bluuebunny/crossref_metadata_2025_split huggingface dataset:
scMEB: A fast and clustering-independentmethod for detecting differentially expressedgenes in single-cell RNA-seq data
Authors: Zhu Jiadi , Yang Youlong 
Published: October 2022

Abstract
Background: Cell clustering is a prerequisite for identifying differentiallyexpressed genes (DEGs) in single-cell RNA sequencing (scRNA-seq) data.Obtaining a perfect clustering result is of central importance for subsequentanalyses, but doing so is not easy. Additionally, the increase in cell throughputdue to the advancement of scRNA-seq protocols exacerbates many computationalissues, especially regarding method runtime. To address these difficulties, a new,accurate, and fast method for detecting DEGs in scRNA-seq data is needed.
Results: Here, we propose single-cell minimum enclosing ball (scMEB), a noveland fast method for detecting single-cell DEGs without prior cell clusteringresults. The proposed method utilizes a small part of known non-DEGs (stablyexpressed genes) to build a minimum enclosing ball and defines the DEGs basedon the distance of a mapped gene to the center of the sphere in a feature space.
Conclusions: We benchmarked scMEB against two other methods that haveimplications for DEG identification without clustering the cells. The analysisresults of 11 real datasets demonstrated that scMEB had a better or at leastcomparable performance with the competing methods in terms of identifyingmarker genes, cell clustering, and predicting genes with biological functions.Moreover, scMEB ran much faster than the other methods, which is especiallyuseful for detecting DEGs in high-throughput scRNA-seq data. Our method“scMEB” has been incorporated into the R package (MEB) and could beaccessed at https://github.com/FocusPaka/MEB.
Efficacy and Safety of Tirofiban in Patient Undergoing Planned Percutaneous Coronary Intervention Based on Real-world Evidence: A Retrospective Study of 1311 Patients
Authors: Huang Bingyu , Zhu Mengying , Zhou Chi , Li Sheng , Lv Jiagao 
Published: October 2022

Abstract
Background
There is no consensus on reductions of ischemic events and bleeding risks of tirofiban for patients receiving planned percutaneous coronary intervention (PCI) yet. In this study, we aim to investigate the real-world efficacy and safety of tirofiban treatment on patients undergoing planned PCI during hospital course and explore potential population who could benefit from tirofiban.
Methods
This real-world study included 1311 patients who received planned PCI and implanted stents. Demographic and clinical characteristics were compared between patients who received tirofiban treatment (n = 829) and those were not given tirofiban as control (n = 482). Correlation of tirofiban and outcome in hospital level was assessed using logistic regression analysis.
Results
More tirofiban patients had multivessel disease and multiple stents implantation. On logistic regression analysis, there was no significant association between the usage of tirofiban and bleeding events (OR [95%CI] = 1.36 [0.65,3.06], p = 0.433), major adverse cardiac and cerebrovascular events (MACCE) (OR [95%CI] = 1.37 [0.65, 3.06], p = 0.425) or net adverse cardiac and cerebrovascular events (NACCE) (OR [95%CI] = 1.01 [0.61, 1.71], P = 0.963). In subgroup analysis, tirofiban used among patients with higher D-dimer level (D-dimer ≥ 0.5 g/ml FEU) was less likely to be associated with MACCE (OR = 0.51 vs OR = 4.59, p for interaction = 0.031).
Conclusions
The use of tirofiban did not decrease MACCE or NACCE during hospital course among patients undergoing planned PCI, however, the risk of bleeding was not increased. Tirofiban receipts were prone to severe illness and complex PCI. Conferring no harm but potential benefits, the use of tirofiban could be considered for patients who received planned PCI and present with comorbidities and complex coronary lesions.
Knowledge-aware Response Selection with Semantics underlying Multi-Turn Open-Domain Conversations
Authors: Nakatsuji Makoto , Ozeki Yuka , Tateishi Shuhei , Kano Yoshihisa , Zhang QingPeng 
Published: October 2022

