bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovering unknown response patterns in progress test data to improve the estimation of student performance
Authors: Sieg Miriam , Roselló Atanet Iván , Tomova Mihaela Todorova , Schoeneberg Uwe , Sehy Victoria , Mäder Patrick , März Maren 
Published: March 2023

Abstract
Background
The Progress Test Medizin (PTM) is a 200-question formative test that is administered to approximately 11,000 students at medical universities (Germany, Austria, Switzerland) each term. Students receive feedback on their knowledge (development) mostly in comparison to their own cohort. In this study, we use the data of the PTM to find groups with similar response patterns.

Methods
We performed k-means clustering with a dataset of 5,444 students, selected cluster number k = 5, and answers as features. Subsequently, the data was passed to XGBoost with the cluster assignment as target enabling the identification of cluster-relevant questions for each cluster with SHAP. Clusters were examined by total scores, response patterns, and confidence level. Relevant questions were evaluated for difficulty index, discriminatory index, and competence levels.

Results
Three of the five clusters can be seen as “performance” clusters: cluster 0 (n = 761) consisted predominantly of students close to graduation. Relevant questions tend to be difficult, but students answered confidently and correctly. Students in cluster 1 (n = 1,357) were advanced, cluster 3 (n = 1,453) consisted mainly of beginners. Relevant questions for these clusters were rather easy. The number of guessed answers increased. There were two “drop-out” clusters: students in cluster 2 (n = 384) dropped out of the test about halfway through after initially performing well; cluster 4 (n = 1,489) included students from the first semesters as well as “non-serious” students both with mostly incorrect guesses or no answers.

Conclusion
Clusters placed performance in the context of participating universities. Relevant questions served as good cluster separators and further supported our “performance” cluster groupings.
The association between patient safety culture and adverse events – a scoping review
Authors: Vikan Magnhild , Haugen Arvid Steinar , Bjørnnes Ann Kristin , Valeberg Berit Taraldsen , Deilkås Ellen Catharina Tveter , Danielsen Stein Ove 
Published: March 2023

Abstract
Background
Adverse events (AEs) affect 10% of in-hospital patients, causing increased costs, injuries, disability and mortality. Patient safety culture (PSC) is an indicator of quality in healthcare services and is thus perceived as a proxy for the quality of care. Previous studies show variation in the association between PSC scores and AE rates. The main objective of this scoping review is to summarise the evidence on the association between PSC scores and AE rates in healthcare services. In addition, map the characteristics and the applied research methodology in the included studies, and study the strengths and limitations of the evidence.

Methods
We applied a scoping review methodology to answer the broad research questions of this study, following the PRISMA-ScR checklist. A systematic search in seven databases was conducted in January 2022. The records were screened independently against eligibility criteria using Rayyan software, and the extracted data were collated in a charting form. Descriptive representations and tables display the systematic mapping of the literature.

Results
We included 34 out of 1,743 screened articles. The mapping demonstrated a statistical association in 76% of the studies, where increased PSC scores were associated with reduced AE rates. Most of the studies had a multicentre design and were conducted in-hospital in high-income countries. The methodological approaches to measuring the association varied, including missing reports on the tools` validation and participants, different medical specialties, and work unit level of measurements. In addition, the review identified a lack of eligible studies for meta-analysis and synthesis and demonstrated a need for an in-depth understanding of the association, including context complexity.

Conclusions
We found that the vast majority of studies report reduced AE rates when PSC scores increase. This review demonstrates a lack of studies from primary care and low- and- middle-income countries. There is a discrepancy in utilised concepts and methodology, hence there is a need for a broader understanding of the concepts and the contextual factors, and more uniform methodology. Longitudinal prospective studies with higher quality can enhance efforts to improve patient safety.
BBB-on-a-chip with integrated micro-TEER for permeability evaluation of multi-functionalized gold nanorods against Alzheimer’s disease
Authors: Palma-Florez Sujey , López-Canosa Adrián , Moralez-Zavala Francisco , Castaño Oscar , Kogan Marcelo J. , Samitier Josep , Lagunas Anna , Mir Mònica 
Published: March 2023

