bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trends and disparities in cardiovascular disease–related mortality among adults with myeloproliferative neoplasms in USA
Authors: Agarwal Siddharth , Qamar Usama , Khan Muhammad Shahzeb , Al-Juhaishi Taha , Naqash Abdul Rafeh , Guha Avirup , Yang Eric H , Barac Ana , Ul Abideen Asad Zain 
Published: December 2024

Abstract

Aims
We aimed to perform a retrospective cohort study using the Centers for Disease Control and Prevention’s (CDC’s) Wide-Ranging Online Data for Epidemiologic Research (WONDER) database to analyse the trends in cardiovascular disease (CVD)–related mortality in patients with myeloproliferative neoplasms (MPNs) from 1999 to 2020.

Methods and results
We analysed the death certificate data from the CDC WONDER database from 1999 to 2020 for CVD with co-morbid myeloproliferative disorders in the US population. Age-adjusted mortality rates (AAMRs) and 95% confidence intervals (CIs) were computed per 1 million population by standardizing crude mortality rates to the 2000 US census population. To assess annual national mortality trends, we employed the Joinpoint regression model, calculating the annual per cent change in AAMR and corresponding 95% CIs. A total of 15 269 deaths related to CVD occurred in patients with co-morbid MPNs from 1999 to 2020. Overall, there was a decreasing trend in CVD-related AAMRs throughout these years. Males contributed to 51% of total deaths, and their AAMR was persistently higher than women throughout the study. Non-Hispanic (NH) Whites had the highest overall AAMR, followed by NH Blacks, NH American Indians or Alaska Natives, Hispanics or Latinos, and NH Asian or Pacific Islanders.

Conclusion
Our findings indicate a significant decline with notable gender, racial/ethnic, and regional differences in CVD-related mortality among patients with MPN over the past two decades. We emphasize the importance of a collaborative approach between oncologists and cardiologists in managing these patients, highlighting the potential benefits of integrating cardio-oncology services to enhance patient outcomes.
Extensive environmental survey of free-living amoebae and their elusive association with Mycobacterium bovis or Mycobacterium avium subsp. paratuberculosis
Authors: Jessu Amélie , Cochard Thierry , Burtin Mélanie , Crapart Stéphanie , Delafont Vincent , Samba-Louaka Ascel , Biet Franck , Moyen Jean-Louis , Héchard Yann 
Published: December 2024

Abstract
Free-living amoebae (FLA) are described as environmental reservoirs for some bacteria able to resist their phagocytosis. In the environment, the fate of Mycobacterium bovis (Mbo) and Mycobacterium avium subsp. paratuberculosis (Map) responsible for bovine tuberculosis and paratuberculosis, respectively, remains poorly understood and is considered potentially problematic in the eradication and control of these diseases. We hypothesize that FLA may play a role in the persistence of Mbo and Map in the environment. In this study, 90 samples were collected from herds affected by one or both diseases to investigate the diversity of amoeba and their associated bacteria. Metabarcoding analyses revealed that Acanthamoeba, Copromyxa, Naegleria, and Vermamoeba were the most represented genera of FLA, with Pseudomonadota being the bacteria most commonly found associated with FLA. Although no Mbo and Map DNA were identified by sequencing, traces were detected by ddPCR (digital droplet PCR), specifically targeting these bacteria. In conclusion, we described a wide diversity of FLA and associated bacteria in this environment. It also suggests that Map and Mbo could be associated, even weakly, with FLA in the environment. However, this needs to be confirmed by detecting a highest amount of DNA and, if possible, cultivable Map and/or Mbo associated with these environmental FLA.
Near telomere-to-telomere genome assembly of Mongolian cattle: implications for population genetic variation and beef quality
Authors: Su Rina , Zhou Hao , Yang Wenhao , Moqir Sorgog , Ritu Xiji , Liu Lei , Shi Ying , Dong Ai , Bayier Menghe , Letu Yibu , Manxi Xin , Chulu Hasi , Nasenochir Narenhua , Meng He , Herrid Muren 
Published: December 2024

Abstract

Background
Mongolian cattle, a unique breed indigenous to China, represent valuable genetic resources and serve as important sources of meat and milk. However, there is a lack of high-quality genomes in cattle, which limits biological research and breeding improvement.

