bluuebunny/crossref_metadata_2025_split huggingface dataset:
A nomogram to predict the pathological complete response in patients with breast cancer based on the TILs-US score
Authors: Shigematsu Hideo , Fukui Kayo , Kanou Akiko , Fujimoto Mutsumi , Suzuki Kanako , Ikejiri Haruka , Amioka Ai , Hiraoka Emiko , Sasada Shinsuke , Emi Akiko , Arihiro Koji , Okada Morihito 
Published: June 2024

Abstract

Background
The tumor-infiltrating lymphocytes-ultrasonography score is a calculation system for predicting lymphocyte-predominant breast cancers in surgical specimens. A nomogram based on the tumor-infiltrating lymphocytes-ultrasonography score was developed to predict the pathological complete response in breast cancer treated with neoadjuvant chemotherapy.

Methods
A retrospective evaluation was conducted on 118 patients with breast cancer treated with neoadjuvant chemotherapy at Hiroshima University Hospital. Tumor-infiltrating lymphocytes-ultrasonography scores ≥4 were classified as high. A nomogram was developed using a stepwise logistic regression model for pathological complete response (ypT0 ypN0), based on the smallest Akaike information criterion. The predictive ability and clinical usefulness of the nomogram were also evaluated.

Results
Among 118 patients, 34 (28.8%) achieved a pathological complete response, and 52 (44.1%) exhibited high tumor-infiltrating lymphocytes-ultrasonography. In multivariate logistic regression analysis, high tumor-infiltrating lymphocytes-ultrasonography (odds ratio, 6.01; P &lt; 0.001), clinical complete response (odds ratio, 4.83; P = 0.004) and hormone receptor (odds ratio, 3.48; P = 0.038) were independent predictors of pathological complete response. A nomogram based on tumor-infiltrating lymphocytes-ultrasonography score, clinical complete response, hormone receptor and clinical N status was developed. The nomogram showed an area under the curve of 0.831 and a bias-corrected area under the curve of 0.809. The calibration plot showed a good fit between the expected and actual pathological complete response values. Decision curve analysis also showed the clinical utility of the nomogram for predicting pathological complete responses.

Conclusions
A nomogram based on the tumor-infiltrating lymphocytes-ultrasonography score exhibited a favorable predictive ability for pathological complete response in patients with breast cancer, which can be useful in predicting the residual disease status after neoadjuvant chemotherapy.
Direct Combat-related U.S. Army Aviation Injuries 2003–2014
Authors: Brozoski Frederick T , Conti Marcy , Dudek Jennifer , Chancey Valeta Carol , Crowley John S 
Published: June 2024

ABSTRACT

Introduction
The U.S. Army Aeromedical Research Laboratory (USAARL), a partner in the Joint Trauma Analysis for the Prevention of Injury in Combat (JTAPIC) partnership, conducted a series of retrospective reviews to investigate injuries sustained by occupants of U.S. Army rotary-wing aircraft involved in combat damage incidents. The reviews were conducted to provide occupant survivability information to the Aviation Survivability Development and Tactics team, an agency within the U.S. Army Aviation Center of Excellence. For these reviews, combat damage incidents that produced casualties were separated into direct events (i.e., events in which an enemy weapon system directly injured occupants) and indirect events (i.e., incidents in which occupants were injured as a result of a crash caused by the enemy weapon system). The previous USAARL reviews provided an overview of injuries sustained during direct and indirect events. The objective of this review was to conduct a detailed analysis of injuries occurring during direct events.

Materials and Methods
A descriptive retrospective review was conducted on injuries sustained by occupants of U.S. Army rotary-wing aircraft involved in combat damage incidents between 2003 and 2014. All Black Hawk, Apache, and Chinook combat aviation damage incidents for the study period were reviewed. Personnel casualty information from the Defense Casualty Information Processing System (DCIPS) was linked to combat damage incident information by matching the aircraft platform, incident date, and circumstantial information found in incident narratives. Injury information for personnel identified in DCIPS as being wounded in action was obtained from the JTAPIC partnership; injury data for personnel killed in action were retrieved from the Armed Forces Medical Examiner System. All injuries were coded using the Abbreviated Injury Scale (AIS). Descriptive statistics were used to describe the frequency and distribution of injuries to personnel involved in direct events.

