bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short reads-based characterization of pathotype diversity and drug resistance among Escherichia coli isolated from patients attending regional referral hospitals in Tanzania
Authors: Kanje Livin E. , Kumburu Happiness , Kuchaka Davis , Shayo Mariana , Juma Masoud A. , Kimu Patrick , Beti Melkiory , van Zwetselaar Marco , Wadugu Boaz , Mmbaga Blandina T. , Mkumbaye Sixbert Isdory , Sonda Tolbert 
Published: April 2024

Abstract
Background
Escherichia coli is known to cause about 2 million deaths annually of which diarrhea infection is leading and typically occurs in children under 5 years old. Although Africa is the most affected region there is little information on their pathotypes diversity and their antimicrobial resistance.

Objective
To determine the pathotype diversity and antimicrobial resistance among E. coli from patients attending regional referral hospitals in Tanzania.

Materials and methods
A retrospective cross-section laboratory-based study where a total of 138 archived E. coli isolates collected from 2020 to 2021 from selected regional referral hospitals in Tanzania were sequenced using the Illumina Nextseq550 sequencer platform. Analysis of the sequences was done in the CGE tool for the identification of resistance genes and virulence genes. SPSS version 20 was used to summarize data using frequency and proportion.

Results
Among all 138 sequenced E. coli isolates, the most prevalent observed pathotype virulence genes were of extraintestinal E. coli UPEC fyuA gene 82.6% (114/138) and NMEC irp gene 81.9% (113/138). Most of the E. coli pathotypes observed exist as a hybrid due to gene overlapping, the most prevalent pathotypes observed were NMEC/UPEC hybrid 29.7% (41/138), NMEC/UPEC/EAEC hybrid 26.1% (36/138), NMEC/UPEC/DAEC hybrid 18.1% (25/138) and EAEC 15.2% (21/138). Overall most E. coli carried resistance gene to ampicillin 90.6% (125/138), trimethoprim 85.5% (118/138), tetracycline 79.9% (110/138), ciprofloxacin 76.1% (105/138) and 72.5% (100/138) Nalidixic acid. Hybrid pathotypes were more resistant than non-hybrid pathotypes.

Conclusion
Whole genome sequencing reveals the presence of hybrid pathotypes with increased drug resistance among E. coli isolated from regional referral hospitals in Tanzania.
DEC1 is involved in circadian rhythm disruption-exacerbated pulmonary fibrosis
Authors: Chen Shuai-Jun , Yu Fan , Feng Xiao , Li Qian , Jiang Ye-Han , Zhao Li-Qin , Cheng Pei-Pei , Wang Meng , Song Lin-Jie , Liang Li-Mei , He Xin-Liang , Xiong Liang , Xiang Fei , Wang Xiaorong , Ye Hong , Ma Wan-Li 
Published: April 2024

Abstract
Background
The alveolar epithelial type II cell (AT2) and its senescence play a pivotal role in alveolar damage and pulmonary fibrosis. Cell circadian rhythm is strongly associated with cell senescence. Differentiated embryonic chondrocyte expressed gene 1 (DEC1) is a very important circadian clock gene. However, the role of DEC1 in AT2 senescence and pulmonary fibrosis was still unclear.

Results
In this study, a circadian disruption model of light intervention was used. It was found that circadian disruption exacerbated pulmonary fibrosis in mice. To understand the underlying mechanism, DEC1 levels were investigated. Results showed that DEC1 levels increased in lung tissues of IPF patients and in bleomycin-induced mouse fibrotic lungs. In vitro study revealed that bleomycin and TGF-β1 increased the expressions of DEC1, collagen-I, and fibronectin in AT2 cells. Inhibition of DEC1 mitigated bleomycin-induced fibrotic changes in vitro and in vivo. After that, cell senescence was observed in bleomycin-treated AT2 cells and mouse models, but these were prevented by DEC1 inhibition. At last, p21 was confirmed having circadian rhythm followed DEC1 in normal conditions. But bleomycin disrupted the circadian rhythm and increased DEC1 which promoted p21 expression, increased p21 mediated AT2 senescence and pulmonary fibrosis.

Conclusions
Taken together, circadian clock protein DEC1 mediated pulmonary fibrosis via p21 and cell senescence in alveolar epithelial type II cells.
The clinical relevance of different antiphospholipid antibody profiles in pediatric rheumatology patients
Authors: Pandya Jheel , Onel Karen , Erkan Doruk 
Published: April 2024

Abstract
Background
The clinical relevance of different antiphospholipid antibody (aPL) profiles, including low level anticardiolipin (aCL) and anti-β2-glycoprotein-I (aβ2GPI) antibodies, is ill-defined in the pediatric population. Our purpose is to describe the demographic, clinical, and laboratory characteristics of aPL positive pediatric patients based on different aPL profiles.

