bluuebunny/crossref_metadata_2025_split huggingface dataset:
Symbiosis of a lytic bacteriophage and
Yersinia pestis
and characteristics of plague in
Marmota himalayana
Authors: Lyu Dongyue , Duan Qun , Duan Ran , Qin Shuai , Zheng Xiaojin , Lu Xinmin , Bukai Asaiti , Zhang Peng , Han Haonan , He Zhaokai , Sha Hanyu , Wu Di , Xiao Meng , Jing Huaiqi , Wang Xin 
Published: July 2024

ABSTRACT

Surveillance for animal plague was conducted in the
Marmota himalayana
plague focus of the Qinghai–Tibet Plateau from 2020 to 2023. A 22.89% positive rate of serum F1 antibody was detected in live-caught marmots, alongside a 43.40% incidence of
Yersinia pestis
isolation from marmot carcasses. Marmot carcasses infected with plague exhibited a significantly higher spleen-somatic index (
P
< 0.05). Twenty-one
Y. pestis-
specific phages were isolated, among which one
Y. pestis
lytic phage (AKS2022HT87GU_phi) was isolated from the bone marrow of a marmot carcass (no. AKS2022HT87) and was found to be symbiotic with
Y. pestis
. Microscopy revealed the coexistence of lysed and non-lysed colonies of
Y. pestis
AKS2022HT87. Genome-wide analysis showed that certain strains of the
Y. pestis
AKS2022HT87 carried phage DNA fragments consistent with phage AKS2022HT87GU_phi. The rare symbiotic relationship between a lytic phage and
Y. pestis
observed
in vitro
was highlighted in this study, laying the basis for further exploring the relationship between
Y. pestis
and its bacteriophages.

IMPORTANCE

Bacteriophages and host bacteria commonly coexist
in vivo
or in soil environments through complex and interdependent microbial interactions. However, recapitulating this symbiotic state remains challenging
in vitro
due to limited medium nutrients. In this work, the natural symbiosis between
Yersinia pestis
and specific phages has been discovered in a
Marmota himalayana
specimen. Epidemiological analysis presented the characteristics of the
Y. pestis
and specific phages in the area with a strong plague epidemic. Crucially, comparative genomics has been conducted to analyze the genetic changes in both the
Y. pestis
and phages over different periods, revealing the dynamic and evolving nature of their symbiosis. These are the critical steps to study the mechanism of the symbiosis.
AcMNPV-miR-2 affects
Autographa californica
nucleopolyhedrovirus infection by regulating the expression of
ac28
and several other viral early genes
Authors: Yu Xinghua , Teng Tingkai , Duan Zhuowen , Wang Jinwen 
Published: July 2024

ABSTRACT

Virus-encoded microRNAs (miRNAs) exert diverse regulatory roles in the biological processes of both viruses and hosts. This study delves into the functions of AcMNPV-miR-2, an early miRNA encoded by
Autographa californica
multiple nucleopolyhedrovirus (AcMNPV). AcMNPV-miR-2 targets viral early genes
ac28
(
lef-6
),
ac37
(
lef-11
),
ac49
, and
ac63
. Overexpression of AcMNPV-miR-2 leads to reduced production of infectious budded virions (BVs) and diminished viral DNA replication. Delayed polyhedron formation was observed through light and transmission electron microscopy, and the larval lifespan extended in oral infection assays. Moreover, the mRNA expression levels of two Lepidoptera-specific immune-related proteins, Gloverin and Spod-11-tox, significantly decreased. These findings indicate that AcMNPV-miR-2 restrains viral load, reducing host immune sensitivity. This beneficial effect enables the virus to combat host defense mechanisms and reside within the host for an extended duration.