AbstractBackgroundThe lack of predictive models that mimic the blood–brain barrier (BBB) hinders the development of effective drugs for neurodegenerative diseases. Animal models behave differently from humans, are expensive and have ethical constraints. Organ-on-a-chip (OoC) platforms offer several advantages to resembling physiological and pathological conditions in a versatile, reproducible, and animal-free manner. In addition, OoC give us the possibility to incorporate sensors to determine cell culture features such as trans-endothelial electrical resistance (TEER). Here, we developed a BBB-on-a-chip (BBB-oC) platform with a TEER measurement system in close distance to the barrier used for the first time for the evaluation of the permeability performance of targeted gold nanorods for theranostics of Alzheimer’s disease. GNR-PEG-Ang2/D1 is a therapeutic nanosystem previously developed by us consisting of gold nanorods (GNR) functionalized with polyethylene glycol (PEG), angiopep-2 peptide (Ang2) to overcome the BBB and the D1 peptide as beta amyloid fibrillation inhibitor, finally obtaining GNR-PEG-Ang2/D1 which showed to be useful for disaggregation of the amyloid in in vitro and in vivo models. In this work, we evaluated its cytotoxicity, permeability, and some indications of its impact on the brain endothelium by employing an animal-free device based on neurovascular human cells.ResultsIn this work, we fabricated a BBB-oC with human astrocytes, pericytes and endothelial cells and a TEER measuring system (TEER-BBB-oC) integrated at a micrometric distance of the endothelial barrier. The characterization displayed a neurovascular network and the expression of tight junctions in the endothelium. We produced GNR-PEG-Ang2/D1 and determined its non-cytotoxic range (0.05–0.4 nM) for plated cells included in the BBB-oC and confirmed its harmless effect at the highest concentration (0.4 nM) in the microfluidic device. The permeability assays revealed that GNR-PEG-Ang2/D1 cross the BBB and this entry is facilitated by Ang2 peptide. Parallel to the permeability analysis of GNR-PEG-Ang2/D1, an interesting behavior of the TJs expression was observed after its administration probably related to the ligands on the nanoparticle surface.ConclusionsBBB-oC with a novel TEER integrated setup which allow a correct read-out and cell imaging monitoring was proven as a functional and throughput platform to evaluate the brain permeability performance of nanotherapeutics in a physiological environment with human cells, putting forward a viable alternative to animal experimentation.
First results of the French OCTOPUS survey among festival attendees: a latent class analysis
Authors: Istvan Marion , Bresdin Vincent , Mainguy Marie , Laigo Pauline , Grall-Bronnec Marie , Eudeline Vincent , Guillet Jean-Emmanuel , Guillo Manon , Babonnaud Laurent , Jolliet Pascale , Schreck Benoit , Victorri-Vigneau Caroline 
Published: March 2023

Abstract
Background
Illicit substance use has constantly evolved over the years, particularly in the party scene. Monitoring these changes is essential to adapt harm reduction strategies. The OCTOPUS survey was implemented to enhance knowledge on drug use at music festivals. The objective of the work presented here was to describe drug use and to characterize profiles of substance use in music festival attendees.

Methods
OCTOPUS was a cross-sectional survey carried out during 13 various music festivals (dub, eclectic and electronic music) in the Loire-Atlantique department (France) from July 2017 to July 2018. Participants were festival attendees. Data were collected by trained research staff using a face-to-face structured interview. We analysed the use of illicit drugs in the last 12 months to describe the prevalence of use and to characterize the profile of substance use using a latent class analysis.

Results
In total, 383 festival attendees were included. Of 314 (82%) participants who reported drug use, the most reported drugs were cannabis, ecstasy/MDMA and cocaine. We identified two profiles of drug use: (i) a “no/low polysubstance use” profile mainly characterized by the use of “classic” stimulants (ecstasy/MDMA, cocaine) and (ii) “moderate/extensive polysubstance use”, with high probabilities of “classic” stimulants use and especially other drugs reported: speed, ketamine, new psychoactive substances (NPSs).

