bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sex differences in long-term heart failure prognosis: a comprehensive meta-analysis
Authors: Qiu Weida , Wang Wenbin , Wu Shiping , Zhu Yanchen , Zheng He , Feng Yingqing 
Published: August 2024

Abstract

Aims
Sex differences in the long-term prognosis of heart failure (HF) remain controversial, and there is a lack of comprehensive pooling of the sex differences in outcomes of HF. This study aims to characterize the sex differences in the long-term prognosis of HF and explore whether these differences vary by age, HF course, left ventricular ejection fraction, region, period of study, study design, and follow-up duration.

Methods and results
A systematic review was conducted using Medline, Embase, Web of Science, and the Cochrane Library, from 1 January 1990 to 31 March 2024. The primary outcome was all-cause mortality (ACM), and the secondary outcomes included cardiovascular mortality (CVM), hospitalization for HF (HHF), all-cause hospitalization, a composite of ACM and HHF, and a composite of CVM and HHF. Pooled hazard ratios (HRs) with corresponding 95% confidence intervals (CIs) were calculated using random-effects meta-analysis. Ninety-four studies (comprising 96 cohorts) were included in the meta-analysis, representing 706,247 participants (56.5% were men; the mean age was 71.0 years). Female HF patients had a lower risk of ACM (HR 0.83; 95% CI 0.80, 0.85; I2 = 84.9%), CVM (HR 0.84; 95% CI 0.79, 0.89; I2 = 70.7%), HHF (HR 0.94; 95% CI 0.89, 0.98; I2 = 84.0%), and composite endpoints (ACM + HHF: HR 0.89; 95% CI 0.83, 0.95; I2 = 80.0%; CVM + HHF: HR 0.85; 95% CI 0.77, 0.93; I2 = 87.9%) compared with males. Subgroup analysis revealed that the lower risk of mortality observed in women was more pronounced among individuals with long-course HF (i.e. chronic HF, follow-up duration &gt; 2 years) or recruited in the randomized controlled trials (P for interaction &lt; 0.05).

Conclusion
Female HF patients had a better prognosis compared with males, with lower risks of ACM, CVM, HHF, and composite endpoints. Despite the underrepresentation of female populations in HF clinical trials, their mortality benefits tended to be lower than in real-world settings.

Registration
PROSPERO: CRD42024526100
Short-Term Coupling Associations Between State Loneliness and Cognitive Performance in Daily Life Among Older Adults
Authors: Kang Jee eun , Graham-Engeland Jennifer E , Martire Lynn M , Almeida David M , Sliwinski Martin J 
Published: August 2024

Abstract

Objectives
Despite extensive efforts to study individual differences in loneliness and neurocognitive health, little is known about how within-person changes in state loneliness relate to cognitive performance. This study addressed this gap by examining the association between within-person variation in state loneliness and cognitive performance assessed objectively in daily life.

Methods
Participants were 313 community-dwelling older adults (70–90 years) who reported momentary feelings of loneliness and completed smartphone-based cognitive tests 5 times daily for 14 consecutive days. Mobile cognitive tests assess visual associative memory, processing speed, and spatial memory.

Results
At the day level, average state loneliness levels were negatively related to cognitive performance on the same day and subsequent day. Consistent with the day-level analysis, momentary assessments of increased loneliness were consistently linked to worse cognitive performance on concurrent assessments. However, moments characterized by lower cognitive performance predicted higher levels of loneliness 3–4 hr later (next occasion), but not vice versa.

Discussion
The findings suggest a prospective association between loneliness and cognitive performance, with higher daily loneliness negatively associated with cognitive performance on the same day and predicting worse performance the following day. Notably, within a single day, lower cognitive performance at a given moment predicted elevated loneliness later in the day. This highlights a complex, reciprocal relationship—loneliness predicting and being predicted by cognitive performance depending on timescale.
Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit
Authors: Lavikka Kari , Oikkonen Jaana , Li Yilin , Muranen Taru , Micoli Giulia , Marchi Giovanni , Lahtinen Alexandra , Huhtinen Kaisa , Lehtonen Rainer , Hietanen Sakari , Hynninen Johanna , Virtanen Anni , Hautaniemi Sampsa 
Published: August 2024

Abstract

Background
Visualization is an indispensable facet of genomic data analysis. Despite the abundance of specialized visualization tools, there remains a distinct need for tailored solutions. However, their implementation typically requires extensive programming expertise from bioinformaticians and software developers, especially when building interactive applications. Toolkits based on visualization grammars offer a more accessible, declarative way to author new visualizations. Yet, current grammar-based solutions fall short in adequately supporting the interactive analysis of large datasets with extensive sample collections, a pivotal task often encountered in cancer research.

