bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protocolised early de-resuscitation in septic shock (REDUCE): protocol for a randomised controlled multicentre feasibility trial
Authors: Messmer Anna , Pietsch Urs , Siegemund Martin , Buehler Philipp , Waskowski Jan , Müller Martin , Uehlinger Dominik E , Hollinger Alexa , Filipovic Miodrag , Berger David , Schefold Joerg C , Pfortmueller Carmen A 
Published: September 2023

BackgroundFluid overload is associated with excess mortality in septic shock. Current approaches to reduce fluid overload include restrictive administration of fluid or active removal of accumulated fluid. However, evidence on active fluid removal is scarce. The aim of this study is to assess the efficacy and feasibility of an early de-resuscitation protocol in patients with septic shock.MethodsAll patients admitted to the intensive care unit (ICU) with a septic shock are screened, and eligible patients will be randomised in a 1:1 ratio to intervention or standard of care. Intervention: Fluid management will be performed according to the REDUCE protocol, where resuscitation fluid will be restricted to patients showing signs of poor tissue perfusion. After the lactate has peaked, the patient is deemed stable and assessed for active de-resuscitation (signs of fluid overload). The primary objective of this study is the proportion of patients with a negative cumulative fluid balance at day 3 after ICU. Secondary objectives are cumulative fluid balances throughout the ICU stay, number of patients with fluid overload, feasibility and safety outcomes and patient-centred outcomes. The primary outcome will be assessed by a logistic regression model adjusting for the stratification variables (trial site and chronic renal failure) in the intention-to-treat population.Ethics and disseminationThe study was approved by the respective ethical committees (No 2020–02197). The results of the REDUCE trial will be published in an international peer-reviewed medical journal regardless of the results.Trial registration numberClinicalTrials.gov,NCT04931485.
Applying clinical decision aids for the assessment and management of febrile infants presenting to emergency care in the UK and Ireland: Febrile Infant Diagnostic Assessment and Outcome (FIDO) Study protocol
Authors: Umana Etimbuk , Mills Clare , Norman-Bruce Hannah , Wilson Kathryn , Mitchell Hannah , McFetridge Lisa , Woolfall Kerry , Lynn Fiona A , McKeeman Gareth , Foster Steven , Barrett Michael , Roland Damian , Lyttle Mark D , Watson Chris , Waterfield Thomas 
Published: September 2023

IntroductionFebrile infants 90 days and younger are at risk of invasive bacterial infections (bacteraemia and meningitis) and urinary tract infections. Together this is previously termed serious bacterial infection with an incidence of approximately 10–20%. The National Institute for Health and Care Excellence guidance advocates a cautious approach with most infants requiring septic screening, parenteral broad-spectrum antibiotics and hospital admission. Internationally, variations exist in the approach to febrile infants, with European and North American guidance advocating a tailored approach based on clinical features and biomarker testing. None of the available international clinical decision aids (CDAs) has been validated in the UK and Irish cohorts. The aim of the Febrile Infant Diagnostic Assessment and Outcome (FIDO) Study is to prospectively validate a range of CDAs in a UK and Irish population including CDAs that use procalcitonin testing.Methods and analysisThe FIDO Study is a prospective multicentre mixed-methods cohort study conducted in UK and Irish hospitals. All infants aged 90 days and younger presenting with fever or history of fever (≥38°C) are eligible for inclusion. Infants will receive standard emergency clinical care without delay. Clinical data and blood samples will be collected, and consent will be obtained at the earliest appropriate opportunity using research without prior consent methodology. The performance and cost-effectiveness of CDAs will be assessed. An embedded qualitative study will explore clinician and caregiver views on different approaches to care and perceptions of risk.Ethics and disseminationThis study was reviewed and approved by the Office for Research Ethics Committees Northern Ireland-Health and Social Care Research Ethics Committee B, Public Benefit and Privacy Panel for Health and Social Care Scotland, and Children’s Health Ireland Research and Ethics Committee Ireland. The results of this study will be presented at academic conferences and in peer-reviewed publications.Trial registration numberNCT05259683.
Sex differences in adverse events following seasonal influenza vaccines: a meta-analysis of randomised controlled trials
Authors: Kiely Marilou , Tadount Fazia , Lo Ernest , Sadarangani Manish , Wei Shu Qin , Rafferty Ellen , Quach Caroline , MacDonald Shannon E 
Published: September 2023