IMPORTANCE
Virus-encoded miRNAs have been extensively studied for their pivotal roles in finetuning viral infections. Baculoviruses, highly pathogenic in insects, remain underexplored concerning their encoded miRNAs. Previous reports outlined three AcMNPV-encoded miRNAs, AcMNPV-miR-1, -miR-3, and -miR-4. This study delves into the functions of another AcMNPV-encoded miRNA, AcMNPV-miR-2 (Ac-miR-2). Through a comprehensive analysis of target gene expression, the impact on larvae, and variations in host immune-related gene expression, we elucidate a functional pathway for Ac-miR-2. This miRNA suppresses viral load and infectivity and prolongs lifespans of infected larva by downregulating specific viral early genes and host immune-related genes. These mechanisms ultimately serve the virus's primary goal of enhanced propagation. Our study significantly contributes to understanding of the intricate regulatory mechanisms of virus-encoded miRNAs in baculovirus infections.
Comparison between patient characteristics, aetiology and outcomes in patients with and without cirrhosis with hepatocellular carcinoma diagnosed in a regional centre
Authors: Lamb Carly , Tham Jennifer , Goh Tee Lin , Barclay Stephen , Priest Matthew , Forrest Ewan H , Fraser Andrew , Kay David , Kasthuri Ram , Evans Jeff , Stanley Adrian J 
Published: July 2024

IntroductionHepatocellular carcinoma (HCC) is increasing in incidence across the UK. Most patients have underlying cirrhosis, but a significant minority do not. Progression and outcomes of HCC in patients without cirrhosis remains unclear.This study aimed to establish the proportion and characteristics of patients with HCC occurring in those with and without cirrhosis in the West of Scotland.MethodsData were collected from our prospectively collected database on patient demographics, liver disease aetiology, stage at presentation and outcomes for patients with a diagnosis of HCC confirmed at the Regional West of Scotland multidisciplinary team from 2009 to 2015.Results638 patients were included. 138 (21.6%) did not have cirrhosis and were older at diagnosis than those with cirrhosis (72 years vs 68 years, p=0.001). A higher proportion of those without cirrhosis presented with more advanced HCC (Barcelona clinic liver cancer (BCLC) score B or above; p=0.003).Patients with cirrhosis had median survival of 8 months, compared with those without cirrhosis (11.5 months) but survival was similar in both groups on Kaplan-Meier analysis (p=0.119). There was no difference in survival between these groups when adjusted for cancer stage.Survival was influenced by BCLC score in both cirrhotic and non-cirrhotic groups, as was survival by Child-Pugh score in patients with cirrhosis. Among the patients who underwent transarterial chemoembolisation (TACE), those with cirrhosis had worse survival (p=0.044).Conclusion21.6% of patients with a new diagnosis of HCC in our region did not have underlying cirrhosis. Patients with non-cirrhotic HCC were diagnosed at an older age, with more advanced stage of HCC. There was no difference in overall survival between patients with HCC with and without cirrhosis, however, survival after TACE was higher in those without cirrhosis.
Ocular protection practice and associated factors among welders in small-scale industries in Hosanna town, Southern Ethiopia, 2023
Authors: Birhan Getenet Shumet , Wossoro Henock Erkeno , Admassu Nebiyat Feleke , Eticha Biruk Lelisa 
Published: July 2024

PurposeGood eye protection is the most important factor in preventing eye injuries. Most eye injuries are due to the improper use or lack of use of eye protection equipment. Therefore, this study aims to assess eye protection practice and associated factors among welders in small-scale industries in Hosanna town of Southern Ethiopia.MethodsA cross-sectional study was conducted on 420 welders between 14 August and 14 September 2023. A structured questionnaire was used to collect the data entered into Epi-data V.4.6 and analysed using a statistical package for social science V.25.0. Descriptive statistics was used to describe the characteristics of study participants. Binary logistic regression analysis was carried out to identify factors associated with eye protection practice. Finally, the OR with a corresponding 95% CI was computed to show the strength of the association. A p value <0.05 was considered to declare statistical significance.ResultsA total of 420 study participants were included. Good eye protection practice was 43.6% (95% CI 43.41 to 43.79). Monthly income between 4000 and 8000 and above 8000 Ethiopian birr, knowledge (adjusted OR (AOR)=3.90, 95% CI 1.96 to 7.78), permanent work pattern (AOR=2.86, 95% CI 1.59 to 5.17), previous ocular trauma (AOR=3.09, 95% CI 1.53 to 6.22) were positively associated with good eye protection practice.ConclusionThe results of this study revealed poor eye protection practice among welders. Factors such as monthly income, previous ocular injury, work pattern and knowledge of eye Personal Protective Equipment were significantly associated with eye protection practice.
Risk assessment for perfluorooctanoic acid (PFOA) in air, blood serum and water: mortality from liver and kidney disease
Authors: Park Robert M 
Published: July 2024

BackgroundCancer and non-cancer associations have been observed with PFAS (perfluoroalkyl and polyfluoroalkyl) substances in the general population, in populations from locally contaminated environments and in exposed workers.MethodsA quantitative risk assessment on the PFAS substance perfluorooctanoic acid (PFOA) was conducted for six outcomes using two occupational mortality studies that reported sufficient data to estimate exposure-relationships in relation to serum PFOA levels. Excess lifetime mortality risks were calculated using a life table procedure that applies an exposure response to time-dependent PFOA serum levels for a surviving hypothetical population from ages 20 to 85. Both occupational and general population exposures were described as serum levels, and as air and drinking water concentrations.ResultsThe estimated occupational inhalation concentrations conferring the benchmark one-per-thousand lifetime risk were 0.21 µg/m3for chronic kidney disease, 1.0 µg/m3for kidney cancer and (from the two studies) 0.67 and 1.97 µg/m3for chronic liver disease. Specific excess lifetime risks estimated in the general population at current PFOA serum levels (~ 1 ng/mL) range 1.5–32 per 100 000 which corresponds to drinking water concentrations of less than 10 ppt.ConclusionOver eight outcome risk estimates, the serum PFOA concentrations conferring 1/1000 occupational lifetime risk ranged 44 to 416 ng/mL corresponding to air concentrations ranging 0.21 to 1.99 µg/m3. The analyses provide a preliminary PFOA quantitative risk assessment for liver and kidney disease mortality which, together with reported assessments for several other end-points, would inform policy on PFAS.
Social determinants of food insecurity experienced by Ecuadorian women during the COVID-19 pandemic of Summer 2020: an online survey at the individual level
Authors: Carpio Arias Tannia Valeria , Guijarro-Garvi Marta , Morejón-Terán Yadira Alejandra , Ruíz-Cantero María Teresa 
Published: July 2024

The COVID-19 pandemic has amplified concerns about food insecurity, prompting its investigation. An online pilot survey anonymously gathered responses from a non-probabilistic sample of 2058 Ecuadorian women. The Food and Agriculture Organization's Food Insecurity Experience Scale was used to measure moderate or severe food insecurity (MSFI). Data quality was assessed using the Rasch item response theory model; this is a single-parameter logistic model that considers food insecurity severity as a latent trait. The analysis produced MSFI prevalence rates with 90% confidence level margins of error (90%MoE). The highest MSFI was found in women: lacking resources for personal expenses (29.53%, 90%MoE = 3.21) compared to those who had them (12.47, 90%MoE = 1.40); who live in the Amazon region (21.37, 90%MoE = 4.24) versus those living in Highlands (17.66%, 90%MoE = 1.77) or in Coast (13.44%, 90%MoE = 2.40); with three or more children (20.97%, 90%MoE = 4.71) against those without children (12.63%, 90%MoE = 3.57); who experienced income reduction during confinement (18.31%, 90%MoE = 2) compared to those who did not (15.71%, 90%MoE = 1.85); and who are rural (18.13%, 90%MoE = 2.83) versus urban residents (16.63%, 90%MoE = 1.55). This study highlights that the most vulnerable Ecuadorian women experienced the highest food insecurity levels during lockdown, emphasizing the need to consider the intersection between income and sociodemographic factors and their impact on women's food insecurity in future research and policymaking.
Establishing Metrics to Encourage Broader Use of Atomic Requirements - A Call for Exchange and Experimentation
Authors: Honig William L. 
Published: July 2024

