bluuebunny/crossref_metadata_2025_split huggingface dataset:
The chemokine CXCL14 is a novel early prognostic biomarker for poor outcome in acetaminophen-induced acute liver failure
Authors: Umbaugh David S. , Nguyen Nga T. , Curry Steven C. , Rule Jody A. , Lee William M. , Ramachandran Anup , Jaeschke Hartmut ,   Acute Liver Failure Study Group
Published: November 2023

Background and Aims:Patients with acetaminophen-induced acute liver failure are more likely to die while on the liver transplant waiting list than those with other causes of acute liver failure. Therefore, there is an urgent need for prognostic biomarkers that can predict the need for liver transplantation early after an acetaminophen overdose.Approach and Results:We evaluated the prognostic potential of plasma chemokine C-X-C motif ligand 14 (CXCL14) concentrations in patients with acetaminophen (APAP) overdose (n=50) and found that CXCL14 is significantly higher in nonsurviving patients compared to survivors with acute liver failure (p< 0.001). Logistic regression and AUROC analyses revealed that CXCL14 outperformed the MELD score, better discriminating between nonsurvivors and survivors. We validated these data in a separate cohort of samples obtained from the Acute Liver Failure Study Group (n = 80), where MELD and CXCL14 had similar AUC (0.778), but CXCL14 demonstrated higher specificity (81.2 vs. 52.6) and positive predictive value (82.4 vs. 65.4) for death or need for liver transplantation. Next, combining the patient cohorts and using a machine learning training/testing scheme to mimic the clinical scenario, we found that CXCL14 outperformed MELD based on AUC (0.821 vs. 0.787); however, combining MELD and CXCL14 yielded the best AUC (0.860).Conclusions:We find in 2 independent cohorts of acetaminophen overdose patients that circulating CXCL14 concentration is a novel early prognostic biomarker for poor outcomes, which may aid in guiding decisions regarding patient management. Moreover, our findings reveal that CXCL14 performs best when measured soon after patient presentation to the clinic, highlighting its importance for early warning of poor prognosis.
High Plasma Presepsin Levels in Children With Hemophagocytic Lymphohistiocytosis
Authors: Yoshinari Hiroki , Kawahara Yuta , Niijima Hitomi , Oh Yukiko , Morimoto Akira 
Published: November 2023

Presepsin is reported as a novel diagnostic and prognostic biomarker for sepsis, and its optimal cutoff value is reported to be 600 to 650 pg/mL. Three children were diagnosed with hemophagocytic lymphohistiocytosis (HLH). The cause of HLH was unknown in cases 1 and 2, while Epstein-Barr virus infection was the cause in case 3. The plasma presepsin levels at the diagnosis were 1020, 1080, and 3160 pg/mL in cases 1, 2, and 3, respectively. In case 1, the plasma level of presepsin decreased to 164 pg/mL on day 19 of her sickness, when symptoms improved. Follow-up plasma presepsin levels were missing for cases 2 and 3. No microbiological pathogens were detected in the blood cultures of any of the patients. Our cases suggest that plasma presepsin levels can be elevated in childhood HLH.
Tailoring parenting styles and family-based interventions cross-culturally as an effective prevention strategy for youth substance use: a scoping review
Authors: Williams Ozge C. , Prasad Sakshi , Khan Ahmed Ali , Ayisire Oghenetega Esther , Naseer Hafsa , Abdullah Muhammad , Nadeem Mahrukh , Ashraf Nauman , Zeeshan Muhammad 
Published: November 2023

Background:
The challenge of substance use among youth continues to be a highly concerning public health issue across the globe. The notion that parenting lifestyles and family-based intervention can help in the prevention of adolescent substance use have received robust attention from policy makers, researchers’ clinicians and general public, nonetheless, there is scarcity of high quality evidence to support these concepts.

Objective:
To review available literature which assessed the effects of parenting styles and family-based interventions on the prevention of adolescent substance use.