BackgroundDespite being a vaccine-preventable disease, influenza remains a major public health threat with vaccine safety concerns reducing vaccine acceptability. Immune responses to vaccines and adverse events may differ between males and females, but most studies do not report results by sex. Using data from clinical trials, we explored sex differences in adverse events following seasonal influenza vaccines.MethodsWe obtained data for phase III randomised controlled trials identified through a systematic review and clinical trials registries, and performed a two-stage meta-analysis. Risk ratios (RR) and 95% confidence intervals (95% CI) comparing solicited reactions in femalesversusmales were pooled using the Mantel-Haenszel method and a random-effects model. We used the ROBINS-I tool to assess risk of bias and the I2statistic for heterogeneity. Main analysis was stratified by age: 18–64 years and ≥65 years.ResultsThe dataset for this analysis included 34 343 adults from 18 studies (12 with individual-level data and 6 with aggregate data). There was a higher risk of injection site reactions in females compared with males for both younger and older participants, with RRs of 1.29 (95% CI 1.21 to 1.37) and 1.43 (95% CI 1.28 to 1.60), respectively. Higher risk in females was also observed for systemic reactions, with RRs of 1.25 (95% CI 1.20 to 1.31) and 1.27 (95% CI 1.20 to 1.34) for younger and older participants, respectively. We also observed elevated risks of severe reactions in females, with a higher RR in youngerversusolder participants for systemic reactions (RRs 2.12 and 1.48, p=0.03, I2=79.7%). RRs were not found to vary between quadrivalent and trivalent vaccines.ConclusionThis meta-analysis suggested a higher risk of solicited reactions following influenza vaccines for females compared with males, irrespective of age and vaccine type. Transparent communication of this risk could increase the trust in vaccines and limit vaccine hesitancy. Future studies should report results stratified by sex and explore the role of gender in the occurrence of adverse events.
Diagnostic genome sequencing improves diagnostic yield: a prospective single-centre study in 1000 patients with inherited eye diseases
Authors: Weisschuh Nicole , Mazzola Pascale , Zuleger Theresia , Schaeferhoff Karin , Kühlewein Laura , Kortüm Friederike , Witt Dennis , Liebmann Alexandra , Falb Ruth , Pohl Lisa , Reith Milda , Stühn Lara G , Bertrand Miriam , Müller Amelie , Casadei Nicolas , Kelemen Olga , Kelbsch Carina , Kernstock Christoph , Richter Paul , Sadler Francoise , Demidov German , Schütz Leon , Admard Jakob , Sturm Marc , Grasshoff Ute , Tonagel Felix , Heinrich Tilman , Nasser Fadi , Wissinger Bernd , Ossowski Stephan , Kohl Susanne , Riess Olaf , Stingl Katarina , Haack Tobias B 
Published: September 2023

PurposeGenome sequencing (GS) is expected to reduce the diagnostic gap in rare disease genetics. We aimed to evaluate a scalable framework for genome-based analyses ‘beyond the exome’ in regular care of patients with inherited retinal degeneration (IRD) or inherited optic neuropathy (ION).MethodsPCR-free short-read GS was performed on 1000 consecutive probands with IRD/ION in routine diagnostics. Complementary whole-blood RNA-sequencing (RNA-seq) was done in a subset of 74 patients. An open-source bioinformatics analysis pipeline was optimised for structural variant (SV) calling and combined RNA/DNA variation interpretation.ResultsA definite genetic diagnosis was established in 57.4% of cases. For another 16.7%, variants of uncertain significance were identified in known IRD/ION genes, while the underlying genetic cause remained unresolved in 25.9%. SVs or alterations in non-coding genomic regions made up for 12.7% of the observed variants. The RNA-seq studies supported the classification of two unclear variants.ConclusionGS is feasible in clinical practice and reliably identifies causal variants in a substantial proportion of individuals. GS extends the diagnostic yield to rare non-coding variants and enables precise determination of SVs. The added diagnostic value of RNA-seq is limited by low expression levels of the major IRD disease genes in blood.
Simultaneous measurement of refractive index and dispersion using optical coherence tomography for restoration of transparent works of art
Authors: Faluweki Mixon K. , Cheung C. S. , Liang Haida 
Published: September 2023

