolites were identified in L1 and HZ1 on day 3 and day 9 of drought stress. The key metabolites (amino acids, nucleotides, peptides, organic acids, lipids and carbohydrates) accumulated differently in quinoa leaves. and HZ1 had the most DEMs in Glycerophospholipid metabolism (ko00564) and ABC transporters (ko02010) pathways.

Conclusion
These results provide a reference for characterizing the response mechanism of quinoa to drought and improving the drought tolerance of quinoa.
Pathogens in PICU before and during the SARS-CoV-2 pandemic in China: a multicenter retrospective study
Authors: Ni Jingwen , Zhao Zhe , Wang Chun , Jin Youpeng , Wang Yi , Liang Zhenhua , Li Shujun , Chen Jie , Du Yanqiang , Li Yipei , Huang Hanwu , Guo Yuxiong , Zhong Yujie , Feng Zhichun , Fang Kenan , Hong Xiaoyang 
Published: October 2023

Abstract
Background
Nonpharmacological interventions for COVID-19 could reduce the incidence of children hospitalized in pediatric intensive care units (PICU) and the incidence of children with bacterial infections. This study aimed to evaluate changes in the bacterial profile of children in PICU before and during the COVID-19 pandemics.

Methods
This is a retrospective study, involving clinical data of children with positive bacterial cultures admitted to the PICU respectively in 2019 and 2021.

Results
In total 652 children were included in this study. The total number of hospitalized patients and the incidence of bacteria-positive children in 2021 were lower than those in 2019. There were no significant differences in the ratio of Gram-positive bacterial infection, Gram-negative bacteria infection or fungi infection between the two years. The rate of Streptococcus pneumoniae in 2021 was higher than that in 2019(p = 0.127). The incidence of Haemophilus influenzae in hospitalized patients decreased with a downward trend(p = 0.002). The distribution of previous underlying diseases in children admitted to PICU with different outcomes of bacterial infection between the two years were homogeneous (p > 0.05).

Conclusion
After the implementation of COVID-19 isolation, prevention and control measures, the number of hospitalizations and bacterial infections in PICU decreased, which may be due to changes in population’s behavior patterns. Meanwhile, the incidence of Haemophilus influenzae in hospitalized patients decreased with a downward trend.
At-home computerized executive-function training to improve cognition and mobility in normal-hearing adults and older hearing aid users: a multi-centre, single-blinded randomized controlled trial
Authors: Downey Rachel , Gagné Nathan , Mohanathas Niroshica , Campos Jennifer L. , Pichora-Fuller Kathleen M. , Bherer Louis , Lussier Maxime , Phillips Natalie A. , Wittich Walter , St-Onge Nancy , Gagné Jean-Pierre , Li Karen 
Published: October 2023

Abstract
Background
Hearing loss predicts cognitive decline and falls risk. It has been argued that degraded hearing makes listening effortful, causing competition for higher-level cognitive resources needed for secondary cognitive or motor tasks. Therefore, executive function training has the potential to improve cognitive performance, in turn improving mobility, especially when older adults with hearing loss are engaged in effortful listening. Moreover, research using mobile neuroimaging and ecologically valid measures of cognition and mobility in this population is limited. The objective of this research is to examine the effect of at-home cognitive training on dual-task performance using laboratory and simulated real-world conditions in normal-hearing adults and older hearing aid users. We hypothesize that executive function training will lead to greater improvements in cognitive-motor dual-task performance compared to a wait-list control group. We also hypothesize that executive function training will lead to the largest dual-task improvements in older hearing aid users, followed by normal-hearing older adults, and then middle-aged adults.

Methods
A multi-site (Concordia University and KITE-Toronto Rehabilitation Institute, University Health Network) single-blinded randomized controlled trial will be conducted whereby participants are randomized to either 12 weeks of at-home computerized executive function training or a wait-list control. Participants will consist of normal-hearing middle-aged adults (45–60 years old) and older adults (65–80 years old), as well as older hearing aid users (65–80 years old, ≥ 6 months hearing aid experience). Separate samples will undergo the same training protocol and the same pre- and post-evaluations of cognition, hearing, and mobility across sites. The primary dual-task outcome measures will involve either static balance (KITE site) or treadmill walking (Concordia site) with a secondary auditory-cognitive task. Dual-task performance will be assessed in an immersive virtual reality environment in KITE’s StreetLab and brain activity will be measured using functional near infrared spectroscopy at Concordia’s PERFORM Centre.

Discussion
This research will establish the efficacy of an at-home cognitive training program on complex auditory and motor functioning under laboratory and simulated real-world conditions. This will contribute to rehabilitation strategies in order to mitigate or prevent physical and cognitive decline in older adults with hearing loss.