Findings
In this single center retrospective cohort study, based on the screening of our pediatric (age ≤ 18) rheumatology electronic medical records (2016–2022), we identified patients who had at least one “positive” aPL (lupus anticoagulant [LA], aCL IgG/M, or aβ2GPI IgG/M) result. Patients were grouped into high- (LA positive and/or aCL/aβ2GPI IgG/M > 40U [ELISA]) and low-risk (LA negative and aCL/aβ2GPI IgG/M 20-39U) aPL profiles; those with persistently positive aPL were descriptively analyzed for demographic and clinical characteristics. Of 57 included patients, 34 (59%) had initial high- and 23 (40%) had initial low-risk profiles. Based on subsequent aPL results available in 42/57 (74%) patients, 25/27 (93%) in the high-, and 7/15 (47%) in the low-risk groups remained still positive. Of these 32 patients with persistently positive aPL, moderate-to-large vessel or microvascular thrombosis occurred in nine (28%) patients with high-risk and in none with low-risk aPL profiles; non-thrombotic aPL-related manifestations were reported in 15 (47%) patients with persistent aPL positivity.

Conclusion
An initial high-risk aPL profile was persistent in approximately 90% of our cohort, a third of whom had thrombosis, and half had non-thrombotic aPL manifestations. Our results underscore the need for a large-scale effort to better characterize aPL-related manifestations in pediatric patients with persistent high-risk aPL-profiles.
Presepsin as a prognostic biomarker in COVID-19 patients: combining clinical scoring systems and laboratory inflammatory markers for outcome prediction
Authors: Wu Zhipeng , Geng Nan , Liu Zhao , Pan Wen , Zhu Yueke , Shan Jing , Shi Hongbo , Han Ying , Ma Yingmin , Liu Bo 
Published: April 2024

Abstract
Background
There is still limited research on the prognostic value of Presepsin as a biomarker for predicting the outcome of COVID-19 patients. Additionally, research on the combined predictive value of Presepsin with clinical scoring systems and inflammation markers for disease prognosis is lacking.

Methods
A total of 226 COVID-19 patients admitted to Beijing Youan Hospital’s emergency department from May to November 2022 were screened. Demographic information, laboratory measurements, and blood samples for Presepsin levels were collected upon admission. The predictive value of Presepsin, clinical scoring systems, and inflammation markers for 28-day mortality was analyzed.

Results
A total of 190 patients were analyzed, 83 (43.7%) were mild, 61 (32.1%) were moderate, and 46 (24.2%) were severe/critically ill. 23 (12.1%) patients died within 28 days. The Presepsin levels in severe/critical patients were significantly higher compared to moderate and mild patients (p < 0.001). Presepsin showed significant predictive value for 28-day mortality in COVID-19 patients, with an area under the ROC curve of 0.828 (95% CI: 0.737–0.920). Clinical scoring systems and inflammation markers also played a significant role in predicting 28-day outcomes. After Cox regression adjustment, Presepsin, qSOFA, NEWS2, PSI, CURB-65, CRP, NLR, CAR, and LCR were identified as independent predictors of 28-day mortality in COVID-19 patients (all p-values < 0.05). Combining Presepsin with clinical scoring systems and inflammation markers further enhanced the predictive value for patient prognosis.

Conclusion
Presepsin is a favorable indicator for the prognosis of COVID-19 patients, and its combination with clinical scoring systems and inflammation markers improved prognostic assessment.
Research progress in the pathogenesis of hormone-induced femoral head necrosis based on microvessels: a systematic review
Authors: Ma Tiancheng , Wang Yan , Ma Jianxiong , Cui Hongwei , Feng Xiaotian , Ma Xinlong 
Published: April 2024