Conclusion
We observed frequent polysubstance use in festival attendees. Harm reduction should be targeted at the increased risk of toxicity linked to polysubstance use, and the reduction in harm caused by particular drugs (ketamine, NPS, speed) could be further strengthened.
Application of triple evaluation method in predicting the efficacy of neoadjuvant therapy for breast cancer
Authors: Han Xu , Li Hui , Dong Sha-Sha , Zhou Shui-Ying , Wang Cai-Hong , Guo Lin , Yang Jie , Zhang Gang-Ling 
Published: March 2023

Abstract
Objective
To analyze the factors related to the efficacy of neoadjuvant therapy for breast cancer and find appropriate evaluation methods for evaluating the efficacy of neoadjuvant therapy

Methods
A total of 143 patients with breast cancer treated by neoadjuvant chemotherapy at Baotou Cancer Hospital were retrospectively analyzed. The chemotherapy regimen was mainly paclitaxel combined with carboplatin for 1 week, docetaxel combined with carboplatin for 3 weeks, and was replaced with epirubicin combined with cyclophosphamide after evaluation of disease progression. All HER2-positive patients were treated with simultaneous targeted therapy, including trastuzumab single-target therapy and trastuzumab combined with pertuzumab double-target therapy. Combined with physical examination, color Doppler ultrasound, and magnetic resonance imaging (MRI), a systematic evaluation system was initially established—the “triple evaluation method.” A baseline evaluation was conducted before treatment. The efficacy was evaluated by physical examination and color Doppler every cycle, and the efficacy was evaluated by physical examination, color Doppler, and MRI every two cycles.

Results
The increase in ultrasonic blood flow after treatment could affect the efficacy of monitoring. The presence of two preoperative time–signal intensity curves is a therapeutically effective protective factor for inflow. The triple evaluation determined by physical examination, color Doppler ultrasound, and MRI in determining clinical efficacy is consistent with the effectiveness of the pathological gold standard.

Conclusion
The therapeutic effect of neoadjuvant therapy can be better evaluated by combining clinical physical examination, color ultrasound, and nuclear magnetic resonance evaluation. The three methods complement each other to avoid the insufficient evaluation of a single method, which is convenient for most prefecty-level hospitals. Additionally, this method is simple, feasible, and suitable for promotion.
Klebsiella quasipneumoniae in intestine damages bile acid metabolism in hematopoietic stem cell transplantation patients with bloodstream infection
Authors: Yin Guankun , Guo Yifan , Ding Qi , Ma Shuai , Chen Fengning , Wang Qi , Chen Hongbin , Wang Hui 
Published: March 2023

Abstract
Background
Bloodstream infection (BSI) is a serious hematopoietic stem cell transplantation (HSCT) complication. The intestinal microbiome regulates host metabolism and maintains intestinal homeostasis. Thus, the impact of microbiome on HSCT patients with BSI is essential.

Methods
Stool and serum specimens of HSCT patients were prospectively collected from the pretransplant conditioning period till 4 months after transplantation. Specimens of 16 patients without BSI and 21 patients before BSI onset were screened for omics study using 16S rRNA gene sequencing and untargeted metabolomics. The predictive infection model was constructed using LASSO and the logistic regression algorithm. The correlation and influence of microbiome and metabolism were examined in mouse and Caco-2 cell monolayer models.

Results
The microbial diversity and abundance of Lactobacillaceae were remarkably reduced, but the abundance of Enterobacteriaceae (especially Klebsiella quasipneumoniae) was significantly increased in the BSI group before onset, compared with the non-BSI group. The family score of microbiome features (Enterobacteriaceae and Butyricicoccaceae) could highly predict BSI (AUC = 0.879). The serum metabolomic analysis showed that 16 differential metabolites were mainly enriched in the primary bile acid biosynthesis pathway, and the level of chenodeoxycholic acid (CDCA) was positively correlated with the abundance of K. quasipneumoniae (R = 0.406, P = 0.006). The results of mouse experiments confirmed that three serum primary bile acids levels (cholic acid, isoCDCA and ursocholic acid), the mRNA expression levels of bile acid farnesol X receptor gene and apical sodium-dependent bile acid transporter gene in K. quasipneumoniae colonized mice were significantly higher than those in non-colonized mice. The intestinal villus height, crypt depth, and the mRNA expression level of tight junction protein claudin-1 gene in K. quasipneumoniae intestinal colonized mice were significantly lower than those in non-colonized mice. In vitro, K. quasipneumoniae increased the clearance of FITC-dextran by Caco-2 cell monolayer.

