bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization and trans-generation dynamics of mitogene pool in the silver carp (Hypophthalmichthys molitrix)
Authors: Li Jinlin , Wu Hengshu , Zhou Yingna , Liu Manhong , Zhou Yongheng , Chu Jianing , Kamili Elizabeth , Wang Wenhui , Yang Jincheng , Lin Lijun , Zhang Qi , Yang Shuhui , Xu Yanchun 
Published: June 2024

Abstract
Multicopied mitogenome are prone to mutation during replication often resulting in heteroplasmy. The derived variants in a cell, organ, or an individual animal constitute a mitogene pool. The individual mitogene pool is initiated by a small fraction of the egg mitogene pool. However, the characteristics and relationship between them has not yet been investigated. This study quantitatively analyzed the heteroplasmy landscape, genetic loads, and selection strength of the mitogene pool of egg and hatchling in the silver carp (Hypophthalmichthys molitrix) using high-throughput resequencing. The results showed heteroplasmic sites distribute across the whole mitogenome in both eggs and hatchlings. The dominant substitution was Transversion in eggs and Transition in hatching accounting for 95.23%±2.07% and 85.38%±6.94% of total HP sites, respectively. The total genetic loads were 0.293±0.044 in eggs and 0.228±0.022 in hatchlings (P=0.048). The dN/dS ratio was 58.03±38.98 for eggs and 9.44±3.93 for hatchlings (P=0.037). These results suggest that the mitogenomes were under strong positive selection in eggs with tolerance to variants with deleterious effects, while the selection was positive but much weaker in hatchlings showing marked quality control. Based on these findings, we proposed a trans-generation dynamics model to explain differential development mode of the two mitogene pool between oocyte maturation and ontogenesis of offspring. This study sheds light on significance of mitogene pool for persistence of populations and subsequent integration in ecological studies and conservation practices.
High Polymorphism Levels of De Novo ORFs in a Yoruba Human Population
Authors: Vara Covadonga , Montañés José Carlos , Albà M Mar 
Published: June 2024

Abstract
During evolution, new open reading frames (ORFs) with the potential to give rise to novel proteins continuously emerge. A recent compilation of noncanonical ORFs with translation signatures in humans has identified thousands of cases with a putative de novo origin. However, it is not known which is their distribution in the population. Are they universally translated? Here, we use ribosome profiling data from 65 lymphoblastoid cell lines from individuals of Yoruba origin to investigate this question. We identify 2,587 de novo ORFs translated in at least one of the cell lines. In line with their de novo origin, the encoded proteins tend to be smaller than 100 amino acids and encode positively charged proteins. We observe that the de novo ORFs are more polymorphic in the population than the set of canonical proteins, with a substantial fraction of them being translated in only some of the cell lines. Remarkably, this difference remains significant after controlling for differences in the translation levels. These results suggest that variations in the level translation of de novo ORFs could be a relevant source of intraspecies phenotypic diversity in humans.
Clinical Characteristics of Older Adults Living in Foster Families in the French West Indies: Baseline Screening of the KArukera Study of Aging in Foster Families (KASAF) Cohort
Authors: Boucaud-Maitre Denis , Villeneuve Roxane , Rambhojan Christine , Simo-Tabué Nadine , Thibault Nathalie , Rinaldo Leila , Dartigues Jean-François , Dramé Moustapha , Amieva Hélène , Tabué-Teguo Maturin 
Published: June 2024

Abstract

Background and Objectives
Foster families for older adults could represent a transitional or alternative model to nursing homes. The aim of this study was to describe the clinical characteristics of older adults in foster families and to compare them with those of residents in nursing homes in French West Indies.

Research Design and Methods
This study is a cross-sectional analysis of the KArukera Study of Aging in Foster Families (KASAF) cohort. Sociodemographic and clinical characteristics were extracted. Dependency was assessed using the Activities of Daily Living (ADL) scale and cognition using the Mini-Mental State Examination (MMSE) scale. Age, gender, ADL, and MMSE scores were compared with nursing home residents from a twin study of KASAF (n = 332).