Methods:
A scoping review of literature to identify studies published in English between 2012 and 2022 was conducted searching Scopus, MEDLINE, PsychInfo, and CINAHL databases focused on effects of parenting styles and family-based interventions in the prevention of adolescent substance use.
Keywords of family-based intervention strategies and possible outcomes of parenting styles on youth substance use were coded from the results, discussion, or conclusion. Strategies were inductively categorized into themes according to the focus of the strategy.

Results:
A total of 47 studies, published between 2012 and 2022 in English language included. Narrative synthesis illustrated that parental involvement, restriction of mature-rated content, parental monitoring, authoritative parenting styles, and parental support and knowledge can help in the prevention of adolescent substance use. On the contrary, poor parent-child bonding, overprotection, permissive parenting, parental frustrations, authoritarian and harsh parenting styles promoted adolescent substance use disorders. Proximal risk factors like peer influence, previous use of other substances, and risky behaviours had more effect than just parenting styles. Culturally tailored family-based intervention strategies such as “Preventive Parenting”, “Parent Training”, and “Parent Involvement”, with focus on “Technology Assisted Intervention”, particularly “SMART “(Substance Misuse among Adolescents in Residential Treatment) are found as effective family-based intervention strategies to mitigate substance use in youth.

Conclusion:
Culturally tailored family-based behavioural strategies psychosocial intervention strategies can be considered of the most effective strategies to prevent substance use disorders in youth.
Efficacy of sexual intercosurse in the spontaneous passage of distal or intramural ureteral stones: a randomsized controlled trial
Authors: Bhatti Kamran Hassan , Bapir Rawa , Bhatti Waseem Sarwar , Muhammad Huda Muhaddien , Abdullah Hiwa O. , Abdalla Berun Anwar , Channa Aftab Ahmed , Rahim Hawbash M. , Cheema Naeem Ahmed , Sohail Nadeem , Gomha Faaz S. , Fattah Fattah H. , Ahmed Nahidah Hamah Ameen , Aghaways Ismael , Kakamad Fahmi H. 
Published: November 2023

Background:
The role of sexual intercourse as an alternative treatment approach for ureteral stones (UTSs) is a recent area of investigation with only small sample-sized studies. This study aims to evaluate the role of sexual intercourse in the spontaneous passage of distal or intramural UTSs via a larger sample size.

Materials and methods:
The study population included cases that had either a distal ureteric or an intramural radiopaque stone. The patients were divided into two groups; group A was instructed to engage in sexual intercourse two to three times per week while also receiving symptomatic treatment for 4 weeks. Group B received symptomatic treatment alone and was instructed to abstain from sexual intercourse or masturbation for the same period.

Results:
A total of 160 male patients were enrolled in this study. The ages of the patients ranged from 21 to 58 years. The rate of stone expulsion after 2 weeks was 68.18% in group A and 53% in group B (P=0.053). The expulsion rate after 4 weeks was 80% in group A and 68.4% in group B (P=0.072). The mean expulsion time was 13.9±5.4 days for the experimental group and 15.2±6.7 days for the control group (P=0.179). The experimental group required fewer analgesic injections in comparison to the control group (P<0.05).

Conclusion:
While the role of sexual intercourse in facilitating the passage of distal or intramural UTSs cannot be fully established, it may aid to some extent. However, it should not be relied upon as a standalone treatment modality.
Evaluation of laboratory risk indicator for necrotizing fasciitis score as an early diagnostic tool for necrotizing fasciitis: a prospective observational study
Authors: Adhil Ibrahim , Dahal Suman , Gyawali Sushil , Neupane Prashansha , Kharel Ashok , Neupane Priyanka , Pachhai Prarthana , Khadka Rabi , Khatiwada Raj D. , Shrestha Jayan M. 
Published: November 2023

Introduction:
From its historical identification to modern times with advancements in management modalities globally, the mortality of necrotizing fasciitis (NF) is high ranging from 19 to 30% for all affected sites. Although many diagnostic adjuncts have been developed to assist with the prompt and accurate diagnosis of NF, the primary diagnosis is still based on high clinical suspicion. The Laboratory Risk Indicator for Necrotizing Fasciitis (LRINEC) score was developed as a tool for distinguishing NF from other soft tissue infections. The main objective of this study is to evaluate LRINEC as a tool for early diagnosis of NF and differentiating it from other soft tissue infections like cellulitis.