Trial registration
Identifier: NCT05418998. https://clinicaltrials.gov/ct2/show/NCT05418998
The value of elevated cerebrospinal fluid lactate concentrations in post-neurosurgical bacterial meningitis
Authors: Wang Qin , Wang YongFang , Yang Yan , Kong YanXi , Peng Yuan 
Published: October 2023

AbstractBacterial meningitis is a serious complication after neurosurgery and has a high mortality rate. Early diagnosis and timely treatment are crucial or will have disastrous consequences. The classic triad of bacterial meningitis lacks sensitivity and specificity. Therefore, the diagnosis of post-neurosurgical bacterial meningitis relies on cerebrospinal fluid. But traditional cerebrospinal fluid parameters are not completely reliable in diagnosing post-neurosurgical bacterial meningitis. Previous studies have found that CSF lactate concentration is related to bacterial meningitis. But, after the craniocerebral operation, the cerebrospinal fluid of most patients is bloody. Whether red blood cells interfere with diagnosing PNBM based on lactate concentration is limited. In the current study, we further analysis on whether red blood cells interfere with diagnosing PNBM based on lactate concentration. This study aimed to investigate the value of cerebrospinal fluid lactate concentrations in post-neurosurgical bacterial meningitis. A prospective observational study was performed on 62 patients at Kunshan First People’s Hospital’s intensive care unit affiliated with Jiangsu University. We found that erythrocytes do not affect cerebrospinal fluid lactate, and elevated lactate concentrations can be used as a marker for postoperative bacterial meningitis.
Tracking tumor alteration in glioma through serum fibroblast activation protein combined with image
Authors: Yang Xiao-song , zhu Peng , Xie Rong-Xing , Chen Peng-fei , Liu Hong , Cheng Xiao-Man , Zhu Zheng-Quan , Peng Xiao-min , Liu Hai-bin , Yang Qun-Ying , Li Jun-Qi , Zhang Ji 
Published: October 2023

Abstract
Purpose
Detecting tumor progression of glioma continues to pose a formidable challenge. The role of fibroblast activation protein (FAP) in gliomas has been demonstrated to facilitate tumor progression. Glioma-circulating biomarkers have not yet been used in clinical practice. This study seeks to evaluate the feasibility of glioma detection through the utilization of a serum FAP marker.

Methods
We adopted enzyme-linked immunosorbent assay (ELISA) technique to quantify the relative FAP level of serum autoantibodies in a cohort of 87 gliomas. The correlation between preoperative serum autoantibody relative FAP levels and postoperative pathology, including molecular pathology was investigated. A series of FAP tests were conducted on 33 cases of malignant gliomas in order to ascertain their efficacy in monitoring the progression of the disease in relation to imaging observations. To validate the presence of FAP expression in tumors, immunohistochemistry was conducted on four gliomas employing a FAP-specific antibody. Additionally, the investigation encompassed the correlation between postoperative tumor burden, as assessed through volumetric analysis, and the relative FAP level of serum autoantibodies.

Results
A considerable proportion of gliomas exhibited a significantly increased level of serum autoantibody relative FAP level. This elevation was closely associated with both histopathology and molecular pathology, and demonstrated longitudinal fluctuations and variations corresponding to the progression of the disease The correlation between the rise in serum autoantibody relative FAP level and tumor progression and/or exacerbation of symptoms was observed.

Conclusions
The measurement of serum autoantibody relative FAP level can be used to detect the disease as a valuable biomarker. The combined utilization of its detection alongside MR imaging has the potential to facilitate a more accurate and prompt diagnosis.
The effect of smoking on latent hazard classes of metabolic syndrome using latent class causal analysis method in the Iranian population
Authors: Khodamoradi Farzad , Nazemipour Maryam , Mansournia Nasrin , Yazdani Kamran , khalili Davood , Arshadi Maedeh , Etminan Mahyar , Mansournia Mohammad Ali 
Published: October 2023

