bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wide reference databases for typing Trypanosoma cruzi based on amplicon sequencing of the minicircle hypervariable region
Authors: Rusman Fanny , Díaz Anahí G. , Ponce Tatiana , Floridia-Yapur Noelia , Barnabé Christian , Diosque Patricio , Tomasini Nicolás 
Published: November 2023

Background
Trypanosoma cruzi, the etiological agent of Chagas Disease, exhibits remarkable genetic diversity and is classified into different Discrete Typing Units (DTUs). Strain typing techniques are crucial for studying T. cruzi, because their DTUs have significant biological differences from one another. However, there is currently no methodological strategy for the direct typing of biological materials that has sufficient sensitivity, specificity, and reproducibility. The high diversity and copy number of the minicircle hypervariable regions (mHVRs) makes it a viable target for typing.

Methodology/Principal findings
Approximately 24 million reads obtained by amplicon sequencing of the mHVR were analyzed for 62 strains belonging to the six main T. cruzi DTUs. To build reference databases of mHVR diversity for each DTU and to evaluate this target as a typing tool. Strains of the same DTU shared more mHVR clusters than strains of different DTUs, and clustered together. Different identity thresholds were used to build the reference sets of the mHVR sequences (85% and 95%, respectively). The 95% set had a higher specificity and was more suited for detecting co-infections, whereas the 85% set was excellent for identifying the primary DTU of a sample. The workflow’s capacity for typing samples obtained from cultures, a set of whole-genome data, under various simulated PCR settings, in the presence of co-infecting lineages and for blood samples was also assessed.

Conclusions/Significance
We present reference databases of mHVR sequences and an optimized typing workflow for T. cruzi including a simple online tool for deep amplicon sequencing analysis (https://ntomasini.github.io/cruzityping/). The results show that the workflow displays an equivalent resolution to that of the other typing methods. Owing to its specificity, sensitivity, relatively low cost, and simplicity, the proposed workflow could be an alternative for screening different types of samples.
The association between polypharmacy and health-related quality of life among non-dialysis chronic kidney disease patients
Authors: Adjeroh Leonie , Brothers Todd , Shawwa Khaled , Ikram Mohammad , Al-Mamun Mohammad A. 
Published: November 2023

Background and objective
The United States government spends over $85 billion annually on treating non-dialysis chronic kidney disease (CKD). Patients with CKD are prescribed a multitude of medications to manage numerous comorbidities associated with CKD. Thus, this study aims to investigate the association between polypharmacy and health-related quality of life (HRQoL) in non-dialysis CKD patients.

Methods
This cross-sectional study utilized data from the Medical Expenditure Panel Survey (MEPS) from 2010 through 2019. We classified polypharmacy into three groups based on the number of medication classes: ≤ 4 (minor polypharmacy), 5 through 9 (major polypharmacy), and ≥ 10 (hyperpolypharmacy). To measure HRQoL, a Physical Component Summary (PCS) and a Mental Component Summary (MCS) were obtained from the 12-item Short-Form Health Survey version 2 and Veteran’s Rand 12 item. We applied multivariable ordinary least squares regression to assess the association between polypharmacy and HRQoL in non-dialysis CKD patients.

Results
A total of 649 CKD patients (weighted n = 667,989) were included. Patients with minor polypharmacy, major polypharmacy, and hyperpolypharmacy were 22.27%, 48.24%, and 29.48%, respectively. Major polypharmacy and hyperpolypharmacy were significantly and negatively associated with lower PCS scores when compared with minor polypharmacy [Beta = -3.12 (95% CI: -3.62, -2.62), p-value<0.001; Beta = -4.13 (95CI: -4.74, -3.52), p-value<0.001]. Similarly, major polypharmacy and hyperpolypharmacy were significantly and negatively associated with lower MCS scores when compared to minor polypharmacy [Beta = -0.38 (95% CI: -0.55, -0.20), p-value<0.001; Beta = -1.70 (95% CI: -2.01, -1.40), p-value<0.001]. The top 5 classes of medications used by CKD patients were antihyperlipidemic (56.31%), beta-adrenergic blockers (49.71%), antidiabetics (42.14%), analgesics (42.17%), and diuretics (39.65%).