Findings
We present GenomeSpy, a grammar-based toolkit for authoring tailored, interactive visualizations for genomic data analysis. By using combinatorial building blocks and a declarative language, users can implement new visualization designs easily and embed them in web pages or end-user–oriented applications. A distinctive element of GenomeSpy’s architecture is its effective use of the graphics processing unit in all rendering, enabling a high frame rate and smoothly animated interactions, such as navigation within a genome. We demonstrate the utility of GenomeSpy by characterizing the genomic landscape of 753 ovarian cancer samples from patients in the DECIDER clinical trial. Our results expand the understanding of the genomic architecture in ovarian cancer, particularly the diversity of chromosomal instability.

Conclusions
GenomeSpy is a visualization toolkit applicable to a wide range of tasks pertinent to genome analysis. It offers high flexibility and exceptional performance in interactive analysis. The toolkit is open source with an MIT license, implemented in JavaScript, and available at https://genomespy.app/.
Resolving Resident Colonic Muscularis Macrophage Diversity and Plasticity During Colitis
Authors: Ohishi Kensuke , Dora David , Han Christopher Y , Guyer Richard A , Ohkura Takahiro , Kazimierczyk Simon , Picard Nicole , Leavitt Abigail R , Ott Leah C , Rahman Ahmed A , Mueller Jessica L , Shpigel Nahum Y , Jain Nitya , Nagy Nandor , Hotta Ryo , Goldstein Allan M , Stavely Rhian 
Published: August 2024

Abstract

Background
Immune cell populations in the intestinal muscularis propria during colitis are poorly resolved. Maintaining homeostasis in this niche is critical, highlighted by the poorer prognosis of inflammatory bowel disease associated with muscularis propria inflammation.

Methods
This study utilizes single-cell RNA sequencing to survey the immune cell populations within the muscularis propria of normal colon and dextran sodium sulfate-induced colitis. Findings are validated by immunohistochemistry, flow cytometry and cell-lineage tracing in vivo, and in vitro assays with muscularis macrophages (MMφ).

Results
In naïve conditions, transcriptional duality is observed in MMφs with 2 major subpopulations: conventional resident Cx3cr1+ MMφs and Lyve1+ MMφs. The Lyve1+ population is phagocytic and expresses several known MMφ markers in mouse and human, confirming their identity as a bona fide MMφ subset. Single-cell transcriptomics indicate that resident MMφs are retained during colitis and exhibit plasticity toward an inflammatory profile. Lyve1+ MMφs, which express anti-inflammatory marker CD163, are absent during colitis, as confirmed by flow cytometry. In contrast, lineage tracing finds that resident Cx3cr1+ MMφs remain during colitis and are not completely replaced by the inflammatory infiltrating monocytes. In vitro studies provide biological evidence of the plasticity of resident Cx3cr1+ MMφs in response to lipopolysaccharide (LPS), mirroring transcriptional observations in vivo of their inflammatory plasticity. Potential markers for colitic MMφs, validated in animal models and in individuals with ulcerative colitis, are identified.

Conclusions
Our findings contribute to the understanding of the immune system in the muscularis propria niche during colitis by resolving the heterogeneity and origins of colitic MMφs.
Performance analysis and emission characteristics of VCR diesel engine using palm stearin oil biodiesel as fuel
Authors: Malayathi Sivaramakrishnaiah , Aetty Ramachandraiah Babu , Patan Babu , Anugolu Ravitheja , Balasubramanian Arun , Paramasivam Prabhu 
Published: August 2024

