bluuebunny/crossref_metadata_2025_split huggingface dataset:
Total versus proximal gastrectomy for proximal gastric cancer after neoadjuvant chemotherapy: a multicenter retrospective propensity score-matched cohort study
Authors: Yuan Zhen , Cui Hao , Xu Qixuan , Gao Jingwang , Liang Wenquan , Cao Bo , Lin Xia , Song Liqiang , Huang Jun , Zhao Ruiyang , Li Hanghang , Yu Zhiyuan , Du Jiajun , Wang Shuyuan , Chen Lin , Cui Jianxin , Zhao Yongliang , Wei Bo 
Published: December 2023

Background:
This study aimed to analyze and compare the short-term and long-term outcomes of proximal gastrectomy (PG) and total gastrectomy (TG) in patients with locally advanced proximal gastric cancer (GC) following neoadjuvant chemotherapy (NACT).

Method:
A multicenter retrospective cohort study and propensity score matching (PSM) were employed. We examined 367 patients with proximal GC who received NACT followed by PG (n=164) or TG (n=203) at two Chinese medical institutions between December 2009 and December 2022. Clinical and pathological parameters, postoperative complications, and 5-year overall survival (OS) and recurrence-free survival (RFS) were compared between the two groups. The dissection status and metastasis rate of each lymph node station were assessed.

Results:
After PSM, 80 patients were enrolled in both TG and PG group, and baseline characteristics were comparable between the groups (all P>0.05). The TG group had a higher total number of lymph nodes retrived (P<0.001) and longer operative time (P=0.007) compared to the PG group. The incidence of Clavien-Dindo grade II or higher postoperative complications was similar between the TG group (21.3%, 17/80) and the PG group (23.8%, 19/80) (P=0.850). The 5-year OS rates were 68.4% for the PG group and 66.0% for the TG group (P=0.881), while the 5-year RFS rates were 64.8% and 61.9%, respectively (P=0.571), with no statistically significant differences. Metastasis rates at lymph node stations #4d, #5, #6, and #12a were notably low in the TG group, with values of 2.74%, 0.67%, 1.33%, and 1.74%, respectively.

Conclusion:
For proximal GC patients following NACT, PG maintains comparable curative potential and oncological efficacy to TG, making it a safe option.
Hemostasis after transradial coronary intervention by rotary compression device with sterile gauze is associated with more adverse events: a retrospective study
Authors: Fan Rong , Yang Zixuan , Wang Ruiping , Liu Haoqi , Feng Can , Wu Feng , Fan Min 
Published: December 2023

Objective
We investigated the relationship between using a rotary compression device (RCD) with or without sterile gauze and adverse events in transradial access (TRA) for coronary intervention.

Methods
In this study involving 933 patients at Yueyang Hospital, we recorded TRA-related adverse events, such as bleeding, forearm hematoma, swollen palms, radial artery occlusion (RAO) and others. Logistic regression was applied to assess the association.

Results
Of the 933 patients (66.7% males, average age 67.8 years), 511 used RCD with sterile gauze, whereas 422 used RCD without sterile gauze. The most common adverse events were radial artery hemorrhage (7.4%), hand swelling (4.8%) and RAO (4.6%). Logistic regression analysis revealed that the use of RCD with sterile gauze was associated with a higher prevalence of adverse events [odds ratio (OR), 1.74; 95% confidence interval (CI), 1.22–2.49), even with the adjustment of potential confounders (OR, 1.71; 95% CI, 1.19–2.45). Moreover, patients who used RCD with sterile gauze exhibited an increased risk of radial artery hemorrhage (OR, 1.83; 95% CI, 1.07–3.12), swelling of the hand (OR, 1.96; 95% CI, 1.02–3.75) and RAO (OR, 3.17; 95% CI, 1.49–6.72).

Conclusions:
The use of RCD with sterile gauze in TRA is associated with a higher incidence of adverse events.
Impact of Diplopia and Ptosis From Lingering Third Nerve Palsy After Treatment of Cerebral Aneurysms
Authors: Shapiro Jeremy N. , Delott Lindsey B. , Trobe Jonathan D. 
Published: December 2023

Background:
Third nerve palsies (TNPs) may not resolve after intervention for intracranial aneurysms that have compressed the nerve. The disability related to this lingering condition has not been assessed with the support of patient self-report.

Methods:
A single-institutional retrospective study of patients with TNP who had undergone interventions for intracranial aneurysms. We used residual primary-position diplopia, a narrow zone of single binocular vision, and vision-obscuring ptosis to divide TNP recovery into complete, incomplete nondisabling, and incomplete disabling outcomes based on medical record documentation and patient self-report derived from telephonic interviews.

Results:
In a cohort of 33 patients, 13 (39%) had complete TNP recovery. There were 11 patients (33%) with lingering visual disability from diplopia or ptosis present before ophthalmic interventions. Of the 6 patients who underwent ophthalmic interventions, visual disability was relieved in only 2 patients, leaving 9 patients (27%) with lingering impairment in instrumental activities of daily living. Telephonic interviews of 23 patients (70% of the cohort) confirmed that the outcome criteria we applied were accurate in assessing visual disability in 17 patients (74%). Univariate analysis using the Fisher exact test showed that aneurysmal clipping as a treatment modality was the only clinical feature associated with a favorable TNP outcome.

Conclusions:
In applying a novel method of assessing disability, this study showed that more than one-quarter of patients undergoing procedures for brain aneurysms had lingering disability from third nerve palsy–associated diplopia or ptosis, despite later ophthalmic interventions. Patient self-report gleaned from telephonic interviews was valuable in largely validating the assessment method derived from medical records and in revealing differences between physician and patient estimation of disability.
Impact of swab removal in the detection of SARS-CoV-2 weakly-positive specimens
Authors: Zorzoli Azul , Bennett-Slater Susan , MacLean Alasdair , McAllister Gina , Gunson Rory , Templeton Kate 
Published: December 2023

Graphical Abstract
Early removal of swabs can accelerate laboratory work and enhance quality by decreasing contamination and errors in downstream procedures. This article aims to compare the traditional testing workflow in a diagnostic laboratory (red), with manual swab removal and aliquoting vs a swab-out laboratory workflow (blue).
Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications
Authors: Timme Ruth E. , Karsch-Mizrachi Ilene , Waheed Zahra , Arita Masanori , MacCannell Duncan , Maguire Finlay , Petit III Robert , Page Andrew J. , Mendes Catarina Inês , Nasar Muhammad Ibtisam , Oluniyi Paul , Tyler Andrea D. , Raphenya Amogelang R. , Guthrie Jennifer L. , Olawoye Idowu , Rinck Gabriele , O’Cathail Colman , Lees John , Cochrane Guy , Cummins Carla , Brister J. Rodney , Klimke William , Feldgarden Michael , Griffiths Emma 
Published: December 2023

Fast, efficient public health actions require well-organized and coordinated systems that can supply timely and accurate knowledge. Public databases of pathogen genomic data, such as the International Nucleotide Sequence Database Collaboration (INSDC), have become essential tools for efficient public health decisions. However, these international resources began primarily for academic purposes, rather than for surveillance or interventions. Now, queries need to access not only the whole genomes of multiple pathogens but also make connections using robust contextual metadata to identify issues of public health relevance. Databases that over time developed a patchwork of submission formats and requirements need to be consistently organized and coordinated internationally to allow effective searches.
To help resolve these issues, we propose a common pathogen data structure called the Pathogen Data Object Model (DOM) that will formalize the minimum pieces of sequence data and contextual data necessary for general public health uses, while recognizing that submitters will likely withhold a wide range of non-public contextual data. Further, we propose contributors use the Pathogen DOM for all pathogen submissions (bacterial, viral, fungal, and parasites), which will simplify data submissions and provide a consistent and transparent data structure for downstream data analyses. We also highlight how improved submission tools can support the Pathogen DOM, offering users additional easy-to-use methods to ensure this structure is followed.
Lack of association between HLA and asymptomatic SARS-CoV-2 infection
Authors: Marchal Astrid , Cirulli Elizabeth T. , Neveux Iva , Bellos Evangelos , Thwaites Ryan S. , Barrett Kelly M. Schiabor , Zhang Yu , Nemes-Bokun Ivana , Kalinova Mariya , Catchpole Andrew , Tangye Stuart G. , Spaan András N. , Lack Justin B. , Ghosn Jade , Burdet Charles , Gorochov Guy , Tubach Florence , Hausfater Pierre ,   COVID Human Genetic Effort,   COVIDeF Study Group,   French COVID Cohort Study Group,   CoV-Contact Cohort,   COVID-STORM Clinicians,   COVID Clinicians,   Orchestra Working Group,   Amsterdam UMC Covid-19 Biobank,   NIAID-USUHS COVID Study Group, Dalgard Clifton L. , Zhang Shen-Ying , Zhang Qian , Chiu Christopher , Fellay Jacques , Grzymski Joseph J. , Sancho-Shimizu Vanessa , Abel Laurent , Casanova Jean-Laurent , Cobat Aurélie , Bolze Alexandre 
Published: December 2023

AbstractHuman genetic studies of critical COVID-19 pneumonia have revealed the essential role of type I interferon-dependent innate immunity to SARS-CoV-2 infection. Conversely, an association between the HLA-B*15:01 allele and asymptomatic SARS-CoV-2 infection in unvaccinated individuals was recently reported, suggesting a contribution of pre-existing T cell-dependent adaptive immunity. We report a lack of association of classical HLA alleles, including HLA-B*15:01, with pre-omicron asymptomatic SARS-CoV-2 infection in unvaccinated participants in a prospective population-based study in the US (191 asymptomatic vs. 945 symptomatic COVID-19 cases). Moreover, we found no such association in the international COVID Human Genetic Effort cohort (206 asymptomatic vs. 574 mild or moderate COVID-19 cases and 1,625 severe or critical COVID-19 cases). Finally, in the Human Challenge Characterisation study, the three HLA-B*15:01 individuals infected with SARS-CoV-2 developed symptoms. As with other acute primary infections, no classical HLA alleles favoring an asymptomatic course of SARS-CoV-2 infection were identified. These findings suggest that memory T-cell immunity to seasonal coronaviruses does not strongly influence the outcome of SARS-CoV-2 infection in unvaccinated individuals.
Association Between use of an Adaptive Cardiac Resynchronization Therapy Algorithm and Healthcare Utilization and Cost
Authors: Gold Michael R. , Zhou Jiani , Higuera Lucas , Lanctin David P. , Chung Eugene S. 
Published: December 2023

ABSTRACTObjectivesTo assess the association between use of adaptive pacing on clinical and economic outcomes of CRT recipients in real-world analysis.BackgroundThe AdaptivCRTTMalgorithm was shown in prior subgroup analyses of prospective trials to achieve clinical benefits, but a large prospective trial showed nonsignificant changes in the endpoint of mortality or heart failure hospitalizations.MethodsCRT-implanted patients from the Optum Clinformatics® database with ≥90 days of follow-up were included. Remote monitoring data was used to classify patients based on CRT setting – adaptive biventricular and left ventricular pacing (aCRT) vs. standard biventricular pacing (Standard CRT). Inverse probability of treatment weighting was used to adjust for baseline differences between groups. Mortality, 30-day readmissions, healthcare utilization, and payer and patient costs were evaluated post-implantation.ResultsThis study included 2,412 aCRT and 1,638 Standard CRT patients (mean follow-up: 2.4 ± 1.4 years), with balanced baseline characteristics after adjustment. The aCRT group was associated with lower all-cause mortality (adjusted hazard ratio = 0.88 [95% confidence interval (CI):0.80, 0.96]), fewer all-cause 30-day readmissions (adjusted incidence rate ratio = 0.87 [CI:0.81, 0.94]), and fewer all-cause and HF-related inpatient, outpatient, and emergency department (ED) visits. The aCRT cohort was also associated with lower all-cause outpatient payer-paid amounts and lower all-cause and HF-related inpatient and ED patient-paid amounts.ConclusionsIn this retrospective analysis of a large real-world cohort, use of an adaptive CRT algorithm was associated with lower mortality, reduced healthcare resource utilization, and lower payer and patient costs.
Structural variation discovery in wheat using PacBio high-fidelity sequencing
Authors: Zhang Zhiliang , Zhang Jijin , Kang Lipeng , Qiu Xuebing , Xu Song , Xu Jun , Guo Yafei , Niu Zelin , Niu Beirui , Bi Aoyue , Zhao Xuebo , Xu Daxing , Wang Jing , Yin Changbin , Lu Fei 
Published: December 2023

AbstractBackgroundStructural variations (SVs) pervade plant genomes and contribute substantially to the phenotypic diversity. However, most SVs were ineffectively assayed because of their complex nature and the limitations of early genomic technologies. The recent advance in third-generation sequencing, particularly the PacBio high-fidelity (HiFi) sequencing technology, produces highly accurate long-reads and offers an unprecedented opportunity to characterize SVs’ structure and functionality. As HiFi sequencing is relatively new to population genomics, it is imperative to evaluate and optimize HiFi sequencing based SV detection before applying the technology at scale.ResultsWe sequenced wheat genomes using HiFi reads, followed by a comprehensive evaluation of mainstream long-read aligners and SV callers in SV detection. The results showed that the accuracy of deletion discovery is markedly influenced by callers, which account for 87.73% of the variance, while both aligners (38.25%) and callers (49.32%) contributed substantially to the accuracy variance for insertions. Among the aligners, Winnowmap2 and NGMLR excelled in detecting deletions and insertions, respectively. For SV callers, SVIM achieved the best performance. We demonstrated that combining the aligners and callers mentioned above is optimal for SV detection. Furthermore, we evaluated the effect of sequencing depth on the accuracy of SV detection, showing that low-coverage HiFi sequencing is sufficiently robust for high-quality SV discovery.ConclusionsThis study thoroughly evaluated SV discovery approaches using HiFi reads, establishing optimal workflows to investigate structural variations in the wheat genome. The notable accuracy of SV discovery from low-coverage HiFi sequencing indicates that skim HiFi sequencing is effective and preferable to characterize SVs at the population level. This study will help advance SV discovery and decipher the biological functions of SVs in wheat and many other plants.
Vitamin B5 Metabolism is Essential for Vacuolar and Mitochondrial Integrity and Xenobiotic Detoxification in Fungi
Authors: Choi Jae-Yeon , Gihaz Shalev , Munshi Muhammad , Singh Pallavi , Vydyam Pratap , Hamel Patrice , Adams Emily M. , Fuller Kevin , Mamoun Choukri Ben 
Published: December 2023

SUMMARYFungal infections, a leading cause of mortality among eukaryotic pathogens, pose a growing global health threat due to the rise of drug-resistant strains. New therapeutic strategies are urgently needed to combat this challenge. The PCA pathway for biosynthesis of Co-enzyme A (CoA) and Acetyl-CoA (AcCoA) from vitamin B5 (pantothenic acid) has been validated as an excellent target for the development of new antimicrobials against fungi and protozoa. The pathway regulates key cellular processes including metabolism of fatty acids, amino acids, sterols, and heme. In this study, we provide genetic evidence that disruption of the PCA pathway results in a significant alteration in the susceptibility of fungi to a wide range of xenobiotics, including clinically approved antifungal drugs through alteration of vacuolar integrity and drug detoxification. The drug potentiation-mediated by genetic regulation of genes in the PCA pathway could be recapitulated using the pantazine analog PZ-2891 as well as the celecoxib derivative, AR-12 through inhibition of fungal AcCoA synthase activity. Collectively, the data validate the PCA pathway as a suitable target for enhancing the efficacy and safety of current antifungal therapies.
Spatially clustered piRNA genes promote the transcription of piRNAs via condensate formation of the H3K27me3 reader UAD-2
Authors: Zhu Chengming , Si Xiaoyue , Hou Xinhao , Xu Panpan , Gao Jianing , Tang Yao , Weng Chenchun , Xu Mingjing , Yan Qi , Jin Qile , Cheng Jiewei , Ruan Ke , Zhou Ying , Shan Ge , Xu Demin , Chen Xiangyang , Xiang Shengqi , Huang Xinya , Feng Xuezhu , Guang Shouhong 
Published: December 2023

AbstractPIWI-interacting RNAs (piRNAs) are essential for maintaining genome integrity and fertility in various organisms. In flies and nematodes, piRNA genes are encoded in heterochromatinized genomic clusters. The molecular mechanisms of piRNA transcription remain intriguing. Through unique molecular indexed-small RNA sequencing and chromosome editing, we discovered that spatial aggregation of piRNA genes enhances their transcription in nematodes. The heterochromatinized piRNA genome recruits the piRNA transcription complex USTC (including PRDE-1, SNPC-4, TOFU-4, and TOFU-5) and the H3K27me3 reader UAD-2, which phase separate into droplets to initiate piRNA transcription. We searched for factors that regulate piRNA condensate formation and isolated the SUMO E3 ligase GEI-17 as inhibiting and the SUMO protease TOFU-3 as promoting condensate formation, thereby regulating piRNA production. Our study revealed that spatial aggregation of piRNA genes, phase separation and deSUMOylation may benefit the organization of functional biomolecular condensates to direct piRNA transcription in the heterochromatinized genome.
Developing Standards for Rapid Evaluation and Appraisal Methods (STREAM): an e-Delphi consensus study
Authors: Clark Sigrún Eyrúnardóttir , Vera San Juan Norha , Vindrola-Padros Cecilia 
Published: December 2023