Conclusion
Our study found that both major polypharmacy and hyperpolypharmacy were associated with lower HRQoL among non-dialysis CKD patients. This study highlights the need for further evaluation of the combination of medications taken by non-dialysis CKD patients to minimize unnecessary and inappropriate medication use.
Host biomarkers and combinatorial scores for the detection of serious and invasive bacterial infection in pediatric patients with fever without source
Authors: Lacroix Laurence , Papis Sebastien , Mardegan Chiara , Luterbacher Fanny , L’Huillier Arnaud , Sahyoun Cyril , Keitel Kristina , Mastboim Niv , Etshtein Liat , Shani Liran , Simon Einav , Barash Eran , Navon Roy , Gottlieb Tanya M. , Oved Kfir , Eden Eran , Combescure Christophe , Galetto-Lacour Annick , Gervaix Alain 
Published: November 2023

Background
Improved tools are required to detect bacterial infection in children with fever without source (FWS), especially when younger than 3 years old. The aim of the present study was to investigate the diagnostic accuracy of a host signature combining for the first time two viral-induced biomarkers, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and interferon γ-induced protein-10 (IP-10), with a bacterial-induced one, C-reactive protein (CRP), to reliably predict bacterial infection in children with fever without source (FWS) and to compare its performance to routine individual biomarkers (CRP, procalcitonin (PCT), white blood cell and absolute neutrophil counts, TRAIL, and IP-10) and to the Labscore.

Methods
This was a prospective diagnostic accuracy study conducted in a single tertiary center in children aged less than 3 years old presenting with FWS. Reference standard etiology (bacterial or viral) was assigned by a panel of three independent experts. Diagnostic accuracy (AUC, sensitivity, specificity) of host individual biomarkers and combinatorial scores was evaluated in comparison to reference standard outcomes (expert panel adjudication and microbiological diagnosis).

Results
241 patients were included. 68 of them (28%) were diagnosed with a bacterial infection and 5 (2%) with invasive bacterial infection (IBI). Labscore, ImmunoXpert, and CRP attained the highest AUC values for the detection of bacterial infection, respectively 0.854 (0.804–0.905), 0.827 (0.764–0.890), and 0.807 (0.744–0.869). Labscore and ImmunoXpert outperformed the other single biomarkers with higher sensitivity and/or specificity and showed comparable performance to one another although slightly reduced sensitivity in children < 90 days of age.

Conclusion
Labscore and ImmunoXpert demonstrate high diagnostic accuracy for safely discriminating bacterial infection in children with FWS aged under and over 90 days, supporting their adoption in the assessment of febrile patients.
The BREAK study protocol: Effects of intermittent energy restriction on adaptive thermogenesis during weight loss and its maintenance
Authors: Cortez Filipa M. , Nunes Catarina L. , Sardinha Luís B. , Silva Analiza M. , Teixeira Vítor H. 
Published: November 2023

Background
Adaptive thermogenesis, defined as the decrease in the energy expenditure components beyond what can be predicted by changes in body mass stores, has been studied as a possible barrier to weight loss and weight maintenance. Intermittent energy restriction (IER), using energy balance refeeds, has been pointed out as a viable strategy to reduce adaptive thermogenesis and improve weight loss efficiency (greater weight loss per unit of energy deficit), as an alternative to a continuous energy restriction (CER). Following a randomized clinical trial design, the BREAK Study aims to compare the effects of IER versus CER on body composition and in adaptive thermogenesis, and understand whether participants will successfully maintain their weight loss after 12 months.

Methods
Seventy-four women with obesity and inactive (20–45 y) will be randomized to 16 weeks of CER or IER (8x2 weeks of energy restriction interspersed with 7x1 week in energy balance). Both groups will start with 2 weeks in energy balance before energy restriction, followed by 16 weeks in energy restriction, then 8 weeks in energy balance and finally a 12-month weight maintenance phase. Primary outcomes are changes in fat-mass and adaptive thermogenesis after weight loss and weight maintenance. Secondary outcomes include weight loss, fat-free mass preservation, alterations in energy expenditure components, and changes in hormones (thyroid function, insulin, leptin, and cortisol).

Discussion
We anticipate that The BREAK Study will allow us to better understand adaptive thermogenesis during weight loss and weight maintenance, in women with obesity. These findings will enable evidence-based decisions for obesity treatment.