AbstractWe describe a novel in situ non-invasive and non-contact technique for simultaneous measurement of refractive index and dispersion of transparent solid materials using optical coherence tomography (OCT). The technique requires multi-angle OCT imaging. It gives typical precision of 0.02 for the refractive index and 0.03 $$\mu$$
μ
m$$^{-1}$$

-
1

for dispersion. The method can be applied to the restoration of modern sculptures made from plastics where it is important to have precise measurement of the refractive index of an object using a non-contact method, so that a resin-based adhesive with a matching refractive index could be found to restore a scratched or broken transparent works of art.
Single-Cell RNA Sequencing Reveals That Adaptation of Human Aortic Endothelial Cells to Antiproliferative Therapies Is Modulated by Flow-Induced Shear Stress
Authors: Salazar-Martín Antonio G. , Kalluri Aditya S. , Villanueva Martin A. , Hughes Travis K. , Wadsworth Marc H. , Dao Tyler T. , Balcells Mercedes , Nezami Farhad R. , Shalek Alex K. , Edelman Elazer R. 
Published: September 2023

BACKGROUND:
Endothelial cells (ECs) are capable of quickly responding in a coordinated manner to a wide array of stresses to maintain vascular homeostasis. Loss of EC cellular adaptation may be a potential marker for cardiovascular disease and a predictor of poor response to endovascular pharmacological interventions such as drug-eluting stents. Here, we report single-cell transcriptional profiling of ECs exposed to multiple stimulus classes to evaluate EC adaptation.

METHODS:

Human aortic ECs were costimulated with both pathophysiological flows mimicking shear stress levels found in the human aorta (laminar and turbulent, ranging from 2.5 to 30 dynes/cm
2
) and clinically relevant antiproliferative drugs, namely paclitaxel and rapamycin. EC state in response to these stimuli was defined using single-cell RNA sequencing.

RESULTS:
We identified differentially expressed genes and inferred the TF (transcription factor) landscape modulated by flow shear stress using single-cell RNA sequencing. These flow-sensitive markers differentiated previously identified spatially distinct subpopulations of ECs in the murine aorta. Moreover, distinct transcriptional modules defined flow- and drug-responsive EC adaptation singly and in combination. Flow shear stress was the dominant driver of EC state, altering their response to pharmacological therapies.

CONCLUSIONS:
We showed that flow shear stress modulates the cellular capacity of ECs to respond to paclitaxel and rapamycin administration, suggesting that while responding to different flow patterns, ECs experience an impairment in their transcriptional adaptation to other stimuli.
A Solution to the Subject(s) of Psalm 7:13–14
Authors: Foth Kevin 
Published: September 2023

Abstract
The antecedent(s) of the 3ms verbal forms and 3ms pronouns in Ps 7:13–14 have long puzzled scholars, stimulating a wide range of interpretations. This article proposes a new solution, that YHWH is the subject of the first line of verse 13 and the remainder of the 3ms forms in verses 13–14 refer to the enemy of the psalmist. This solution accounts for the available data of grammar and syntax in addition to the context of the overall poem, where the description of the enemy and the actions of YHWH have verbal and thematic echoes with the content in vv. 13–14.
Changes in Biblical Orthography Reflecting the Development of the Language
Authors: Ariel Chanan 
Published: September 2023

Abstract
It is well established in the literature that the vocalization of verbs in the Bible occasionally reflects late linguistic developments, specifically, changes in the Hebrew stem system during the Second Temple period, which affected the vocalization but not the consonantal orthography of the verb. This paper discusses five phenomena involving changes in the tense system, rather than the stem system, during the Second Temple period which are reflected in the orthography itself, namely, in the addition or omission of matres lectionis. I argue that the Second Temple scribes did not consider orthographical amendments involving matres lectionis as actual changes of the biblical text. As a result, they sometimes made such amendments, even in the conservative text of the Pentateuch. The five phenomena discussed here are examples of such amendments, reflecting changes in the Hebrew tense system during the Second Temple period. The reason tense-system developments are evident in the verbal orthography, while stem-system developments are not, is that the latter affected not only the vowels but also the consonants of the verbal forms, which the scribes avoided changing.
Unclear relationships in interference competition among three sympatric medium-sized carnivores in a heavy snowy environment
Authors: Watanabe Kazuma , Saito Masayuki U. 
Published: September 2023

