bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing methods for constructing and representing human pangenome graphs
Authors: Andreace Francesco , Lechat Pierre , Dufresne Yoann , Chikhi Rayan 
Published: November 2023

Abstract
Background
As a single reference genome cannot possibly represent all the variation present across human individuals, pangenome graphs have been introduced to incorporate population diversity within a wide range of genomic analyses. Several data structures have been proposed for representing collections of genomes as pangenomes, in particular graphs.

Results
In this work, we collect all publicly available high-quality human haplotypes and construct the largest human pangenome graphs to date, incorporating 52 individuals in addition to two synthetic references (CHM13 and GRCh38). We build variation graphs and de Bruijn graphs of this collection using five of the state-of-the-art tools: , , , and . We examine differences in the way each of these tools represents variations between input sequences, both in terms of overall graph structure and representation of specific genetic loci.

Conclusion
This work sheds light on key differences between pangenome graph representations, informing end-users on how to select the most appropriate graph type for their application.
Effects of microbes in pig farms on occupational exposed persons and the environment
Authors: Han Jinyi , Li Mengyu , Li Xin , Liu Chuang , Li Xiu-Ling , Wang Kejun , Qiao Ruimin , Yang Feng , Han Xuelei , Li Xin-Jian 
Published: November 2023

AbstractIn terms of pig farming, pig gut microbes have a significant effect on farmers and the farm environment. However, it is still unclear which microbial composition is more likely to contribute to this effect. This study collected a total of 136 samples, including pigs’ faeces samples, farmers’ faeces samples, samples from individuals who had no contact with any type of farm animal (referred to as ‘non-exposed’ persons), and environmental dust samples (collected from inside and outside pig houses and the farm) from two pig farms, pig farm A and pig farm B. Whereafter, 16S rRNA sequencing and taxonomic composition analysis were performed. According to the study, compared to non-exposed persons, pig farmers had a significantly higher abundance of 7 genera. In addition, the farmers were grouped according to the duration of their occupational exposure, and it was shown that 4 genera, including Turicibacter, Terrisporobacter, and Clostridium_sensu_stricto_1, exhibited a rise in more frequent contact with pigs. As compared to outside the pig house, the environmental dust has a greater concentration of the 3 bacteria mentioned before. Therefore, these 3 microbes can be considered as co-occurring microbes that may exist both in humans and the environment. Also, the 3 co-occurring microbes are involved in the fermentation and production of short-chain fatty acids and their effectiveness decreased as distance from the farm increased. This study shows that the 3 microbes where pig farmers co-occur with the environment come from pig farms, which provides fresh ideas for preventing the spread of microbial aerosols in pig farms and reducing pollution.
Integrating compositional and functional content to describe vaginal microbiomes in health and disease
Authors: Holm Johanna B. , France Michael T. , Gajer Pawel , Ma Bing , Brotman Rebecca M. , Shardell Michelle , Forney Larry , Ravel Jacques 
Published: November 2023

Abstract
Background
A Lactobacillus-dominated vaginal microbiome provides the first line of defense against adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microbiome modulates protection, as prior work mostly described its composition through morphologic assessment and marker gene sequencing methods that do not capture functional information. To address this gap, we developed metagenomic community state types (mgCSTs) which use metagenomic sequences to describe and define vaginal microbiomes based on both composition and functional potential.

Results
MgCSTs are categories of microbiomes classified using taxonomy and the functional potential encoded in their metagenomes. MgCSTs reflect unique combinations of metagenomic subspecies (mgSs), which are assemblages of bacterial strains of the same species, within a microbiome. We demonstrate that mgCSTs are associated with demographics such as age and race, as well as vaginal pH and Gram stain assessment of vaginal smears. Importantly, these associations varied between mgCSTs predominated by the same bacterial species. A subset of mgCSTs, including three of the six predominated by Gardnerellavaginalis mgSs, as well as mgSs of L. iners, were associated with a greater likelihood of bacterial vaginosis diagnosed by Amsel clinical criteria. This L. iners mgSs, among other functional features, encoded enhanced genetic capabilities for epithelial cell attachment that could facilitate cytotoxin-mediated cell lysis. Finally, we report a mgSs and mgCST classifier for which source code is provided and may be adapted for use by the microbiome research community.