Trial registration
ClinicalTrials.gov: NCT05184361.
Incidence trends and survival analysis of appendiceal tumors in the United States: Primarily changes in appendiceal neuroendocrine tumors
Authors: Wang Dan , Ge Heming , Lu Yebin , Gong Xuejun 
Published: November 2023

Background
Appendiceal tumors are considered to be a relatively rare tumor of the gastrointestinal tract and the prognosis is unclear. This study comprehensively investigated trends in the epidemiology and survival of appendiceal tumors in the United States over the past approximately 20 years.

Methods
Patients with pathologically confirmed appendiceal tumors from 2000 to 2017 were selected from the Surveillance, Epidemiology and End Results (SEER) database. Age-adjusted incidence rates were calculated by SEER*Stat 8.4.0. The Kaplan-Meier method was used to analyze survival and prognostic factors were investigated by a multivariate Cox proportional risk model.

Results
Ultimately, 13,546 patients with appendiceal tumors between 2000 and 2017 were included. The annual incidence of colonic adenocarcinoma and mucinous adenocarcinoma remained relatively stable. Interestingly, the annual incidence of appendiceal neuroendocrine tumors (aNETs) increased significantly, from 0.03 to 0.90 per 100,000 person-years, with the most dramatic increase in the number of patients with localized disease. Patients with aNETs showed a significant improvement in survival between 2009–2017, compared to the period 2000–2008. Moreover, this improvement in survival over time was seen at all stages (localized, regional, distant) of aNETs. However, this improved survival over time was not seen in colonic and mucinous adenocarcinoma.

Conclusions
The incidence of appendiceal neoplasms has increased significantly over the past nearly two decades, which is mainly due to the increased incidence and significant migration to earlier stages in aNETs. We must note that despite the increased incidence of aNETs, survival rates have improved at different disease stages.
Retaining public health volunteers beyond COVID-19
Authors: Retzer Ameeta , Jones Janet , Damery Sarah , Ullah Habib , Omonijo Modupe , Varney Justin , Jolly Kate 
Published: November 2023

Objectives
The COVID-19 pandemic has led to a change in people’s volunteering behaviours; participation has increased in informal volunteering (giving unpaid help to those who are not a relative) while decreasing in formal volunteering (unpaid help to groups or clubs). There is an interest from stakeholders who have experienced increased participation in maintaining the positive patterns of volunteering, aligning with National Health Service (NHS) objectives and realising benefits in a wider public health context. This research uses a local COVID-19 public health volunteering programme case study to explore the volunteer’s journey and perspective using volunteers’ reported experiences to consider the potential for volunteer retention and role expansion into other public health issues beyond the COVID-19 pandemic.

Methods
Recruitment was undertaken by Birmingham City Council Public Health Team via the COVID-19 Community Champions programme mailing list. Semi-structured focus group discussions, one-to-one interviews and email interviews were conducted with volunteers. Data were analysed through directed thematic analysis using an iteratively developed coding frame.

Results
Data were collected from three focus group discussions, four interviews, and one email interview involving a total of 16 participants. Six themes were identified: volunteer motivations and expectations; volunteer management; programme organisation; feeling valued; continued need for role, and interest in new responsibilities.

Conclusion
Our findings indicate that the factors which are conducive to volunteer recruitment, retention and re-purposing were: maintaining the original terms of engaging with the volunteering opportunity (including retaining the original brief and remit), adjusting these through consultative processes with an emphasis on seeking permission from the volunteers already involved and ensuring a reliable and consistent management and support structure. While some of the learning is specific to the local volunteer programme in question and the context of the COVID-19 pandemic, there are lessons that can be generalised to other scenarios and settings.
Urinary phenotyping of SARS-CoV-2 infection connects clinical diagnostics with metabolomics and uncovers impaired NAD+ pathway and SIRT1 activation
Authors: Lonati Caterina , Berezhnoy Georgy , Lawler Nathan , Masuda Reika , Kulkarni Aditi , Sala Samuele , Nitschke Philipp , Zizmare Laimdota , Bucci Daniele , Cannet Claire , Schäfer Hartmut , Singh Yogesh , Gray Nicola , Lodge Samantha , Nicholson Jeremy , Merle Uta , Wist Julien , Trautwein Christoph 
Published: November 2023

Abstract

Objectives
The stratification of individuals suffering from acute and post-acute SARS-CoV-2 infection remains a critical challenge. Notably, biomarkers able to specifically monitor viral progression, providing details about patient clinical status, are still not available. Herein, quantitative metabolomics is progressively recognized as a useful tool to describe the consequences of virus-host interactions considering also clinical metadata.

Methods
The present study characterized the urinary metabolic profile of 243 infected individuals by quantitative nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography mass spectrometry (LC–MS). Results were compared with a historical cohort of noninfected subjects. Moreover, we assessed the concentration of recently identified antiviral nucleosides and their association with other metabolites and clinical data.

Results
Urinary metabolomics can stratify patients into classes of disease severity, with a discrimination ability comparable to that of clinical biomarkers. Kynurenines showed the highest fold change in clinically-deteriorated patients and higher-risk subjects. Unique metabolite clusters were also generated based on age, sex, and body mass index (BMI). Changes in the concentration of antiviral nucleosides were associated with either other metabolites or clinical variables. Increased kynurenines and reduced trigonelline excretion indicated a disrupted nicotinamide adenine nucleotide (NAD+) and sirtuin 1 (SIRT1) pathway.

Conclusions
Our results confirm the potential of urinary metabolomics for noninvasive diagnostic/prognostic screening and show that the antiviral nucleosides could represent novel biomarkers linking viral load, immune response, and metabolism. Moreover, we established for the first time a casual link between kynurenine accumulation and deranged NAD+/SIRT1, offering a novel mechanism through which SARS-CoV-2 manipulates host physiology.
Effects of minor alloying elements (Si, Mn and Al) on the corrosion behavior of stainless steels in molten carbonate fuel cell cathode environment
Authors: Ahn SooHoon , Kim MinJoong , Kim YoungJun , Youn JuYoung 
Published: November 2023

Abstract
Effects of minor alloying elements (Si, Mn, and Al) on the corrosion resistance behaviors of stainless steel (SS) modified 310S used as a cathode current collector (CCC) material for molten carbonate fuel cells (MCFC) were examined in a mixture of 62 mol% Li2CO3–38 mol% K2CO3 at 650 °C by measuring the change in corrosion potential and the potentio-dynamic, potentio-static polarization responses. The corrosion potential of modified 310S gradually increased after 9 h of immersion due to an active to passive transition and that of SSs added with minor alloying elements drastically increased before 6 h of immersion due to the reactive alloys. Si, Mn, and Al addition to base SS led to a decrease in corrosion resistance due to the rapid corrosion rate at the cathode operation potential, −40 mV, of the MCFC. The steady state current densities of SSs added with minor alloying elements were higher than that of 310S and modified 310S. Addition of Si, Mn, and Al induced a decrease in corrosion resistance of CCC materials in molten carbonate fuel cell operating temperatures, 650 °C.
Forest biomass assessment combining field inventorying and remote sensing data
Authors: Qasim Mohammad , Csaplovics Elmar , Villegas Mike Harvey Salazar 
Published: November 2023

Abstract
Forests offer high potential for the fight against climate change. However, forests are faced with increased deforestation. REDD+ is a financial mechanism that offers hope to developing countries for tackling deforestation. Aboveground (AGB) estimation, however, is necessary for such financial mechanisms. Remote sensing methods offer various advantages for AGB estimation. A study, therefore, was conducted for the estimation of AGB using a combination of remote sensing Sentinel-1 (S1) and Sentinel-2 (S2) satellite data and field inventorying. The mean AGB for Sub-tropical Chir Pine Forest was recorded as 146.73 ± 65.11 Mg ha−1, while for Sub-tropical Broadleaved Evergreen Forest it was 33.77 ± 51.63 Mg ha−1. Results revealed weak associations between the S1 and S2 data with the AGB. Nonetheless, S1 and S2 offer advantages such as free data resources that can be utilized by developing countries for forest biomass and carbon monitoring.
Revisiting incidence rates comparison under right censorship
Authors: Martínez-Camblor Pablo , Díaz-Coto Susana 
Published: November 2023