Findings
In this study, we conducted whole-genome sequencing on a Mongolian bull. This effort yielded a 3.1 Gb Mongolian cattle genome sequence, with a BUSCO integrity assessment of 95.9%. The assembly achieved both contig N50 and scaffold N50 values of 110.9 Mb, with only 3 gaps identified across the entire genome. Additionally, we successfully assembled the Y chromosome among the 31 chromosomes. Notably, 3 chromosomes were identified as having telomeres at both ends. The annotation data include 54.31% repetitive sequences and 29,794 coding genes. Furthermore, a population genetic variation analysis was conducted on 332 individuals from 56 breeds, through which we identified variant loci and potentially discovered genes associated with the formation of marbling patterns in beef, predominantly located on chromosome 12.

Conclusions
This study produced a genome with high continuity, completeness, and accuracy, marking the first assembly and annotation of a near telomere-to-telomere genome in cattle. Based on this, we generated a variant database comprising 332 individuals. The assembly of the genome and the analysis of population variants provide significant insights into cattle evolution and enhance our understanding of breeding selection.
A dataset profiling the multiomic landscape of the prefrontal cortex in amyotrophic lateral sclerosis
Authors: Hausmann Fabian , Caldi Gomes Lucas , Hänzelmann Sonja , Khatri Robin , Oller Sergio , Gebelin Marie , Parvaz Mojan , Tzeplaeff Laura , Pasetto Laura , Zhou Qihui , Zelina Pavol , Edbauer Dieter , Pasterkamp R Jeroen , Rehrauer Hubert , Schlapbach Ralph , Carapito Christine , Bonetto Valentina , Bonn Stefan , Lingor Paul 
Published: December 2024

Abstract
Amyotrophic lateral sclerosis (ALS) is the most common motor neuron disease, which still lacks effective disease-modifying therapies. Similar to other neurodegenerative disorders, such as Alzheimer and Parkinson disease, ALS pathology is presumed to propagate over time, originating from the motor cortex and spreading to other cortical regions. Exploring early disease stages is crucial to understand the causative molecular changes underlying the pathology. For this, we sampled human postmortem prefrontal cortex (PFC) tissue from Brodmann area 6, an area that exhibits only moderate pathology at the time of death, and performed a multiomic analysis of 51 patients with sporadic ALS and 50 control subjects. To compare sporadic disease to genetic ALS, we additionally analyzed PFC tissue from 4 transgenic ALS mouse models (C9orf72-, SOD1-, TDP-43-, and FUS-ALS) using the same methods. This multiomic data resource includes transcriptome, small RNAome, and proteome data from female and male samples, aimed at elucidating early and sex-specific ALS mechanisms, biomarkers, and drug targets.
Patterns and Cofactors of Polyfunctional Mycobacteria-Specific T-Cell Response Restoration Following 6-Month Antiretroviral Treatment in Children With HIV
Authors: Day Cheryl L , Njuguna Irene N , Cranmer Lisa Marie , Whatney Wendy E , Pearson Rachel A , Lindestam Arlehamn Cecilia S , Sette Alessandro , LaCourse Sylvia M , Escudero Jaclyn N , Sasser Loren E , Mugo Cyrus , Okinyi Hellen Moraa , Maleche-Obimbo Elizabeth , Wamalwa Dalton C , John-Stewart Grace C 
Published: December 2024

Abstract

Background
Despite immune restoration after initiation of antiretroviral treatment (ART), the risk of tuberculosis (TB) persists in children with HIV (CHIV). We determined patterns of immune restoration of mycobacteria-specific T cells following ART in CHIV.

Methods
CD4 and CD8 T-cell activation and memory phenotype and functional profiles before and 6 months after ART were evaluated in peripheral blood mononuclear cells from CHIV enrolled in the PUSH study (NCT02063880) in Nairobi, Kenya. T-cell expression of cytokines and activation-induced markers were measured following stimulation of peripheral blood mononuclear cells with a pool of 300 peptides from TB (MTB300) or staphylococcal enterotoxin B.

Results
Among 47 CHIV (median age, 1.5 years), staphylococcal enterotoxin B–induced Th1 cytokine+ and activation-induced marker+ CD4 cell frequencies increased significantly after 6 months of ART. Although MTB300-specific CD4 and CD8 cell frequency did not increase after ART, polyfunctional capacity of MTB300-specific CD4 cells expressing combinations of Th1 cytokines with CD40L increased significantly after ART. Baseline age, immune activation, and effector memory CD4 levels were associated with less restoration of MTB300-specific polyfunctional CD4 cells, whereas CD4 percentage and levels of naive CD4 cells following ART were associated with improved MTB300-specific polyfunctional capacity.