Methods:
This is a single-centered, prospective observational study. Patients presenting with soft tissue infections of the limbs to the emergency department from November 2020 to October 2021 were included in this study. The clinical findings and blood parameters for the LRINEC score were collected and the score was calculated. Based on clinical suspicion of NF, patients underwent debridement and had a tissue biopsy to confirm the diagnosis. The data obtained was analyzed using SPSS version 24 and MS Excel. The AUC curve was used to calculate a cutoff, sensitivity, specificity, positive predictive value, and negative predictive values for the LRINEC score based on our study.

Results:
Forty-five patients with 28 males and 17 females were included. The average age was 53.667 years within a range of 19–79 years. Among them 44.4% of the patients had NF and 66.6% had other minor forms of soft tissue infections. The ROC curve obtained a cutoff value of greater than or equal to 6, with an AUC of 0.751. At this cut of value study showed a sensitivity of 85% with a specificity of 52%. Similarly, positive predictive value was found to be 58.62%, negative predictive values of 81.25%, and overall accuracy of 66.67% in early diagnosis of NF.

Conclusion:
In conclusion, our study showed that the LRINEC score can be a reliable tool for the early diagnosis of NF in an ED setting. This scoring system is best to be used to rule out NF.
Mechanisms and intervention strategies of emotional dysregulation in individuals with nonsuicidal self-injury
Authors: Li Mengyuan , Li Qiuhong , Wu Chao 
Published: November 2023

Abstract
Nonsuicidal self-injury (NSSI) is a deliberate, direct, socially unacceptable, and nonsuicidal form of self-hurt, with a high incidence rate among adolescents. NSSI harms people’s bodies and minds, dampening their social function and increasing the risk of suicide. The Benefit and Barrier Model of NSSI proposes that the core benefit of NSSI is emotional gain, in other words, the emotion regulation effect of the NSSI behaviors. The purpose of this study was to elucidate the relationship between NSSI and emotional dysregulation (ED), analyze the possible behavioral and neural mechanisms underlying ED in NSSI, and summarize the application of emotion regulation strategies in the intervention for NSSI. This review provides evidence and implications for further research on the mechanisms and interventions related to ED in people with NSSI.
SecDATA: Secure Data Access and de novo Transcript Assembly protocol - To meet the challenge of reliable NGS data analysis
Authors: Mondal Sudip , Bhattacharya Namrata , Das Troyee , Ghosh Zhumur , Khatua Sunirmal 
Published: November 2023

AbstractRecent developments in sequencing technologies have created new opportunities to generate high-throughput biological data at an affordable price. Such high-throughput data needs immense computational resources for performing transcript assembly. Further, a high-end storage facility is needed to store the analyzed data and raw data. Here comes the need for centralized repositories to store such mountains of raw and analyzed data. Hence, it is of utmost importance to ensure data privacy for storing the data while performing transcript assembly. In this paper, we have developed a protocol namedSecDATAwhich performs de novo transcript assembly ensuring data security. It consists of two modules. The first module deals with a framework for secured access and storage of data. The novelty of the first module lies in the employment of distributed ledger technology for data storage that ensures the privacy of the data. The second module deals with the development of an optimized graph-based method for de novo transcript assembly. We have compared our results with the state-of-art method de Bruijn graph and the popular pipeline Trinity, for transcript reconstruction, and our protocol outperforms them.
Soquelitinib, A Selective Inhibitor of Interleukin-2-Inducible T Cell Kinase (ITK), is Active in Several Murine Models of T Cell-Mediated Inflammatory Disease
Authors: Hsu Lih-Yun , Rosenbaum James T. , Lindner Sarah , Allanore Yannick , Cauvet Anne , Pawar Rahul D. , Li Dan , Van Den Brink Marcel , Miller Richard A. 
Published: November 2023

