bluuebunny/crossref_metadata_2025_split huggingface dataset:
Treating relapsed/refractory mature T- and NK-cell neoplasms with tislelizumab: a multicenter open-label phase 2 study
Authors: Bachy Emmanuel , Savage Kerry J. , Huang Huiqiang , Kwong Yok-Lam , Gritti Giuseppe , Zhang Qingyuan , Liberati Anna Marina , Cao Junning , Yang Haiyan , Hao Siguo , Hu Jianda , Zhou Keshu , Petrini Mario , Russo Filomena , Zhang Huilai , Sang Wei , Ji Jie , Ferreri Andrés José María , Damaj Gandhi Laurent , Liu Hui , Zhang Wei , Ke Xiaoyan , Ghiggi Chiara , Huang Sha , Li Xiaotong , Yao Hui , Paik Jason , Novotny William , Zhou Wenxiao , Zhu Hongjie , Zinzani Pier Luigi 
Published: June 2023

Abstract
Patients with relapsed/refractory (R/R) mature T- and natural killer (NK)–cell neoplasms lack effective treatments after failure of standard therapies. This phase 2 study evaluated the efficacy and safety of the programmed cell death protein 1 inhibitor tislelizumab in these patients. Seventy-seven patients were treated with 200 mg tislelizumab every 3 weeks. Twenty-two patients with extranodal NK-/T-cell lymphomas were enrolled in cohort 1; 44 patients with peripheral T-cell lymphoma (PTCL) were enrolled in cohort 2 (21 patients had PTCL not otherwise specified, 11 patients had angioimmunoblastic T-cell lymphoma, and 12 patients had anaplastic large-cell lymphoma). Cohort 3 comprised 11 patients with cutaneous T-cell lymphoma, of which 8 patients had mycosis fungoides (MF) and 3 had Sézary syndrome. Of the 77 patients, 76.6% had advanced-stage disease, 51.9% had refractory disease, and 49.4% received ≥3 prior systemic regimens. Promising efficacy was observed in cohort 3 (median follow-up [FU], 16.6 months; overall response rate [ORR], 45.5%; complete response [CR], 9.1%; median duration of response [DOR], 11.3 months; median progression-free survival, 16.8 months; median overall survival, not reached). Modest efficacy was observed in cohort 1 (median FU, 8.4 months; ORR, 31.8%; CR, 18.2%; median DOR, not reached) and cohort 2 (median FU, 9.3 months; ORR, 20.5%; CR, 9.1%; median DOR, 8.2 months). Most treatment-related adverse events were grade 1 or 2, and the safety profile was consistent with the known safety profile of tislelizumab. In conclusion, tislelizumab was well tolerated, achieving modest efficacy in R/R mature T- and NK-cell neoplasms, with some long-lasting remissions. This trial was registered at www.clinicaltrials.gov as #NCT03493451.
Uptake of long-chain fatty acids from the bone marrow suppresses CD8+ T-cell metabolism and function in multiple myeloma
Authors: Gudgeon Nancy , Giles Hannah , Bishop Emma L. , Fulton-Ward Taylor , Escribano-Gonzalez Cristina , Munford Haydn , James-Bott Anna , Foster Kane , Karim Farheen , Jayawardana Dedunu , Mahmood Ansar , Cribbs Adam P. , Tennant Daniel A. , Basu Supratik , Pratt Guy , Dimeloe Sarah 
Published: June 2023

Abstract
T cells demonstrate impaired function in multiple myeloma (MM) but suppressive mechanisms in the bone marrow microenvironment remain poorly defined. We observe that bone marrow CD8+ T-cell function is decreased in MM compared with controls, and is also consistently lower within bone marrow samples than in matched peripheral blood samples. These changes are accompanied by decreased mitochondrial mass and markedly elevated long-chain fatty acid uptake. In vitro modeling confirmed that uptake of bone marrow lipids suppresses CD8+ T function, which is impaired in autologous bone marrow plasma but rescued by lipid removal. Analysis of single-cell RNA-sequencing data identified expression of fatty acid transport protein 1 (FATP1) in bone marrow CD8+ T cells in MM, and FATP1 blockade also rescued CD8+ T-cell function, thereby identifying this as a novel target to augment T-cell activity in MM. Finally, analysis of samples from cohorts of patients who had received treatment identified that CD8+ T-cell metabolic dysfunction resolves in patients with MM who are responsive to treatment but not in patients with relapsed MM, and is associated with substantial T-cell functional restoration.
Role of small airway dysfunction in unexplained exertional dyspnoea
Authors: Sharpe Alexis L. , Reibman Joan , Oppenheimer Beno W. , Goldring Roberta M. , Liu Mengling , Shao Yongzhao , Bohart Isaac , Kwok Benjamin , Weinstein Tatiana , Addrizzo-Harris Doreen , Sterman Daniel H. , Berger Kenneth I. 
Published: June 2023

