bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiota in adult perianal abscess revealed by metagenomic next-generation sequencing
Authors: Hong Jian-Chen , Chen Jian-Sheng , Jiang Zai-Jie , Chen Zhi-Chuan , Ruan Ning , Yao Xiang-Ping 
Published: February 2024

ABSTRACT

The microbiota of perianal abscesses is scarcely investigated. Identifying causative bacteria is essential to develop antibiotic therapy. However, culture-based methods and molecular diagnostics through 16S PCR technology are often hampered by the polymicrobial nature of perianal abscesses. We sought to characterize the microbiota composition of perianal abscesses via metagenomic next-generation sequencing (mNGS). Fourteen patients suffering from perianal abscesses between March 2023 and August 2023 underwent retrospective assessment. Information from medical records was used, including clinical information, laboratory data, and culture and mNGS results. Forty bacterial taxa were identified from perianal abscesses through mNGS, with
Bilophila wadsworthia
(71.4%),
Bacteroides fragilis
(57.1%), and
Escherichia coli
(50.0%) representing the most prevalent species. mNGS identified an increased number of bacterial taxa, with an average of 6.1 compared to a traditional culture-based method which only detected an average of 1.1 in culture-positive perianal abscess patients, predominantly
E. coli
(75.0%), revealing the polymicrobial nature of perianal abscesses. Our study demonstrates that a more diverse bacterial profile is detected by mNGS in perianal abscesses, and that
Bilophila wadsworthia
is the most prevalent microorganism, potentially serving as a potential biomarker for perianal abscess.

IMPORTANCE

Accurately, identifying the bacteria causing perianal abscesses is crucial for effective antibiotic therapy. However, traditional culture-based methods and 16S PCR technology often struggle with the polymicrobial nature of these abscesses. This study employed metagenomic next-generation sequencing (mNGS) to comprehensively analyze the microbiota composition. Results revealed 40 bacterial taxa, with
Bilophila wadsworthia
(71.4%),
Bacteroides fragilis
(57.1%), and
Escherichia coli
(50.0%) being the most prevalent species. Compared to the culture-based approach, mNGS detected a significantly higher number of bacterial taxa (average 6.1 vs 1.1), highlighting the complex nature of perianal abscesses. Notably,
Bilophila wadsworthia
emerged as a potential biomarker for these abscesses. This research emphasizes the importance of mNGS in understanding perianal abscesses and suggests its potential for improving diagnostic accuracy and guiding targeted antibiotic therapy in the future.
Paleo-Pacific plate subduction direction change (122–118 Ma): Insight from late kinematic plutons in the Wulian metamorphic core complex, Jiaodong Peninsula, eastern China
Authors: Ni Jinlong , Wang Ruijie , Liu Junlai , Wang Zhengzheng , Li Chaoyang , Ji Lei , Zhang Jian 
Published: February 2024

Abstract
The late Mesozoic subduction of the paleo-Pacific plate (Izanagi plate) beneath Eurasia involved complex changes in the direction and angle of subduction, which have been controversial in recent decades. This study investigated Early Cretaceous late kinematic plutons of the Wulian metamorphic core complex that formed in the southern Jiaodong Peninsula. Based on geochemical and Sr-Nd isotopic analyses, we conclude that the granites in the Heshan (122 Ma) and Kuaijishan (118 Ma) plutons are I-type granites that formed in a back-arc extensional environment, and tensile fractures played an important role in the process of magma emplacement. Gravity anomaly inversion revealed the significant role of tension fractures in the uplift of the late kinematic plutons. Analysis of magnetic fabrics showed that the dominant plunging direction of magnetic lineation in the late kinematic plutons is NW-SE (127°–307°), while the plunging direction of the mineral stretching lineation in the wall rock is nearly E-W (102°–282°). We posit that the extensional stress field in the Jiaodong Peninsula underwent a significant transformation during the Early Cretaceous period, specifically from 135 Ma to 122 Ma, when it was dominated by a regional E-W or WNW-ESE extensional stress field. Later, from 122 Ma to 118 Ma, the stress field was controlled by a NW-SE extensional stress field. This variation in the regional stress field in the Jiaodong Peninsula indirectly indicates the changing subduction and slab rollback direction of the paleo-Pacific plate. From 135 Ma to 122 Ma, the paleo-Pacific plate subducted beneath Eurasia along a WNW-ESE direction. However, back-arc extension and slab rollback led to extensive extension in the Jiaodong Peninsula. Subsequently, the subduction direction of the paleo-Pacific plate shifted to the NW, with rollback occurring eastward at a high angle under the Jiaodong Peninsula from 122 Ma to 118 Ma. This shift resulted in extensive magmatism and widespread gold mineralization. The findings of this study offer new insights into the complex geodynamic processes that occurred during the Early Cretaceous period in the region.
Paediatric norms for photopic electroretinogram testing based on a large cohort of Chinese preschool children
Authors: Chan Sonia Seen-hang , Choi Kai Yip , Chan Henry Ho-lung 
Published: February 2024