AbstractInterleukin-2-inducible T cell kinase (or ITK) is a tyrosine kinase predominantly expressed by T lymphocytes. It plays a major role in T cell activation, differentiation, and receptor signaling. Studies in mouse models have established that the absence or inhibition of ITK reduces the secretion of Th2 and Th17 cytokines, while favoring the production of Th1 cytokines and the differentiation of T cells to regulatory T cells (T regs). We recently characterized the activity of soquelitinib (SQL), a selective, covalent inhibitor of ITKin vitrousing mouse or human T cells andin vivoin murine models of cancer. We hypothesized that selective pharmacologic blockade of ITK could attenuate a variety of T cell-mediated inflammatory diseases including murine models that resemble asthma, pulmonary fibrosis, systemic sclerosis, psoriasis, and acute graft versus host disease. In each model, SQL demonstrated substantial ability to ameliorate the disease process along with effects on cytokines and/or T cell subsets consistent with the reported function of ITK. Our studies demonstrate that selective inhibition of ITK by SQL is potentially a novel therapeutic approach for several forms of T cell-mediated, inflammatory diseases.
Cryo-EM Heterogeneity Analysis using Regularized Covariance Estimation and Kernel Regression
Authors: Gilles Marc Aurèle , Singer Amit 
Published: November 2023

AbstractProteins and the complexes they form are central to nearly all cellular processes. Their flexibility, expressed through a continuum of states, provides a window into their biological functions. Cryogenic electron microscopy (cryo-EM) is an ideal tool to study these dynamic states as it captures specimens in non-crystalline conditions and enables high-resolution reconstructions. However, analyzing the heterogeneous distributions of conformations from cryo-EM data is challenging. We present RECOVAR, a method for analyzing these distributions based on principal component analysis (PCA) computed using a REgularized COVARiance estimator. RECOVAR is fast, robust, interpretable, expressive, and competitive with the state-of-art neural network methods on heterogeneous cryo-EM datasets. The regularized covariance method efficiently computes a large number of high-resolution principal components that can encode rich heterogeneous distributions of conformations and does so robustly thanks to an automatic regularization scheme. The novel reconstruction method based on adaptive kernel regression resolves conformational states to a higher resolution than all other tested methods on extensive independent benchmarks while remaining highly interpretable. Additionally, we exploit favorable properties of the PCA embedding to estimate the conformational density accurately. This density allows for better interpretability of the latent space by identifying stable states and low free-energy motions. Finally, we present a scheme to navigate the high-dimensional latent space by automatically identifying these low free-energy trajectories. We make the code freely available athttps://github.com/ma-gilles/recovar.
B cell-stromal cell cross talk drives mesenteric lymph node eosinophilia during intestinal helminth infection
Authors: Bessell Emily , Finlay Rachel , James Louisa K. , Ludewig Burkhard , Harris Nicola L. , Hepworth Matthew R. , Dubey Lalit Kumar 
Published: November 2023

AbstractEosinophils are involved in host protection against multicellular organisms including helminths and often participate in regulating long-lasting humoral responses. However, their recruitment to the gut-draining mesenteric lymph node (mLN), where they support the development of the adaptive immune response is still elusive. Here, we demonstrate the mechanism underlying the recruitment of eosinophils to the murine mLN post gastrointestinal helminth infection. We found that mLN eosinophils accumulated at immune interactive sites such as the interfollicular and paracortical regions in an IL-4Rα-dependent manner and was directly associated with the reduced availability of stromal derived eosinophil chemoattractants. Using multiplex imaging we confirmed that eosinophils associate within a stromal niche containing Lyve1+lymphatic vessels, ER-TR7+Pdpn+FRCs, and extrafollicular CD138+plasma cells. Experiments utilising complete and mixed bone marrow chimeras demonstrated that mice lacking IL-4Rα expression or LTβ expression selectively on B cells had diminished eosinophilia and reduced extrafollicular plasma cell numbers within the mLN. When co-cultured with LTβR activated FRCs, eosinophils gained an active phenotype with enhancedIl1rl1(ST2) receptor expression. LTβR ligation on FRCs resulted in enhanced IL-33 expression along with enrichment of distinct reactomes. Additionally, deletion of LTβR in FRCs reduced the homing capability of eosinophils to the mLN, confirming the significance of lymphotoxin signalling in granulocyte recruitment. Overall, these results highlight the previously unknown role of B cell-stromal cell crosstalk in driving mLN eosinophilia and their potential role in regulating the quality and magnitude of the humoral immune response generated within the mLN.
Spatial trajectories of coffee harvesting in large-scale plantations: ecological and management drivers and implications
Authors: Van Cauwelaert Emilio Mora , Boyer Denis , Jiménez-Soto Estelí , González Cecilia González , Benítez Mariana 
Published: November 2023