Conclusions
Despite increases in Th1 cytokine production, deficits in mycobacteria-specific CD4 cells persisted 6 months after ART, with higher deficits in older CHIV with more immunosuppression, higher immune activation, and lower proportion of naive CD4 cells. These findings may explain persistent TB risk during early ART among CHIV and identify those at highest risk.
Candida albicans Recovered From Persistent Candidemia Exhibits Enhanced Virulence Traits
Authors: Ribeiro Felipe de Camargo , Kemmerich Karoline Kristina , Gonçale Juliana Caparroz , Junqueira Juliana Campos , Mannan Mohammad , Nabeela Sunna , Colombo Arnaldo Lopes , Uppuluri Priya 
Published: December 2024

Abstract
Candida albicans catheter-related candidemia is largely driven by microbial adhesion and biofilm formation on central venous catheters. Cells that disperse from these biofilms can enter the bloodstream, spread to distant organs, and sustain the cycle of infection. In this study, we investigated the virulence potential of C. albicans isolates obtained from the blood of catheterized patients experiencing persistent candidemia, comparing them to isolates that were cleared from the bloodstream early in the infection. Our results show that isolates persisting in the bloodstream for 4 days or longer, despite antifungal treatment, exhibited enhanced adherence, filamentation, and biofilm formation in vitro, along with increased expression of key virulence-related genes. Notably, cells dispersed from second-generation biofilms formed by these persistent isolates displayed even more pronounced pathogenic characteristics, including improved immune evasion. Furthermore, in vivo experiments using Galleria mellonella revealed that persistent isolates were significantly more virulent than their nonpersistent counterparts.
A systematic review and individual bacterial species level meta-analysis of in vitro studies on the efficacy of ceftazidime/avibactam combined with other antimicrobials against carbapenem-resistant Gram-negative bacteria
Authors: Assefa Getnet M , Roberts Jason A , Aslan Abdullah T , Mohammed Solomon A , Sime Fekade B 
Published: December 2024

Abstract

Background
Carbapenem-resistant Gram-negative bacteria (CR-GNB) develop resistance to many antimicrobials. To effectively manage infections caused by these organisms, novel agents and/or combinations of antimicrobials are required.

Objectives
Evaluated the in vitro efficacy of ceftazidime/avibactam in combination with other antimicrobials against CR-GNB.

Methods
PubMed, Web of Science, Embase and Scopus were searched. Study outcomes were quantified by counting the number of isolates exhibiting synergy, defined as a fractional inhibitory concentration index ≤ 0.5 for checkerboard and Etest, and a &gt;2 log cfu/mL reduction for time-kill studies. The proportion of synergy was calculated as the ratio of isolates exhibiting synergy to the total number of isolates tested. These proportions were analysed using a random-effects model, following the Freeman–Tukey double-arcsine transformation.

Results
Forty-five in vitro studies were included. A total of 734 isolates were tested, and 69.3% of them were resistant to ceftazidime/avibactam. The combination of ceftazidime/avibactam with aztreonam showed a high synergy rate against carbapenem-resistant Klebsiella pneumoniae (effect size, ES = 0.91–0.98) and Escherichia coli (ES = 0.75–1.00). Ceftazidime/avibactam also demonstrated a high synergy rate (ES = 1) in time-kill studies when combined with azithromycin, fosfomycin and gentamicin against K. pneumoniae. Compared to ceftazidime/avibactam alone, a higher bactericidal rate was reported when ceftazidime/avibactam was combined with other antimicrobials against carbapenem-resistant K. pneumoniae (57% versus 31%) and E. coli (93% versus 0%).

Conclusions
Ceftazidime/avibactam frequently demonstrates synergistic bactericidal activity when combined with various antimicrobials against CR-GNB in in vitro tests. Further pre-clinical and clinical studies are warranted to validate the utility of ceftazidime/avibactam-based combination regimens for CR-GNB infections.
Leveraging local public health to advance antimicrobial stewardship (AMS) implementation and mitigate antimicrobial resistance (AMR): a scoping review
Authors: Leung Valerie , Ashiru-Oredope Diane , Hicks Lauri , Kabbani Sarah , Aloosh Mehdi , Armstrong Irene E , Brown Kevin A , Daneman Nick , Lam Kevin , Meghani Hamidah , Nur Mahad , Schwartz Kevin L , Langford Bradley J 
Published: December 2024

Abstract

Objective
To explore the role of local public health organisations in antimicrobial stewardship (AMS) and antimicrobial resistance (AMR) surveillance.

