bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid review methods series: Guidance on the use of supportive software
Authors: Affengruber Lisa , Nussbaumer-Streit Barbara , Hamel Candyce , Van der Maten Miriam , Thomas James , Mavergames Chris , Spijker Rene , Gartlehner Gerald 
Published: January 2024

This paper is part of a series of methodological guidance from the Cochrane Rapid Reviews Methods Group. Rapid reviews (RRs) use modified systematic review methods to accelerate the review process while maintaining systematic, transparent and reproducible methods. This paper guides how to use supportive software for RRs.We strongly encourage the use of supportive software throughout RR production. Specifically, we recommend (1) using collaborative online platforms that enable working in parallel, allow for real-time project management and centralise review details; (2) using automation software to support, but not entirely replace a human reviewer and human judgement and (3) being transparent in reporting the methodology and potential risk for bias due to the use of supportive software.
Time to death and predictors of mortality among asphyxiated neonates in southwest Ethiopia, 2022: prospective cohort study
Authors: Kebede Belete Fenta , Biyazin Tesfa Tsegaw , Yetwale Hiwot Aynalem , Mulu Kassa Kindie , Adugnaw Emebet , Mihretu Esmelalem , Sewmehone Enatfenta , Genie Yalemtsehay Dagnaw 
Published: January 2024

ObjectiveThis study aimed to determine the time to death and predictors of mortality among asphyxiated neonates admitted to public hospitals in the southwest region of Ethiopia.DesignAn institution-based prospective cohort study was conducted.SettingPublic hospitals in southwest Ethiopia.ParticipantsA total of 144 asphyxiated neonates, who were admitted to the neonatal intensive care unit, and their mothers participated from March 2022 to 30 September 2022. Data were entered into EpiData V.4.4.2.1 and exported to STATA V.16 for analysis. The Cox proportional hazards model using bivariate (p<0.25) and multivariate (p<0.05) analyses was used to identify the predictors of mortality. The median survival time was estimated using Kaplan-Meier survival estimates.Primary outcomeTime to death from asphyxia and its predictors in neonates.ResultsThe mortality incidence rate of asphyxiated neonates was 9.1 deaths per 1000 person-days of observation (95% CI: 7.11 to 11.52) with a median survival time of 8 days, and 45.83% (95% CI: 37.81% to 54.08%) of asphyxiated neonates died. Being male (adjusted HR (AHR) 0.32 (95% CI: 0.14 to 0.76)), neonatal sepsis (AHR 0.321 (95% CI: 0.13 to 0.77)), not receiving kangaroo mother care (AHR 0.16 (95% CI: 0. 07 to 0.39)) and vaginal delivery (AHR 0.39 (95% CI: 0.16 to 0.95)) were independent predictors of mortality of asphyxiated neonates.ConclusionsIn this study, asphyxiated neonates had a higher incidence of mortality with a median survival time of only 8 days. Being male, vaginal delivery, not receiving kangaroo mother care and comorbidities such as neonatal sepsis were independent predictors of mortality among asphyxiated neonates. Therefore, healthcare providers and other stakeholders should provide timely initiation of advanced diagnosis and appropriate therapeutic interventions for neonates with asphyxia to reduce neonatal mortality.
Challenges and knowledge gaps in the management of non-tuberculous mycobacterial pulmonary disease in sub-Saharan African countries with a high tuberculosis burden: a scoping review
Authors: Abbew Elizabeth Tabitha , Lorent Natalie , Mesic Anita , Wachinou Ablo Prudence , Obiri-Yeboah Dorcas , Decroo Tom , Rigouts Leen , Lynen Lutgarde 
Published: January 2024