Conclusions
MgCSTs are a novel and easily implemented approach to reduce the dimension of complex metagenomic datasets while maintaining their functional uniqueness. MgCSTs enable the investigation of multiple strains of the same species and the functional diversity in that species. Future investigations of functional diversity may be key to unraveling the pathways by which the vaginal microbiome modulates the protection of the genital tract. Importantly, our findings support the hypothesis that functional differences between vaginal microbiomes, including those that may look compositionally similar, are critical considerations in vaginal health. Ultimately, mgCSTs may lead to novel hypotheses concerning the role of the vaginal microbiome in promoting health and disease, and identify targets for novel prognostic, diagnostic, and therapeutic strategies to improve women’s genital health.
Effects of open and closed skill exercise interventions on executive function in typical children: a meta-analysis
Authors: Feng Xiaosu , Zhang Ziyun , Jin Teng , Shi Peng 
Published: November 2023

Abstract
Background
The effects of open and closed skill exercise interventions for executive function in children and adolescents have received widespread attention. Open skill refers to the skill of performing motor tasks in an unpredictable environment; closed skill refers to the skill of performing motor tasks in a stable environment. However, the results of related studies are currently controversial and Meta-analysis is urgently needed.

Methods
After computer searches of CNKI, Wan-Fang, VIP, WOS, PubMed, and EBSCO databases, two researchers independently screened articles, extracted information, and evaluated the quality of the articles. This study was statistical analyzed using Stata 16.0 software.

Results
A total of 31 articles were included, including 2988 typical children. Open, closed, continuous and sequential skills all improved executive function in typical children to varying degrees, but open and sequential skills were more effective in improving executive function, particularly in the former in the working memory (SMD=-0.833, P < 0.001) and in the latter in the inhibitory control (SMD=-0.834, P < 0.001) and cognitive flexibility (SMD=-0.903, P < 0.001). Long-term, moderate- intensity interventions were better than acute, vigorous-intensity interventions for executive function, with long-term interventions reflected in working memory (SMD=-0.579, P < 0.001) and moderate-intensity interventions reflected in all three dimensions of executive function (P < 0.01). Intervention periods, intervention intensity and continuous and sequential skills classified by action structure play a significant moderating role. Better results for long-term, sequential structural action interventions based on open skills (P < 0.001); better results for acute, moderate intensity, sequential structural action interventions based on closed (P < 0.05). Whereas intervention intensity had a non-significant moderating effect in the open skills intervention, both moderate and vigorous intensity had a significant effect on executive function (P < 0.001).

Conclusion
Open and closed skills have different levels of facilitation effects on executive function in typical children, but open skills are more effective. The facilitation effects of open and closed skills were moderated by the qualitative characteristics and action structure of the intervention.
Using intensive longitudinal methods to quantify the sources of variability for situational engagement in science learning environments
Authors: Rosenberg Joshua M. , Beymer Patrick N. , Phun Vicky , Schmidt Jennifer A. 
Published: November 2023

Abstract
Background
Situational engagement in science is often described as context-sensitive and varying over time due to the impact of situational factors. But this type of engagement is often studied using data that are collected and analyzed in ways that do not readily permit an understanding of the situational nature of engagement. The purpose of this study is to understand—and quantify—the sources of variability for learners’ situational engagement in science, to better set the stage for future work that measures situational factors and accounts for these factors in models.

Results
We examined how learners' situational cognitive, behavioral, and affective engagement varies at the situational, individual learner, and classroom levels in three science learning environments (classrooms and an out-of-school program). Through the analysis of 12,244 self-reports of engagement collected using intensive longitudinal methods from 1173 youths, we found that the greatest source of variation in situational engagement was attributable to individual learners, with less being attributable to—in order—situational and classroom sources. Cognitive engagement varied relatively more between individuals, and affective engagement varied more between situations.