BackgroundIsolated small airway abnormalities may be demonstrable at rest in patients with normal spirometry; however, the relationship of these abnormalities to exertional symptoms remains uncertain. This study uses an augmented cardiopulmonary exercise test (CPET) to include evaluation of small airway function during and following exercise to unmask abnormalities not evident with standard testing in individuals with dyspnoea and normal spirometry.MethodsThree groups of subjects were studied: 1) World Trade Center (WTC) dust exposure (n=20); 2) Clinical Referral (n=15); and Control (n=13). Baseline evaluation included respiratory oscillometry. Airway function during an incremental workload CPET was assessed by: 1) tidal flowversusvolume curves during exercise to assess for dynamic hyperinflation and expiratory flow limitation; and 2) post-exercise spirometry and oscillometry to evaluate for airway hyperreactivity.ResultsAll subjects demonstrated normal baseline forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC). Dyspnoea was reproduced during CPET in WTC and Clinical Referral groupsversusControl without abnormality in respiratory pattern and minute ventilation. Tidal flow–volume curves uncovered expiratory flow limitation and/or dynamic hyperinflation with increased prevalence in WTC and Clinical ReferralversusControl (55%, 87%versus15%; p<0.001). Post-exercise oscillometry uncovered small airway hyperreactivity with increased prevalence in WTC and Clinical ReferralversusControl (40%, 47%versus0%, p<0.05).ConclusionsWe uncovered mechanisms for exertional dyspnoea in subject with normal spirometry that was attributable to either small airway dysfunction during exercise and/or small airway hyperreactivity following exercise. The similarity of findings in WTC environmentally exposed and clinically referred cohorts suggests broad relevance for these evaluations.
Biotite: new tools for a versatile Python bioinformatics library
Authors: Kunzmann Patrick , Müller Tom David , Greil Maximilian , Krumbach Jan Hendrik , Anter Jacob Marcel , Bauer Daniel , Islam Faisal , Hamacher Kay 
Published: June 2023

Abstract
Background
Biotite is a program library for sequence and structural bioinformatics written for the Python programming language. It implements widely used computational methods into a consistent and accessible package. This allows for easy combination of various data analysis, modeling and simulation methods.

Results
This article presents major functionalities introduced into Biotite since its original publication. The fields of application are shown using concrete examples. We show that the computational performance of Biotite for bioinformatics tasks is comparable to individual, special purpose software systems specifically developed for the respective single task.

Conclusions
The results show that Biotite can be used as program library to either answer specific bioinformatics questions and simultaneously allow the user to write entire, self-contained software applications with sufficient performance for general application.
LAPIS is a fast web API for massive open virus sequencing data
Authors: Chen Chaoran , Taepper Alexander , Engelniederhammer Fabian , Kellerer Jonas , Roemer Cornelius , Stadler Tanja 
Published: June 2023

Abstract
Background
Recent epidemic outbreaks such as the SARS-CoV-2 pandemic and the mpox outbreak in 2022 have demonstrated the value of genomic sequencing data for tracking the origin and spread of pathogens. Laboratories around the globe generated new sequences at unprecedented speed and volume and bioinformaticians developed new tools and dashboards to analyze this wealth of data. However, a major challenge that remains is the lack of simple and efficient approaches for accessing and processing sequencing data.

Results
The Lightweight API for Sequences (LAPIS) facilitates rapid retrieval and analysis of genomic sequencing data through a REST API. It supports complex mutation- and metadata-based queries and can perform aggregation operations on massive datasets. LAPIS is optimized for typical questions relevant to genomic epidemiology. Using a newly-developed in-memory database engine, it has a high speed and throughput: between 25 January and 4 February 2023, the SARS-CoV-2 instance of LAPIS, which contains 14.5 million sequences, processed over 20 million requests with a mean response time of 411 ms and a median response time of 1 ms. LAPIS is the core engine behind our dashboards on genspectrum.org and we currently maintain public LAPIS instances for SARS-CoV-2 and mpox.

Conclusions
Powered by an optimized database engine and available through a web API, LAPIS enhances the accessibility of genomic sequencing data. It is designed to serve as a common backend for dashboards and analyses with the potential to be integrated into common database platforms such as GenBank.
Systematically identifying genetic signatures including novel SNP-clusters, nonsense variants, frame-shift INDELs, and long STR expansions that potentially link to unknown phenotypes existing in dog breeds
Authors: Li Zicheng , Wang Zuoheng , Chen Zhiyuan , Voegeli Heidi , Lichtman Judith H. , Smith Peter , Liu Ju , DeWan Andrew T. , Hoh Josephine 
Published: June 2023

AbstractBackgroundIn light of previous studies that profiled breed-specific traits or used genome-wide association studies to refine loci associated with characteristic morphological features in dogs, the field has gained tremendous genetic insights for known dog traits observed among breeds. Here we aim to address the question from a reserve perspective: whether there are breed-specific genotypes that may underlie currently unknown phenotypes. This study provides a complete set of breed-specific genetic signatures (BSGS). Several novel BSGS with significant protein-altering effects were highlighted and validated.ResultsUsing the next generation whole-genome sequencing technology coupled with unsupervised machine learning for pattern recognitions, we constructed and analyzed a high-resolution sequence map for 76 breeds of 412 dogs. Genomic structures including novel single nucleotide polymorphisms (SNPs), SNP clusters, insertions, deletions (INDELs) and short tandem repeats (STRs) were uncovered mutually exclusively among breeds. We also partially validated some novel nonsense variants by Sanger sequencing with additional dogs.Four novel nonsense BSGS were found in the Bernese Mountain Dog, Samoyed, Bull Terrier, and Basset Hound, respectively. Four INDELs resulting in either frame-shift or codon disruptions were found in the Norwich Terrier, Airedale Terrier, Chow Chow and Bernese Mountain Dog, respectively. A total of 15 genomic regions containing three types of BSGS (SNP-clusters, INDELs and STRs) were identified in the Akita, Alaskan Malamute, Chow Chow, Field Spaniel, Keeshond, Shetland Sheepdog and Sussex Spaniel, in which Keeshond and Sussex Spaniel each carried one amino-acid changing BSGS in such regions.ConclusionGiven the strong relationship between human and dog breed-specific traits, this study might be of considerable interest to researchers and all. Novel genetic signatures that can differentiate dog breeds were uncovered. Several functional genetic signatures might indicate potentially breed-specific unknown phenotypic traits or disease predispositions. These results open the door for further investigations. Importantly, the computational tools we developed can be applied to any dog breeds as well as other species. This study will stimulate new thinking, as the results of breed-specific genetic signatures may offer an overarching relevance of the animal models to human health and disease.
The effect of erector spinae plane block on fentanyl consumption during open abdominal hysterectomy: a randomised controlled study
Authors: Hamed Mohamed Ahmed , Boules Maged Labib , Mahmoud Mohamed Abd El Moniem , Abdelghaffar Rana Ahmed 
Published: June 2023

Abstract
Background
Perioperative analgesia is very important during an abdominal hysterectomy. Determining the impact of the erector spinae plane block (ESPB) on patients undergoing an open abdominal hysterectomy while under general anesthesia was our aim.

Methods
In order to create equal groups, 100 patients who underwent elective open abdominal hysterectomies under general anesthesia were enlisted. The preoperative bilateral ESPB with 20 ml of bupivacaine 0.25% was administered to the ESPB group (n = 50). The same procedure was performed on the control group (n = 50), but they received a 20-ml saline injection instead. The primary outcome is the total amount of fentanyl consumed during surgery.

Results
We found that the mean (SD) intraoperative fentanyl consumption was significantly lower in the ESPB group than in the control group (82.9 (27.4) g vs. 148.5 (44.8) g, with a 95% CI = -80.3 to -50.8; p 0.001). Likewise, mean (SD) postoperative fentanyl consumption was significantly lower in the ESPB group than in the control group (442.4 (17.8) g vs. 477.9 (10.4) g, with a 95% CI = -41.3 to -29.7; p 0.001). On the other hand, there is no statistically significant difference between the two study groups regarding sevoflurane consumption (89.2 (19.5) ml vs. 92.4 (15.3) ml, with a 95% CI = -10.1 to 3.8; p 0.4).
We documented that during the post-operative period (0–24 h), VAS scores at rest were, on average, 1.03 units lower in the ESPB group (estimate = -1.03, 95% CI = -1.16-(-0.86), t = -14.9, p-value 0.001), and VAS scores during cough were, on average, 1.07 units lower in the ESPB group (estimate = -1.07, 95% CI = -1.21-(-0.93), t = -14.8, p-value 0.001).