ObjectiveFull-field electroretinogram (ffERG) is an objective test to determine the electroretinal activities in response to light stimulation for investigating retinal physiology and diagnosing retinal diseases. This study aimed to establish a reference data set of photopic electroretinogram (ERG) of Chinese preschool children in Hong Kong to facilitate clinical and research studies.Methods and analysisPreschool children aged 3–7 years with normal vision were recruited from local kindergartens. Eye examinations, including cycloplegic spherical equivalent refraction (SER), axial length (AL) and keratometry (K) measurements, were performed. ffERGs of the International Society for Clinical Electrophysiology of Vision (ISCEV) standard photopic flash and 30-Hz flicker protocols were measured using RETeval with Sensor Strip skin electrodes. ERG waveform characteristics were extracted, and relationships between ERG, age, SER, AL and K were evaluated.ResultsA total of 479 children completed the measurements (mean age: 5.0±0.9 years, 45.5% female). Mean, 95% CIs, 5th–95th percentile range of the ERG parameters were reported. Age was positively associated with amplitudes of b-wave and 30-Hz flicker (p<0.01), but negatively associated with implicit times of b-wave and 30-Hz flicker (p<0.01). AL was significantly associated with all amplitudes of a-wave, b-wave and 30-Hz flicker (p≤0.01) and implicit time of both a-wave and 30-Hz flicker (p<0.05). K was positively associated only with 30-Hz flicker amplitude (p=0.01), and no association between all responses and SER.ConclusionReference data set of photopic ERG of Chinese preschool children was established. Cross-sectional investigations revealed associations between ERG, age, SER and AL, which were speculated to further implicate the role of retina in refractive error development.
Genetic analysis of ocular tumour-associated genes using large genomic datasets: insights into selection constraints and variant representation in the population
Authors: Tanner Alexander , Sagoo Mandeep S , Mahroo Omar A , Pulido Jose S 
Published: February 2024

BackgroundLarge genomic databases enable genetic evaluation in terms of haploinsufficiency and prevalence of missense and synonymous variants. We explored these parameters in ocular tumour-associated genes.MethodsA curated list of ocular tumour-associated genes was assessed using the genomic databases Genome Aggregation Database (gnomAD) and DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources (DECIPHER) and compared with breast and lung cancer-associated gene lists. Haploinsufficiency was determined based on specific criteria: probability of loss of function index ≥0.9 in gnomAD, upper CI O/E limit <0.35 for loss of function variants in gnomAD and/or a DECIPHER pHaplo ≥0.86. UniProt was used for further gene characterisation, and gene ontology Protein Analysis THrough Evolutionary Relationships was explored for common biological pathways. In addition, we identified genes with under-representation/over-representation of missense/synonymous variants.ResultsFifty-seven genes were identified in association with ocular and extraocular tumours.Regarding haploinsufficiency, 41% of genes met the criteria for negative selection, with 57% categorised as tumour-suppressing and 39% as oncogenic. Most genes were involved in regulatory processes. Regarding triplosensitivity, 33% of genes reached significance and 83% of these were haploinsufficient. Analysis of variants revealed under-representation of missense variants in 23% of genes and over-representation of synonymous variants in 5% of genes. Ocular tumour-associated genes exhibited higher scores for haploinsufficiency and triplosensitivity compared with breast and lung cancer-associated genes. Pathway analysis revealed significant enrichment in cellular proliferation, differentiation and division. Encoded proteins of ocular tumour-associated genes were generally longer than the median of the UniProt database.ConclusionOur findings highlight the importance of negative selection in ocular tumour genes, supporting cranial gene conservation. This study provides insights into ocular tumourigenesis and future research avenues.
Association between statin use and tuberculosis risk in patients with bronchiectasis: a retrospective population-based cohort study in Taiwan
Authors: Liao Kuang-Ming , Lee Chung-Shu , Wu Yu-Cih , Shu Chin-Chung , Ho Chung-Han 
Published: February 2024