AbstractBackgroundThe prevalence of metabolic syndrome is increasing worldwide. Clinical guidelines consider metabolic syndrome as an all or none medical condition. One proposed method for classifying metabolic syndrome is latent class analysis (LCA). One approach to causal inference in LCA is using propensity score (PS) methods. The aim of this study was to investigate the causal effect of smoking on latent hazard classes of metabolic syndrome using the method of latent class causal analysis.MethodsIn this study, we used data from the Tehran Lipid and Glucose Cohort Study (TLGS). 4857 participants aged over 20 years with complete information on exposure (smoking) and confounders in the third phase (2005–2008) were included. Metabolic syndrome was evaluated as outcome and latent variable in LCA in the data of the fifth phase (2014–2015). The step-by-step procedure for conducting causal inference in LCA included: (1) PS estimation and evaluation of overlap, (2) calculation of inverse probability-of-treatment weighting (IPTW), (3) PS matching, (4) evaluating balance of confounding variables between exposure groups, and (5) conducting LCA using the weighted or matched data set.ResultsBased on the results of IPTW which compared the low, medium and high risk classes of metabolic syndrome (compared to a class without metabolic syndrome), no association was found between smoking and the metabolic syndrome latent classes. PS matching which compared low and moderate risk classes compared to class without metabolic syndrome, showed that smoking increases the probability of being in the low-risk class of metabolic syndrome (OR: 2.19; 95% CI: 1.32, 3.63). In the unadjusted analysis, smoking increased the chances of being in the low-risk (OR: 1.45; 95% CI: 1.01, 2.08) and moderate-risk (OR: 1.68; 95% CI: 1.18, 2.40) classes of metabolic syndrome compared to the class without metabolic syndrome.ConclusionsBased on the results, the causal effect of smoking on latent hazard classes of metabolic syndrome can be different based on the type of PS method. In adjusted analysis, no relationship was observed between smoking and moderate-risk and high-risk classes of metabolic syndrome.
Maternal weight trajectories and associations with infant growth in South African women
Authors: Madlala Hlengiwe P. , Bengtson Angela M. , Hannan Luke , Malaba Thokozile R. , Kalk Emma , Nyemba Dorothy , Boulle Andrew , Myer Landon 
Published: October 2023

Abstract
Background
Despite the close relationship between pre-pregnancy body mass index (BMI), gestational weight gain (GWG) and postpartum weight (PPW), these factors are often studied separately. There are no data characterising longitudinal weight trajectories among pregnant and postpartum women in urban African populations. We examined maternal weight trajectories from pregnancy through to 12 months postpartum, factors associated with higher weight trajectory class membership and associations of weight trajectories with infant growth at 12 months.

Methods
Data from 989 women were examined for weight trajectories from first antenatal care visit in pregnancy to 12 months postpartum using latent-class growth models. Baseline factors associated with class membership were assessed using multinomial logistic regression. Of the enrolled women, 613 of their infants were assessed for growth at 12 months. Anthropometry measurements for mothers and infants were conducted by a trained study nurse. Associations between maternal weight trajectory class and infant weight-for-age (WAZ), length-for-age (LAZ), weight-for-length (WLZ) at 12 months of age were analysed using linear regression.

Results
Four distinct classes of maternal weight trajectories were identified. The classes included consistent low (29%), consistent medium (37%), medium–high (24%) and consistent high (10%) trajectories. Similar to trends observed with medium–high trajectory, baseline factors positively associated with consistent high class membership included age (OR 1.05, 95% CI 1.01–1.09), pre-pregnancy BMI (OR 2.24, 95% CI 1.97–2.56), stage 1 hypertension (OR 3.28, 95% CI 1.68–6.41), haemoglobin levels (OR 1.39, 95% CI 1.11–1.74) and parity (OR 1.39, 95% CI 1.15–1.67); living with HIV (OR 0.47, 95% CI 0.30–0.74) was inversely associated. In adjusted analyses, compared to consistent medium weight trajectory, consistent low weight trajectory (mean difference -0.41, 95% CI -0.71;-0.12) was associated with decreased, and consistent high weight trajectory (mean difference 1.21, 95% CI 0.59–1.83) with increased infant WAZ at 12 months of age.

Conclusion
Identification of unique longitudinal weight trajectory groupings might inform comprehensive efforts targeted at improving healthy maternal weight and infant outcomes.
Conditional diagnostic accuracy according to inflammation status and age for diagnosing tuberculous effusion
Authors: Jeon Da Som , Kim Sung-Hoon , Lee Jang Ho , Choi Chang-Min , Park Hyung Jun 
Published: October 2023

Abstract
Background
Tuberculous effusion varies from lymphocyte-dominant to neutrophilic effusion according to inflammation status. The criteria of adenosine deaminase (ADA) and lymphocyte/neutrophil (L/N) ratio have yet not been evaluated across different disease conditions.

Methods
Patients who conducted pleural fluid analysis from 2009 to 2019 at Asan Medical Center were included. Criteria (ADA of 50 and L/N ratio of 0.75) were evaluated by quantile subgroups according to age, C-reactive protein (CRP), white blood cell (WBC), and lactate dehydrogenase (LD) by the Monte Carlo simulation method to diagnose tuberculosis. The model for the ADA and L/N ratio was evaluated by AUROC.

Results
Among the 2,918 reviewed cases, 2034 were included with 229 (11.26%) tuberculosis cases. The mean baseline ADA AUROC was 0.88 across all patients. Increased CRP and WBC showed high proportions of neutrophilic tuberculous effusion, with low sensitivity of approximately 45% and 33% in the fifth WBC and CRP groups, respectively. The AUROC of the models decreased with the increase in WBC and CRP groups (ADA model: 0.69 [the top quantile WBC group], 0.74 [the top quantile CRP group]). The AUROC of the models did not show a trend according to the increase in LD and age.