Results
A total of 107 older adults (mean age 81.8 years; 61.7% women) were recruited in 56 foster families between September 2020 and May 2021. In all, 25.5% had diabetes mellitus and 45.8% suffered from hypertension. The mean MMSE score was 9.3 ± 10.1 and 76.0% had major cognitive impairment (MMSE score &lt;18); 12.5% were diagnosed with Parkinson’s disease, and 42.0% of the residents were confined to bed or in a wheelchair, with a mean ADL score of 1.5 ± 1.8. Almost all the residents (96.3%) benefited from a medical follow-up by a nurse who visited once or twice a day. Compared to older adults living in nursing homes, those in foster families were more frequently women (61.7% vs 49.4%) and had lower ADL score (1.5 vs 2.4) and lower MMSE score (9.3 vs 11.3).

Discussion and Implications
The clinical profile of foster families’ residents was quite similar to that of nursing home residents in terms of demographics, dementia, and dependency. Foster families might represent an interesting strategy to address the unmet clinical and social needs of dependent older adults, especially in countries where nursing homes are not sufficiently developed.

Clinical Trials Registration Number
NCT04545775
The Copyright Amendment Bill: A New Vista for Fair Remuneration for South African Creators and Performers?
Authors: Oriakhogba Desmond O , Erhagbe Eunice O 
Published: June 2024

Abstract
The South African Copyright Amendment Bill (CAB) was passed by parliament on 29 February 2024. From the formal commencement of the legislative process for the enactment of the CAB, by way of its introduction to parliament in 2017 to its eventual passage and afterwards, there has been very serious debate about whether or not the CAB will live up to the objectives it is formulated to achieve. The debate has mainly been centred around the limitations and exceptions the CAB seeks to introduce into the copyright regime in South Africa. This debate has the effect of blurring other key proposals in the CAB that are geared towards ensuring and promoting fair remuneration for creators and performers in South Africa’s creative industries. Building on previous work and based on desk research, this report undertakes an in-depth analysis of key clauses in the CAB relating to equitable remuneration and fair royalty, reversionary right, licensing of orphan works, artist resale royalty and regulation of collective management organisations (CMOs) in order to illuminate and ignite debate on the CAB’s proposals aimed at ensuring fair remuneration for South African creators and performers.
Incorporation of observation uncertainty in stock assessment using spatio-temporal modeling of catch-at-length and age-at-length survey data
Authors: Breivik Olav Nikolai , Zimmermann Fabian , Johannesen Edda , Ono Kotaro , Fall Johanna , Howell Daniel , Nielsen Anders 
Published: June 2024

Abstract
Spatio-temporal models are essential tools for estimating abundance indices and quantifying the associated uncertainty. Time series of index uncertainties can be used to objectively determine the influence each index has on the assessment. This can involve reducing the influence of indices in years with limited data. However, incorporating uncertainty in age-length conversion into assessment models has remained a challenge. In this research, we propose an index estimation approach that combines an abundance-at-length model with a model for age-at-length to generate age-specific abundance indices. By jointly modeling abundance-at-length and age-at-length, we address uncertainties in both components of the index-at-age. Using North East Arctic haddock (Melanogrammus aeglefinus) as a case study, we validate the uncertainty of the indices by integrating them into the state space assessment model SAM. The results indicate that the uncertainty estimates are realistic, and we further demonstrate that incorporating uncertainty in age conversion has effects on the assessment results. Our case study demonstrates that incorporating the uncertainty in age-at-length data improves the characterization of uncertainty in stock assessment, and hence better accounts for risk in precautionary management.
Restorative benefits of classroom windows: a study on the effect of window:wall ratio on task load and learning performance based on VR technology
Authors: Zhang Yalin , Jing Xiaotong , Liu Chao , Sun Yinan , Wang Wenhao , Gao Weijun 
Published: June 2024