Conclusions
Given the observed variability of situational engagement across learners and contexts, it is vital for studies targeting dynamic psychological and social constructs in science learning settings to appropriately account for situational fluctuations when collecting and analyzing data.
Superior bone fixation of conical compared with hemispherical trapezial cup design: an experimental radiostereometry study
Authors: Stilling Maiken , Dremstrup Lene , Hansen Torben Bæk , Thillemann Janni Kjærgaard 
Published: November 2023

AbstractPurposeThe most used cup designs for trapeziometacarpal (TMC) arthroplasty are of hemispherical and conical geometrical shape. Using a validated pig bone model, we compared the bone fixation using radiostereometry (RSA).MethodsTwenty saddle‐shaped pig forefoot bones were prepared with insertion of bone markers and reaming. Hemispherical Type T cups (Beznoska, Kladno, Czech Republic) (N = 10) and conical Moovis cups (Stryker, Pusignan, France) (N = 10) of 9‐mm diameter were inserted press‐fit. The bones were fixed in cement blocks for stability, and the cups were loaded in a motorized test stand. First, a low‐pressure cyclic load test (0—150N) with 130 compression cycles was performed. Next, a push‐in test of progressive loads with 50N increments (range: 150–900N) was applied until a visual change in cup position appeared. Cup migration was evaluated with RSA after every new load application. Cup failure was defined as total translation > 0.5 mm between two load applications.ResultsBoth cup types tolerated a compression load of 450 N without failure. Beyond this load level, the total translation cup migration of mean 0.20 mm (95% CI 0.11; 0.30) for the Type T group was higher than mean 0.10 mm (95% CI 0.06; 0.15) of the Moovis group (p = 0.046). The Hazard ratio for failure was 0.52 (95% CI 0.12; 2.17) (p = 0.37), indicating that the risk of failure was two‐fold higher in the Type T group.ConclusionWe conclude that conical TMC cups have superior fixation as compared to hemispherical cups above a loading level of 450 N, which correspond to a 3.8 kg tip‐pinch.In a clinical perspective, based on the fixation strength of both cup types, it seems safe to allow light‐load activities of daily living such as buttoning a shirt and using a key shortly after surgery and until sufficient osseointegration is achieved.
Circulating endothelial extracellular vesicle signatures correspond with ICU requirement: an exploratory study in COVID-19 patients
Authors: Zipperle Johannes , Oesterreicher Johannes , Hackl Matthias , Krammer Teresa Lara , Thumfart Helena , Bobbili Madhusudhan Reddy , Wiegele Marion , Grillari Johannes , Osuchowski Marcin F. , Schöchl Herbert , Holnthoner Wolfgang , Schlimp Christoph J. , Schiefer Judith , Pesce Marco Valerio , Ulbing Stefan , Gratz Johannes 
Published: November 2023

AbstractExtracellular vesicles (EVs) represent nanometer-sized, subcellular spheres, that are released from almost any cell type and carry a wide variety of biologically relevant cargo. In severe cases of coronavirus disease 2019 (COVID-19) and other states of systemic pro-inflammatory activation, EVs, and their cargo can serve as conveyors and indicators for disease severity and progression. This information may help distinguish individuals with a less severe manifestation of the disease from patients who exhibit severe acute respiratory distress syndrome (ARDS) and require intensive care measures. Here, we investigated the potential of EVs and associated miRNAs to distinguish normal ward patients from intensive care unit (ICU) patients (N = 10/group), with 10 healthy donors serving as the control group. Blood samples from which plasma and subsequently EVs were harvested by differential ultracentrifugation (UC) were obtained at several points in time throughout treatment. EV-enriched fractions were characterized by flow cytometry (FC), nanoparticle tracking analysis (NTA), and qPCR to determine the presence of selected miRNAs. Circulating EVs showed specific protein signatures associated with endothelial and platelet origin over the course of the treatment. Additionally, significantly higher overall EV quantities corresponded with increased COVID-19 severity. MiR-223-3p, miR-191-5p, and miR-126-3p exhibited higher relative expression in the ICU group. Furthermore, EVs presenting endothelial-like protein signatures and the associated miR-126-3p showed the highest area under the curve in terms of receiver operating characteristics regarding the requirement for ICU treatment. In this exploratory investigation, we report that specific circulating EVs and miRNAs appear at higher levels in COVID-19 patients, especially when critical care measures are indicated. Our data suggest that endothelial-like EVs and associated miRNAs likely represent targets for future laboratory assays and may aid in clinical decision-making in COVID-19.
Atypical pattern of ocular toxoplasmosis: recurrent inner foveal toxoplasmic retinitis (rifter)
Authors: Souza Guilherme Macedo , Biccas Laurentino , Maia André , Silveira Claudio , Belfort Rubens 
Published: November 2023