AbstractHormonal necrosis of the femoral head is caused by long-term use of glucocorticoids and other causes of abnormal bone metabolism, lipid metabolism imbalance and blood microcirculation disorders in the femoral head, resulting in bone trabecular fracture, bone tissue necrosis collapse, and hip dysfunction. It is the most common type of non-traumatic necrosis of the femoral head, and its pathogenesis is complex, while impaired blood circulation is considered to be the key to its occurrence. There are a large number of microvessels in the femoral head, among which H-type vessels play a decisive role in the “angiogenesis and osteogenesis coupling”, and thus have an important impact on the occurrence and development of femoral head necrosis. Glucocorticoids can cause blood flow injury of the femoral head mainly through coagulation dysfunction, endothelial dysfunction and impaired angiogenesis. Glucocorticoids may inhibit the formation of H-type vessels by reducing the expression of HIF-1α, PDGF-BB, VGEF and other factors, thus causing damage to the “angiogenesis-osteogenesis coupling” and reducing the ability of necrosis reconstruction and repair of the femoral head. Leads to the occurrence of hormonal femoral head necrosis. Therefore, this paper reviewed the progress in the study of the mechanism of hormone-induced femoral head necrosis based on microvascular blood flow at home and abroad, hoping to provide new ideas for the study of the mechanism of femoral head necrosis and provide references for clinical treatment of femoral head necrosis.
Carbon sequestration costs and spatial spillover effects in China's collective forests
Authors: Zhou Yifan , Xue Caixia , Liu Shuohua , Zhang Jinrong 
Published: April 2024

Abstract
Background
Global climate change is one of the major challenges facing the world today, and forests play a crucial role as significant carbon sinks and providers of ecosystem services in mitigating climate change and protecting the environment. China, as one of the largest developing countries globally, owns 60% of its forest resources collectively. Evaluating the carbon sequestration cost of collective forests not only helps assess the contribution of China’s forest resources to global climate change mitigation but also provides important evidence for formulating relevant policies and measures.

Results
Over the past 30 years, the carbon sequestration cost of collective forests in China has shown an overall upward trend. Except for coastal provinces, southern collective forest areas, as well as some southwestern and northeastern regions, have the advantage of lower carbon sequestration costs. Furthermore, LSTM network predictions indicate that the carbon sequestration cost of collective forests in China will continue to rise. By 2030, the average carbon sequestration cost of collective forests is projected to reach 125 CNY per ton(= 16.06 Euros/t). Additionally, there is spatial correlation in the carbon sequestration cost of collective forests. Timber production, labor costs, and labor prices have negative spatial spillover effects on carbon sequestration costs, while land opportunity costs, forest accumulation, and rural resident consumption have positive spatial spillover effects.

Conclusion
The results of this study indicate regional disparities in the spatial distribution of carbon sequestration costs of collective forests, with an undeniable upward trend in future cost growth. It is essential to focus on areas with lower carbon sequestration costs and formulate targeted carbon sink economic policies and management measures to maximize the carbon sequestration potential of collective forests and promote the sustainable development of forestry.
Clinical manifestation, epidemiology, genetic basis, potential molecular targets, and current treatment of polycystic liver disease
Authors: Mahboobipour Amir Ali , Ala Moein , Safdari Lord Javad , Yaghoobi Arash 
Published: April 2024

AbstractPolycystic liver disease (PLD) is a rare condition observed in three genetic diseases, including autosomal dominant polycystic liver disease (ADPLD), autosomal dominant polycystic kidney disease (ADPKD), and autosomal recessive polycystic kidney disease (ARPKD). PLD usually does not impair liver function, and advanced PLD becomes symptomatic when the enlarged liver compresses adjacent organs or increases intra-abdominal pressure. Currently, the diagnosis of PLD is mainly based on imaging, and genetic testing is not required except for complex cases. Besides, genetic testing may help predict patients’ prognosis, classify patients for genetic intervention, and conduct early treatment. Although the underlying genetic causes and mechanisms are not fully understood, previous studies refer to primary ciliopathy or impaired ciliogenesis as the main culprit. Primarily, PLD occurs due to defective ciliogenesis and ineffective endoplasmic reticulum quality control. Specifically, loss of function mutations of genes that are directly involved in ciliogenesis, such as Pkd1, Pkd2, Pkhd1, and Dzip1l, can lead to both hepatic and renal cystogenesis in ADPKD and ARPKD. In addition, loss of function mutations of genes that are involved in endoplasmic reticulum quality control and protein folding, trafficking, and maturation, such as PRKCSH, Sec63, ALG8, ALG9, GANAB, and SEC61B, can impair the production and function of polycystin1 (PC1) and polycystin 2 (PC2) or facilitate their degradation and indirectly promote isolated hepatic cystogenesis or concurrent hepatic and renal cystogenesis. Recently, it was shown that mutations of LRP5, which impairs canonical Wnt signaling, can lead to hepatic cystogenesis. PLD is currently treated by somatostatin analogs, percutaneous intervention, surgical fenestration, resection, and liver transplantation. In addition, based on the underlying molecular mechanisms and signaling pathways, several investigational treatments have been used in preclinical studies, some of which have shown promising results. This review discusses the clinical manifestation, complications, prevalence, genetic basis, and treatment of PLD and explains the investigational methods of treatment and future research direction, which can be beneficial for researchers and clinicians interested in PLD.
SF3B3-regulated mTOR alternative splicing promotes colorectal cancer progression and metastasis
Authors: Xu Tong , Li Xichuan , Zhao Wennan , Wang Xue , Jin Leixin , Feng Zhiqiang , Li Huixiang , Zhang Mingzhe , Tian Yiqing , Hu Ge , Yue Yuan , Dai Xintong , Shan Changliang , Zhang Weihua , Zhang Chunze , Zhang Youcai 
Published: April 2024

Abstract
Background
Aberrant alternative splicing (AS) is a pervasive event during colorectal cancer (CRC) development. SF3B3 is a splicing factor component of U2 small nuclear ribonucleoproteins which are crucial for early stages of spliceosome assembly. The role of SF3B3 in CRC remains unknown.

Methods
SF3B3 expression in human CRCs was analyzed using publicly available CRC datasets, immunohistochemistry, qRT-PCR, and western blot. RNA-seq, RNA immunoprecipitation, and lipidomics were performed in SF3B3 knockdown or overexpressing CRC cell lines. CRC cell xenografts, patient-derived xenografts, patient-derived organoids, and orthotopic metastasis mouse models were utilized to determine the in vivo role of SF3B3 in CRC progression and metastasis.

Results
SF3B3 was upregulated in CRC samples and associated with poor survival. Inhibition of SF3B3 by RNA silencing suppressed the proliferation and metastasis of CRC cells in vitro and in vivo, characterized by mitochondria injury, increased reactive oxygen species (ROS), and apoptosis. Mechanistically, silencing of SF3B3 increased mTOR exon-skipped splicing, leading to the suppression of lipogenesis via mTOR-SREBF1-FASN signaling. The combination of SF3B3 shRNAs and mTOR inhibitors showed synergistic antitumor activity in patient-derived CRC organoids and xenografts. Importantly, we identified SF3B3 as a critical regulator of mTOR splicing and autophagy in multiple cancers.

Conclusions
Our findings revealed that SF3B3 promoted CRC progression and metastasis by regulating mTOR alternative splicing and SREBF1-FASN-mediated lipogenesis, providing strong evidence to support SF3B3 as a druggable target for CRC therapy.
The skåne emergency medicine (SEM) cohort
Authors: Ekelund Ulf , Ohlsson Bodil , Melander Olle , Björk Jonas , Ohlsson Mattias , Forberg Jakob Lundager , de Capretz Pontus Olsson , Nyström Axel , Björkelund Anders 
Published: April 2024

Abstract
Background
In the European Union alone, more than 100 million people present to the emergency department (ED) each year, and this has increased steadily year-on-year by 2–3%. Better patient management decisions have the potential to reduce ED crowding, the number of diagnostic tests, the use of inpatient beds, and healthcare costs.

Methods
We have established the Skåne Emergency Medicine (SEM) cohort for developing clinical decision support systems (CDSS) based on artificial intelligence or machine learning as well as traditional statistical methods. The SEM cohort consists of 325 539 unselected unique patients with 630 275 visits from January 1st, 2017 to December 31st, 2018 at eight EDs in the region Skåne in southern Sweden. Data on sociodemographics, previous diseases and current medication are available for each ED patient visit, as well as their chief complaint, test results, disposition and the outcome in the form of subsequent diagnoses, treatments, healthcare costs and mortality within a follow-up period of at least 30 days, and up to 3 years.

Discussion
The SEM cohort provides a platform for CDSS research, and we welcome collaboration. In addition, SEM’s large amount of real-world patient data with almost complete short-term follow-up will allow research in epidemiology, patient management, diagnostics, prognostics, ED crowding, resource allocation, and social medicine.
Polygenic scores for longitudinal prediction of incident type 2 diabetes in an ancestrally and medically diverse primary care physician network: a patient cohort study
Authors: Mandla Ravi , Schroeder Philip , Porneala Bianca , Florez Jose C. , Meigs James B. , Mercader Josep M. , Leong Aaron 
Published: April 2024

Abstract
Background
The clinical utility of genetic information for type 2 diabetes (T2D) prediction with polygenic scores (PGS) in ancestrally diverse, real-world US healthcare systems is unclear, especially for those at low clinical phenotypic risk for T2D.