IntroductionIn sub-Saharan African (SSA) countries endemic for tuberculosis (TB), previous TB is a significant risk factor for non-tuberculous mycobacterial pulmonary disease (NTM-PD). The deployment of GeneXpert MTB/RIF in pulmonary TB diagnostic work-up regularly identifies symptomatic patients with a positive smear microscopy but negative GeneXpert, indicative of NTM presence. This scoping review outlines recent evidence for NTM-PD diagnosis and management in SSA.ObjectiveThe review’s objective was to outline the risk factors, available diagnostics, management options and outcomes of NTM-PD in high-burden TB settings in SSA using the population-concept-context framework.Design and data sourcesWe searched existing literature from PubMed, Web of Science, African Journals Online, Google Scholar and grey literature. Studies published between January 2005 and December 2022 were retained. Data were extracted into Rayyan software and Mendeley and summarised using Excel.ResultsWe identified 785 potential articles, of which 105 were included in the full-text review, with 7 papers retained. Included articles used international criteria for diagnosing NTM-PD. Multiple papers were excluded due to non-application of the criteria, suggesting challenging application in the SSA setting. Identified risk factors include previous TB, smoking and mining. Most commonly, chest radiography and not CT was used for the radiological diagnosis of PD, which may miss early changes related to NTM-PD. Molecular methods for NTM species identification were employed in research settings, usually at referral centres, but were unavailable for routine care. Most studies did not report a standardised approach to treatment and they were not offered treatment for the specific disease, marking a lack of guidance in treatment decision-making. When treatment was provided, the outcome was often not reported due to the lack of implementation of standardised outcome definitions.ConclusionsThese outlined challenges present a unique opportunity for researchers to undertake further studies in NTM-PD and proffer solutions more applicable to SSA.
HIP fracture Supplemental Therapy to Enhance Recovery (HIPSTER): a protocol for a randomised controlled trial
Authors: Kimmel Lara A , Raper Eleanor , Harris Ian A , Ackerman Ilana N , Page Richard , Naylor Justine M , Burge Angela T , Hepworth Graham , Harris Anthony , Woode Maame Esi , Gabbe Belinda J , Ekegren Christina L , Holland Anne E 
Published: January 2024

IntroductionHip fractures result in substantial health impacts for patients and costs to health systems. Many patients require prolonged hospital stays and up to 60% do not regain their prefracture level of mobility within 1 year. Physical rehabilitation plays a key role in regaining physical function and independence; however, there are no recommendations regarding the optimal intensity. This study aims to compare the clinical efficacy and cost-effectiveness of early intensive in-hospital physiotherapy compared with usual care in patients who have had surgery following a hip fracture.Methods and analysisThis two-arm randomised, controlled, assessor-blinded trial will recruit 620 participants who have had surgery following a hip fracture from eight hospitals. Participants will be randomised 1:1 to receive usual care (physiotherapy according to usual practice at the site) or intensive physiotherapy in the hospital over the first 7 days following surgery (two additional sessions per day, one delivered by a physiotherapist and the other by an allied health assistant). The primary outcome is the total hospital length of stay, measured from the date of hospital admission to the date of hospital discharge, including both acute and subacute hospital days. Secondary outcomes are functional mobility, health-related quality of life, concerns about falling, discharge destination, proportion of patients remaining in hospital at 30 days, return to preadmission mobility and residence at 120 days and adverse events. Twelve months of follow-up will capture data on healthcare utilisation. A cost-effectiveness evaluation will be undertaken, and a process evaluation will document barriers and facilitators to implementation.Ethics and disseminationThe Alfred Hospital Ethics Committee has approved this protocol. The trial findings will be published in peer-reviewed journals, submitted for presentation at conferences and disseminated to patients and carers.Trial registration numberACTRN12622001442796.
Interventions to improve continence for children and young people with neurodisability: a national survey of practitioner and family perspectives and experiences
Authors: Eke Helen , Ball Susan , Allinson Annette , Anderson Rob , Hunt Harriet , Hutton Eve , Lindsay Claire , Logan Stuart , Madden Nicholas , Melluish Julia , Richardson Davina , Rogers June , Thompson Coon Jo , Whear Rebecca , Wright Anne , Morris Christopher 
Published: January 2024