There are seemingly many advantages to being able to identify, document, test, and trace single or "atomic" requirements during system development and maintenance. Ongoing work with Agile development has focused on "user stories" that can capture individual features for implementation. However, it is still difficult to evaluate the quality of such requirements and teaching their creation is difficult.
Based on a working definition of atomic requirement, this paper proposes a set of metrics for their evaluation. Ten metrics designed to measure atomic requirements are presented here: five used on individual requirements statements and five applied to a requirements document or set of requirement statements.
Example metrics for individual requirements include Requirement Atomic Completeness and Requirement Atomic Verifiability. Requirement Traceability is a proposed metric for a set of atomic requirements (such as a traditional requirements specification document.)
Further work is needed to make the suggested metrics more consistent and precise, including exploring the use of tools that may automate some of the measures. However, a first step is to refine the metrics themselves and ensure they adequately measure atomic requirement quality.
Hence this note shares the proposed metrics to encourage discussion and to recommend experimentation. The author is applying the metrics in software engineering courses doing team software development.
The goal is the eventual acceptance of a set of requirements metrics specifically designed to evaluate atomic requirements. Better metric definitions may lead to wider utilization of atomic requirements and improved requirements engineering in general.
NAT10 Phase Separation Regulates YTHDF1 Splicing to Promote Gastric Cancer Progression
Authors: Liu Songyi , Lin Chunlin , Lin Xiang , Lin Penghang , He Ruofan , Pan Xiaoyu , Lin Yan , Ye Jianxin , Zhu Guangwei 
Published: July 2024

Abstract
Gastric cancer is an aggressive malignancy with poor patient outcomes. N-Acetyltransferase 10 (NAT10) is an acetyltransferase that has been reported to contribute to gastric cancer progression. In-depth investigation into the underlying molecular mechanisms driven by NAT10 could help identify therapeutic targets to improve gastric cancer treatment. In this study, we found that NAT10 forms condensates to regulate RNA dynamics and promote gastric cancer progression. In samples of patients with gastric cancer, elevated NAT10 expression correlated with an unfavorable prognosis, advanced disease stage, and metastasis. NAT10 enhanced the proliferation, migration, and invasion of gastric cancer cells; supported the growth of patient-derived organoids; and accelerated tumor development. A C-terminal intrinsically disordered region-mediated liquid–liquid phase separation of NAT10 and was essential for its tumor-promoting function in gastric cancer. Moreover, NAT10 interacted with the splicing factor serine/arginine-rich splicing factor 2 (SRSF2), leading to its acetylation and increased stability. Acetylated SRSF2 directly bound to the pre-mRNA of the m6A reader YTHDF1, resulting in enhanced YTHDF1 exon 4 skipping and upregulation of a short YTHDF1 transcript that could stimulate gastric cancer cell proliferation and migration. Furthermore, YTHDF1 exon 4 skipping correlated with NAT10 and SRSF2 expression and was associated with a more aggressive phenotype in samples of patients with gastric cancer. Together, this study uncovers the role of NAT10 liquid–liquid phase separation in modulating YTHDF1 splicing through SRSF2 acetylation to drive gastric cancer progression, providing insights into the oncogenic mechanism of NAT10.
Significance: Phase separation of NAT10 enables acetylation of SRSF2 that enhances YTHDF1 exon 4 skipping, which is a tumor-promoting axis in gastric cancer that represents potential therapeutic targets and prognostic biomarkers.
Transgender and Nonbinary Individuals’ Perceptions Regarding Gender-Affirming Hormone Therapy and Cardiovascular Health: A Qualitative Study
Authors: Rytz Chantal L. , Pattar Badal S.B. , Mizen Sara J. , Lieb Parker , Parsons Leigh Jeanna , Saad Nathalie , Dumanski Sandra M. , Beach Lauren B. , Marshall Zack , Newbert Amelia M. , Peace Lindsay , Ahmed Sofia B. 
Published: July 2024

BACKGROUND:
Transgender and nonbinary individuals face substantial cardiovascular health uncertainties. The use of gender-affirming hormone therapy can be used to achieve one’s gender-affirming goals. As self-rated health is an important predictor of health outcomes, an understanding of how this association is perceived by transgender and nonbinary individuals using gender-affirming hormone therapy is required. The objective of this research was to explore transgender and nonbinary individuals’ perceptions of cardiovascular health in the context of using gender-affirming hormone therapy.

METHODS:
In this qualitative study, English-speaking transgender and nonbinary adults using gender-affirming hormone therapy for 3 months or more were recruited from across Canada using purposive and snowball sampling methods. Semistructured interviews were conducted through videoconference to explore transgender and nonbinary individuals’ perceptions of the association between gender-affirming hormone therapy and cardiovascular health between May and August 2023. Data were transcribed verbatim, and transcripts were analyzed independently by 3 reviewers using thematic analysis.