Abstract
As a connection to the outdoor environment, windows can relieve the stress, emotional, and cognitive fatigue that building users face from long hours of study. It provides restorative function for building users between study and work, thus reducing task load and improving learning performance. To investigate the effects of different window:wall ratios (WWRs) on task load and learning performance, virtual reality (VR) technology was used to build virtual classrooms with WWRs of 25%, 40%, 55%, 70%, and 85%. The task performances, physiological data, and subjective evaluations of 34 college studies were analyzed. It was found that the highest subjective psychological loads were in classrooms with a 25% WWR and were lowest when the WWR was 55%. Participants performed best in classrooms with a WWR of 55%. Further multiobjective optimization with particle swarm optimization found that 58.41–62.24% WWR not only contributed to the users’ physical and mental happiness but also improved their learning efficiency. In addition, the participant’s HRV-LF/HF and EEG β wave values were significantly correlated with their performance on the task test. These findings provide a reference for the spatial design of school classrooms and a foundation for further research into the relationship between HRV and EEG physiological indicators and learning efficiency.
Quality of life, clinical outcomes and cost utilization of endoscopic therapy in patients with Barrett’s esophagus and early esophageal cancer—an 8-year Canadian experience
Authors: David Joel , Woo Matthew , Congly Stephen , Andrews Christopher N , Jeyalingam Thurarshen , Belletrutti Paul J , Gupta Milli 
Published: June 2024

Abstract

Background and Aims
Endoscopic treatment is a definitive and cost-effective management strategy for early neoplasia in Barrett’s oesophagus (BE). However, little is known of its impact on quality of life (QoL). This study reports outcomes of endoscopic eradication treatment (EET), focusing on QoL and costs in a Canadian tertiary referral centre.

Methods
A retrospective cohort study using a prospectively maintained clinical database captured validated QoL metrics during and at the end of EET, risk factors for BE, treatment response, complications, costs, and follow-up response of all treated Barrett patients in Calgary and Southern Alberta, Canada.

Results
A total of 147 BE patients were treated from 2013 to 2021. All patients showed significant improvement in almost all QoL parameters except depression. There was significant improvement in 7 of the 8 QoL metrics in those who achieved complete eradication of intestinal metaplasia (CEIM). EET was successful in achieving complete eradication of dysplasia (CED) and CEIM in 93.4% and 74.3% of patients, respectively, with a median of 3 radio frequency ablation treatments. Longer circumferential segments of BE (Cx) predicted a lower likelihood of achieving CEIM. The average total cost to achieve CED and CEIM were $10 414.58 and $9347.93CAD, respectively (compared to oesophagectomy estimated at $58 332.30 CAD).

Conclusion
This Canadian cohort reports significant post-treatment improvement in QoL parameters in patients treated to CEIM or CED over an 8-year period. EET for BE eradication is cost-effective compared to oesophagectomy. There was a low rate of complications and recurrence post-CEIM.
Associations between early changes in the neutrophil-to-lymphocyte ratio after radical nephroureterectomy and treatment outcomes
Authors: Saito Shun , Takahashi Hidetsugu , Yata Yuji , Takamizawa Shigeyoshi , Hara Shuhei , Miyajima Keiichiro , Iwatani Kosuke , Yasue Keiji , Nishikawa Hideomi , Yamamoto Toshihiro , Koide Haruhisa , Sadakane Ibuki , Atsuta Mahito , Mori Keiichiro , Imai Yu , Kayano Sotaro , Murakami Masaya , Tashiro Kojiro , Tsuzuki Shunsuke , Yamada Hiroki , Miki Jun , Urabe Fumihiko , Kimura Takahiro , On behalf of JIKEI-SCRUM Collaborative Group  
Published: June 2024

Abstract

Objectives
This study explored the impacts of peri-operative changes in the neutrophil-to-lymphocyte ratio (NLR) on the survival rate after radical nephroureterectomy.

Methods
This retrospective analysis included a multicentric cohort of patients diagnosed with upper tract urothelial carcinoma (UTUC) who had undergone radical nephroureterectomy from 2012 to 2021. We assessed the preoperative NLR, postoperative NLR, delta-NLR (difference between postoperative and preoperative NLRs), and NLR change (ratio of postoperative to preoperative NLR). Additionally, patients were categorized according to increases in their preoperative and/or postoperative NLRs. Associations of survival with peri-operative changes in the NLR were investigated using Cox multivariate regression models.

Results
A total of 488 patients were included in the study, with a median age of 73 years. Among the patients, 105 (21.5%) exhibited elevated preoperative and postoperative NLRs, 88 (18.0%) exhibited elevated preoperative NLR only, 53 (10.9%) exhibited elevated postoperative NLR only, and 242 (49.6%) exhibited normal NLRs. Multivariate analysis indicated significant negative correlations between both preoperative and postoperative increased NLRs and oncological outcomes, including nonurothelial tract recurrence-free survival and cancer-specific survival (hazard ratio [HR]: 1.65, P = 0.017; HR: 2.12, P = 0.014, respectively).

Conclusion
This is the first study to evaluate the association between peri-operative changes in the NLR and the outcomes of patients with UTUC who underwent radical nephroureterectomy. Patients with elevated NLRs at both time points experienced considerably worse outcomes. Further research should explore whether increases in the NLR during long-term follow-up could indicate impending disease recurrence.
Radiation-induced eCIRP impairs macrophage bacterial phagocytosis
Authors: Yamaga Satoshi , Murao Atsushi , Zhou Mian , Aziz Monowar , Brenner Max , Wang Ping 
Published: June 2024

Abstract
Macrophages are essential immune cells for host defense against bacterial pathogens after radiation injury. However, the role of macrophage phagocytosis in infection following radiation injury remains poorly examined. Extracellular cold-inducible RNA-binding protein is a damage-associated molecular pattern that dysregulates host immune system responses such as phagocytosis. We hypothesized that radiation-induced extracellular cold-inducible RNA-binding protein release impairs macrophage phagocytosis of bacteria. Adult healthy mice were exposed to 6.5 Gy total body irradiation. Primary peritoneal macrophages isolated from adult healthy mice were exposed to 6.5 Gy radiation. Extracellular cold-inducible RNA-binding protein–neutralizing monoclonal antibody was added to the cell culture prior to irradiation. Bacterial phagocytosis by peritoneal macrophages was assessed using pHrodo Green-labeled Escherichia coli 7 d after irradiation ex vivo and in vitro. Bacterial phagocytosis was also assessed after treatment with recombinant murine cold-inducible RNA-binding protein. Rac1 and ARP2 protein expression in cell lysates and extracellular cold-inducible RNA-binding protein levels in the peritoneal lavage were assessed by western blotting. Bacterial phagocytosis by peritoneal macrophages was significantly decreased after irradiation compared with controls ex vivo and in vitro. Rac1 and ARP2 expression in the peritoneal macrophages were downregulated after total body irradiation. Total body irradiation significantly increased extracellular cold-inducible RNA-binding protein levels in the peritoneal cavity. Recombinant murine cold-inducible RNA-binding protein significantly decreased bacterial phagocytosis in a dose-dependent manner. Extracellular cold-inducible RNA-binding protein monoclonal antibody restored bacterial phagocytosis by peritoneal macrophages after irradiation. Ionizing radiation exposure impairs bacterial phagocytosis by macrophages after irradiation. Neutralization of extracellular cold-inducible RNA-binding protein restores the phagocytic ability of macrophages after irradiation. Our findings elucidate a novel mechanism of immune dysfunction and provide a potential new therapeutic approach for limiting infection after radiation injury.
Urban landscape as a determinant of sarcosaprophagous fly assemblages of sanitary interest: a comparative field study between larviparous and oviparous reproductive strategies
Authors: Battán Horenstein Moira , Montes Marcela , Gleiser Raquel M 
Published: June 2024

Abstract
In Diptera, reproductive strategies vary according to the stage of development of the newly deposited offspring and their abundance. The aim of our study is to establish connections between the reproductive strategies of flies (larviparous or oviparous) and the prevailing local conditions (sun or shade) as well as landscape attributes (low or high urbanization) in an urban setting. We collected flies using 2 baited traps (in the sun or shade) at each of the 13 study sites with varying levels of urbanization. We used generalized linear mixed models to examine the impact of landscape and local characteristics on the diversity (abundance and richness of larviparous and oviparous Diptera) of sarcosaprophagous flies. Our findings indicate that while the abundance and diversity of both larviparous and oviparous flies are affected by urbanization, larviparous flies would be less sensitive to more urbanized environments. Larviparous also exhibit a preference for resources under sun exposure, while the responses of oviparous seem more species-dependent. The observed patterns can be explained by the known biology of the studied groups.
The risk and benefit profiles of US-eligible lung cancer screening attendees vs nonattendees
Authors: Zhang Elizabeth Y , Cheung Li C , Katki Hormuzd A , Graubard Barry I , Jemal Ahmedin , Chaturvedi Anil K , Landy Rebecca 
Published: June 2024