ObjectiveDescribe families’ experiences of interventions to improve continence in children and young people with neurodisability, and health professionals’ and school and social care staff’s perspectives regarding factors affecting intervention use.DesignFour online surveys were developed and advertised to parent carers, young people with neurodisability, health professionals and school and social care staff, via societies, charities, professional contacts, schools, local authorities, and national parent carer and family forums, who shared invitations with their networks. Survey questions explored: difficulties helping children and young people use interventions; acceptability of interventions and waiting times; ease of use and availability of interventions, and facilitators and barriers to improving continence.Results1028 parent carers, 26 young people, 352 health professionals and 202 school and social care staff registered to participate. Completed surveys were received from 579 (56.3%) parent carers, 20 (77%) young people, 193 (54.8%) health professionals, and 119 (58.9%) school and social care staff. Common parent carer-reported difficulties in using interventions to help their children and young people to learn to use the toilet included their child’s lack of understanding about what was required (reported by 337 of 556 (60.6%) parent carers who completed question) and their child’s lack of willingness (343 of 556, 61.7%). Almost all (142 of 156, 91%) health professionals reported lack of funding and resources as barriers to provision of continence services. Many young people (14 of 19, 74%) were unhappy using toilet facilities while out and about.ConclusionsPerceptions that children lack understanding and willingness, and inadequate facilities impact the implementation of toileting interventions for children and young people with neurodisability. Greater understanding is needed for children to learn developmentally appropriate toileting skills. Further research is recommended around availability and acceptability of interventions to ensure quality of life is unaffected.
Pregnancy outcomes in women with rheumatoid arthritis: an 11-year French nationwide study
Authors: Pina Vegas Laura , Drouin Jérôme , Weill Alain , Dray-Spira Rosemary 
Published: January 2024

BackgroundRheumatoid arthritis (RA) can affect women of childbearing age. The management of patients with RA during pregnancy has evolved over the past decades, especially with the availability of new therapeutic molecules.ObjectivesTo describe pregnancy in women with RA, to compare pregnancy outcomes with those of women in the general population and to compare pregnancy outcomes in women with active and inactive RA.MethodsUsing the French National Health Data System, we identified all pregnancies ending between 2010 and 2020 in patients with and without RA. Characteristics were described. Active RA was defined by conventional synthetic/biological/targeted synthetic disease-modifying antirheumatic drug initiation, systemic or intra-articular corticosteroid administration and/or RA-related hospitalisation. Pregnancy outcomes were compared computing multivariable logistic marginal regression model using generalised estimating equation (GEE).ResultsWe included 11 792 RA and 10 413 681 non-RA pregnancies. Among RA pregnancies, 74.5% ended in live births and 0.4% in stillbirths. RA pregnancies resulted more frequently in preterm births (adjusted OR (ORa) 1.84; 95% CI 1.69 to 2.00) and very preterm births (ORa1.43; 95% CI 1.20 to 1.71), low birth weight (ORa1.65; 95% CI: 1.52 to 1.90), caesarean section (ORa1.46; 95% CI 1.38 to 1.55) and pregnancy-related hospitalisation (ORa1.30; 95% CI 1.22 to 1.39). Disease activity decreased during pregnancy. Active RA had higher rates of prematurity (ORa2.02; 95% CI 1.71 to 2.38), small for gestational age (ORa1.53; 95% CI 1.28 to 1.83) and caesarean section (ORa1.25; 95% CI 1.11 to 1.40) than non-active RA.ConclusionPregnancies in women with RA were associated with more adverse outcomes, especially if the disease was active. These findings should encourage physicians to closely monitor RA during this crucial period.
Data Management for ML-Based Analytics and Beyond
Authors: Kang Daniel , Guibas John , Bailis Peter , Hashimoto Tatsunori , Sun Yi , Zaharia Matei 
Published: January 2024

The increasing capabilities of machine learning (ML) has enabled the deployment of ML methods in a variety of applications, ranging from unstructured data analytics to autonomous vehicles. Due to the volumes of data over which ML is deployed, it is infeasible for humans to monitor deployments: the Tesla fleet of vehicles produces exabytes of data and millions of hours of video per day. As a result, ML deployments can fail in unexpected and catastrophic ways.
In this work, we highlight three important but underlooked aspects of ML deployment pipelines: (1) managing high-quality training data, (2) monitoring ML errors at deployment time, and (3) connecting end use to deployment algorithms. We first demonstrate that training labels are often erroneous, contrary to standard practice, even when labeled by leading vendors. We then demonstrate that standard methods of deploying ML methods can lead to downstream errors. As a first step toward addressing these issues, we review and contextualize two abstractions for finding errors in training data and deployments. We further describe how to improve algorithms for analytics queries as a case study for optimizing ML pipelines end to end.
N6-Methyladenosine Reader YTHDF1 Promotes Stemness and Therapeutic Resistance in Hepatocellular Carcinoma by Enhancing NOTCH1 Expression
Authors: Zhang Xinyue , Su Tianhong , Wu Yifan , Cai Yuhong , Wang Lina , Liang Cong , Zhou Lei , Wang Shiyan , Li Xiao-Xing , Peng Sui , Kuang Ming , Yu Jun , Xu Lixia 
Published: January 2024