Results
Overall, the extremities were the most commonly injured body regions, with lower extremities suffering more injuries than upper extremities. Penetrating injuries were identified as the primary injury mechanism for all body regions. Injuries to each AIS body region were predominantly of minor (AIS 1) and moderate (AIS 2) severity.

Conclusions
Although injury severities were generally low (AIS 1 or AIS 2), the results of this effort indicate which body regions may benefit from additional protection during rotary-wing operations in hostile environments. The influence of occupant position within the aircraft and the use and effectiveness of personal protective equipment could not be effectively analyzed due to a lack of information.
Recurrent Duplication and Diversification of a Vital DNA Repair Gene Family Across Drosophila
Authors: Brand Cara L , Oliver Genevieve T , Farkas Isabella Z , Buszczak Michael , Levine Mia T 
Published: June 2024

Abstract
Maintaining genome integrity is vital for organismal survival and reproduction. Essential, broadly conserved DNA repair pathways actively preserve genome integrity. However, many DNA repair proteins evolve adaptively. Ecological forces like UV exposure are classically cited drivers of DNA repair evolution. Intrinsic forces like repetitive DNA, which also imperil genome integrity, have received less attention. We recently reported that a Drosophila melanogaster-specific DNA satellite array triggered species-specific, adaptive evolution of a DNA repair protein called Spartan/MH. The Spartan family of proteases cleave hazardous, covalent crosslinks that form between DNA and proteins (“DNA–protein crosslink repair”). Appreciating that DNA satellites are both ubiquitous and universally fast-evolving, we hypothesized that satellite DNA turnover spurs adaptive evolution of DNA–protein crosslink repair beyond a single gene and beyond the D. melanogaster lineage. This hypothesis predicts pervasive Spartan gene family diversification across Drosophila species. To study the evolutionary history of the Drosophila Spartan gene family, we conducted population genetic, molecular evolution, phylogenomic, and tissue-specific expression analyses. We uncovered widespread signals of positive selection across multiple Spartan family genes and across multiple evolutionary timescales. We also detected recurrent Spartan family gene duplication, divergence, and gene loss. Finally, we found that ovary-enriched parent genes consistently birthed functionally diverged, testis-enriched daughter genes. To account for Spartan family diversification, we introduce a novel mechanistic model of antagonistic coevolution that links DNA satellite evolution and adaptive regulation of Spartan protease activity. This framework promises to accelerate our understanding of how DNA repeats drive recurrent evolutionary innovation to preserve genome integrity.
Analysis of Evolutionary Conservation, Expression Level, and Genetic Association at a Genome-wide Scale Reveals Heterogeneity Across Polygenic Phenotypes
Authors: Giel Ann-Sophie , Bigge Jessica , Schumacher Johannes , Maj Carlo , Dasmeh Pouria 
Published: June 2024

Abstract
Understanding the expression level and evolutionary rate of associated genes with human polygenic diseases provides crucial insights into their disease-contributing roles. In this work, we leveraged genome-wide association studies (GWASs) to investigate the relationship between the genetic association and both the evolutionary rate (dN/dS) and expression level of human genes associated with the two polygenic diseases of schizophrenia and coronary artery disease. Our findings highlight a distinct variation in these relationships between the two diseases. Genes associated with both diseases exhibit a significantly greater variance in evolutionary rate compared to those implicated in monogenic diseases. Expanding our analyses to 4,756 complex traits in the GWAS atlas database, we unraveled distinct trait categories with a unique interplay among the evolutionary rate, expression level, and genetic association of human genes. In most polygenic traits, highly expressed genes were more associated with the polygenic phenotypes compared to lowly expressed genes. About 69% of polygenic traits displayed a negative correlation between genetic association and evolutionary rate, while approximately 30% of these traits showed a positive correlation between genetic association and evolutionary rate. Our results demonstrate the presence of a spectrum among complex traits, shaped by natural selection. Notably, at opposite ends of this spectrum, we find metabolic traits being more likely influenced by purifying selection, and immunological traits that are more likely shaped by positive selection. We further established the polygenic evolution portal (evopolygen.de) as a resource for investigating relationships and generating hypotheses in the field of human polygenic trait evolution.
Clinical Presentation and Outcomes Following Infection With Vibrio spp, Aeromonas spp, Chromobacterium violaceum, and Shewanella spp Water-Associated Organisms in Tropical Australia, 2015–2022
Authors: Campbell Stuart , MacGregor Kirsten , Smith Emma L , Kanitkar Tanmay , Janson Sonja , Baird Robert W , Currie Bart J , Venkatesan Sudharsan 
Published: June 2024

Abstract

Background
Water-associated bacterial infections cause a wide spectrum of disease. Although many of these infections are typically due to human host commensal Staphylococcal or Streptococcal spp, water exposure can result in infections with environmental gram negatives such as Vibrio spp, Aeromonas spp, Chromobacterium violaceum, and Shewanella spp (collectively VACS).

Methods
We performed a retrospective analysis of the epidemiology, clinical presentation, and outcomes of deep and superficial infections associated with VACS organisms in our health service between 1 January 2015 and 31 December 2023.

Results
We identified 317 patient episodes of infection with VACS organisms over this period. Of these, Aeromonas spp (63%) was the most common, followed by Vibrio spp (19%), Shewanella spp (13%), and C violaceum (5%). The majority were isolated from males (74.4%) and involved the lower limb (67.5%). Mild infections were more common than severe presentations, with only 15 (4.7%) admissions to the intensive care unit and 8 (2.5%) deaths. Colonization occurred in 6.9% of patients, in contrast to the perceived severity of some of these bacteria. Copathogens were common and included Staphylococcus aureus (48%) and enteric bacteria (57%). The majority of patients (60%) had no documented water exposure. Initial empiric antimicrobial therapy presumptively covered the susceptibilities of the isolated organisms in 47.3% of patients; however, a lack of VACS-covering empirical therapy was not associated with readmission.

Conclusions
The isolation of a VACS organism in our setting was often not associated with documented water exposure, which has implications for empiric antimicrobial therapy. Severe disease and death were uncommon.
Culture-Free Whole Genome Sequencing of Mycobacterium tuberculosis Using Ligand-Mediated Bead Enrichment Method
Authors: Vasanthaiah Shruthi , Verma Renu , Kumar Ajay , Bandari Aravind K , George John , Rastogi Mona , Manjunath Gowrang Kasaba , Sharma Jyoti , Kumar Abhishek , Subramani Janavi , Chawla Kiran , Pandey Akhilesh 
Published: June 2024

Abstract

Background
Direct whole genome sequencing (WGS) of Mycobacterium tuberculosis (Mtb) can be used as a tool to study drug resistance, mixed infections, and within-host diversity. However, WGS is challenging to obtain from clinical samples due to low number of bacilli against a high background.

Methods
We prospectively collected 34 samples (sputum, n = 17; bronchoalveolar lavage, n = 13; and pus, n = 4) from patients with active tuberculosis (TB). Prior to DNA extraction, we used a ligand-mediated magnetic bead method to enrich Mtb from clinical samples and performed WGS on Illumina platform.

Results
Mtb was definitively identified based on WGS from 88.2% (30/34) of the samples, of which 35.3% (12/34) were smear negative. The overall median genome coverage was 15.2% (interquartile range [IQR], 7.7%–28.2%). There was a positive correlation between load of bacilli on smears and genome coverage (P &lt; .001). We detected 58 genes listed in the World Health Organization mutation catalogue in each positive sample (median coverage, 85% [IQR, 61%–94%]), enabling the identification of mutations missed by routine diagnostics. Mutations causing resistance to rifampicin, isoniazid, streptomycin, and ethambutol were detected in 5 of 34 (14.7%) samples, including the rpoB S441A mutation that confers resistance to rifampicin, which is not covered by Xpert MTB/RIF.

Conclusions
We demonstrate the feasibility of magnetic bead–based enrichment for culture-free WGS of Mtb from clinical specimens, including smear-negative samples. This approach can also be integrated with low-cost sequencing workflows such as targeted sequencing for rapid detection of Mtb and drug resistance.
Navigating stormy waters: a middle power perspective
Authors: Fried Jonathan T 
Published: June 2024

Abstract
Structural shifts in patterns of international production, trade, and investment have been spurred by the globalization of supply chains. Today, however, a range of factors, including wars and sanctions, the increasing divide between Western and Chinese approaches to the economy, the increasing links between economic security and national security, and between trade and environmental regulation, are contributing to the fragmentation of international economic frameworks and growing populist and protectionist sentiment. Competition for advantage through industrial subsidies and the setting of digital and environmental standards risks enshrining a less-than-global economic order. In many fields, however, multilateral cooperation, rulemaking, and enforcement in serving shared objectives, in various international organizations, multi-stakeholder forums, and by the private sector, continues to function well. In this ever-more complex international context, where clubs, coalitions, and informal networks among nations are increasingly prevalent, middle powers are wise to remain both agile and resolute in ensuring that national interests are advanced through smart diplomacy, encompassing working with like-minded in caucuses and informal settings that serve to build broader consensus, engaging business and other stakeholders at home and abroad in support. Canada’s experience and current efforts provide a constructive example for middle powers.
Post-neoliberal globalization: international trade rules for global prosperity
Authors: Guzman Martin , Stiglitz Joseph E 
Published: June 2024

Abstract
This paper analyses frameworks for the design of the rules for international trading, assuming that it is possible to have some rule of law. In the Arrow–Debreu benchmark, where there is no economic power and political power is seemingly irrelevant, there is no need for trade agreements—free trade is the optimal policy for each country. But under even minimal deviations from that benchmark, trade agreements matter. We focus on environments in which there are market failures, technology is endogenous, and there is political power. Power dynamics play, for instance, a critical role in the design, implementation, and enforcement of agreements, with the latter being a critical difference between international agreements and domestic contracts and a key determinant of the feasibility and consequences of agreements. With endogenous technology, trade rules proscribing industrial policies may lead to lower growth and greater cross-country inequalities. Finally, we develop a normative framework which may be useful in the design and implementation of trade rules.
A review of crime trends in Hong Kong during COVID-19: Empirical analysis based on ARIMA model
Authors: Gao Yifan 
Published: June 2024

Abstract
This study uses the crime dynamics in Hong Kong as the research object and builds an autoregressive integrated moving average model to compare the expected crime rates of common criminal activities with the observed crime rates in order to analyse the impact of COVID-19 on criminal activities in detail. Findings reveal distinct patterns in crime rates, with significant decreases observed in serious assault, burglary, and theft from vehicles, alongside increases in fraud-related crimes and incidents of child abuse. These trends underscore the relationship between changes in routine activities, availability of potential targets, and negative emotions experienced by individuals during the pandemic. The study highlights the importance of considering both Routine Activities Theory and General Strain Theory when analysing the multifaceted impacts of societal changes on crime dynamics. The findings offer valuable implications for researchers, policymakers, and law enforcement agencies in understanding changes of criminal behaviours and developing proactive strategies for crime prevention, and promoting societal well-being in the post-pandemic era.
Potentialist set theory and the nominalist’s dilemma
Authors: Berry Sharon 
Published: June 2024

Abstract
Mathematicalnominalists have argued that we can reformulate scientific theories without quantifying over mathematical objects.However, worries about the nature and meaningfulness of these nominalistic reformulations have been raised, like Burgess and Rosen’s dilemma. In this paper, I’ll review (what I take to be) a kind of emerging consensus response to this dilemma: appeal to the idea of different levels of analysis and explanation, with philosophy providing an extra layer of analysis “below” physics, much as physics does below chemistry. I’ll argue that one can address certain lingering worries for this approach by appeal to the apparent usefulness of a distinction between foundational and non-foundational contexts within mathematics and certain (admittedly controversial) arguments for Potentialism about set theory.
Various investigations of ameliorative role of Ashwagandha seeds (Withania somnifera) against amoxicillin toxicity
Authors: Elnasharty Mohamed M M , Elwan Azhar M , Elhadidy Mohamed E , Mohamed Mona A , Abd El-Rahim Abeer H , Hafiz Naglaa A , Abd-El-Moneim Omaima M , Abd El-Aziz Kamilia B , Abdalla Aboelfetoh M , Farag Ibrahim M 
Published: June 2024

Abstract
Several studies showed the adverse effects of amoxicillin on various body organs. So, this research has been designed to evaluate the modulatory role of Ashwagandha seed extract (ASE) against amoxicillin (AM) toxicity. Rats treated with AM (90 mg/kg), protected by ASE doses (100, 200 and 300 mg/kg), and treated by ASE at the same three doses. At the end of the experimental period, DNA comet assay, cytogenetic examinations, sperm-shape analysis, evaluation of the malondialdehyde (MDA) percentages, histopathological examinations, and biophysical tests (modulus, relaxation time, permittivity, entropy, and internal energy change of brain) were documented. The results confirmed that AM treatment induced significant elevation of DNA damage, cytogenetic aberrations, and MDA content in brain, liver, and testis tissues and sperm-shape anomalies. ASE treatment significantly minimized the genetic changes, sperm-shape anomalies, and MDA generation. These enhancements were more pronounced by protective ASE and increased by increasing the dose level. In histopathological examinations, AM treatment caused neurotoxicity in brain tissue. ASE treatment, partially, minimized these damages and the positive effects of therapeutic ASE were more noticeable. Biophysical parameters showed that therapeutic ASE was better for relaxation time, permittivity, and free energy change. Protective and therapeutic ASE were able to recover entropy and internal energy changes in variant degrees.
The efficacy and safety of ureteroscopic lithotripsy and flexible ureteroscopy with continuous anticoagulant or antiplatelet drugs: A multicenter retrospective real-world study
Authors: Xu Zijie , He Chujiang , Cao Jianwei , Wu Jianhong , Wang Dawei , Da Jun , Xu Dongliang , Tan Mingyue , Gao Xiaofeng , Peng Yonghan , Chen Jie , Chen Rong , Wu Pengfei , Jiang Juntao , Chen Lei , Xia Shujie , Shao Yi 
Published: June 2024

Abstract

Objective
The objective of this study is to assess the effectiveness and safety of ureteroscopic lithotripsy and flexible ureteroscopy (fURS) for treating patients on anticoagulant (AC) or antiplatelet (AP) medications.

Patients and Methods
The study included 213 patients with urinary stones who underwent ureteroscopic lithotripsy or fURS between January 2019 and October 2022 at the Shanghai Municipal Hospital Urology Specialist Alliance. Among these patients, 15 received AC therapy, 193 received AP therapy, and 5 received both AC and AP therapy. Patients were divided into 3 groups based on the real-world management of antithrombotic drugs: the continuation group (n = 62), the discontinuation group (n = 91), and the discontinuation and bridge heparin group (n = 60). Intraoperative and postoperative outcomes were compared among the 3 groups.

Results
Age, sex, body mass index, stone location, stone size, stone side, and residual fragments were not different among the groups. None of the patients received blood transfusions or had thromboembolic events, emergencies for gross hematuria, significant bleeding-related complications, or unplanned secondary ureteroscopic surgery. The mean duration of hospital stay of the continuation group (3.97 days) was significantly lower than that of the discontinuation group (5.99 days) and the discontinuation and bridge heparin group (5.75 days) (p < 0.001).

Conclusions
Ureteroscopic lithotripsy and fURS can be performed safely and effectively in patients on AC or AP drugs, resulting in reduced duration of hospital stay.