bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing a nomogram for predicting acute complicated course in pediatric acute hematogenous osteomyelitis
Authors: Zhao Chaochen , Jiang Qizhi , Wu Wangqiang , Shen Yiming , Zhu Yujie , Wang Xiaodong 
Published: July 2024

Abstract
Background
The objective of this study was to develop and validate a nomogram for predicting the risk of an acute complicated course in pediatric patients with Acute Hematogenous Osteomyelitis (AHO).

Methods
A predictive model was developed based on a dataset of 82 pediatric AHO patients. Clinical data, imaging findings, and laboratory results were systematically collected for all patients. Subsequently, biomarker indices were calculated based on the laboratory results to facilitate a comprehensive evaluation. Univariate and multivariate logistic regression analyses were conducted to identify factors influencing early adverse outcomes in AHO. A nomogram model was constructed based on independent factors and validated internally through bootstrap methods. The discriminative ability, calibration, and clinical utility of the nomogram model were assessed using receiver operating characteristic (ROC) curves, calibration plots, and decision curve analysis (DCA), respectively. The developed nomogram model was compared with previously published A-score and Gouveia scoring systems.

Results
Logistic regression analysis identified delayed source control, suppurative arthritis, albumin on admission, and platelet to lymphocyte ratio (PLR) as independent predictors of early adverse outcomes in pediatric AHO patients. The logistic regression model was formulated as: Log(P) = 7. 667–1.752 × delayed source control − 1.956 × suppurative arthritis − 0.154 × albumin on admission + 0.009 × PLR. The nomogram’s AUC obtained through Bootstrap validation was 0.829 (95% CI: 0.740–0.918). Calibration plots showed good agreement between predictions and observations. Decision curve analysis demonstrated that the model achieved net benefits across all threshold probabilities. The predictive efficacy of our nomogram model for acute complicated course in pediatric AHO patients surpassed that of the A-score and Gouveia scores.

Conclusions
A predictive model for the acute complicated course of pediatric AHO was established based on four variables: delayed source control, suppurative arthritis, albumin on admission, and PLR. This model is practical, easy to use for clinicians, and can aid in guiding clinical treatment decisions.
RETRACTED ARTICLE: Early or delayed cord clamping during transition of term newborns: does it make any difference in cerebral tissue oxygenation?
Authors: Arcagok Baran Cengiz , Bilgen Hulya , Ozdemir Hulya , Memisoglu Asli , Save Dilsad , Ozek Eren 
Published: July 2024

Abstract
Background
According to the World Health Organization’s recommendation,
delayed cord clamping in term newborns can have various benefits. Cochrane
metaanalyses reported no differences for mortality and early neonatal morbidity
although a limited number of studies investigated long-term neurodevelopmental
outcomes. The aim of our study is to compare the postnatal cerebral tissue
oxygenation values in babies with early versus delayed cord clamping born after
elective cesarean section.

Methods
In this study, a total of 80 term newborns delivered by elective
cesarean section were included. Infants were randomly grouped as early (clamped
within 15 s, n:40) and delayed cord clamping (at the 60th second, n:40)
groups. Peripheral arterial oxygen saturation (SpO2) and heart rate were
measured by pulse oximetry while regional oxygen saturation of the brain (rSO2)
was measured with near-infrared spectrometer. Fractional tissue oxygen
extraction (FTOE) was calculated for every minute between the 3rd and 15th
minute after birth. (FTOE = pulse oximetry value-rSO2/pulse
oximetry value). The measurements were compared for both groups.

Results
The demographical characteristics, SpO2 levels (except postnatal
6th, 8th, and 14th minutes favoring DCC p < 0.05), heart rates and umbilical cord blood
gas values were not significantly different between the groups (p > 0.05). rSO2 values were
significantly higher while FTOE values were significantly lower for every minute
between the 3rd and 15th minutes after birth in the delayed cord clamping group
(p < 0.05).