Conclusion
Inflammatory status affects the diagnostic metrics for tuberculous effusion due to the progression of tuberculous effusion. Clinicians should consider the low accuracy of tuberculous effusion criteria in high-inflammatory conditions when diagnosing tuberculosis.
Dietary caffeine intake is associated with favorable metabolic profile among apparently healthy overweight and obese individuals
Authors: Alshahrani Shadia Hamoud , Atia Yasir A. , Badir Raheem Atiya , Almalki Sami G. , Tayyib Nahla A , Shahab Sana , Romero-Parra Rosario Mireya , Abid Mohammed Kadhem , Hussien Beneen M. , Ramaiah Pushpamala 
Published: October 2023

Abstract
Background
Recent studies have revealed some conflicting results about the health effects of caffeine. These studies are inconsistent in terms of design and population and source of consumed caffeine. In the current study, we aimed to evaluate the possible health effects of dietary caffeine intake among overweight and obese individuals.

Methods
In this cross-sectional study, 488 apparently healthy individuals with overweight and obesity were participated. Dietary intake was assessed by a Food Frequency Questionnaire (FFQ) and the amount of dietary caffeine was calculated. Body composition was determined by bioelectrical impedance analysis (BIA). Enzymatic methods were used to evaluate serum lipid, glucose, and insulin concentrations.

Results
Those at the highest tertile of dietary caffeine intake had lower percentage of fat mass, higher fat free mass and appetite score (P < 0.05). Also, lower total cholesterol (TC) and low density lipoprotein cholesterol (LDL-c) was observed in higher tertiles of dietary caffeine intake compared with lower tertiles. In multinomial adjusted models, those at the second tertile of dietary caffeine intake were more likely to have higher serum insulin (P = 0.04) and lower homeostatic model assessment of insulin resistance (HOMA-IR) values compared with first tertile (P = 0.03) in crude model. While, in the age, body mass index (BMI), sex, physical activity, socio-economic status (SES) and energy intake –adjusted model (Model III), those at the third tertile of dietary caffeine intake were more likely to have low serum LDL concentrations [odds ratio (OR) = 0.957; CI = 0.918–0.997; P = 0.04]. With further adjustment to dietary vegetable, fiber and grain intake, those at the third tertile of dietary caffeine intake were more likely to have low systolic blood pressure (SBP), LDL and high HDL levels compared with those at the first tertile (P < 0.05).

Conclusion
High intakes of dietary caffeine was associated with lower LDL, SBP, insulin resistance and higher HDL concentrations among overweight and obese individuals. However, due to observational design of the study, causal inference is impossible and further studies are warranted to confirm our findings.
The impact and the challenges of implementing a faculty development program on health professions education in a Brazilian Medical School: a case study with mixed methods
Authors: Cintra Karine Angélica , Borges Marcos Carvalho , Panúncio-Pinto Maria Paula , de Almeida Troncon Luiz Ernesto , Bollela Valdes Roberto 
Published: October 2023

Abstract
Purpose
Faculty development in health professions education is still challenging in developing countries like Brazil. Work overload and the lack of financial support hinder faculty members' participation. Ribeirão Preto Medical School founded its Center for Faculty Development in 2016. Since then, an essential skills module (ESMo) on health professions education (HPE) has been offered regularly to faculty members and preceptors of seven undergraduate programs. This case study aims to evaluate the impact of this Essential Skills Module on the educational practices of participants two years after attending the module and the challenges faced during the process.

Method
The study used a mixed-method approach with a description of the demographic and professional profile data of the ESMo participants. Immediate post-ESMo perceptions (satisfaction and learning) of the participants were determined with structured instruments. Two years later, a semi-structured interview was conducted and recorded to determine the long-term effects (application of learning and behavior changing as an educator). NVIVO® software was used to store and systematize the thematic discourse analysis with a socio-constructivist theoretical framework interpretation.

Results
One hundred forty-six participants were included: 86 (59%) tenured faculty members, 49 (33,5%) clinical preceptors, and 11 (7,5%) invited teachers. Most were female (66%), and 56% had teaching experience shorter than ten years. 52 (69%) out of 75 eligible participants were interviewed. The immediate reaction to participating in the module was quite positive and 80% have already implemented an educational intervention in their daily activities. Discourses thematic analysis showed five emerging themes appearing in different frequencies: Changes in teaching activities (98%); Lack of previous pedagogical training (92.3%); Commitment and enthusiasm towards teaching (46.15%); Overlapping functions inside the institution (34.6%) and Challenges for student assessment (23%).

Conclusion
This first in-depth evaluation of the long-term effects of a faculty development intervention in a Brazilian Health Profession Education school showed that participation positively changed participants' teaching & learning practices. These interventions consistently fostered a community of practice and valued faculty development processes in local and national scenarios.