Abstract
Response selection is a critical issue in the AI community with important applications on the Web. The accuracy of the selected responses, however, tends to be insufficient due to the lack of contextual awareness, especially in open-domain conversations where words tend to have several meanings in different contexts. Our solution, SemSol, is a knowledge-aware response selection model that tackles this problem by utilizing the context-specific semantics behind words that are implicitly shared among users throughout the dialogue. SemSol simultaneously learns word sense disambiguations (WSD) for the words in the dialogue on the basis of an open-domain knowledge graph, i.e. WordNet, while learning the match between the context and the response candidates. Then, SemSol improves the accuracy of the response by exploiting the semantic information in knowledge graph in accordance with the dialogue context. Our model learns the topics of utterances in the context of the whole training dataset. This topic-level knowledge can provide topic-specific information in the dialogue context. This improves the WSDs and the response selection accuracy. Experimens with two open-domain conversational datasets, Douban (Chinese) and Reddit (English), demonstrated that the proposed SemSol model outperformed state-of-the-art baselins. SemSol is ranked #1 in the Douban leaderboard.
Impact of off-label under-dose direct oral anticoagulant on coagulation and fibrinolytic markers in patients with atrial fibrillation
Authors: Watanabe Tetsuya , Tachibana Koichi , Shinoda Yukinori , Minamisaka Tomoko , Fukuoka Hidetada , Inui Hirooki , Ueno Keisuke , Inoue Souki , Mine Kentaro , Hoshida Shiro 
Published: October 2022

Abstract
Objectives: Direct oral anticoagulants (DOAC) have been approved for oral anticoagulation in patients with non-valvular atrial fibrillation (AF). On the other hand, DOAC are sometimes prescribed off-label under-doses for patients with AF. This study aimed to compare the effects of different DOAC doses on coagulation and fibrinolytic markers.
Methods:A total of 88 patients with AF (age, 68 ± 11 years; male sex, 45%; persistent AF, 43%) were analyzed. All patients received edoxaban (60 or 30 mg) once daily. For this study, patients were divided into three groups according to whether they had been treated before the ablation procedure under an appropriate standard-dose group (n = 30 [34.1%]), appropriate low-dose group (n = 35 [39.8%]), or off-label under-dose group (n = 23 [26.1%]). Coagulation and fibrinolytic markers and echocardiographic parameters were examined before ablation.
Results:There were no significant baseline differences in AF type, plasma B-type natriuretic peptide, protein C, fibrinogen, D-dimer level, left ventricular ejection fraction, or left atrial dimension among the three groups. The prothrombin fragment 1+2 (F1+2) level was significantly different among the appropriate standard-dose, appropriate low-dose, and off-label under-dose groups (105.9 ± 29.4, 142.6 ± 41.3, and 142.8 ± 84.9 pmol/L, respectively; P = 0.011). After multivariate analysis, the F1+2 was significantly higher in the off-label low-dose group than in the standard-dose group when compared among the three groups (P = 0.034, Bonferroni test).
Conclusion:Our results suggest that an appropriate standard dose of edoxaban is required to suppress hypercoagulability in patients with AF.
Binge drinking, parental substance use and family socio-economic status in France: evidence for an alcohol harm paradox in adolescence
Authors: Legleye Stéphane , Khlat Myriam , Aubin Henri-Jean , Bricard Damien 
Published: October 2022

Abstract
Background
Adolescent heavy episodic drinking (HED) represents a serious health threat. We explore the relation of HED and of emergency room visit because of acute alcoholic intoxication during life (ERV) with family socioeconomic status (SES), family living arrangement (living in a non-intact family or living independently) and parental substance use.
Setting: A cross-sectional nationwide exhaustive 12-day survey in March 2017 of French youth aged 17-18.5 participating in the national mandatory civic information day.
Participants: 13,314 adolescents answering a pen and paper questionnaire about their own alcohol consumption and the consumption of tobacco and alcohol of their parents.
Measurements: Outcomes were the number of past month heavy drinking episodes and ERV. Risk ratios (RR) were computed using modified Poisson regressions.
Results
Compared to the adolescents with the highest SES, those from the lowest SES were less likely to report 1-2 or 3-5 episodes of heavy drinking instead of none (RR=0.58, 95% CI=[0.50; 0.66] and 0.35 [0.27; 0.45]) but there was no difference for 6 episodes and above (RR=0.81 [0.59; 1.12]). At the extreme, ERV was more frequent among adolescents with the lowest SES (RR=1.86 [1.05; 3.30]).
SES, parental substance use and family living arrangement were associated independently with HED; they were not confounded by each other and no interaction between these factors was significant.
Conclusion
Adolescents from disadvantaged families report fewer episodes of heavy drinking, but are more likely to report alcohol-related emergency room visit, showing the existence of a robust “alcohol harm paradox”.
Colonization of Patients Hospitalized at Orthopedic Department of Tertiary Hospital in Uganda with Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae
Authors: Bizimana Jules , Ndayisenga Jerome , Kajumbura Henry , Mulepo Phillip , Najjuka Florence Christine 
Published: October 2022

Abstract
Background
Beta-lactamase production remains the most contributing factor to beta-lactam resistance. Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae (ESBL-PE) are associated with risk factors both in hospital and community settings.
Objectives
To assess the incidence and risk factors for intestinal carriage of extended spectrum beta lactamase producing Enterobacteriaceae among patients admitted to orthopedic ward of Mulago National Referral Hospital, and to analyze the acquisition of ESBL-PE during hospital stay and associated factors.
Methods
We screened 172 patients aged 18 years old and above who got admitted to the orthopedic ward of Mulago National Referral Hospital between May to July 2017. Stool samples or rectal swabs were collected at admission, every 3 days until fourteen days and screened for ESBL-PE. Data on demographic status, antibiotic use, admission and travel, length of hospital stay, hygiene practices and drinking boiled water were analyzed by logistic regression and cox regression model.
Results
At admission, 61% of patients showed intestinal ESBL-PE carriage. Co- resistance was common but no Carbapenem resistance was detected. Of the ESBL-PE negative, 49 % were colonized during hospitalization. On admission, prior antibiotic use was significantly associated with carriage, but none was associated with acquisition during hospitalization at p-value < 0.05.
Conclusion
Carriage of ESBL-PE on admissions and acquisition at orthopedic ward of Mulago Hospital were high, and dissemination into the community are of substantial concern. We suggested refinement of empirical treatment based on risk stratification, and enhanced infection control measures that target health care workers, patients and attendants.
A Phase I/II Study of Preoperative Letrozole, Everolimus, and Carotuximab in Stage 2 and 3 Hormone Receptor-positive and Her2-negative Breast Cancer.
Authors: Vaklavas Christos , Stringer-Reasor Erica M , Elkhanany Ahmed M , Ryan Kevin J , Li Yufeng , Theuer Charles P , Acosta Edward P , Wei Shi , Yang Eddy S , Grizzle William E , Forero-Torres Andres 
Published: October 2022

Abstract
Purpose: In nonmetastatic hormone receptor-positive and Her2-negative breast cancer, preoperative endocrine therapies can yield outcomes similar with chemotherapy. We evaluated the tolerability and preliminary antitumor activity of preoperative letrozole, everolimus, and carotuximab, a monoclonal antibody targeting endoglin, in nonmetastatic breast cancer.
Methods: Eligible patients had newly diagnosed, stage 2 or 3, hormone receptor-positive and Her2/neu-negative breast cancer. Patients received escalating doses of everolimus; the dose of letrozole and carotuximab were fixed at 2.5 mg PO daily and 15 mg/kg intravenously every 2 weeks, respectively. The primary objective was to determine the safety and tolerability of the combination. Secondary objectives included pharmacokinetic and pharmacodynamic studies and assessments of antitumor activity.
Results: fifteen patients enrolled. The recommended phase 2 dose of everolimus in combination with letrozole and carotuximab was 10 mg PO daily. The most frequent adverse events were headache (67%), fatigue (47%), facial flushing and swelling (47%), gingival hemorrhage (40%), epistaxis (33%), nausea and vomiting (27%). Headache constituted a dose limiting toxicity. At least two signs of mucocutaneous telangiectasia developed in 92% of patients. Carotuximab accumulated in the extravascular space and accelerated the biodistribution and clearance of everolimus. All patients had residual disease. Gene expression analyses were consistent with downregulation of genes involved in proliferation and DNA repair. Among 6 patients with luminal B breast cancer, 5 converted to luminal A after one cycle of therapy.
Conclusion: Letrozole, everolimus, and carotuximab were tolerated in combination at their single-agent doses. Pharmacokinetic studies revealed an interaction between everolimus and carotuximab.
Trial Registration: This trial is registered with ClinicalTrials.gov (Identifier: NCT02520063), first posted on August 11, 2015, and is active, not recruiting.
Biochemical Variations in Vitrified-warmed in Vitro Matured Porcine Oocytes
Authors: Morado Sergio , Aparicio Ailén , Pinchetti Daniela , Arraztoa Claudia Cecilia , Alvarez Gabriel , Gutnisky Cynthia , Neild Deborah , Dalvit Gabriel , Cetica Pablo 
Published: October 2022

Abstract
As the porcine oocyte is the most sensitive to low temperature damage, it has been difficult to cryopreserve compared to those from other domestic animals. However, at present, vitrification is used as a method for the cryopreservation of both oocytes and embryos in this species. Our aim was to analyze biochemical variations in vitrified-warmed in vitro matured porcine oocytes at different recovery times using a minimum volume vitrification system. Additionally, metaphase II plate recovery time analysis, in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI) were carried out to evaluate oocyte maturational capacity recovery. Oocytes were vitrified-warmed and then incubated for 0h, 3h or 21h post-warming to assess biochemical parameters. Oocyte viability or morphology were not affected by vitrification-warming. Cytosolic oxidative status, active mitochondria and reactive oxygen species levels presented variations at the different time points in both control and vitrified-warmed oocytes (P < 0.05) as well as differences between one group and the other (P < 0.05). NAD(P)H levels remained constant throughout different recovery times, but were significantly lower in vitrified-warmed oocytes (P < 0.05). Metaphase II plate recovery occurred mostly between 3 and 4h post-warming, but the percentage of metaphase II was reduced by vitrification-warming process. Sperm head decondensation and pronuclear formation capacities were not modified. In conclusion, vitrification-warming generates biochemical modifications in porcine oocytes that would be in part responsible for affecting their performance. So, although the technique is a possible alternative for porcine oocyte cryopreservation, improvements in the vitrification-warming protocols should be included to minimize the metabolic variations produced during this process.
Newly Synthesized Aminothiazole Based Disazo Dyes and Their Theoretical Calculations
Authors: GÖKALP Merve , ATAY Çiğdem KARABACAK , TİLKİ Tahir 
Published: October 2022

Abstract
This study consists of two parts, experimental and theoretical. In the first part, ten new aminothiazole based disazo dyes (4a-e, 5a-e) were synthesized. Structures of these synthesized dyes were confirmed by 1H-NMR, FT-IR and UV–Vis spectra. In the second part, employing the B3LYP level with the 6-311G(d,p) basis set, in the ground state, the molecular geometry and vibrational frequency calculations were performed by the density functional theory (DFT). The gauge independent atomic orbital (GIAO) method was carried out to investigate the chemical shifts values. Time-dependent DFT (TD-DFT) approach was used to determine the HOMO–LUMO calculations. As a result of our study, it was observed that the computational spectroscopic values of the synthesized disazo compounds were compatible with the experimental values.
Transmission of negative biases through social commentary included in neonatal intensive care unit progress notes
Authors: Shaikh Henna , Billimoria Zeenia , Vandeleur Daron , Weiss Elliott , Batra Maneesh , Hedstrom Anna 
Published: October 2022