AbstractFailure to recognize the different possible clinical presentations of ocular toxoplasmosis may delay diagnosis and treatment, compromising visual prognosis. The aim of this paper is to describe an atypical pattern of ocular toxoplasmosis, not yet described. Five Brazilian patients, from 4 different referral centers, presented similar atypical pattern of ocular toxoplasmosis characterized by mild vitritis, foveal cavitation involving predominantly all retinal layers associated with adjacent inner retinal necrosis (a necrotizing retinitis with a persisting inner retinal tissue bridge and loss of subjacent retinal layers). The appearance of the OCT image resembling a “rift”, led the authors to define this pattern as a Recurrent Inner Foveal Toxoplasmic Retinitis (RIFTER), which can be considered as a new description of an atypical pattern of toxoplasma retinochoroiditis, and clinicians should be aware of it and consider testing for toxoplasmosis in patients with similar findings.
Clinical situations for which 3D Printing is considered an appropriate representation or extension of data contained in a medical imaging examination: vascular conditions
Authors: Lee Joonhyuk , Chadalavada Seetharam C. , Ghodadra Anish , Ali Arafat , Arribas Elsa M. , Chepelev Leonid , Ionita Ciprian N. , Ravi Prashanth , Ryan Justin R. , Santiago Lumarie , Wake Nicole , Sheikh Adnan M. , Rybicki Frank J. , Ballard David H. 
Published: November 2023

Abstract
Background
Medical three-dimensional (3D) printing has demonstrated utility and value in anatomic models for vascular conditions. A writing group composed of the Radiological Society of North America (RSNA) Special Interest Group on 3D Printing (3DPSIG) provides appropriateness recommendations for vascular 3D printing indications.

Methods
A structured literature search was conducted to identify all relevant articles using 3D printing technology associated with vascular indications. Each study was vetted by the authors and strength of evidence was assessed according to published appropriateness ratings.

Results
Evidence-based recommendations for when 3D printing is appropriate are provided for the following areas: aneurysm, dissection, extremity vascular disease, other arterial diseases, acute venous thromboembolic disease, venous disorders, lymphedema, congenital vascular malformations, vascular trauma, vascular tumors, visceral vasculature for surgical planning, dialysis access, vascular research/development and modeling, and other vasculopathy. Recommendations are provided in accordance with strength of evidence of publications corresponding to each vascular condition combined with expert opinion from members of the 3DPSIG.

Conclusion
This consensus appropriateness ratings document, created by the members of the 3DPSIG, provides an updated reference for clinical standards of 3D printing for the care of patients with vascular conditions.
Dutch–Flemish translation and validation of the gastrointestinal symptom scales from the patient‑reported outcomes measurement information system (PROMIS)®
Authors: van der Ende-van Loon Mirjam , Korteling Dorinde , Willekens Hilde , Schilders Monique , Curvers Wouter , Bisschops Raf , Schoon Erik , Terwee Caroline 
Published: November 2023

Abstract
Purpose
To translate the eight PROMIS® GastrointestinaI Symptom Scales into Dutch–Flemish and to evaluate their psychometric properties.

Methods
This study consisted of two parts: (1) translation according to the Functional Assessment of Chronic Illness Therapy (FACIT) translation methodology and (2) evaluation of psychometric properties: structural validity, using confirmatory factor analysis; and construct validity using hypothesis testing.