Methods
A scoping review was conducted. Peer-reviewed and grey literature from countries within the organisation for economic co-operation and development was searched between 1999 and 2023 using the concepts of local public health, AMR and AMS. Thematic analysis was performed to identify themes.

Results
There were 63 citations illustrating 122 examples of AMS and AMR surveillance activities with local public health involvement. Common AMS activities (n = 105) included healthcare worker education (n = 22), antimicrobial use (AMU) evaluation (n = 21), patient/public education (n = 17), clinical practice guidelines (n = 10), and antibiograms (n = 10). Seventeen citations described local public health activities in AMR surveillance; the majority focussed on communicable diseases (n = 11) and/or AMR organisms (n = 6).

Conclusions
Local public health capabilities should be leveraged to advance high-impact activities to mitigate AMR, particularly in the areas of knowledge translation/mobilisation, optimising surveillance and establishing strategic collaborations.

Policy implications
Future work should focus on better understanding barriers and facilitators, including funding, to local public health participation in these activities.
‘Some patients demand for a prescription of an antibiotic’: an assessment of barriers and facilitators to rational antimicrobial use in a private health facility in Uganda
Authors: Kizito Mark , Lalitha Rejani , Kajumbula Henry , Muhumuza Richard , Kintu Moses Grace , Muyanja David , Byakika-Kibwika Pauline 
Published: December 2024

Abstract

Background
Antimicrobial misuse and overuse propagate antimicrobial resistance, yet data on factors influencing antibiotic prescription decisions in low-resource settings are limited. We describe factors influencing antimicrobial prescription at a large tertiary care private not-for-profit hospital in Uganda.

Methods
We conducted a descriptive phenomenology qualitative study involving face-to-face in-depth interviews of 12 purposively selected prescribers (four intern doctors, six medical officers and two Internal Medicine physicians) in a private not-for-profit hospital in Kampala, Uganda. Audio recordings and filed notes were transcribed verbatim and analysed manually by content analysis. Emerging themes and sub-themes were recorded and reported.

Results
Three broad themes emerged: experience with antimicrobial use in Uganda, barriers and facilitators to rational antimicrobial prescription and measures to address irrational antimicrobial use. Participants recognized that antibiotics are often used irrationally, prescribed even when there is uncertainty regarding clinical evidence for infection, and influenced by drug promoters, and noted high levels of antibiotic resistance. Patients’ symptoms and clinical signs, previous experience using antibiotics, fear of bad outcomes, patient demand and expectations, influence from senior colleagues, the turnaround time of clinical investigations and drug marketers were the barriers and facilitators to antimicrobial prescription. Prescribers also acknowledged the need to update clinical guidelines, set up hospital antibiograms, and provide continuous medical education on rational antimicrobial use.

Conclusions
A complex interplay of intrinsic and extrinsic factors influences antibiotic prescribing decisions in this hospital. Targeted interventions through continuous education and training for prescribers, providing local prescription guidelines and antibiograms and implementing regulations on over-the-counter antibiotic sales are needed to implement robust antimicrobial stewardship programmes to curb antimicrobial resistance successfully.
Short-term outcomes of periacetabular osteotomy versus periacetabular osteotomy with concomitant femoral osteochondroplasty: a propensity matched analysis
Authors: Houlihan Nathan V , Sucato Daniel J , Thornton Tanner , Nepple Jeffrey J , Clohisy John C , Sankar Wudbhav N 
Published: December 2024