BackgroundChronic airway diseases have been associated with an increased risk of tuberculosis (TB); however, data in patients with bronchiectasis is limited. Statins have been shown to exhibit anti-inflammatory effects by modulating the inflammatory response. This study investigated whether statin treatment could reduce the risk of TB in patients with bronchiectasis.MethodsWe conducted a retrospective cohort study using a nationwide population database of patients with bronchiectasis who did or did not receive statin treatment. The defined daily dose (DDD) of statin, current or past statin user and statin exposure time were measured for the impact of statin use. The primary outcome was the incidence of new-onset TB. Considering of potential immortal time bias due to stain exposure time, Cox regression models with time-dependent covariates were employed to estimate HRs with 95% CIs for TB incidence among patients with bronchiectasis.ResultsPatients with bronchiectasis receiving statin treatment had a decreased risk of TB. After adjusting for age, sex, income, comorbidities and Charlson Comorbidity Index, statin users had a 0.59-fold lower risk of TB incidence compared with non-statin users (95% CI 0.40 to 0.88; p=0.0087). Additionally, compared with non-statin users, statin treatment was a protective factor against TB in users with a cumulative DDD greater than 180 per year, with an HR of 0.32 (95% CI 0.12 to 0.87; p=0.0255).ConclusionsStatin treatment demonstrated a dose-dependent protective effect and was associated with a reduced risk of TB in patients with bronchiectasis. These findings suggest that statins may play a role in lowering TB risk by modulating airway inflammation in this patient population.
Comprehensive analysis of environmental exposure to hazardous trace elements and lung function: a national cross-sectional study
Authors: Yu Yun-Jiang , Zheng Tong , Perret Jennifer L , Han Yajing , Li Hongyan , Meng Wenjie , Bui Dinh , Wu Qi-Zhen , Dong Chenyin , Fang Qiu-Ling , Li Zhenchi , Kuang Hongxuan , Chen Xiaowen , Xiang Mingdeng , Qin Xiaodi , Dharmage Shyamali C , Dong Guang-Hui , Zhou Yang 
Published: February 2024

BackgroundThere is growing interest in the joint effects of hazardous trace elements (HTEs) on lung function deficits, but the data are limited. This is a critical research gap given increased global industrialisation.MethodsA national cross-sectional study including spirometry was performed among 2112 adults across 11 provinces in China between 2020 and 2021. A total of 27 HTEs were quantified from urine samples. Generalised linear models and quantile-based g-computation were used to explore the individual and joint effects of urinary HTEs on lung function, respectively.ResultsOverall, there were negative associations between forced expiratory volume in 1 s (FEV1) and urinary arsenic (As) (z-score coefficient, −0.150; 95% CI, −0.262 to –0.038 per 1 ln-unit increase), barium (Ba) (−0.148, 95% CI: −0.258 to –0.039), cadmium (Cd) (−0.132, 95% CI: −0.236 to –0.028), thallium (Tl) (−0.137, 95% CI: −0.257 to –0.018), strontium (Sr) (−0.147, 95% CI: −0.273 to –0.022) and lead (Pb) (−0.121, 95% CI: −0.219 to –0.023). Similar results were observed for forced vital capacity (FVC) with urinary As, Ba and Pb and FEV1/FVC with titanium (Ti), As, Sr, Cd, Tl and Pb. We found borderline associations between the ln-quartile of joint HTEs and decreased FEV1(−20 mL, 95% CI: −48 to +8) and FVC (−14 mL, 95% CI: −49 to+2). Ba and Ti were assigned the largest negative weights for FEV1and FVC within the model, respectively.ConclusionOur study investigating a wide range of HTEs in a highly polluted setting suggests that higher urinary HTE concentrations are associated with lower lung function, especially for emerging Ti and Ba, which need to be monitored or regulated to improve lung health.
Mapping the Earth's igneous record: a geospatial database approach
Authors: Markwick Paul J. , Paton Douglas A. 
Published: February 2024