Conclusions
This study demonstrated that the intestinal opportunistic pathogen, K. quasipneumoniae, was increased in HSCT patients before BSI onset, causing increased serum primary bile acids. The colonization of K. quasipneumoniae in mice intestines could lead to mucosal integrity damage. The intestinal microbiome features of HSCT patients were highly predictive of BSI and could be further used as potential biomarkers.
Fast-track transformation and genome editing in Brachypodium distachyon
Authors: Soulhat Camille , Wehbi Houssein , Fierlej Yannick , Berquin Patrick , Girin Thomas , Hilson Pierre , Bouchabké-Coussa Oumaya 
Published: March 2023

Abstract
Background
Even for easy-to-transform species or genotypes, the creation of transgenic or edited plant lines remains a significant bottleneck. Thus, any technical advance that accelerates the regeneration and transformation process is welcome. So far, methods to produce Brachypodium distachyon (Bd) transgenics span at least 14 weeks from the start of tissue culture to the recovery of regenerated plantlets.

Results
We have previously shown that embryogenic somatic tissues grow in the scutellum of immature zygotic Bd embryos within 3 days of in vitro induction with exogenous auxin and that the development of secondary embryos can be initiated immediately thereafter. Here, we further demonstrate that such pluripotent reactive tissues can be genetically transformed with Agrobacterium tumefaciens right after the onset of somatic embryogenesis. In brief, immature zygotic embryos are induced for callogenesis for one week, co-cultured with Agrobacterium for three days, then incubated on callogenesis selective medium for three weeks, and finally transferred on selective regeneration medium for up to three weeks to obtain plantlets ready for rooting. This 7-to-8-week procedure requires only three subcultures. Its validation includes the molecular and phenotype characterization of Bd lines carrying transgenic cassettes and novel CRISPR/Cas9-generated mutations in two independent loci coding for nitrate reductase enzymes (BdNR1 and BdNR2).

Conclusions
With a short callogenesis stage and streamlined in vitro regeneration following co-cultivation with Agrobacterium, transgenic and edited T0 Bd plantlets can be produced in about 8 weeks, a gain of one to two months compared to previously published methods, with no reduction in transformation efficiency and at lower costs.
Effectiveness of intraoperative peritoneal lavage with saline in patient with intra-abdominal infections: a systematic review and meta-analysis
Authors: Zhou Qi , Meng Wenbo , Ren Yanhan , Li Qinyuan , Boermeester Marja A. , Nthumba Peter Muli , Rickard Jennifer , Zheng Bobo , Liu Hui , Shi Qianling , Zhao Siya , Wang Zijun , Liu Xiao , Luo Zhengxiu , Yang Kehu , Chen Yaolong , Sawyer Robert G. 
Published: March 2023

Abstract
Background
Intraoperative peritoneal lavage (IOPL) with saline has been widely used in surgical practice. However, the effectiveness of IOPL with saline in patients with intra-abdominal infections (IAIs) remains controversial. This study aims to systematically review randomized controlled trials (RCTs) evaluating the effectiveness of IOPL in patients with IAIs.

Methods
The databases of PubMed, Embase, Web of Science, Cochrane library, CNKI, WanFang, and CBM databases were searched from inception to December 31, 2022. Random-effects models were used to calculate the risk ratio (RR), mean difference, and standardized mean difference. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) was used to rate the quality of the evidence.