Abstract
The increasing depletion of fossil fuels has prompted international efforts to search for diesel substitutes. One way to considerably reduce fuel shortages would be to use bio-derived fuels as replacements. Transesterification of edible or nonedible vegetable oils yields biodiesel, which is one example of a bio-origin fuel and a workable solution. Biodiesel’s characteristics are often more advantageous than those of diesel. One well-known example of a nonedible vegetable oil is palm stearin. In this work, we investigate the potential use of transesterified palm stearin methyl esters (PSME) as a substitute fuel. A rated compression ratio (CR) of 17.5 and 210 bar of fuel injection pressure were employed in the experimental investigations, which were carried out at a constant speed of 1500 rpm. Our main goals were to reduce emissions and improve engine performance. The evaluation parameters encompassed brake thermal efficiency (BTE), brake-specific fuel consumption (BSFC), and emission indices. It was observed that using PSME led to better performance and fewer emissions when compared to using conventional diesel, especially when the CR was 17.5. Increased BTE, decreased BSFC, lower air–fuel ratios, and decreased volumetric efficiencies were all correlated with higher CR. As a byproduct of palm oil, PSME shows promise as a seasonally and geographically specific feedstock for biodiesel production, providing benefits over conventional diesel fuels in terms of performance and the environment.
Association of Pneumococcal Conjugate Vaccination With Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Older Adult Recipients of Coronavirus Disease 2019 Vaccines: A Longitudinal Cohort Study
Authors: Lewnard Joseph A , Hong Vennis , Grant Lindsay R , Ackerson Bradley K , Bruxvoort Katia J , Pomichowski Magdalena , Arguedas Adriano , Cané Alejandro , Jodar Luis , Gessner Bradford D , Tartof Sara Y 
Published: August 2024

Abstract

Background
Pneumococcal carriage is associated with increased acquisition and duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among adults. While pneumococcal conjugate vaccines (PCVs) prevent carriage of vaccine-serotype pneumococci, their potential impact on coronavirus disease 2019 (COVID-19)–related outcomes remains poorly understood in populations with prevalent immunity against SARS-CoV-2.

Methods
We undertook a retrospective cohort study of adults aged ≥65 years in the Kaiser Permanente Southern California healthcare system who had received ≥2 COVID-19 vaccine doses, comparing risk of SARS-CoV-2 infection between 1 January 2021 and 31 December 2022 among recipients and nonrecipients of 13-valent PCV (PCV13) employing multiple strategies to mitigate bias from differential test-seeking behavior.

Results
The ajusted hazard ratio of confirmed SARS-CoV-2 infection comparing PCV13 recipients to nonrecipients was 0.92 (95% confidence interval [CI], .90–.95), corresponding to prevention of 3.9 (95% CI, 2.6–5.3) infections per 100 person-years. Following receipt of 2, 3, and ≥4 COVID-19 vaccine doses, aHRs (95% CI) were 0.85 (.81–.89), 0.94 (.90–.97), and 0.99 (.93–1.04), respectively. The aHR (95% CI) for persons who had not received COVID-19 vaccination in the preceding 6 months was 0.90 (.86–.93), versus 0.94 (.91–.98) within 6 months after COVID-19 vaccination. Similarly, aHRs (95% CI) were 0.92 (.89–.94) for persons without history of documented SARS-CoV-2 infection, versus 1.00 (.90–1.12) for persons with documented prior infection.

Conclusions
Among older adults who had received ≥2 COVID-19 vaccine doses, PCV13 was associated with modest protection against SARS-CoV-2 infection. Protective effects of PCV13 were greater among individuals expected to have weaker immune protection against SARS-CoV-2 infection.
Field abundance and spatial patterns of ear-feeding insect pests in relation to levels of defective kernels in processing sweet corn
Authors: Dively Galen P , Yurchak Veronica , Hooks Cerruti R R , Farcuh Macarena 
Published: August 2024

Abstract
In this study, we investigated the within-field distribution of sweet corn insect pests in relation to adjacent habitats and determined the level and specific causes of defective kernels affecting the quality of the final product at the processing cannery. Sap beetles [primarily Carpophilus lugubris (Murray, 1864) (Coleoptera: Nitidulidae)] and stink bugs [primarily Euschistus servus (Say) ((Heteroptera: Pentatomidae)] infested 27.6% and 73.6% of the fields, respectively. Densities of stink bugs were highest along field edges adjacent to wheat, soybean, vegetable crops, and woodlots. Levels of kernel injury were consistently higher in truckloads of ears harvested first from the outer rows. Earworm damage was confined to the ear tip and had no measurable impact on the quality of the final product. Sap beetles and blemished kernels were the major causes of defective kernels in the cannery, even though stink bugs were more abundant in the fields. Defective kernels were more positively related to physiological blemishes than to other causal factors. For all fields, defective kernel levels averaged less than 1%, resulting in excellent quality of the processed product throughout the entire season. Results provided a better understanding of the quality control issues, resulting in practical implications for improvements in field monitoring and decision-making in the cannery to minimize grading problems.
NCI SEER-Linked Virtual Tissue Repository Pilot
Authors: Sanchez Pamela , Van Dyke Alison L , Petkov Valentina I , Yuan Yao , Bonds Sarah , Valenzuela Connor , Tuan Alyssa W , Moravec Radim , Altekruse Sean F , Singhi Aatur D , Serdy Kate M , Wu Yun , Cress Rosemary D , Doherty Jennifer A , Mueller Lloyd , Hernandez Brenda Y , Lynch Charles F , Tucker Thomas C , Wu Xiao-Cheng , Matrisian Lynn , Penberthy Lynne 
Published: August 2024