Conclusion
Our study revealed a significant increase in cerebral rsO2 values
and a decrease in FTOE values in the delayed cord clamping (DCC) group,
indicating a positive impact on cerebral oxygenation and hemodynamics.
Furthermore, the DCC group exhibited a higher proportion of infants with
cerebral rSO2 levels above the 90th percentile. This higher proportion, along
with a lower of those with such parameter below the 10th percentile, suggest
that DCC may lead to the targeted/optimal cerebral oxygenetaion of these babies.
As a result, we recommend measuring cerebral oxygenation, in addition to
peripheral SpO2, for infants experiencing perinatal hypoxia and receiving
supplemental oxygen.
Mining alternative splicing patterns in scRNA-seq data using scASfind
Authors: Song Yuyao , Parada Guillermo , Lee Jimmy Tsz Hang , Hemberg Martin 
Published: July 2024

AbstractSingle-cell RNA-seq (scRNA-seq) is widely used for transcriptome profiling, but most analyses focus on gene-level events, with less attention devoted to alternative splicing. Here, we present scASfind, a novel computational method to allow for quantitative analysis of cell type-specific splicing events using full-length scRNA-seq data. ScASfind utilizes an efficient data structure to store the percent spliced-in value for each splicing event. This makes it possible to exhaustively search for patterns among all differential splicing events, allowing us to identify marker events, mutually exclusive events, and events involving large blocks of exons that are specific to one or more cell types.
Commentary: The North West London Clinical Trials Alliance: efficiency and innovation in clinical trial delivery
Authors: Kierkegaard Patrick , Su Bowen , Wong Richard , Boffito Marta , Balendra Suki 
Published: July 2024

Abstract
Background
The set-up, activation, and delivery of clinical trials is pivotal for the advancement of medical science, serving as the primary mechanism through which new therapeutic interventions are validated for clinical use. Despite their critical role, the execution of these trials is often encumbered by a multitude of challenges. The North West London Clinical Trials Alliance (The Alliance) was established to address these complexities. It aims to bridge the gap between emerging scientific research and its clinical application through strategic collaborations among healthcare and research entities, thereby enhancing the regional ecosystem for clinical trials.

Main text
This commentary aims to offer clarity on the fundamental insights that underlie The Alliance, providing a comprehensive understanding of its operational structure and the ecosystem it has fostered to optimise clinical trial delivery and revenue generation. The strategy employed by The Alliance centres on the cultivation of strategic partnerships across a broad spectrum of stakeholders. This approach addresses key operational challenges in clinical trial management, facilitating improvements in the development, setup, activation, and recruitment stages. Notably, The Alliance has reduced the average time to initiate trials to 19 days, compared to the standard 75 days typically observed for commercial setups in North West London. The effectiveness of The Alliance’s framework was notably demonstrated during the COVID-19 pandemic, particularly with the expedited recruitment performance in the Janssen COVID-19 vaccine study conducted at Charing Cross Hospital. This instance highlighted the Alliance’s capability to meet and exceed recruitment targets promptly while maintaining diversity within study cohorts. Additionally, The Alliance has effectively harnessed digital technology and infrastructure, enhancing its attractiveness to commercially funded studies and illustrating a sustainable model for clinical trial financing and execution.

Conclusion
The North West London Clinical Trials Alliance represents a strategic response to the conventional challenges faced in clinical trial management, emphasising the importance of cross-sectoral collaboration and resource optimisation. Its efforts, particularly highlighted by its response to the COVID-19 pandemic, provide a case study in enhancing trial delivery and efficiency with significant implications for both regional and global clinical trials research communities.
The association of inflammatory biomarkers with clinical outcomes in diabetic retinopathy participants: data from NHANES 2009–2018
Authors: Si Yueqiao , Chen Qingwei , Xiong XiaoJing , Zheng Minming 
Published: July 2024

Abstract
Objective
The aim of this study was to assess the association of neutrophil lymphocyte ratio (NLR), monocyte to lymphocyte ratio (MLR), and system inflammation response index (SIRI) with the all-cause mortality and diabetes-cardiovascular mortality in participants with diabetic retinopathy (DR).

Methods
A total of 572 participants with DR from NHANES were included, and divided into survival group (n = 440) and all-cause death group (n = 132). NLR = neutrophil count/lymphocyte count, MLR = monocyte count/lymphocyte count, SIRI = (neutrophil count × monocyte count)/lymphocyte count. We utilized the NHANES Public-Use Linked Mortality File through April 26, 2022, to determine mortality status. Diabetes-cardiovascular death was defined as death resulting from heart disease, cerebrovascular disease, or diabetes mellitus. The Spearson Correlation Analysis, Kaplan-Meier curves, Cox proportional hazards regression models, Restricted cubic spline plots and Decision Curve Analysis were used.