Conclusion
Bilateral ESPB can be utilized as an adjuvant method to reduce intraoperative fentanyl consumption and enhance postoperative pain control in patients undergoing open total abdominal hysterectomy under general anesthesia. It is effective, secure, and little obtrusive.

Trial registration
No protocol revisions or study amendments have been made since the trial's inception, according to the information on ClinicalTrials.gov (NCT05072184; principal investigator: Mohamed Ahmed Hamed; date of registration: October 28, 2021).
Albumin infusion may decrease the mortality of hypoalbuminemia patients with severe acute pancreatitis: a retrospective cohort study
Authors: Xu Huiting , Wan Jianhua , He Wenhua , Zhu Yong , Zeng Hao , Liu Pi , Liu Jing , Xia Liang , Liu Fen , Zhu Yin , Chen Youxiang , Lu Nonghua 
Published: June 2023

Abstract
Background
At present, the relationship between severe acute pancreatitis (SAP) and albumin infusion is not clear. We aimed to identify the impact of serum albumin on the prognosis of SAP and the association between albumin infusions and mortality for hypoalbuminemia patients.

Methods
This was a retrospective cohort study that analyzed 1000 patients with SAP who were admitted to the First Affiliated Hospital of Nanchang University between January 2010 and December 2021 using data from a prospectively maintained database. Multivariate logistic regression analysis was conducted to reveal the relationship between serum albumin within 1 week after admission and poor prognosis of SAP. Propensity score matching (PSM) analysis was adopted to evaluate the effect of albumin infusion for hypoalbuminemia patients with SAP.

Results
The prevalence of hypoalbuminemia (≤ 30 g/L) was 56.9% within 1 week after admission. Multivariate logistic regression identified that age (OR: 1.02; 95% CI: 1.00-1.04; P = 0.012), serum urea (OR: 1.08; 95% CI: 1.04–1.12; P < 0.001), serum calcium (OR: 0.27; 95% CI: 0.14–0.50; P < 0.001), lowest albumin level within 1 week after admission (OR: 0.93; 95% CI: 0.89–0.97; P = 0.002), and APACHE II score ≥ 15 (OR: 1.73; 95% CI: 1.19–2.51; P = 0.004) were independently associated with mortality. The PSM analysis demonstrated that mortality (OR: 0.52, 95% CI: 0.29–0.92, P = 0.023) was less common in albumin-infused than non-albumin-infused hypoalbuminemia patients. In subgroup analyses, doses > 100 g within 1 week after admission for hypoalbuminemia patients with albumin infusions was associated with lower mortality than doses ≤ 100 g (OR: 0.51, 95% CI: 0.28–0.90, P = 0.020).

Conclusions
Hypoalbuminemia in early-stage SAP is significantly related to poor prognosis. However, albumin infusions could significantly decrease mortality in hypoalbuminemia patients with SAP. Additionally, infusing sufficient albumin within a week after admission may decrease mortality in hypoalbuminemia patients.
Effect of metal artifact removal modes on the accuracy of linear measurement around titanium implants by applying different voltages: an original article
Authors: Goodarzi Pour Daryoush , Emami Meybodi Elham , Sodagar Kosar , Emami Meybodi Zahra Alsadat , Safari Sanaz 
Published: June 2023

Abstract
Background
This study aims to evaluate the effects of the artifact removal algorithm on linear measurements of the buccal cortical plate by altering the voltage.

Methods
Ten titanium fixtures were inserted at the site of central, lateral, canine, premolars and molars of dry human mandibles. Vertical height of buccal plate was measured using a digital caliper as a gold standard. Mandibles were scanned with 54 and 58 kVp. Other parameters were constant. Images were reconstructed with none, low, medium and high artifact removal modes. Two Oromaxillofacial radiologists evaluated and measured the buccal plate height using Romexis software. Statistical package for the social sciences (SPSS) version 24 was used for data analysis.

Results
In medium and high modes, the difference between 54 and 58 kVp was significant (p < 0.001). No significance was noted by using low ARM (artifact removal mode) at the 54 kVp and 58 kVp.