Abstract

Background
The Surveillance, Epidemiology, and End Results (SEER) Program with the National Cancer Institute tested whether population-based cancer registries can serve as honest brokers to acquire tissue and data in the SEER-Linked Virtual Tissue Repository (VTR) Pilot.

Methods
We collected formalin-fixed, paraffin-embedded tissue and clinical data from patients with pancreatic ductal adenocarcinoma (PDAC) and breast cancer (BC) for two studies comparing cancer cases with highly unusual survival (≥5 years for PDAC and ≤30 months for BC) to pair-matched controls with usual survival (≤2 years for PDAC and ≥5 years for BC). Success was defined as the ability for registries to acquire tissue and data on cancer cases with highly unusual outcomes.

Results
Of 98 PDAC and 103 BC matched cases eligible for tissue collection, sources of attrition for tissue collection were tissue being unavailable, control paired with failed case, second control that was not requested, tumor necrosis ≥20%, and low tumor cellularity. In total, tissue meeting the study criteria was obtained for 70 (71%) PDAC and 74 (72%) BC matched cases. For patients with tissue received, clinical data completeness ranged from 59% for CA-19-9 after treatment to &gt;95% for margin status, whether radiation therapy and chemotherapy were administered, and comorbidities.

Conclusions
The VTR Pilot demonstrated the feasibility of using SEER cancer registries as honest brokers to provide tissue and clinical data for secondary use in research. Studies using this program should oversample by 45% to 50% to obtain sufficient sample size and targeted population representation and involve subspecialty matter expert pathologists for tissue selection.
Occurrence and Case Fatality Rate of Invasive Aspergillosis in Children With Acute Leukemia: A Systematic Review and Meta-analysis
Authors: Duus Rasmus Moeller , Moeller Jesper Bonnet , Rathe Mathias 
Published: August 2024

Abstract
Invasive aspergillosis (IA) is a potentially life-threatening complication of childhood acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). We conducted a systematic review and meta-analyses of studies on acute leukemia in children aged 0–17 years since 2000. Findings were reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. We included 24 studies with 3661 ALL patients and 1728 AML patients. IA cumulative incidence varied (0%–10% for ALL and 0%–18% for AML) across the studies. Pooled cumulative IA incidences were estimated at 3.2% (95% CI: 1.8%–5.8%) in ALL and 5.2% (95% CI: 3.1%–8.6%) in AML, with corresponding case fatality rates of 13.3% (95% CI: 6.3%–25.9%), and 7.8% (95% CI: 0.7%–51.2%), respectively. Our analysis highlights the impact of IA in childhood leukemia, underscoring the need to address strategies for prevention, early detection, and treatment of IA in pediatric leukemia.
Risk factors for adverse drug reactions to sulfamethoxazole-trimethoprim prophylaxis in patients with rheumatic and musculoskeletal diseases
Authors: Hiramoto Kazuoto , Akiyama Mitsuhiro , Kaneko Yuko 
Published: August 2024

ABSTRACT

Objectives
Risk factors for adverse drug reactions (ADRs) associated with prophylactic sulfamethoxazole-trimethoprim (SMX/TMP) in patients with rheumatic and musculoskeletal diseases undergoing immunosuppressive therapy remain unclear; we aimed to identify the risk factors associated with ADRs.

Methods
Consecutive patients with rheumatic and musculoskeletal diseases, who were admitted to Keio University Hospital and received prophylactic administration of SMX/TMP, were included. Data regarding ADRs to SMX/TMP were collected to identify the associated risk factors using multivariable analysis.