Abstract
This study compared outcomes of periacetabular osteotomy (PAO) with and without femoral osteochondroplasty (OCP) in treating symptomatic acetabular dysplasia through propensity score matching. Data from a prospective multicenter cohort of patients undergoing PAO from 2007 to 2014 were analyzed. Inclusion criteria were a lateral center edge angle &lt;25°. The exclusion criteria were history of previous procedure and age &gt;45 years. A 2- to 5-year follow-up interval was utilized; patients outside this follow-up window were excluded. Propensity matching variables included sex, baseline hip internal rotation at 90° flexion, preoperative alpha angle, lateral center edge angle, modified Harris Hip score (mHHS), and arthroscopy at the time of surgery. Propensity scores were calculated using logistic regression with treatment as the dependent variable. Clinical failure was defined as failure to meet the minimal clinically important difference and patient acceptable symptom state for mHHS or a need for reoperation. There were 219 patients that met the inclusion criteria. Of these, 116 patients were matched, representing 58 pairs (PAO/OCP = 58; PAO without OCP = 58). Preoperative functional scores were similar between groups. At mean 4.1 years follow-up, there were no significant differences in the rates of clinical failure or reoperation between the two groups [PAO/OCP = 13 (22%), PAO without OCP = 8 (14%); P = .23] Similarly, the final mHHS was 83.2 ± 16.2 for the PAO/OCP group and 84.1 ± 15.9 for the isolated PAO group, with no significant difference (P = .74). In the treatment of symptomatic acetabular dysplasia, isolated PAO is noninferior to combined PAO/OCP at short-term follow-up in patients who are likely to be treated by either method.
The spatiotemporal patterns of the beet webworm (Lepidoptera: Crambidae) in China and possible dynamics under future climate scenarios
Authors: Zhang Jinping , Yang Qin , Zhao Zhengxue , Yu Xiaofei , Wei Jianzhou , Cheng Hua , Zhao Xuechun , Yang Maofa , Jin Baocheng 
Published: December 2024

Abstract
The beet webworm (BWW), Loxostege sticticalis (L.), is a notorious migratory agriculture pest of crops and fodder plants, inducing sudden outbreaks and huge losses of food and forage production. Quantifying its spatiotemporal patterns and possible dynamics under future climate scenarios may have significant implications for management policies and practices against this destructive agriculture pest. In this paper, a database containing nearly 7,000 occurrence records for the spatiotemporal distribution of BWW in China was established and its possible dynamics under future climate scenarios predicted using Maxent. We found that BWW could affect a vast geographic range of Northern China, about one third of the country’s land area. The beet webworm overwintered in most of its distribution regions. Maxent model found a northward movement and distribution reduction for BWW in China under future climate scenarios. The occurrence and overwintering regions will move northward about 0.3°N–0.9°N under warming climate scenarios, and about 40%–70% of the suitable habitat and overwintering habitat will disappear by 2100. Most of the northward movement and suitable area reduction likely will happen in 2 decades. Given the vast affected area, the abrupt outbreaks, the diverse host plants, the sensitivity to climate change, as well as their long-distance migration capacity, global scale research, and monitoring the population dynamics of BWW are essential for developing effective management strategies and mitigating its impact on agriculture and ecosystems.
Physical activity and incident cardiovascular disease in breast cancer survivors: the Pathways Study
Authors: Kresovich Jacob K , Richards Alicia R , Ergas Isaac J , Cannioto Rikki , Thomsen Catherine , Laurent Cecile A , Shariff-Marco Salma , Rillamas-Sun Eileen , Kolevska Tatjana , Yao Song , Ambrosone Christine , Kushi Lawrence , Greenlee Heather , Kwan Marilyn L 
Published: December 2024

Abstract

Background
Breast cancer survivors experience higher rates of cardiovascular disease (CVD) than women without breast cancer, due in part to cardiotoxic cancer treatments and shared lifestyle risk factors. Physical activity is associated with lower mortality risk in breast cancer survivors, but associations with CVD have not been examined in detail.

Methods
The Pathways Study is a prospective cohort study of 4504 women diagnosed with invasive breast cancer between 2005 and 2013. At enrollment, women self-reported their physical activities during the previous 6 months, which were dichotomized as meeting the Centers for Disease Control and Prevention’s Physical Activity Guidelines for Americans (≥150 minutes of moderate-intensity or ≥75 minutes of vigorous-intensity activity per week) vs not. Incident CVD events (heart failure, cardiomyopathy, cardiac arrest, ischemic heart disease, stroke) occurring between enrollment and December 2021 were identified from electronic health records. Covariate-adjusted, competing-risks Cox regression models estimated associations between meeting physical activity guidelines and CVD risk.

Results
Compared with women who did not meet physical activity guidelines at their diagnosis, those who did had a 25% lower risk of CVD (HR = 0.75, 95% CI = 0.60 to 0.94). Among the individual CVD outcomes, meeting physical activity guidelines was protective against incident cardiomyopathy (hazard ratio [HR] = 0.54, 95% CI = 0.31 to 0.95), heart failure (HR = 0.66, 95% CI = 0.50 to 0.87), and cardiac arrest (HR = 0.68, 95% CI = 0.49 to 0.99).

Conclusions
Meeting physical activity guidelines at breast cancer diagnosis was associated with lower risk of CVD after diagnosis. Studies investigating changes in physical activity after a breast cancer diagnosis and CVD risk are warranted.