Abstract
Data description is the first step for understanding the nature of the problem at hand. Usually, it is a simple task that does not require any particular assumption. However, the interpretation of the used descriptive measures can be a source of confusion and misunderstanding. The incidence rate is the quotient between the number of observed events and the sum of time that the studied population was at risk of having this event (person-time). Despite this apparently simple definition, its interpretation is not free of complexity. In this piece of research, we revisit the incidence rate estimator under right-censorship. We analyze the effect that the censoring time distribution can have on the observed results, and its relevance in the comparison of two or more incidence rates. We propose a solution for limiting the impact that the data collection process can have on the results of the hypothesis testing. We explore the finite-sample behavior of the considered estimators from Monte Carlo simulations. Two examples based on synthetic data illustrate the considered problem. The R code and data used are provided as Supplementary Material.
The preparation of cellulose acetate capsules using emulsification techniques: high-shear bulk mixing and microfluidics
Authors: Mystek Katarzyna , Andreasson Bo , Reid Michael S. , Françon Hugo , Fager Cecilia , Larsson Per A. , Svagan Anna J. , Wågberg Lars 
Published: November 2023

Abstract
This work describes an emulsification-solvent-evaporation method for the preparation of liquid-filled capsules made from cellulose acetate. Two different emulsification techniques were applied: bulk emulsification by high-shear mixing, and droplet generation using microfluidics. The bulk emulsification method resulted in the formation of oil-in-water emulsions composed of an organic mixture of isooctane and cellulose acetate in methyl acetate, and an aqueous phase of high-molecular-weight polyvinyl alcohol (PVA). Upon the solvent evaporation, the emulsion droplets evolved into isooctane-filled cellulose acetate capsules. In contrast, microfluidics led to the formation of monodisperse droplets composed of the aqueous PVA solution dispersed in the organic phase. Upon the solvent evaporation, the emulsion droplets evolved into water-filled cellulose acetate capsules. Owing to the thermoplastic properties of the cellulose acetate, the capsules formed with the bulk mixing demonstrated a significant expansion when exposed to an increased temperature. Such expanded capsules hold great promise as building blocks in lightweight materials.
Blending and functionalisation modification of 3D printed polylactic acid for fused deposition modeling
Authors: Li Yishan , Huang Lijie , Wang Xiyue , Wang Yanan , Lu Xuyang , Wei Zhehao , Mo Qi , Sheng Yao , Zhang Shuya , Huang Chongxing , Duan Qingshan 
Published: November 2023

Abstract
Polylactic acid (PLA) is extensively used as a raw material in fused deposition modeling (FDM)-based three-dimensional printing (3DP), owing to its abundant resources, simple production processes, decent biodegradability, and adequate mechanical strength. However, it has disadvantages such as poor toughness and straightforward bending deformation. Given the considerable application potential of PLA materials in FDM-based 3DP technology, herein, studies conducted over the last 5 years toward the enhancement of the characteristics of PLA for FDM are summarized. In particular, modification approaches (chemical or physical methods) that have been employed to improve the mechanical and processing attributes of PLA are discussed, along with the development of PLA composites with unique functionalities. The insights provided herein can help expand the scope of application of PLA composites in FDM-based 3DP for utilization in fields such as transportation, aerospace engineering, industrial equipment fabrication, consumer/electronic product manufacturing, and biomedicine/medicine.
Die sechste Kirchenmitgliedschaftsuntersuchung: Zentrale Erkenntnisse und Herausforderungen für Religionspädagogik und Gemeindepädagogik
Authors: Ilg Wolfgang 
Published: November 2023

Zusammenfassung
Die Kirchenmitgliedschaftsuntersuchungen (KMU) sind die wohl wichtigsten religionssoziologischen Studien für die evangelische (und seit der sechsten KMU auch für die katholische) Kirche in Deutschland. Die aktuelle KMU VI (Erhebungsjahr 2022) nimmt im Vergleich zur Vorgängerstudie aus 2012 das kirchliche Bildungshandeln verstärkt in den Blick. Zentrale Ergebnisse werden vorgestellt: Der Religionsunterricht in seiner konfessionell getrennten Organisationsform hat nur noch einen geringen Rückhalt in der Bevölkerung. Die Arbeit der kirchlichen Kindertagesstätten führt bei den meisten Eltern nicht zu einer Einstellungsänderung gegenüber der Kirche. Bei der religiösen Sozialisation spielen die erstmals abgefragten gemeindepädagogischen Angebote, insbesondere die Konfirmation, eine wichtige Rolle. Der Artikel schließt mit möglichen Konsequenzen für Religions- und Gemeindepädagogik, Kirche und Gesellschaft.