Abstract

Background
The US Preventive Services Task Force (USPSTF) recommend lung cancer screening for individuals aged 50-80 years with at least 20 pack-years and no more than 15 quit-years, but uptake is low. The risk and benefit profiles of screening attendees are unknown; consequently, the impact and lost opportunity of ongoing lung cancer screening in the United States remains unclear.

Methods
We estimated lung cancer death risk (using the Lung Cancer Death Risk Assessment Tool) and life gained from screening (using the Life Years Gained From Screening-Computed Tomography model) for individuals aged 50-79 years who ever-smoked in the US representative 2022 Behavioral Risk Factor Surveillance System. We compared lung cancer death risk and life gained among USPSTF-eligible individuals by screening status (self-reported screened vs not screened in past year) and estimated the number of lung cancer deaths averted and life-years gained under current screening levels and if everyone eligible was screened.

Results
USPSTF eligibility was 33.7% (95% confidence interval [CI] = 33.1% to 34.4%), of whom 17.9% (95% CI = 17.0% to 18.8%) self-reported screening. Screening uptake increased with increasing lung cancer death risk quintile (Q1 = 5.2%, 95% CI = 3.0% to 8.8%; Q5 = 21.8%, 95% CI = 20.3% to 23.3%) and life-gain from screening quintile (Q1 = 6.2%, 95% CI = 3.8% to 9.9%; Q5 = 20.8%, 95% CI = 19.5% to 22.2%). Screened individuals had higher lung cancer death risk (risk ratio [RR] = 1.35, 95% CI = 1.26 to 1.46) and life-years gained (RR = 1.19, 95% CI = 1.12 to 1.25) than unscreened individuals. Currently, screening averts 19 306 lung cancer deaths and gains 237 564 life-years; screening everyone eligible would additionally avert 56 956 lung cancer deaths and gain 751 850 life-years. Two-thirds of USPSTF lung-eligible women were up to date with breast cancer screening, but only 17.3% attended lung screening in the past year.

Conclusions
Eligible screening attendees had higher lung cancer death risk and benefit from screening. Higher rates of screening could substantially increase the number of lung cancer deaths prevented.
Racial discrimination and health-care system trust among American adults with and without cancer
Authors: Brown Jordyn A , Taffe Brianna D , Richmond Jennifer A , Roberson Mya L 
Published: June 2024

Abstract

Background
Racial and ethnic minoritized groups report disproportionately lower trust in the health-care system. Lower health-care system trust is potentially related to increased exposure to racial discrimination in medical settings, but this association is not fully understood. We examined the association between racial discrimination in medical care and trust in the health-care system among people with and without a personal cancer history.

Methods
We examined racial discrimination and trust in a nationally representative American adult sample from the Health Information National Trends Survey 6. Racial discrimination was defined as any unfair treatment in health care on the basis of race or ethnicity. Trust in the health-care system (eg, hospitals and pharmacies) was grouped into low, moderate, and high trust. Multinomial logistic regression models were used to compare low and moderate trust relative to high trust in the health-care system and estimate odds ratios (ORs) and 95% confidence intervals (CIs).

Results
A total of 5813 respondents (15% with a personal cancer history) were included; 92% (n = 5355) reported no prior racial discrimination experience during medical treatment. Prior experiences of racial discrimination were positively associated with low (OR = 6.12, 95% CI = 4.22 to 8.86) and moderate (OR = 2.70, 95% CI = 1.96 to 3.72) trust in the health-care system relative to high trust. Similar associations were observed when stratifying by personal cancer history.

Conclusion
Respondents who reported racial discrimination during medical encounters had lower trust in the health-care system, especially respondents with a personal cancer history. Our findings highlight the need to address racial discrimination experiences during medical care to build patient trust and promote health-care access.