Results
Ten RCTs with 1318 participants were included, of which eight studies on appendicitis and two studies on peritonitis. Moderate-quality evidence showed that the use of IOPL with saline was not associated with a reduced risk of mortality (0% vs. 1.1%; RR, 0.31 [95% CI, 0.02–6.39]), intra-abdominal abscess (12.3% vs. 11.8%; RR, 1.02 [95% CI, 0.70–1.48]; I2 = 24%), incisional surgical site infections (3.3% vs. 3.8%; RR, 0.72 [95% CI, 0.18–2.86]; I2 = 50%), postoperative complication (11.0% vs. 13.2%; RR, 0.74 [95% CI, 0.39–1.41]; I2 = 64%), reoperation (2.9% vs. 1.7%; RR,1.71 [95% CI, 0.74–3.93]; I2 = 0%) and readmission (5.2% vs. 6.6%; RR, 0.95 [95% CI, 0.48–1.87]; I2 = 7%) in patients with appendicitis when compared to non-IOPL. Low-quality evidence showed that the use of IOPL with saline was not associated with a reduced risk of mortality (22.7% vs. 23.3%; RR, 0.97 [95% CI, 0.45–2.09], I2 = 0%) and intra-abdominal abscess (5.1% vs. 5.0%; RR, 1.05 [95% CI, 0.16–6.98], I2 = 0%) in patients with peritonitis when compared to non-IOPL.

Conclusion
IOPL with saline use in patients with appendicitis was not associated with significantly decreased risk of mortality, intra-abdominal abscess, incisional surgical site infection, postoperative complication, reoperation, and readmission compared with non-IOPL. These findings do not support the routine use of IOPL with saline in patients with appendicitis. The benefits of IOPL for IAI caused by other types of abdominal infections need to be investigated.
Successful in vitro fertilization following conservative surgery for synchronous endometrioid tumor of ovary and uterus
Authors: Suri Vanita , Bansal Ramandeep , Aggarwal Neelam , Sikka Pooja , Chopra Seema , Saha Subhash Chandra , Gupta Nalini , Rai Bhavana 
Published: March 2023

AbstractBackgroundSuccessful pregnancy outcome in women with synchronous ovarian and endometrial cancers is very rare. We report successful pregnancy outcome in a young woman managed conservatively for synchronous endometrial and ovarian cancer.Case presentationThirty years old nulliparous lady presented following exploratory laparotomy, left salpingo-oophorectomy and hysteroscopic polypectomy for left adnexal mass. Histology revealed endometrioid carcinoma of left ovary and moderately differentiated adenocarcinoma in the resected polyp. She underwent staging laparotomy along with hysteroscopy which confirmed above findings without any evidence of further tumor spread. She was treated conservatively with high dose oral progestin (megestrol acetate, 160 mg) and leuprolide acetate 3.75 mg monthly injections for three months along with four cycles of carboplatin and paclitaxel based chemotherapy followed by monthly injection of leuprolide for further three months. After failure of spontaneous conception, she underwent ovulation induction for six cycles along with intrauterine insemination which failed. She underwent in vitro fertilization with donor egg followed by elective cesarean section at 37 weeks of gestation. She delivered a healthy baby of weight 2.7 kg. Intraoperatively 5 × 6 cm right ovarian cyst was found which drained chocolate coloured fluid on puncture and cystectomy was carried out. Histological examination revealed endometrioid cyst of right ovary. Uterus was spared as she wanted to preserve her fertility. She is being followed periodically and is normal nine months following delivery. She is on injection Depot medroxy progesterone acetate once every three months.
BIND&MODIFY: a long-range method for single-molecule mapping of chromatin modifications in eukaryotes
Authors: Weng Zhe , Ruan Fengying , Chen Weitian , Chen Zhichao , Xie Yeming , Luo Meng , Xie Zhe , Zhang Chen , Wang Juan , Sun Yuxin , Fang Yitong , Guo Mei , Tan Chen , Chen Wenfang , Tong Yiqin , Li Yaning , Wang Hongqi , Tang Chong 
Published: March 2023

AbstractEpigenetic modifications of histones are associated with development and pathogenesis of disease. Existing approaches cannot provide insights into long-range interactions and represent the average chromatin state. Here we describe BIND&MODIFY, a method using long-read sequencing for profiling histone modifications and transcription factors on individual DNA fibers. We use recombinant fused protein A-M.EcoGII to tether methyltransferase M.EcoGII to protein binding sites to label neighboring regions by methylation. Aggregated BIND&MODIFY signal matches bulk ChIP-seq and CUT&TAG. BIND&MODIFY can simultaneously measure histone modification status, transcription factor binding, and CpG 5mC methylation at single-molecule resolution and also quantifies correlation between local and distal elements.