Results
In the first part of the study, in 19 out of the 77 items (24.7%) translation was challenging. After discussion between the translators, consensus could be achieved. In the cognitive debriefing interview phase, ten minor changes in the wording of items were made. A universal Dutch–Flemish translation for all 77 items was obtained. In de second part of the study a good fit was found for three DF-PROMIS GI Scales: Bowel Incontinence, Gas and Bloating, and Belly Pain. Four scales (Reflux, Disrupted Swallowing, Diarrhea, and Constipation) did not show sufficient fit and fit for the Nausea and Vomiting scale could not be assessed because of skewed responses. Construct validity was considered sufficient for six out of eight DF-PROMIS GI Scales. Less than 75% of hypothesis for de Constipation and Disrupted Swallowing scales could be confirmed.

Conclusion
The PROMIS GI Symptom Scales were successfully translated into DutchFlemish. The findings suggest a sufficient structural validity for the PROMIS GI Scales. Bowel Incontinence, Gas and Bloating and Belly Pain. Construct validity was sufficient for the Scales Gas and Bloating, Incontinence, Nausea and Vomiting, Reflux, Belly Pain, and Diarrhea.
Validation of a German-language modified Rankin Scale structured telephone interview at 3 months in a real-life stroke cohort
Authors: Milles Lennart Steffen , Pommeranz Doreen , Chae Woon Hyung , Kühne Escolà Jordi , Kleinschnitz Christoph , Köhrmann Martin , Frank Benedikt 
Published: November 2023

Abstract
Background
The modified Rankin scale (mRS) at 3 months is established as the primary outcome measure in clinical stroke trials. Traditionally, the mRS is assessed through an unstructured face-to-face interview. This approach can be labor-intensive and lead to suboptimal inter-rater reliability. Recently, the Covid-19 pandemic made face-to-face contact even more challenging. To address these issues, we developed and validated a structured German-language questionnaire for mRS testing by telephone.

Methods
In this prospective cohort study, we compared the mRS testing results of the standard face-to-face interview with those obtained in a structured interview by telephone using Cohen’s Kappa.

Results
At our tertiary care stroke center, we included 108 patients who underwent both assessments. In 80.6% of cases (87/108) face-to-face and telephone interview reached identical scores. Linear weighted Kappa was 0.82 (p < 0.001). Unweighted Kappa for dichotomized mRS between fair (0–2) and poor (3–6) functional outcome was κ = 0.97 (p < 0.001).

Conclusions
Our study validates the use of the German-language structured telephone interview as a reliable instrument for the use in clinical trials. We encourage others to utilize the questionnaire. It is available as an Appendix (Additional file 1) to this publication.
Native pulmonary valve massive endocarditis in a drug-addicted patients with Covid-19 pneumonia: a case report
Authors: Garatti Andrea , Daprati Andrea , Ronco Lorenzo Lora , Sassi Carlo Gaetano , De Vincentiis Carlo 
Published: November 2023

Abstract
Background
Pulmonary valve (PV) infective endocarditis is a rare pathology. Association between acute endocarditis and Covid pneumonia is equally poorly investigated.

Case presentation
We present the case of a 50-year-old male active drug-abuser admitted for native PV endocarditis with huge and mobile vegetations and a concomitant interstitial SARS-Cov2 pneumonia. Surgical timing was carefully evaluated, and the patient was first treated with Remdesivir to prevent ARDS evolution. After 5 days he underwent PV replacement with bioprosthesis via patch enlargement of RVOT and a tricuspid valve De-Vega annuloplasty. The postoperative course was uneventful with complete resolution of sepsis and viremia.

Conclusions
The association between infective endocarditis and Covid pneumonia is emerging in the recent months. The reorganization in cardiac surgery hub centers resulted in an increase of urgencies referral, with consequent relative observation of some pathologies (i.e., endocarditis). The widespread administration of antibiotics and corticosteroids during the first phase of the pandemic could have contributed to the development of a moderate immunodepression of the general population and, during the pandemic, patients have been reluctant to access to hospital care, and this diagnostic delay could contribute to misdiagnosis or late presentation. We believe that in the present case, the strategy of immediate viral and respiratory stabilization, followed by a timely surgical procedure, allowed an excellent outcome in a very complicated situation.