Abstract

N6-methyladenosine (m6A) RNA modification is the most common and conserved epigenetic modification in mRNA and has been shown to play important roles in cancer biology. As the m6A reader YTHDF1 has been reported to promote progression of hepatocellular carcinoma (HCC), it represents a potential therapeutic target. In this study, we evaluated the clinical significance of YTHDF1 using human HCC samples and found that YTHDF1 was significantly upregulated in HCCs with high stemness scores and was positively associated with recurrence and poor prognosis. Analysis of HCC spheroids revealed that YTHDF1 was highly expressed in liver cancer stem cells (CSC). Stem cell–specific conditional Ythdf1 knockin (CKI) mice treated with diethylnitrosamine showed elevated tumor burden as compared with wild-type mice. YTHDF1 promoted CSCs renewal and resistance to the multiple tyrosine kinase inhibitors lenvatinib and sorafenib in patient-derived organoids and HCC cell lines, which could be abolished by catalytically inactive mutant YTHDF1. Multiomic analysis, including RNA immunoprecipitation sequencing, m6A methylated RNA immunoprecipitation sequencing, ribosome profiling, and RNA sequencing identified NOTCH1 as a direct downstream of YTHDF1. YTHDF1 bound to m6A modified NOTCH1 mRNA to enhance its stability and translation, which led to increased NOTCH1 target genes expression. NOTCH1 overexpression rescued HCC stemness in YTHDF1-deficient cells in vitro and in vivo. Lipid nanoparticles targeting YTHDF1 significantly enhanced the efficacy of lenvatinib and sorafenib in HCC in vivo. Taken together, YTHDF1 drives HCC stemness and drug resistance through an YTHDF1–m6A–NOTCH1 epitranscriptomic axis, and YTHDF1 is a potential therapeutic target for treating HCC.

Significance:
Inhibition of YTHDF1 expression suppresses stemness of hepatocellular carcinoma cells and enhances sensitivity to targeted therapies, indicating that targeting YTHDF1 may be a promising therapeutic strategy for liver cancer.
Nutrient Sensing in Macrophages Linked to Reorganized Tumor Vasculature
Authors: Chan Hilda L. , Zhang Xiang H.-F. 
Published: January 2024

Abstract
Macrophages are plastic immune cells that have varying functions dependent on stimulation from their environment. In a recent issue of Immunity, Do and colleagues demonstrated that activating mechanistic target of rapamycin complex 1 signaling in tumor macrophages alters their metabolism, localization, and function. Specifically, these tumor macrophages promote vascular remodeling that develops a hypoxic environment toxic to cancer cells. This culminates in a tangible reduction in tumor burden in a murine model of breast cancer. Their findings reveal a unique strategy to promote vascular remodeling through macrophage polarization and thereby highlight the intimate connections between macrophage metabolism and function. Additionally, their model highlights parallels between tumor progression and wound healing contexts while emphasizing the amplified effect of small perturbations to a tumor ecosystem.
T-cell States, Repertoire, and Function in Classical Hodgkin Lymphoma Revealed through Single-Cell Analyses
Authors: Chen Xiufen , Yu Jovian , Venkataraman Girish , Smith Sonali M. , Chen Mengjie , Cooper Alan , Tumuluru Sravya , Brody Joshua D. , Godfrey James , Kline Justin 
Published: January 2024