Results
The all-cause mortality and diabetes-cardiovascular mortality were significantly higher in NLR ≥ 1.516, MLR ≥ 0.309, SIRI ≥ 0.756, and NLR + MLR + SIRI subgroups than NLR < 1.516, MLR < 0.309, SIRI < 0.756 subgroups, and other participants except NLR + MLR + SIRI (all P < 0.05). The HR of NLR, MLR, SIRI, NLR + MLR + SIRI for all-cause mortality were 1.979(1.13–3.468), 1.850(1.279–2.676), 1.821(1.096–3.025), 1.871(1.296–2.703), respectively. The hazard ratio of NLR, MLR, SIRI, NLR + MLR + SIRI for diabetes-cardiovascular mortality were 2.602(1.028–6.591), 2.673(1.483–4.818), 2.001(0.898–4.459), 2.554(1.426–4.575), respectively. In the restricted cubic spline plots, the relationship between NLR, MLR, SIRI and HR of all-cause mortality and diabetes-cardiovascular mortality was overall as “J” shaped. In both age < 60 and age > 60 years participants, the all-cause mortality and diabetes-cardiovascular mortality were significantly higher in NLR ≥ 1.516, MLR ≥ 0.309, SIRI ≥ 0.756, and NLR + MLR + SIRI subgroups than NLR < 1.516, MLR < 0.309, SIRI < 0.756 subgroups, and other participants except NLR + MLR + SIRI (all P < 0.05).

Conclusion
NLR, MLR, and SIRI may be three independent prognostic predictors for all-cause mortality and diabetes-cardiovascular mortality among individuals with DR. In practical clinical applications, combining NLR, MLR, and SIRI may enhance the prediction of all-cause mortality and diabetes-cardiovascular mortality in DR.
Effect of capsular polysaccharide phase variation on biofilm formation, motility and gene expression in Vibrio vulnificus
Authors: Zhang Tingting , Ji Shenjie , Zhang Miaomiao , Wu Fei , Li Xue , Luo Xi , Huang Qinglian , Li Min , Zhang Yiquan , Lu Renfei 
Published: July 2024

AbstractVibrio vulnificus, a significant marine pathogen, undergoes opaque (Op)-translucent (Tr) colony switching based on whether capsular polysaccharide (CPS) is produced. CPS phase variation is sometime accompanied by genetic variation or down-regulation of particular genes, such as wzb. In addition, CPS prevents biofilm formation and is important to the virulence of V. vulnificus. However, the extent to which there is a difference in gene expression between Tr and Op colonies and the impact of CPS phase variation on other behaviors of V. vulnificus remain unknown. In this work, the data have shown that CPS phase variation of V. vulnificus is affected by incubation time. Tr and Op strains exhibited similar growth rates. However, Tr strains had enhanced biofilm formation capacities but reduced swimming motility compared to Op strains. The RNA-seq assay revealed 488 differentially expressed genes, with 214 downregulated and 274 upregulated genes, between Tr and Op colonies. Genes associated with Tad pili and CPS were downregulated, whereas those involved in flagellum were upregulated, in Tr colonies compared with Op colonies. In addition, 9 putative c-di-GMP metabolism-associated genes and 28 genes encoding putative regulators were significantly differentially expressed, suggesting that CPS phase variation is probably strictly regulated in V. vulnificus. Moreover, 8 genes encoding putative porins were also differentially expressed between the two phenotypic colonies, indicating that bacterial outer membrane was remodeled during CPS phase variation. In brief, this work highlighted the gene expression profiles associated with CPS phase variation, but more studies should be performed to disclose the intrinsic mechanisms in the future.
Insulin promotes the bone formation capability of human dental pulp stem cells through attenuating the IIS/PI3K/AKT/mTOR pathway axis
Authors: E Lingling , Shan Yanbo , Luo Yuxi , feng Lin , Dai Yawen , Gao Mingzhu , Lv Yan , Zhang Chaoran , Liu Hongchen , Wen Ning , Zhang Rong 
Published: July 2024

Abstract
Background
Insulin has been known to regulate bone metabolism, yet its specific molecular mechanisms during the proliferation and osteogenic differentiation of dental pulp stem cells (DPSCs) remain poorly understood. This study aimed to explore the effects of insulin on the bone formation capability of human DPSCs and to elucidate the underlying mechanisms.