Abstract

The record of igneous activity (magmatism and volcanism) can significantly affect natural resource exploration and exploitation, including the search for hydrocarbons, critical minerals, natural hydrogen and geothermal energy sources, as well as using mafic igneous rocks as storage sites for CO
2
. These effects will vary depending on the nature and timing of the activity, the structural framework and the crustal architecture of the affected country-rock. To understand these effects and the interplay with other factors, we must first know the igneous record's distribution, timing, and petrology. In this paper, we describe a new geospatial database of the igneous rock record designed to provide a baseline digital resource that is application-agnostic and can be applied across the broadest range of research and resource exploration activities. We discuss the challenges we have faced and solved at each of the three main stages of geospatial mapping: database design, database population and database visualization. This includes the importance of a comprehensive audit trail so that users can differentiate between well and poorly-constrained interpretations, helping identify areas requiring additional work and data acquisition. The result is a geospatial database that will facilitate a better understanding of the Earth system and natural resource exploration.
Broad Next-Generation Integrated Sequencing of Myelofibrosis Identifies Disease-Specific and Age-Related Genomic Alterations
Authors: Kandarpa Malathi , Robinson Dan , Wu Yi-Mi , Qin Tingting , Pettit Kristen , Li Qing , Luker Gary , Sartor Maureen , Chinnaiyan Arul , Talpaz Moshe 
Published: February 2024

Abstract

Purpose:
Myeloproliferative neoplasms (MPN) are characterized by the overproduction of differentiated myeloid cells. Mutations in JAK2, CALR, and MPL are considered drivers of Bcr-Abl−ve MPN, including essential thrombocythemia (ET), polycythemia vera (PV), prefibrotic primary myelofibrosis (prePMF), and overt myelofibrosis (MF). However, how these driver mutations lead to phenotypically distinct and/or overlapping diseases is unclear.

Experimental Design:
To compare the genetic landscape of MF to ET/PV/PrePMF, we sequenced 1,711 genes for mutations along with whole transcriptome RNA sequencing of 137 patients with MPN.

Results:
In addition to driver mutations, 234 and 74 genes were found to be mutated in overt MF (N = 106) and ET/PV/PrePMF (N = 31), respectively. Overt MF had more mutations compared with ET/PV/prePMF (5 vs. 4 per subject, P = 0.006). Genes frequently mutated in MF included high-risk genes (ASXL1, SRSF2, EZH2, IDH1/2, and U2AF1) and Ras pathway genes. Mutations in NRAS, KRAS, SRSF2, EZH2, IDH2, and NF1 were exclusive to MF. Advancing age, higher DIPSS, and poor overall survival (OS) correlated with increased variants in MF. Ras mutations were associated with higher leukocytes and platelets and poor OS. The comparison of gene expression showed upregulation of proliferation and inflammatory pathways in MF. Notably, ADGRL4, DNASE1L3, PLEKHGB4, HSPG2, MAMDC2, and DPYSL3 were differentially expressed in hematopoietic stem and differentiated cells.

Conclusions:
Our results illustrate that evolution of MF from ET/PV/PrePMF likely advances with age, accumulation of mutations, and activation of proliferative pathways. The genes and pathways identified by integrated genomics approach provide insight into disease transformation and progression and potential targets for therapeutic intervention.
Attribution of Moisture Sources for Summer Precipitation in the Upstream Catchment of the Three Gorges Dam
Authors: Shao Shuaibing , Zeng Xin-Min , Wang Ning , Ullah Irfan , Lv Haishen 
Published: February 2024