Abstract
Interference competition, a category of interspecific competition, is a critical aspect of understanding the dynamics of carnivore communities, as it can result in a decline in the health and reduced opportunity for resource acquisition of one or both competing species. Heavy snowfall environments during winter are expected to exacerbate interference competition due to decreased food resources and limited foraging opportunities caused by snow cover. However, knowledge on interference competition in such environments is limited. Using camera traps with baits, we evaluated the interference competition among three sympatric medium-sized carnivores, red foxes, raccoon dogs, and Japanese martens, within a heavy snowfall region of northeastern Japan. As in previous studies, we hypothesized that body weight would serve as a determining factor for superiority in winter snow environments. Diel activity patterns using the visitation time to baits did not reveal any clear differences. Nevertheless, the daytime occurrence frequency of Japanese martens during the snowfall season was higher than that of the other two species, indicating inferiority to the other species. The analysis of time intervals between species visiting baits revealed no clear superiority among the target species. These findings suggest that the interspecific relationships among medium-sized carnivores in winter snowy environments are complex and not easily determined.
The Right Kind of Reason for the Wrong Kind of Thing
Authors: Makin Laura Tomlinson 
Published: September 2023

Abstract
This paper offers a novel solution to the Wrong Kind of Reason problem that afflicts Fitting-Attitude analyses of value. I argue that we can distinguish reasons of the right kind from reasons of the wrong kind by being clear about what our reasons are for. In Wrong Kind of Reason cases, our reason to have a certain affective attitude is a reason for an action, and it is this category-mistake that is the source of the problem.
Glycolysis of Flexible Polyurethane Foams
Authors: Simioni F. , Modesti M. 
Published: September 2023

Flexible water blown polyurethanes are polymers with repeating urethane and urea groups. When they undergo heating in the presence of glycols the reaction of these groups leads to soluble products. The transesterification reaction of the urethane groups, that leads to the formation of new carbamate is faster than that of the urea groups. Carbamates in turn undergo aminolysis due to the amines formed in the glycolysis of the urea groups. The use of ethylene glycol (EG) allows the process to be carried out with high polymer/glycol ratio (up to 4:1). A polyphase product is obtained with a top liquid phase mainly formed by the polyether polyol from the polymer, an intermediate liquid phase formed by the solution of carbamates, ureas and amines in EG and a bottom solid phase with compounds with prevalent urea bonds.
Consumption Habits of Recorded Music: Determinants of Flamenco Albums Acquisition
Authors: Heredia-Carroza Jesús , Palma Luis , de Sancha-Navarro Jesús , Chavarría-Ortiz Carlos 
Published: September 2023

The article analyses the determinants of acquisition of flamenco albums. Flamenco is a musical genre recognized by UNESCO as intangible heritage of humanity. A methodology divided into three phases has been used for this purpose: firstly, interviews with experts from the Spanish music industry where new variables are identified that can affect flamenco consumption habits; then 586 surveys of flamenco spectators who valued these variables and, finally, the application of econometric models to obtain the coefficients of the variables. The results show how the valuation of the composition, the performer and its virtuosity, of the existing trends, and the sociodemographic characteristics of the spectators directly affect the acquisition of flamenco-recorded music. The article contributes to the scarce empirical literature that relates the determinants of recorded music acquisition with traditional popular genres, by adding never studied before variables, focusing on the case of flamenco. JEL Classification: C2; D2; Z1. MSC2010: 00A65; 00A66.
Cardiopulmonary response to exercise in adults born very preterm
Authors: Delfrate Jacques , Girard-Bock Camille , Curnier Daniel , Perie Delphine , Cloutier Anik , Gascon Gabrielle , Landry Jennifer S. , Masse Benoît , Stickland Michael K. , Nuyt Anne Monique , Luu Thuy Mai 
Published: September 2023

This study aims to compare cardiopulmonary response to aerobic exercise between young adults born very preterm, including a subgroup with bronchopulmonary dysplasia (BPD), and term controls.Seventy-one adults (18–29 years) born <30 weeks’ gestational age (24 with BPD) and 73 term controls were recruited. Assessment included cardiopulmonary exercise testing with impedance cardiography. We compared group differences in peak O2consumption (peak VO2) and in ventilatory and cardiovascular responses to exercise using linear regression analyses.Preterm participants had reduced peak VO2(mean difference −2.7; 95% CI −5.3, −0.1 mL·kg−1lean body mass·min−1)versuscontrols. Those with BPD achieved lower peak work-rate compared to term controls (−21; 95% CI −38, −5 watts). There was no difference across groups in breathing reserve, ventilatory efficiency, peak heart rate and cardiac output. VO2to work-rate relationship (ΔVO2/ΔWR) was reduced in pretermversusterm. Peak systolic blood pressure and circulatory power (systolic blood pressure*VO2) were also lower in BPDversusterm controls. In the preterm group, longer NICU stay and lower peak cardiac output were associated with lower peak VO2.Results suggest limitations with peripheral O2uptake in the muscle with reduced ΔVO2/ΔWR and peak circulatory power, but normal cardiac output. Investigations into skeletal muscle perfusion and O2use during exercise are warranted to better understand mechanisms of exercise limitation.
Critical assessment of on-premise approaches to scalable genome analysis
Authors: Al-Aamri Amira , Kamarul Azman Syafiq , Daw Elbait Gihan , Alsafar Habiba , Henschel Andreas 
Published: September 2023

Abstract
Background
Plummeting DNA sequencing cost in recent years has enabled genome sequencing projects to scale up by several orders of magnitude, which is transforming genomics into a highly data-intensive field of research. This development provides the much needed statistical power required for genotype–phenotype predictions in complex diseases.

Methods
In order to efficiently leverage the wealth of information, we here assessed several genomic data science tools. The rationale to focus on on-premise installations is to cope with situations where data confidentiality and compliance regulations etc. rule out cloud based solutions. We established a comprehensive qualitative and quantitative comparison between BCFtools, SnpSift, Hail, GEMINI, and OpenCGA. The tools were compared in terms of data storage technology, query speed, scalability, annotation, data manipulation, visualization, data output representation, and availability.

Results
Tools that leverage sophisticated data structures are noted as the most suitable for large-scale projects in varying degrees of scalability in comparison to flat-file manipulation (e.g., BCFtools, and SnpSift). Remarkably, for small to mid-size projects, even lightweight relational database.

Conclusion
The assessment criteria provide insights into the typical questions posed in scalable genomics and serve as guidance for the development of scalable computational infrastructure in genomics.
Identification of disease-related genes in Plasmodium berghei by network module analysis
Authors: Lin Junhao , Zeng Shan , Chen Qiong , Liu Guanghui , Pan Suyue , Liu Xuewu 
Published: September 2023

Abstract
Background
Plasmodium berghei has been used as a preferred model for studying human malaria, but only a limited number of disease-associated genes of P. berghei have been reported to date. Identification of new disease-related genes as many as possible will provide a landscape for better understanding the pathogenesis of P. berghei.

Methods
Network module analysis method was developed and applied to identify disease-related genes in P. berghei genome. Sequence feature identification, gene ontology annotation, and T-cell epitope analysis were performed on these genes to illustrate their functions in the pathogenesis of P. berghei.

Results
33,314 genes were classified into 4,693 clusters. 4,127 genes shared by six malaria parasites were identified and are involved in many aspects of biological processes. Most of the known essential genes belong to shared genes. A total of 63 clusters consisting of 405 P. berghei genes were enriched in rodent malaria parasites. These genes participate in various stages of parasites such as liver stage development and immune evasion. Combination of these genes might be responsible for P. berghei infecting mice. Comparing with P. chabaudi, none of the clusters were specific to P. berghei. P. berghei lacks some proteins belonging to P. chabaudi and possesses some specific T-cell epitopes binding by class-I MHC, which might together contribute to the occurrence of experimental cerebral malaria (ECM).

Conclusions
We successfully identified disease-associated P. berghei genes by network module analysis. These results will deepen understanding of the pathogenesis of P. berghei and provide candidate parasite genes for further ECM investigation.