Methods
We tested the association of PGS with T2D incidence in patients followed within a primary care practice network over 16 years in four hypothetical scenarios that varied by clinical data availability (N = 14,712): (1) age and sex; (2) age, sex, body mass index (BMI), systolic blood pressure, and family history of T2D; (3) all variables in (2) and random glucose; and (4) all variables in (3), HDL, total cholesterol, and triglycerides, combined in a clinical risk score (CRS). To determine whether genetic effects differed by baseline clinical risk, we tested for interaction with the CRS.

Results
PGS was associated with incident T2D in all models. Adjusting for age and sex only, the Hazard Ratio (HR) per PGS standard deviation (SD) was 1.76 (95% CI 1.68, 1.84) and the HR of top 5% of PGS vs interquartile range (IQR) was 2.80 (2.39, 3.28). Adjusting for the CRS, the HR per SD was 1.48 (1.40, 1.57) and HR of the top 5% of PGS vs IQR was 2.09 (1.72, 2.55). Genetic effects differed by baseline clinical risk ((PGS-CRS interaction p = 0.05; CRS below the median: HR 1.60 (1.43, 1.79); CRS above the median: HR 1.45 (1.35, 1.55)).

Conclusions
Genetic information can help identify high-risk patients even among those perceived to be low risk in a clinical evaluation.
Successful preimplantation genetic testing for fibrodysplasia ossificans progressiva: a case report
Authors: Murugesu Sughashini , Jones Benjamin P. , Serhal Paul , Ben-Nagi Jara 
Published: April 2024

Abstract
Purpose of the study
Fibrodysplasia ossificans progressiva (FOP) is a rare autosomal dominant condition that leads to significant disability and morbidity, characterised by the formation of heterotopic hard tissues within connective tissues. The condition has an incidence of approximately one per two million people worldwide. There is no known single effective treatment available for FOP. We report the world’s first case of a healthy infant born following in vitro fertilisation (IVF) and preimplantation genetic testing for monogenic disorder (PGT-M) using Karyomapping for FOP.

Case presentation
A 30-year-old Caucasian female with FOP presented with her partner seeking IVF with PGT-M to achieve a healthy pregnancy with an embryo unaffected by FOP.

Methods
The couple underwent IVF and PGT-M using Karyomapping as the testing method. A multi-disciplinary team approach was utilised in planning this case, considering the additional risks of oocyte retrieval, pregnancy and childbirth in women with FOP.

Main findings
The oocyte retrieval was covered with a 5-day course of prednisolone to reduce the risk of a localised inflammatory reaction, which could result in subsequent heterotopic ossification. This was subsequently weaned down with reducing doses every two days. The patient underwent uncomplicated oocyte retrieval, yielding 12 mature oocytes. Following intracytoplasmic sperm injection (ICSI), ten zygotes having two pro-nuclei were cultured, and six underwent trophoectoderm biopsy and vitrification 5–6 days after retrieval. PGT-M via Karyomapping revealed four out of six (66.7%) of blastocysts were not carriers of the maternal high-risk FOP allele. In total, the patient had three separate embryo transfers. Pregnancy was achieved following the third frozen embryo transfer, which went to 37 weeks’ gestation, and delivered by Caesarean section. The baby was born in excellent condition and is unaffected by FOP.

Conclusion
IVF/ICSI and PGT-M using Karyomapping was successfully implemented to identify embryos carrying the high-risk FOP allele resulting in a healthy livebirth.
Classification of battery compounds using structure-free Mendeleev encodings
Authors: Zhuang Zixin , Barnard Amanda S. 
Published: April 2024

Abstract
Machine learning is a valuable tool that can accelerate the discovery and design of materials occupying combinatorial chemical spaces. However, the prerequisite need for vast amounts of training data can be prohibitive when significant resources are needed to characterize or simulate candidate structures. Recent results have shown that structure-free encoding of complex materials, based entirely on chemical compositions, can overcome this impediment and perform well in unsupervised learning tasks. In this study, we extend this exploration to supervised classification, and show how structure-free encoding can accurately predict classes of material compounds for battery applications without time consuming measurement of bonding networks, lattices or densities.

Scientific contribution
The comprehensive evaluation of structure-free encodings of complex materials in classification tasks, including binary and multi-class separation, inclusive of three classifiers based on different logic function, is measured four metrics and learning curves. The encoding is applied to two data sets from computational and experimental sources, and the outcomes visualised using 5 approaches to confirms the suitability and superiority of Mendeleev encoding. These methods are general and accessible using source software, to provide simple, intuitive and interpretable materials informatics outcomes to accelerate materials design.