Abstract
Objective:
To determine how the perception of families elicited after reading progress note social commentary differs by patient race.
Study Design:
Retrospectively performed content analysis of social commentary in physician progress notes for Neonatal Intensive Care Unit patients hospitalized from 2018-2019. Neonatologists blinded to patient race rated how commentary impacted their perception of the patient’s family on a 5-point Likert scale. Frequency of negative ratings was compared across reported race using chi-squared tests.
Results:
We reviewed charts of 460 neonates. 225 (49%) contained social commentary beyond parents’ names. 12 neonatologists rated how commentaries impacted their perception of the patient’s family; 79%, 18%, and 3% were rated neutrally, negatively, and positively, respectively. Frequency of negative ratings was significantly greater among American Indian/Alaska Native than other patients (35% vs. 22%, p<0.001).
Conclusions:
Physician documentation of social commentary in patient notes may reflect and perpetuate implicit biases that contribute to race-based healthcare disparities.
Artificial temperature-compensated circadian rhythm using Belousov-Zhabotinsky gels
Authors: Yamada Yuhei , Ito Hiroshi , Maeda Shingo 
Published: October 2022

Abstract
A circadian rhythm is a fundamental physiological function for a wide range of organisms. The molecular machinery for generating rhythms has been elucidated over the last few decades. Nevertheless, the mechanism for temperature compensation of the oscillation period, which is a prominent property of the circadian rhythm, is still controversial. In this study, we propose a new mechanism through a chemically synthetic approach (i.e., we realized temperature compensation by the Belousov-Zhabotinsky (BZ) gels). The BZ gels are prepared by embedding a metal catalyst of the BZ reaction into the gel polymer. We made the body of BZ gels using a temperature-sensitive polymer gel, which enabled temperature compensation of the oscillation. Moreover, we constructed a simple mathematical model for the BZ oscillation in temperature-sensitive gels. The model can reproduce temperature compensation of BZ gels, even though all reactions are temperature sensitive according to the Arrhenius rule, suggesting that temperature compensation does not require a special temperature-insensitive process but can be embodied as an oscillatory body. Our finding hints that oscillation-body coupling underlies temperature-compensated biological functions, including circadian rhythms.
A randomised controlled feasibility trial of an early years language development intervention: Results of the ‘outcomes of Talking Together evaluation and results’ (oTTer) project
Authors: Nielsen Dea , d'Apice Katrina , Cheung Rachael , Bryant Maria , Heald Rebecca , Storr Chloe , Tracey Louise , Rashid Rukhsana , Dickerson Josie , Bowyer-Crane Claudine 
Published: October 2022

Abstract

Background

Early language difficulties are associated with poor school readiness and can impact lifelong attainment. The quality of the early home language environment is linked to language outcomes. However, few home-based language interventions have sufficient evidence of effectiveness in improving preschool children’s language abilities. This study reports the first stage in the evaluation of a theory-based programme, Talking Together (developed and delivered by BHT Early Education and Training) given over 6 weeks to families in the home setting. We aimed to test the feasibility and acceptability of delivering Talking Together in the Better Start Bradford community prior to a definitive trial, using a two-armed randomised controlled feasibility study.

Methods

Families from a single site within the Better Start Bradford reach area were randomly allocated (1:1) to the Talking Together intervention or a wait list control group. Child language and parent-level outcome measures were administered before randomisation (baseline), pre-intervention (pre-test), 2 months post-intervention start (post-test), and 6 months post-intervention start (follow-up). Routine monitoring data from families and practitioners were also collected for eligibility, consent, protocol adherence, and attrition rates. Descriptive statistics on the feasibility and reliability of potential outcome measures were analysed alongside qualitative feedback on trial design acceptability. Pre-defined progression-to-trial criteria using a traffic light system were assessed using routine monitoring data.

Results

Two-hundred and twenty-two families were assessed for eligibility; of these, 164 were eligible. A total of 102 families consented and were randomised (intervention: 52, waitlist control: 50); 68% of families completed outcome measures at 6-month follow-up. Recruitment (eligibility and consent) reached ‘green’ progression criteria; however, adherence reached ‘amber’ and attrition reached ‘red’ criteria. Child and parent-level data were successfully measured, and the Oxford-CDI was identified as a suitable primary outcome measure for a definitive trial. Qualitative data indicated that the procedures were largely acceptable to practitioners and families, but also identified areas for improvement in adherence and attrition rates.

Conclusions

Referral rates indicate that Talking Together is a much-needed service, and was positively received by the community. A full trial is feasible with adaptations to improve adherence and reduce attrition.

Trial registration

ISRCTN13251954, retrospectively registered 21 February 2019