Results
Of 438 patients included in the analysis, 82 (18.7%) experienced ADRs. Patients in the ADR group were significantly older, had chronic kidney disease, and exhibited lower lymphocyte and platelet counts, lower albumin levels, lower estimated glomerular filtration rates, higher aspartate aminotransferase levels, and higher ferritin levels than those in the non-ADR group. Regarding the underlying rheumatic and musculoskeletal diseases, adult-onset Still’s disease (ASD) was associated with a significantly higher incidence of ADRs (67%) than other diseases. Multivariable analysis identified the presence of ASD and low lymphocyte counts as independent risk factors for allergic ADRs and older age and use of angiotensin-converting enzyme inhibitors/angiotensin receptor blockers for nonallergic ADRs.

Conclusions
Risk factors for ADRs associated with prophylactic SMX/TMP treatment in patients with rheumatic and musculoskeletal diseases were identified.
Potential Health Benefits of a Diet Rich in Organic Fruit and Vegetables versus a Diet Based on Conventional Produce: A Systematic Review
Authors: Komati Nathalie , Cravedi Jean-Pierre , Lecerf Jean-Michel , Belzunces Luc P , Tailliez Delphine , Chambrier Claire , Calvarin Johanna , Amiot Marie-Josèphe 
Published: August 2024

Abstract

Context
Over the past decade, the production and consumption of organic food (OF) have received increasing interest. Scientific studies have shown better quality of organic fruit and vegetables (FV) in terms of nutrients and pesticide contents, but it appears difficult to conclude if there are potentially greater health benefits of these products compared with conventional food (CF).

Objective
To determine whether the current scientific literature demonstrates that a diet rich in organic FV is healthier than 1 based on conventional produce.

Methods
A systematic search was conducted using the PubMed and Web of Science databases for articles published between January 2003 and December 2022. Articles were analyzed uniformly by 2 reviewer, using a specific template summary sheet, and scored from 1 to 5. The level of evidence and the quality of studies in humans were assessed using the Jadad score and the French National Authority for Health method.

Results
A total of 12 human studies were included. Studies often reported contradictory or even opposite results, with methodological limitations. Only 6 of the 12 studies found significant associations between OF and the health outcomes evaluated.

Conclusion
The current data do not enable a firm conclusion about a greater health benefit for a diet rich in FV based on products grown organically compared with conventional farming. There is a paucity of available data and considerable heterogeneity in study designs (participants, exposures, durations, health outcomes, and residual confounding factors). Well-designed interventional studies are required.
Multiple Acquisitions of XopJ2 Effectors in Populations of Xanthomonas perforans
Authors: Sharma Anuj , Iruegas-Bocardo Fernanda , Bibi Shaheen , Chen Yun-Chu , Kim Jung-Gun , Abrahamian Peter , Minsavage Gerald V. , Hurlbert Jason C. , Vallad Gary E. , Mudgett Mary B. , Jones Jeffrey B. , Goss Erica M. 
Published: August 2024

Type III effectors (T3Es) are major determinants of Xanthomonas virulence and targets for resistance breeding. XopJ2 (synonym AvrBsT) is a highly conserved YopJ-family T3E acquired by X. perforans, the pathogen responsible for bacterial spot disease of tomato. In this study, we characterized a new variant (XopJ2b) of XopJ2, which is predicted to have a similar three-dimensional (3D) structure as the canonical XopJ2 (XopJ2a) despite sharing only 70% sequence identity. XopJ2b carries an acetyltransferase domain and the critical residues required for its activity, and the positions of these residues are predicted to be conserved in the 3D structure of the proteins. We demonstrated that XopJ2b is a functional T3E and triggers a hypersensitive response (HR) when translocated into pepper cells. Like XopJ2a, XopJ2b triggers HR in Arabidopsis that is suppressed by the deacetylase, SOBER1. We found xopJ2b in genome sequences of X. euvesicatoria, X. citri, X. guizotiae, and X. vasicola strains, suggesting widespread horizontal transfer. In X. perforans, xopJ2b was present in strains collected in North America, Africa, Asia, Australia, and Europe, whereas xopJ2a had a narrower geographic distribution. This study expands the Xanthomonas T3E repertoire, demonstrates functional conservation in T3E evolution, and further supports the importance of XopJ2 in X. perforans fitness on tomato. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .