bluuebunny/crossref_metadata_2025_split huggingface dataset:
Safety and feasibility study of uniportal video-assisted thoracoscopic pulmonary wedge resection without postoperative chest tube drainage: a retrospective propensity score-matched study
Authors: Yang Qingjie , Lv Shenghua , Li Qingtian , Lan Linhui , Sun Xiaoyan , Feng Xinhai , Han Kaibao 
Published: December 2023

Abstract

OBJECTIVES
The aim of this study was to assess the impact of postoperative chest tube drainage (CTD) on safety and postoperative recovery by comparing patients with pulmonary nodule undergoing uniportal video-assisted thoracoscopic pulmonary wedge resection with and without postoperative CTD.

METHODS
We retrospectively analysed the data of patients who underwent video-assisted thoracoscopic pulmonary wedge resection for pulmonary nodule at our hospital between 2018 and 2022. In cases where a 12-Fr chest tube was used following the procedure, the tube was not usually removed until the day after surgery. Therefore, the eligible patients were categorized into the drainage tube or the no-drainage tube group according to the use of postoperative CTD. Propensity score matching at a ratio of 1:1 was performed using clinicopathologic and demographic variables. The highest postoperative pain score, postoperative complication rate, postoperative length of stay and hospitalization costs were compared between the 2 groups.

RESULTS
A total of 275 eligible patients, including 150 and 125 patients in the drainage tube and no-drainage tube groups, respectively, were included in the study. After propensity score matching, there were 102 patients in each group. The postoperative complication rate during hospitalization and at 1 week and 1 month after discharge were not significantly different between the 2 groups (P &gt; 0.05 for all). The highest postoperative pain score was significantly lower in the no-drainage tube group than in the drainage tube group [2.02 (standard deviation: 0.81) days vs 2.31 (standard deviation: 0.76) days, P = 0.008]. The postoperative length of stay was significantly shorter in the no-drainage tube group than in the drainage tube group {3.00 [interquartile ranges (IQRs): 2.00–4.00] days vs 2.00 (IQRs: 1.00–3.00) days, P &lt; 0.001}. Similarly, the total hospitalization costs were significantly lower in the no-drainage tube group than in the drainage tube group [33283.74 (IQRs: 27098.61–46718.56) yuan vs 26598.67 (IQRs: 22965.14–29933.67) yuan, P &lt; 0.001].

CONCLUSIONS
Omission of postoperative CTD was safe and feasible in patients with pulmonary nodule undergoing wedge resection. The no-postoperative-drainage policy can substantially shorten the length of hospital stay and reduce the postoperative pain and hospitalization costs without increasing the risk of postoperative complications.
Nirmatrelvir/ritonavir for COVID-19: an overview of systematic reviews
Authors: Cruciani Mario , Pati Ilaria , Masiello Francesca , Pupella Simonetta , De Angelis Vincenzo 
Published: December 2023

Abstract

Objectives
A reappraisal of the validity of the conclusions of systematic reviews (SRs) related to nirmatrelvir/ritonavir for the treatment of COVID-19.

Methods
An overview of SRs (umbrella review). The methodological quality of the SRs was assessed using the AMSTAR 2 checklist; quality of the evidence from the trials included in each SR was appraised following the GRADE approach.

Results
Sixteen SRs with meta-analysis published between 2020 and 2023 were included in this overview. The SRs reported data from 108 overlapping reports, based on 43 individual primary studies [3 randomized clinical trials (RCTs), 40 non-RCTs]. In outpatient settings the use of nirmatrelvir/ritonavir reduced overall mortality, hospital admission and progression of disease compared with controls (from moderate to low certainty of evidence); nirmatrelvir/ritonavir reduced mortality, hospital admission and progression of disease in both immunized and non-immunized patients. No differences in the occurrence of any adverse events between groups were observed in the large majority of SRs; serious adverse events, including adverse events requiring discontinuation of treatment, were reported with lower prevalence in nirmatrelvir recipients compared with controls (from low to moderate certainty of evidence).

Conclusions
There is low to moderate certainty of evidence from SRs that nirmatrelvir/ritonavir reduces mortality, clinical progression and hospitalization rate in COVID-19 patients compared with controls, without increasing the occurrence of overall and serious adverse events. Based on the overall methodological assessment, on average we can have high confidence in the quality of results generated by the SRs.
Combined purebred and crossbred genetic evaluation of Columbia, Suffolk, and crossbred lamb birth and weaning weights: systematic effects and heterogeneous variances
Authors: Vargas Jurado Napoleón , Notter David R , Taylor Joshua B , Brown Daniel J , Mousel Michelle R , Lewis Ronald M 
Published: December 2023

Abstract
Despite the benefits of crossbreeding on animal performance, genetic evaluation of sheep in the U.S. does not directly incorporate records from crossbred lambs. Crossbred animals may be raised in different environments as compared to purebreds. Systemic factors such as age of dam and birth and rearing type may, therefore, affect purebred and crossbred performance differently. Furthermore, crossbred performance may benefit from heterozygosity, and genetic and environmental variances may be heterogeneous in different breeds and their crosses. Such issues must be accounted for in a combined (purebred and crossbred) genetic evaluation. The objectives of this study were to i) determine the effect of dam age and birth type on birth weight, and dam age and birth-rearing type on weaning weight, in purebred and crossbred lambs, ii) test for heterogeneous genetic and environmental variances in those weights, and iii) assess the impact of including weights on crossbred progeny on sire estimated breeding values (EBV). Performance records were available on purebred Columbia and Suffolk lambs. Crossbred information was available on lambs sired by Suffolk, Columbia or Texel rams mated to Columbia, Suffolk, or crossbred ewes. A multiple-trait animal model was fitted in which weights from Columbia, Suffolk, or crossbred lambs were considered different traits. At birth, there were 4,160, 2,356, and 5,273 Columbia, Suffolk, and crossbred records, respectively, with means (SD) of 5.14 (1.04), 5.32 (1.14), and 5.43 (1.23) kg, respectively. At weaning, on average at 122 (12) d, there were 2,557, 980, and 3,876 Columbia, Suffolk, and crossbred records, respectively, with corresponding means of 39.8 (7.2), 40.3 (7.9), and 39.6 (8.0) kg. Dam age had a large positive effect on birth and weaning weight in pure and crossbred lambs. At birth, however, the predicted effect was larger in crossbred and Suffolk lambs. While an increase in a number of lambs born and reared had a strong and negative influence on birth and weaning weight, the size of the effect did not differ across-breed types. Environmental variances were similar at birth and weaning, but additive variances differed among breed types for both weights. Combining purebred and crossbred information in the evaluation not only improved predictions of genetic merit in purebred sires but also allowed for direct comparisons of sires of different breeds. Breeders thus can benefit from an additional tool for making selection decisions.
The use of R in forestry research
Authors: Lai Jiangshan , Zhu Weijie , Cui Dongfang , Fan Dayong , Mao Lingfeng 
Published: December 2023

Abstract
The field of forestry research has greatly benefited from the integration of computational tools and statistical methods in recent years. Among these tools, the programming language R has emerged as a powerful and versatile platform for forestry research, ranging from data analysis, modeling to visualization. However, the key trends in general reported R use and patterns in forestry research remain unknown. We analyzed R and R package usage frequencies for 14 800 research articles published in eight top forestry journals across a span of 10 years, from 2013 to 2022. Among these articles, a notable number of 6790 (accounting for 45.7%) explicitly utilized R as their primary tool for data analysis. The adoption of R exhibited a linear growth trend, rising from 28.3% in 2013 to 60.9% in 2022. The top five used packages reported were vegan, lme4, nlme, MuMIn, and ggplot2. Diverse journals have their unique areas of emphasis, resulting in disparities in the frequency of R package application among journals. The average number of R packages used per article also showed an increasing trend over time. The study underscores the recognition that R, with its powerful data statistical and visualization capabilities, plays a pivotal role in enabling researchers to conduct thorough analyses and acquire comprehensive insights into various aspects of forestry science.
Identifying dietary consumption patterns from survey data: a Bayesian nonparametric latent class model
Authors: Stephenson Briana J K , Wu Stephanie M , Dominici Francesca 
Published: December 2023

Abstract
Dietary assessments provide the snapshots of population-based dietary habits. Questions remain about how generalisable those snapshots are in national survey data, where certain subgroups are sampled disproportionately. We propose a Bayesian overfitted latent class model to derive dietary patterns, accounting for survey design and sampling variability. Compared to standard approaches, our model showed improved identifiability of the true population pattern and prevalence in simulation. We focus application of this model to identify the intake patterns of adults living at or below the 130% poverty income level. Five dietary patterns were identified and characterised by reproducible code/data made available to encourage further research.
Into the Hills: Challenges of Writing Postemancipation Agency in the Caribbean
Authors: Eller Anne 
Published: December 2023

Abstract
As Caribbean postemancipation scholarship has deepened so richly in recent decades, writers have been able to shake major distortions such as the progressive teleologies of freedom that lurk as the very scaffolding of congratulatory imperial records. The full dynamism of repression directed at postslavery generations still demands attention, as does the difficult task of reconstructing communities’ and individuals’ responses to these serious restraints, efforts that sometimes yielded nothing. Especially given archival difficulties, Johnson’s exhortation to seek everyday understandings and actions, ineffable registers like love and fear, and internal community politics, including discord, continue to present high aims for scholars seeking to conceive and describe agency in such an archivally and politically difficult era.
Effects of onset of phase transition on binary neutron star mergers
Authors: Haque Shamim , Mallick Ritam , Thakur Shashikesh K 
Published: December 2023

ABSTRACT
Quantum Chromodynamics predicts phase transition from hadronic matter to quark matter at high density, which is highly probable in astrophysical systems like binary neutron star mergers. To explore the critical density where such phase transition can occur, we performed numerical relativity simulations of binary neutron star mergers with various masses (equal and unequal binaries). We aim to understand the effect of the onset of phase transition on the merger dynamics and gravitational wave spectra. We generated a set of equations of states by agnostically changing the onset of phase transition, having the hadronic matter part and quark matter part fixed. This particular arrangement of the equation of states explores the scenario of mergers where mixed phases of matter are achieved before or during the merger. Under these circumstances, if the matter properties with hadronic and quark degrees differ significantly, it is reflected in the stability of the final merger product for the intermediate mass binary. We performed a case study on mixed species merger, where one of the binary companions is hybrid star. If quark matter appears at low densities, we observe significant change in post-merger gravitational wave analysis in terms of higher peak frequencies and post-merger frequencies in power spectral density. We report indications expressed as spikes in phase difference plots at merger time for mixed mergers. We found that the expression of phase transition in post-merger gravitational wave signals is more significant for unequal mass binary than for equal mass binary having the same total baryonic mass.
Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses
Authors: Flores Samuel Coulbourn , Malý Michal , Hrebík Dominik , Plevka Pavel , Černý Jiří 
Published: December 2023

Abstract
The revolution in cryo-electron microscopy has resulted in unprecedented power to resolve large macromolecular complexes including viruses. Many methods exist to explain density corresponding to proteins and thus entire protein capsids have been solved at the all-atom level. However methods for nucleic acids lag behind, and no all-atom viral double-stranded DNA genomes have been published at all. We here present a method which exploits the spiral winding patterns of DNA in icosahedral capsids. The method quickly generates shells of DNA wound in user-specified, idealized spherical or cylindrical spirals. For transition regions, the method allows guided semiflexible fitting. For the kuravirus SU10, our method explains most of the density in a semiautomated fashion. The results suggest rules for DNA turns in the end caps under which two discrete parameters determine the capsid inner diameter. We suggest that other kuraviruses viruses may follow the same winding scheme, producing a discrete rather than continuous spectrum of capsid inner diameters. Our software may be used to explain the published density maps of other double-stranded DNA viruses and uncover their genome packaging principles.
A developmentally controlled cellular decompartmentalization process executes programmed cell death in the Arabidopsis root cap
Authors: Wang Jie , Bollier Norbert , Buono Rafael Andrade , Vahldick Hannah , Lin Zongcheng , Feng Qiangnan , Hudecek Roman , Jiang Qihang , Mylle Evelien , Van Damme Daniel , Nowack Moritz K 
Published: December 2023

Abstract
Programmed cell death (PCD) is a fundamental cellular process crucial to development, homeostasis, and immunity in multicellular eukaryotes. In contrast to our knowledge on the regulation of diverse animal cell death subroutines, information on execution of PCD in plants remains fragmentary. Here, we make use of the accessibility of the Arabidopsis (Arabidopsis thaliana) root cap to visualize the execution process of developmentally controlled PCD. We identify a succession of selective decompartmentalization events and ion fluxes as part of the terminal differentiation program that is orchestrated by the NO APICAL MERISTEM, ARABIDOPSIS THALIANA ACTIVATING FACTOR, CUP-SHAPED COTYLEDON (NAC) transcription factor SOMBRERO. Surprisingly, the breakdown of the large central vacuole is a relatively late and variable event, preceded by an increase of intracellular calcium levels and acidification, release of mitochondrial matrix proteins, leakage of nuclear and endoplasmic reticulum lumina, and release of fluorescent membrane reporters into the cytosol. In analogy to animal apoptosis, the plasma membrane remains impermeable for proteins during and after PCD execution. Elevated intracellular calcium levels and acidification are sufficient to trigger cell death execution specifically in terminally differentiated root cap cells, suggesting that these ion fluxes act as PCD-triggering signals. This detailed information on the cellular processes occurring during developmental PCD in plants is a pivotal prerequisite for future research into the molecular mechanisms of cell death execution.
Immunohistochemical Expression of Angiotensin-Converting Enzyme 2 in the Skin of Patients Affected by COVID-19
Authors: Abdou Asmaa Gaber , Fayed Mona , Farag Azza Gaber Antar 
Published: December 2023

Background:
After many recorded cases of acute pneumonia of unknown cause, the World Health Organization announced COVID-19 as the start of a new coronavirus disease pandemic in 2019. Angiotensin-converting enzyme-2 (ACE2) is reduced by a protease known as transmembrane serine type 2 in the host cell, which then activates the S protein of SARS-CoV-2 regulating coronavirus entry into the host cells.

Aim:
The aim of this study was to assess the immunohistochemical expression of ACE 2 in the skin of patients affected by COVID-19 with and without cutaneous manifestations and to correlate ACE2 expression with clinical and pathologic parameters.

Methods:
Skin biopsies were obtained from skin lesions of 25 patients presenting with cutaneous manifestations and from the left forearm of 22 patients without cutaneous manifestations. The specimens were processed for evaluation of histopathologic changes and ACE2 immunohistochemical evaluation.

Results:
Positive ACE2 expression was significantly higher in patients without cutaneous manifestations (96%) than those with cutaneous manifestations (72.7%). Positive ACE2 expression in the skin of affected patients was significantly associated with the presence of comorbidities, positive family history, high ABCD score, elevated lactate dehydrogenase, high D-dimer, rapid respiratory rate, and low oxygen saturation.

Conclusions:
The skin could be involved in COVID-19 infection in the form of inflammatory changes, such as pityriasis rosea–like lesions. Patients with COVID-19 who presented with cutaneous manifestations are usually less severe. The presence of ACE2 in the skin of patients with COVID-19 is an indicator of worse status. Patients with COVID-19 without skin manifestations showed higher positivity for ACE2, which may explain the severity of the cases.
Hemodynamic effects of positive end-expiratory pressure
Authors: Joseph Adrien , Petit Matthieu , Vieillard-Baron Antoine 
Published: December 2023

Purpose of review
Positive end-expiratory pressure (PEEP) is required in the Berlin definition of acute respiratory distress syndrome and is a cornerstone of its treatment. Application of PEEP increases airway pressure and modifies pleural and transpulmonary pressures according to respiratory mechanics, resulting in blood volume alteration into the pulmonary circulation. This can in turn affect right ventricular preload, afterload and function. At the opposite, PEEP may improve left ventricular function, providing no deleterious effect occurs on the right ventricle.

Recent findings
This review examines the impact of PEEP on cardiac function with regards to heart-lung interactions, and describes its consequences on organs perfusion and function, including the kidney, gut, liver and the brain. PEEP in itself is not beneficious nor detrimental on end-organ hemodynamics, but its hemodynamic effects vary according to both respiratory mechanics and association with other hemodynamic variables such as central venous or mean arterial pressure. There are parallels in the means of preventing deleterious impact of PEEP on the lungs, heart, kidney, liver and central nervous system.

Summary
The quest for optimal PEEP settings has been a prominent goal in ARDS research for the last decades. Intensive care physician must maintain a high degree of vigilance towards hemodynamic effects of PEEP on cardiac function and end-organs circulation.
Latent Class Analysis of Social Needs in Medicaid Population and Its Impact on Risk Adjustment Models
Authors: Pandya Chintan J. , Wu JunBo , Hatef Elham , Kharrazi Hadi 
Published: December 2023

Background:
A growing number of US states are implementing programs to address the social needs (SNs) of their Medicaid populations through managed care contracts. Incorporating SN might also improve risk adjustment methods used to reimburse Medicaid providers.

Objectives:
Identify classes of SN present within the Medicaid population and evaluate the performance improvement in risk adjustment models of health care utilization and cost after incorporating SN classes.

Research Design:
A secondary analysis of Medicaid patients during the years 2018 and 2019. Latent class analysis (LCA) was used to identify SN classes. To evaluate the impact of SN classes on measures of hospitalization, emergency (ED) visits, and costs, logistic and linear regression modeling for concurrent and prospective years was used. Model performance was assessed before and after incorporating these SN classes to base models controlling for demographics and comorbidities.

Subjects:
262,325 Medicaid managed care program patients associated with a large urban academic medical center.

Results:
7.8% of the study population had at least one SN, with the most prevalent being related to safety (3.9%). Four classes of SN were determined to be optimal based on LCA, including stress-related needs, safety-related needs, access to health care–related needs, and socioeconomic status–related needs. The addition of SN classes improved the performance of concurrent base models’ AUC (0.61 vs. 0.58 for predicting ED visits and 0.61 vs. 0.58 for projecting hospitalizations).

Conclusions:
Incorporating SN clusters significantly improved risk adjustment models of health care utilization and costs in the study population. Further investigation into the predictive value of SN for costs and utilization in different Medicaid populations is merited.