Methods
Cell proliferation was assessed using a CCK-8 assay. Cell phenotype was analyzed by flow cytometry. Colony-forming unit-fibroblast ability and multilineage differentiation potential were evaluated using Toluidine blue, Oil red O, Alizarin red, and Alcian blue staining. Gene and protein expressions were quantified by real-time quantitative polymerase chain reaction and Western blotting, respectively. Bone metabolism and biochemical markers were analyzed using electrochemical luminescence and chemical colorimetry. Cell adhesion and growth on nano-hydroxyapatite/collagen (nHAC) were observed with a scanning electron microscope. Bone regeneration was assessed using micro-CT, fluorescent labeling, immunohistochemical and hematoxylin and eosin staining.

Results
Insulin enhanced the proliferation of human DPSCs as well as promoted mineralized matrix formation in a concentration-dependent manner. 10− 6 M insulin significantly up-regulated osteogenic differentiation-related genes and proteins markedly increased the secretion of bone metabolism and biochemical markers, and obviously stimulated mineralized matrix formation. However, it also significantly inhibited the expression of genes and proteins of receptors and receptor substrates associated with insulin/insulin-like growth factor-1 signaling (IIS) pathway, obviously reduced the expression of the phosphorylated PI3K and the ratios of the phosphorylated PI3K/total PI3K, and notably increased the expression of the total PI3K, phosphorylated AKT, total AKT and mTOR. The inhibitor LY294002 attenuated the responsiveness of 10− 6 M insulin to IIS/PI3K/AKT/mTOR pathway axis, suppressing the promoting effect of insulin on cell proliferation, osteogenic differentiation and bone formation. Implantation of 10− 6 M insulin treated DPSCs into the backs of severe combined immunodeficient mice and the rabbit jawbone defects resulted in enhanced bone formation.

Conclusions
Insulin induces insulin resistance in human DPSCs and effectively promotes their proliferation, osteogenic differentiation and bone formation capability through gradually inducing the down-regulation of IIS/PI3K/AKT/mTOR pathway axis under insulin resistant states.
Leveraging oncovirus-derived antigen against the viral malignancies in adoptive cell therapies
Authors: Zhang Wei , Zeng Miao , Li Yisheng , Yu Li 
Published: July 2024

AbstractAdoptive cell therapies (ACTs) have revolutionized cancer immunotherapy, prompting exploration into their application against oncoviruses. Oncoviruses such as human papillomavirus (HPV), hepatitis B virus (HBV), hepatitis C virus (HCV), and Epstein-Barr virus (EBV) contribute significantly (12-25%) to human malignancies through direct or indirect oncogenic mechanisms. These viruses persistently or latently infect cells, disrupt cellular homeostasis and pathways, challenging current antiviral treatment paradigms. Moreover, viral infections pose additional risks in the setting of long-term cancer therapy and lead to morbidity and mortality. Virally encoded oncoproteins, which are tumor-restricted, immunologically foreign, and even uniformly expressed, represent promising targets for patient-tailored ACTs. This review elucidates the rationale for leveraging viral antigen-specific ACTs in combating viral-associated malignancies. On this basis, ongoing preclinical studies consolidate our understanding of harnessing ACTs against viral malignancies, underscoring their potential to eradicate viruses implicated in cancer progression. Furthermore, we scrutinize the current landscape of clinical trials focusing on virus-specific ACTs and discuss their implications for therapeutic advancement.
Development of an opto-electrochemical sensor for the detection of malathion using manganese metal–organic framework (Mn-MOF)
Authors: Sankhla Lakshya , Kushwaha Himmat Singh 
Published: July 2024