RESULTS:
Twenty-one participants were interviewed (8 transgender women, 9 transgender men, and 3 nonbinary individuals; median [range] age, 27 [20–69] years; 80% White participants). Three main themes were identified: cardiovascular health was not a primary concern in the decision-making process with regard to gender-affirming hormone therapy, the improved well-being associated with gender-affirming hormone therapy was felt to contribute to improved cardiovascular health, and health care provider knowledge and attitude facilitate the transition process.

CONCLUSIONS:
Gender-affirming hormone therapy in transgender and nonbinary individuals is perceived to improve cardiovascular health. Given the positive associations between care aligned with patient priorities, self-rated health, and health outcomes, these findings should be considered as part of shared decision-making and person-centered care.
Supercooled large droplet size distribution effects on airfoil icing: A numerical investigation based on a new coupled Eulerian method
Authors: Guo Wei , Bian Qingyong , Zhu Chengxiang , Zhao Ning , Zhu Chunling 
Published: July 2024

Supercooled large droplets (SLDs) under natural icing conditions have the characteristics of easy deformation in motion and easy splashing on impact, and a bimodal droplet size distribution that has received less attention. The modified form of the Rosin-Rammler function was improved to achieve a more accurate nonlinear fitting of the SLD distribution curve. The droplet size distribution was divided into non-equipartition continuous multiple components. The drag source term of each component was coupled with the overall droplet size distribution, and the Eulerian equations of each component of SLDs were solved simultaneously. A new coupled Eulerian method for non-equipartition continuous multi-size droplets was proposed to simulate the impact characteristics of SLDs, and the SLD collection coefficients were validated. Effects of the ratio between the number of large and small droplet components and the number of all components on the simulation results were investigated to select a better combination based on stable convergence calculation steps and the calculation time. This new method was added to the multi-step icing numerical method, and the accuracy and robustness of the method in icing shape prediction were verified based on the freezing drizzle, median volume diameter < 40 μm (FZDZ, MVD < 40 μm) icing condition. Airfoil icing characteristics based on the bimodal and monomodal distribution were compared, and the icing shapes at the leading edge were similar. Still, the upper and lower limits of the icing shapes with the bimodal distribution were nearer to the trailing edge and the ice layer was thicker there.
Impact of patient demographics on treatment outcomes in AML: a population-based registry in England, 2013-2020
Authors: Liu Hanhua , Stanworth Simon J. , McPhail Sean , Bishton Mark , Rous Brian , Bacon Andrew , Coats Thomas 
Published: July 2024

Abstract
We report 1- and 5-year survival after acute myeloid leukemia (AML) diagnosis and early mortality within 30 days of systemic anticancer therapy (SACT) treatments, using national cancer registry data in England. Patients aged 18 to 99 years diagnosed between 2013 and 2020 were included. Overall survival (OS) was calculated using Kaplan-Meier methodology, and adjusted hazard ratios (aHRs; adjusted for intensity of treatment, age at diagnosis, sex, ethnicity, socioeconomic deprivation, comorbidity, and year of diagnosis) using Cox proportional hazards regression. Odds of 30-day mortality (adjusted odds ratios [aORs], adjusted for aforementioned characteristics), along with performance status and body mass index, were calculated using logistic regression. Among 17 107 patients identified, older age and comorbidity were associated with worse survival. Asian and Black patients had better survival than White patients: 5-year OS of 34.6%, 29.7%, and 17.8%, respectively; aHR of 0.86; (95% confidence interval [CI], 0.77-0.96) Asian vs White, and 0.84 (95% CI, 0.73-0.96) Black vs White. Socioeconomic deprivation was associated with worse survival. Overall, 7906 (46.2%) patients were documented as having received SACT. Thirty-day mortality was lower for patients receiving intensive rather than nonintensive SACT. After adjustment for cofactors, the risk was higher in those treated intensively (aOR, 0.74; 95% CI, 0.60-0.92). We show that ethnicity and socioeconomic status affects outcomes in AML. Further work is needed to understand how these effects may differ in different health care settings, and whether this because of effects on disease biology, responsiveness to treatment, or drug toxicity. Selection of intensive vs nonintensive treatment should be based on individual patient factors, balancing improved long-term survival against higher early mortality.