Abstract
Currently, there is a lack of investigating moisture sources for precipitation over the upstream catchment of the Three Gorges Dam (UCTGD), the world’s largest dam. Using the dynamical recycling model (DRM), trajectory frequency method (TFM), and the Climate Forecast System Reanalysis (CFSR), this study quantifies moisture sources and transport paths for UCTGD summer precipitation from 1980 to 2009 based on two categories of sources: region-specific and source-direction. Overall, the land and oceanic sources contribute roughly 63% and 37%, respectively, of the moisture to UCTGD summer precipitation. UCTGD and the Indian Ocean are the most important land and oceanic sources, respectively, in which the southern Indian Ocean with over 10% of moisture contribution was overlooked previously. Under the influence of the Asian monsoon and prevailing westerlies, the land contribution decreases to 57.3% in June, then gradually increases to 68.8%. It is found that for drought years with enhanced southwest monsoon, there is a weakening of the moisture contribution from the C-shaped belt along the Arabian Sea, South Asia, and UCTGD, and vice versa. TFM results show three main moisture transport paths and highlight the importance of moisture from the southwest. Comparison analysis indicates that, generally, sink regions are more affected by land evaporation with their locations more interior to the center of the mainland. Furthermore, correlations between moisture contributions and indices of general circulation and sea surface temperature are investigated, suggesting that these indices affect precipitation by influencing moisture contributions of the subregions. All of these are useful for comprehending the causes of summer UCTGD precipitation.

Significance Statement
Quantitative research on the moisture sources of summer precipitation has been implemented for the upstream catchment of the Three Gorges Dam (UCTGD), which is of particular hydrological significance but has not been investigated previously. The dynamical recycling model (DRM)–trajectory frequency method (TFM) approach is used to quantify and interpret the results of the moisture sources both in different specific subregions and directions, which produce more meaningful results than a single method for the areal division of moisture sources. Furthermore, antecedent indices that significantly influence the following moisture contributions of the subregions and then summer UCTGD precipitation are studied in terms of large-scale general circulation indices, which would help our understanding of precipitation forecast for UCTGD.
Common femoral vein wall thickness measurement by Doppler ultrasonography is an accurate diagnostic test for Behçet’s Disease both in supine and standing positions
Authors: Ergelen Rabia , Kutluğ Ağaçkıran Seda , Direskeneli Haner , Alibaz-Oner Fatma 
Published: February 2024

Objectives We recently reported the first controlled Doppler ultrasonography (US) study demonstrating increased common femoral vein (CFV) thickness in Behçet’s Disease (BD). Standard lower extremity venous Doppler US is performed in erect position. In order to confirm accuracy and applicability of method, we measured CFV thickness in both supine and standing positions in this study. Method We included sex and age-matched 42 BD patients and 41 healthy controls (HCs). After routine visits, bilateral CFV thickness was measured with Doppler US both in supine and standing positions. Results Bilateral CFV thickness was significantly higher in BD than in HC. There were no statistically significant differences in measurements of CFV wall thickness between standing and supine positions in both groups. Conclusions CFV measurement by Doppler US is a new and non-invasive diagnostic tool for the diagnosis of BD. Our study confirmed that patient position does not affect CFV wall thickness measurement for diagnosis of BD.
Effects of the Omaha System- and HeartScore®-Based Impaired-Risk Perception Reduction Program on the Risk Perception of Individuals Aged 50–65 Years: A One-Group Pre-Test–Post-Test Study
Authors: Akgöz Ayşe Dağıstan , Gözüm Sebahat 
Published: February 2024

Purpose This study evaluates the impact of interventions in the Omaha System and HeartScore®-based program to reduce impaired-risk perception. Design and setting: This study utilized a one-group pre-test–post-test design. Subjects The program was conducted among participants aged over 50 years from different social settings. Intervention The program had three parts: a briefing on HeartScore® recommendations, Omaha System interventions, and referral to a doctor. Measures HeartScore® determined cardiovascular disease (CVD) risk, body mass index (BMI) was calculated from height and weight, and the International PA Questionnaire evaluated physical activity (PA) levels. Self-assessment was used to perceived CVD risk, BMI, and PA. Analysis We used the Wilcoxon signed-rank test to compare the pre-test and post-test scores of the Omaha System, the problem rating scale (PRS) subscales and McNemar test to measure changes in CVD risk perception, BMI, and PA level. Results 310 high-risk individuals out of 522 had impaired perception of their CVD risk. Only 201 responded to follow-up phone calls. Interventions based on HeartScore® and Omaha System improved CVD risk and PA perceptions ( P < .001) but not BMI. The program significantly increased knowledge, status, and behavior scores ( P < .001). After participating, 39% saw a cardiologist, and 57.2% saw a family physician within six months to reduce impaired risk perception. CVD risk perception increased to the actual level after the intervention, mostly in the group with low education level. Conclusions The program using the Omaha System and HeartScore® can help middle-aged individuals better understand their risk of cardiovascular disease.