AbstractThis paper presents a new method for detecting malathion pesticides using a modified screen-printed electrode (SPE) with a fluorescence quenching technique. The manganese-based MOF was synthesized using the solvothermal method. The synthesized MOFs were characterized by transmission electron microscopy (TEM), x-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), and Raman spectroscopy. The material’s electrocatalytic properties were assessed via electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). Within the concentration range of 0.89 µM to 5.95 µM, the material’s response to malathion was analyzed with square wave voltammetry (SWV), giving rise to a detection limit of 39.097 nM. Fluorescence quenching studies have been carried out between 0.039 and 0.56 µM, with a lower detection limit of 62.03 nM. A sensor with good anti-interference properties was tested for selectivity and practicability in detecting malathion in real samples, proving its potential use in this area.
Pancreaticoduodenectomy after postoperative gastric tube reconstruction for esophageal cancer with median arcuate ligament syndrome: a case report
Authors: Izumi Hideki , Yoshii Hisamichi , Fujino Rika , Takeo Shigeya , Kojima Yukiko , Kaneko Junichi , Mukai Masaya , Chino Osamu , Makuuchi Hiroyasu 
Published: July 2024

Abstract
Background
Pancreaticoduodenectomy (PD) is considered a challenging surgery for resecting the gastroduodenal artery (GDA), right gastric artery (RGA), and lymph node tumors. In cases of pancreatic head cancer surgery, vascular anastomosis or right gastroepiploic artery (RGEA)/GDA preservation is necessary after postoperative gastric tube reconstruction for esophageal cancer. Therefore, we report for the first time an extremely rare case of PD in a patient with pancreatic head cancer and median arcuate ligament syndrome (MALS) after gastric tube reconstruction following esophageal cancer surgery, in which the entire pancreatic head arcade was preserved.

Case presentation
The patient was a 76-year-old man who had undergone esophageal cancer surgery after sternal gastric tube reconstruction 7 years ago. He was referred to our hospital because of the suspicion of intraductal papillary mucinous carcinoma (IPMC) owing to an enlarged cystic lesion and a substantial component in the uncinate process of the pancreas. Preoperative three-dimensional computed (3D-CT) tomography angiography showed celiac axis stenosis and pancreatic head arcade dilation. The diagnosis was IPMC without evidence of invasion; therefore, gastric tube blood flow was maintained by preserving the GDA and RGEA. Due to MALS, the GDA blood flow was supplied through the pancreatic head arcade, necessitating its preservation. The GDA-RGEA, right gastroepiploic vein, and anterior superior pancreaticoduodenal artery were taped over the entire pancreatic head for preservation. The inferior pancreaticoduodenal artery (IPDA) was also taped on the dorsal pancreas and the posterior or anterior IPDA, which further bifurcates were taped to preserve them. Subsequently, PD was performed.

Conclusion
We report a case of PD after gastric tube reconstruction for esophageal cancer with MALS, in which the pancreatic head arcade vessels were successfully preserved using 3D-CT to confirm the operation of the vessels.
Influence of enhanced self-efficacy on English performance through English medium instruction: a mixed methods research
Authors: Huang Wen-Chi 
Published: July 2024

AbstractThe adoption of English-Medium Instruction (EMI) has gained global traction, spurred on by higher education internationalization trends. Despite the widespread usage of EMI, its influence on students’ language development remains relatively unexplored. This study investigated the impact of EMI instruction on the self-efficacy and English performance of Taiwanese English as a Foreign Language (EFL) undergraduates. The research aimed to discern whether EMI courses improve EFL undergraduates’ self-efficacy and how this self-efficacy can predict English performance. 272 Taiwanese EFL undergraduates were recruited for the study, and all of them joined the EMI courses for at least one semester. Data collection instruments included a revised questionnaire and TOEIC test, and a mixed approach was applied for data analyses. Quantitative analyses of repeated measure of ANOVA revealed a significant enhancement in the students’ self-efficacy across all four English skills (listening, speaking, reading, and writing) following EMI instruction. Moreover, the regression analysis established a moderate to strong positive relationship between English self-efficacy and English performance. The qualitative analysis of structured interview specifically elaborated on what participants’ attitudes were toward the implementation of EMI. These findings underscore the positive influence of EMI instruction on EFL undergraduates’ English self-efficacy and performance, substantiating the role of self-efficacy as a significant predictor of performance. These insights offer valuable implications for curriculum design, learner motivation, and academic success in EFL contexts.