Abstract
The classical Hodgkin lymphoma (cHL) environment is comprised of a dense and complex immune cell infiltrate interspersed with rare malignant Hodgkin-Reed-Sternberg (HRS) cells. HRS cells are actively surveilled by endogenous T cells, but data linking phenotypic and functional T-cell states with clonality at the single-cell level in cHL is lacking. To address this knowledge gap, we performed paired single-cell RNA and T-cell receptor sequencing on 14 cHL and 5 reactive lymphoid tissue specimens. Conventional CD4+ T cells dominated the cHL landscape. However, recurrent clonal expansion within effector and exhausted CD8+ T-cell and regulatory T-cell clusters was uniquely observed in cHL specimens. Multiplex flow cytometric analysis revealed that most lymphoma-resident T cells produced effector cytokines upon ex vivo restimulation, arguing against a profound dysfunctional T-cell state in cHL. Our results raise new questions about the nature of T cells that mediate the antilymphoma response following programmed cell death protein 1 (PD-1) blockade therapy in cHL.
Fast region based convolutional neural network ResNet-50 model for on tree Mango fruit yield estimation
Authors: Managali Vasanth Neethi , PPandian Raviraj 
Published: January 2024

<p><span>The foundation of the Indian economy is agriculture, the amount of land available for agricultural activities has decreased due to numerous factors. To fulfill the demands of the expanding population, the maximum yield must be produced on the least amount of land that is accessible. To overcome the challenges of agriculture, many researches have been carried out to adopt technology into agriculture. As India is one of the world's top producers of Mangoes and has a vast market, and has encouraged extensive Mango farm development. Automatic yield estimation of Mangoes in the early stage is important to improve the quality and quantity of production which improves both domestic and export markets. The work proposes a fast region (FR) based convolutional neural network (CNN) residual network (ResNet)-50 model for efficient deep learning-based Mango crop yield estimation system to count the Mango fruit from the images of individual trees. A temporal Mango fruit database is used to estimate the yield of on tree Mango fruits, and a framework is provided to estimate Mango fruit yield in red, green, and blue (RGB) image. This experiment shows that the suggested FRCNN ResNet-50 model attained a better accuracy of 98.20% on the proposed dataset.</span></p>
Spark-MLlib intrusion detection mechanism using machine learning models
Authors: Sarwath Asra , Gulmeher Raafiya , Sultana Zeenath 
Published: January 2024

<p align="justify"><span>Typically, a single method is employed in machine learning (ML) based intrusion detection to identify intrusion information. However, this approach lacks flexibility, has a low detection rate, and struggles to handle high-dimensional data. Consequently, it is not efficient in addressing these challenges. This study proposes a new intrusion detection architecture that utilizes Spark and ensures resilient data dissemination across the platform to improve its effectiveness. It consists of preprocessing module, a label encoder module, a feature extraction module, a classification module and a database module. The preprocessing module compresses information by utilizing the module for label encoding. This generates a lower-dimensional reconstruction and classification characteristic. The database module has the capability to store the compressed characteristics of all traffic. This enables the classifier to be tested and then returns these features back into the original traffic, facilitating retraining. In order to evaluate the efficacy of the framework, simulations were conducted using the CICIDS 2017 dataset to accurately replicate the network traffic. Based on the test findings, the accuracy of both multiclass and binary classification surpasses that of earlier studies. High precision was achieved for the traffic that was restored. The possible application of the proposed architecture for edge/fog networks is discussed in the conclusion.</span></p>
Design of battery state of charge monitoring and control system using coulomb counting method based
Authors: Syafii Syafii , El Fakhri Irfan , Kurnia Agung Thoriq , Azizah Farah 
Published: January 2024

<span>Lead-acid batteries are commonly used in photovoltaic systems to store solar energy for continuous use. However, lead-acid batteries have a relatively short lifespan due to frequent over-charging and over-discharging. A battery management system (BMS) is essential for accurately predicting the battery state of charge (SoC) value in order to extend the battery lifespan. In this research, a BMS is developed using the coulomb counting method to estimate the SoC value of a lead-acid battery. The coulomb counting algorithm provides a reliable estimation of the battery’s SoC value by calculating the incoming and outgoing currents. The BMS also uses two normally closed relays to prevent overcharging and over-discharging. The first relay turns on when the SoC reaches 100% full charge and turns off when the SoC decreases to 70%. The second relay turns on when the SoC reaches 20%. The BMS was tested using Blynk, a cloud-based internet of things (IoT) platform. The results showed that the BMS successfully provided monitoring and reliable control of the lead-acid battery, with a low margin of error. This demonstrates that the developed BMS can be practically implemented in photovoltaic (PV)-battery systems to extend the battery lifespan and improve the overall performance of the system.</span>