ABSTRACTCONTEXTCoffee is produced under different management systems and scales of production categorized as Syndromes of Production. The “Capitalist Syndrome” is characterized by the high use of capital and labor inputs to increase agricultural outputs. This syndrome results in practices like high planting densities that may promote the development and dispersal of plant pathogens like coffee leaf rust. The spatial arrangement of coffee trees drives the spatial movement of the harvesters, who can bear and disperse pathogens across and within plantations. In most capitalist coffee plantations, harvesters work multiple hours to maximize the daily harvest, which might increase their dispersal potential. However, their spatial movement has not yet been described, nor its relationship with the scale or management of the plantation, and even less its ecological implications for pathogens dispersal.OBJECTIVEWe describe and analyze the daily spatial movement of coffee harvesters in two large-scale capitalist plantations: an organic and a conventional plantation.METHODSUsing state-space models, we recorded and analyzed the spatial movements of harvesters. We then constructed a driver tree for harvest dynamics, which incorporated qualitative variables related to climate, coffee plants, and management aspects reported by the harvesters.RESULTS AND CONCLUSIONSOur model differentiated two kinds of movements: 1) when trees have berries, harvesters remain in the coffee rows or areas nearby (Collect state; 94-98% of the steps); 2) when not, harvesters make longer steps within the harvesting location or move to another area (Search state; 2-6% of the steps). In the organic plantation, the Search state had a longer-tailed step-length distribution than in the conventional plantation, resulting in a significantly higher visited area per worker (p<0.05). This might be related to a) a lower fruit load or percentage of trees with ripe fruits when we took the data or b) smaller harvesting locations (“pantes”) per number of harvesters. Harvesting movements that explore a wider area, either by visiting more plants or by changing locations on the same day, could create more foci of CLR infection across the plantation.SIGNIFICANCEOur results highlight practices that can reduce the possible impact of human dispersal of pathogens like shorter harvesting trajectories by working fewer hours a day or avoiding harvesting at the end of the maturation season when few trees have berries and harvesters have to travel longer distances. This calls for organic coffee management that could prevent diseases, increase diversity, and guarantee just and safe conditions for workers.
piRNAs are regulators of metabolic reprogramming in stem cells
Authors: Rojas-Ríos Patricia , Chartier Aymeric , Enjolras Camille , Cremaschi Julie , Garret Céline , Boughlita Adel , Ramat Anne , Simonelig Martine 
Published: November 2023

AbstractStem cells preferentially use glycolysis instead of oxidative phosphorylation and this metabolic rewiring plays an instructive role in their fate; however, the underlying molecular mechanisms remain largely unexplored. PIWI-interacting RNAs (piRNAs) and PIWI proteins have essential functions in a range of adult stem cells across species. Here, we show that piRNAs and the PIWI protein Aubergine (Aub) are instrumental in activating glycolysis inDrosophilagermline stem cells (GSCs). High glycolysis is required for GSC self-renewal andaubloss-of-function induces a metabolic switch in GSCs leading to their differentiation. Aub directly binds glycolytic mRNAs andEnolasemRNA regulation by Aub depends on its 5’UTR. Furthermore, deletion of a piRNA target site inEnolase5’UTR leads to GSC loss. These data reveal an Aub/piRNA function in translational activation of glycolytic mRNAs in GSCs, and pinpoint a new mode of regulation of metabolic reprogramming in stem cells based on small RNAs.