AbstractTimeliness is key to influencing the utility of evaluation and research findings and has given rise to a range of rapid evaluation and appraisal approaches. However, issues in the design, implementation and transparency in their reporting has led to concerns around their rigour and validity. To address this, we have developed the Standards for Rapid Evaluation and Appraisal Methods (STREAM). We followed a four-stage consensus process, starting with a (1) steering group consultation; (2) three-stage e-Delphi study; (3) stakeholder consensus workshop; and (4) piloting exercise. The stakeholders invited to participate in the consensus process had experience in conducting, being part of, or commissioning rapid evaluations or appraisals. As a result, 38 standards were developed with the purpose of guiding the design and implementation of rapid evaluations and appraisals and supporting the reporting of methods used. We suggest strengthening STREAM by testing it in alternative contexts to assess its generalisability.
P-tau217 and other blood biomarkers of dementia: variation with time of day
Authors: della Monica Ciro , Revell Victoria , Atzori Giuseppe , Laban Rhiannon , Skene Simon S. , Heslegrave Amanda , Hassanin Hana , Nilforooshan Ramin , Zetterberg Henrik , Dijk Derk-Jan 
Published: December 2023

AbstractPlasma biomarkers of dementia, including phosphorylated tau (p-tau217), offer promise as tools for diagnosis, stratification for clinical trials, monitoring disease progression, and assessing the success of interventions in those living with Alzheimer’s disease. However, currently, it is unknown whether these dementia biomarker levels vary with time of day, which could have implications for their clinical value. In two protocols, we studied 38 participants (70.8 ± 7.6 years; mean ± SD) in a 27-hour laboratory protocol with either two samples taken 12 hours apart or 3-hourly blood sampling for 24 hours in the presence of a sleep-wake cycle. The study population comprised people living with mild Alzheimer’s disease (PLWA, n = 8), partners/caregivers of PLWA (n = 6) and cognitively intact older adults (n = 24). Single molecule array technology was used to measure phosphorylated tau (p-tau217) (ALZpath), amyloid-beta 40 (Aβ40), amyloid-beta 42 (Aβ42), glial fibrillary acidic protein (GFAP), and neurofilament light (NfL) (Neuro 4-Plex E). Analysis with a linear mixed model (SAS, PROC MIXED) revealed a significant effect of time of day for p-tau217, Aβ40, Aβ42, and NfL, and a significant effect of participant group for p-tau217. For p-tau217, lowest levels were observed in the morning upon waking and highest values in the afternoon/early evening. The magnitude of the diurnal variation for p-tau217 was similar to the reported increase in p-tau217 over one year in amyloid-β-positive mild cognitively impaired people. Currently, the factors driving this diurnal variation are unknown and could be related to sleep, circadian mechanisms, activity, posture, or meals. Overall, this work implies that time of day of sample collection may be relevant in the implementation and interpretation of plasma biomarkers in dementia research and care.
The dark side of leadership communication: the impact of supervisor verbal aggressiveness on workplace culture, employee–organization relationships and counterproductive work behaviors
Authors: Yue Cen April , Qin Yufan Sunny , Men Linjuan Rita 
Published: December 2023

PurposeThis study is designed to bridge a gap in the existing leadership communication literature by delving into lesser-explored facets of the field. It particularly concentrates on investigating how the verbal aggressiveness of supervisors influences various aspects of the workplace, including workplace emotional culture, the quality of employee–organization relationships (EORs) and the prevalence of counterproductive work behaviors (CWB).Design/methodology/approachThis study employed a quantitative research design to investigate the impact of supervisors' verbal aggressiveness on employee and organizational outcomes. The data were collected from 392 full-time employees across various organizations and industries in the USA using a self-report questionnaire. The researchers used structural equation modeling (SEM) to analyze the data and test hypotheses.FindingsThe findings of this study showed that supervisors' verbal aggressiveness had a significant positive association with negative emotional culture and employee CWB. However, it had no direct impact on employee–organization relationships. The effect of supervisor verbal aggressiveness on employee CWB was found to be mediated by a negative team-level emotional culture.Originality/valueThis study advances the literature on leadership communication by highlighting the detrimental influence of the dark side of leadership communication. More specifically, by identifying negative emotional culture and employee CWB as the direct outcomes of supervisor verbal aggressiveness, the authors add to the existing theoretical knowledge on verbal aggressiveness in the workplace. Additionally, this study provides empirical evidence of the impact of a negative emotional culture on eliciting employees' CWBs and diminishing relationship quality, adding to the body of knowledge on why managing emotional culture is crucial for organizations and workgroups.