Conclusion
Using artifact removal in low voltage decreases the accuracy of linear measurement and buccal crest visibility. By using high voltage, artifact removal would have no significant effect on accuracy of linear measurements.
A dynamic nomogram for predicting the probability of irreversible neurological dysfunction after cervical spinal cord injury: research based on clinical features and MRI data
Authors: Chen Si , Li Guangzhou , Li Feng , Wang Gaoju , Wang Qing 
Published: June 2023

Abstract
Background
Irreversible neurological dysfunction (IND) is an adverse event after cervical spinal cord injury (CSCI). However, there is still a shortage of objective criteria for the early prediction of neurological function. We aimed to screen independent predictors of IND and use these findings to construct a nomogram that could predict the development of neurological function in CSCI patients.

Methods
Patients with CSCI attending the Affiliated Hospital of Southwest Medical University between January 2014 and March 2021 were included in this study. We divided the patients into two groups: reversible neurological dysfunction (RND) and IND. The independent predictors of IND in CSCI patients were screened using the regularization technique to construct a nomogram, which was finally converted into an online calculator. Concordance index (C-index), calibration curves analysis and decision curve analysis (DCA) evaluated the model's discrimination, calibration, and clinical applicability. We tested the nomogram in an external validation cohort and performed internal validation using the bootstrap method.

Results
We enrolled 193 individuals with CSCI in this study, including IND (n = 75) and RND (n = 118). Six features, including age, American spinal injury association Impairment Scale (AIS) grade, signal of spinal cord (SC), maximum canal compromise (MCC), intramedullary lesion length (IMLL), and specialized institution-based rehabilitation (SIBR), were included in the model. The C-index of 0.882 from the training set and its externally validated value of 0.827 demonstrated the model's prediction accuracy. Meanwhile, the model has satisfactory actual consistency and clinical applicability, verified in the calibration curve and DCA.

Conclusion
We constructed a prediction model based on six clinical and MRI features that can be used to assess the probability of developing IND in patients with CSCI.
Enhancing equity and diversity in palliative care clinical practice, research and education
Authors: Koffman Jonathan , Shapiro Gilla K. , Schulz-Quach Christian 
Published: June 2023

AbstractHealth disparities in palliative care are preventable consequences of structural discrimination and marginalization. The first step in addressing a problem is recognizing there is one and devotion to fully understanding its multifaceted nature. Palliative care clinicians, educators and researchers must prioritize investigating and mitigating the effects of racial, social, and intersectional injustice.
Australian nursing students’ perception, knowledge, and attitude towards oral healthcare of older people and associated factors: a national cross-sectional survey
Authors: Bhagat Vandana , Hoang Ha , Crocombe Leonard A. , Goldberg Lynette R. 
Published: June 2023

Abstract
Background
The oral health of many older Australians is poor and associated with many systemic health problems. However, nurses often have a limited understanding of the importance of oral healthcare for older people. This study aimed to investigate Australian nursing students’ perception, knowledge, and attitude toward providing oral healthcare for older people and associated factors.

Methods
A cross-sectional study was conducted among final year nursing students studying at accredited nursing programs using an online self-reported 49-item survey. The data were analysed using univariate and bivariate analysis (t-test, ANOVA, Spearman’s correlation test).

Results
A total of 416 final-year nursing students from 16 accredited programs in Australia completed the survey. Mean scores showed that more than half of the participants felt they lacked confidence (55%, n = 229) and had limited knowledge about oral healthcare for older people (73%, n = 304); however, their attitude towards providing such care was favourable (89%, n = 369). A positive correlation was found between students’ confidence in delivering oral healthcare to older people and their perceived knowledge (r = 0.13, p < 0.01). Results revealed a statistically significant positive association between students’ experience in providing oral healthcare to older people and students’ perception (t = 4.52, p < 0.001), knowledge (t = 2.87, p < 0.01), and attitude (t = 2.65, p < 0.01) mean scores in such care. Nearly 60% (n = 242) of participants received education/training in oral healthcare for older people at university, but this was often for less than one hour. Around 56% (n = 233) believed that the current nursing curriculum did not prepare them to provide effective oral healthcare to older people.

Conclusion
Findings suggested a need for nursing curricula to be revised to include oral health education and clinical experience. Knowledge of evidence-based oral healthcare by nursing students may improve the quality of oral healthcare for older people.