bluuebunny/crossref_metadata_2025_split huggingface dataset:
Value-based healthcare in fertility care using relevant outcome measures for the full cycle of care leading towards shared decision-making: a retrospective cohort study
Authors: Bensink Milou , Volkerink Joy , Teklenburg Gijs , van Bavel Casandra C A W , Kuchenbecker Walter K H , Cohlen Ben J , Curfs Max H J M 
Published: September 2023

ObjectiveTo determine if the introduction of value-based healthcare (VBHC) in fertility care can help to create realistic expectations in patients resulting in increased patient value, by demonstrating the relevance of defining outcome measures that truly matter to subfertile patients.DesignRetrospective cohort study.SettingTertiary fertility centre.ResultsTime to pregnancy (TTP) and ongoing pregnancy rate (OPR), as a proxy for the live birth rate, for the full cycle of fertility care, regardless of which and how many treatment cycles performed, were identified as the most relevant medical outcome measures. Outcome measures were incorporated into a digital dashboard by using anonymised and validated patient data from the electronic patient file. We were able to present the TTP and OPR for the population as a whole as well as stratified for age, diagnosis, gravidity and type of gamete source used thereby resulting in a virtual ‘patient like me’ resembling the individual patient in the consultation room.ConclusionWe have shown that, by applying VBHC principles, relevant outcome measures can be generated and stratified for different patient characteristics, in order to develop a virtual ‘patient like me’. This virtual ‘patient like me’ can be used in the consulting room in the form of a digital dashboard, attributing to create realistic patient expectations. This facilitates healthcare providers and patients in shared decision-making.
Delirium in patients with musculoskeletal tumours: incidence and risk factors – single-centre prospective study
Authors: Mihara Noriaki , Yazawa Yasuo , Imanishi Jungo , Torigoe Tomoaki , Onishi Hideki , Ishida Mayumi 
Published: September 2023

ObjectivesDelirium, a neurocognitive disorder, typically occurs in older patients and those with advanced cancer. Although there have been numerous reports on delirium in patients with cancer in various conditions, there are no reports that specifically focus on patients with musculoskeletal tumours. This prospective study aimed to investigate the incidence, risk factors and prognostic implications of delirium in patients with musculoskeletal tumours.MethodsIn this single institutional study, 148 patients with musculoskeletal oncology were enrolled. The estimated risk factors included age, sex, alcohol abuse, performance status (PS), dietary status, admission route, tumour malignancy, oncological stage and blood test results. The significance of delirium in survival was also examined.ResultsOnly 18 patients with malignant tumours had delirium (12.2%). Based on univariate analysis, older age, poor PS, dietary status, admission from another hospital, malignant tumour, carcinoma rather than sarcoma, anaemia and some laboratory abnormalities were found to be significant risk factors for delirium. Multivariate analysis showed that poor PS was significantly correlated with delirium. Additionally, delirium was significantly correlated with poor survival.ConclusionsThe incidence of delirium among patients with musculoskeletal tumours was 12.2% and was observed only in patients with malignant tumours. PS is a significant risk factor for delirium. Delirium is correlated with poor prognosis.
Short-season high-moisture shelled corn, snaplage, or corn silage as a partial replacement for dry-rolled barley grain or barley silage in western Canadian beef cattle finishing diets
Authors: Carey R.E. , Ribeiro G.O. , Paddock Z.D. , Moya D. , McAllister T.A. , Penner G.B. 
Published: September 2023

The objective was to evaluate the replacement of barley-based ingredients with short-season high-moisture corn products on steer growth performance and carcass characteristics. Over 2 years, 320 beef steers (528 ± 36.2 kg initial body weight) were assigned to 32 pens (4 pens/treatment/year). Treatments were finishing diets that contained dry-rolled barley grain and barley silage (BGBS; control), barley grain and corn silage (BGCS), high-moisture shelled corn and barley grain with barley silage (HCBS), or snaplage (included as a silage and grain source) with barley grain (SNAP). Steers were fed for 99 days and 72 days in years 1 and 2, respectively. Steers fed BGCS did not differ ( P ≥ 0.13) from BGBS for dry matter intake, average daily gain, gain:feed, or carcass characteristics. Steers fed HCBS had greater ( P ≤ 0.05) hot carcass weight and dressing percentage than BGBS. A lesser ( P = 0.02) proportion of steers fed SNAP had severe liver abscesses than BGBS. We concluded that corn silage can replace barley silage, 50% replacement of barley grain with high-moisture shelled corn may improve hot carcass weight, and replacement of barley silage and some barley grain with snaplage decreases the proportion of cattle with severe liver abscesses at slaughter.
Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
Authors: Grillo Giacomo , Keshavarzian Tina , Linder Simon , Arlidge Christopher , Mout Lisanne , Nand Ankita , Teng Mona , Qamra Aditi , Zhou Stanley , Kron Ken J. , Murison Alex , Hawley James R. , Fraser Michael , van der Kwast Theodorus H. , Raj Ganesh V. , He Housheng Hansen , Zwart Wilbert , Lupien Mathieu 
Published: September 2023

Abstract

Transposable elements hold regulatory functions that impact cell fate determination by controlling gene expression. However, little is known about the transcriptional machinery engaged at transposable elements in pluripotent and mature versus oncogenic cell states. Through positional analysis over repetitive DNA sequences of H3K27ac chromatin immunoprecipitation sequencing data from 32 normal cell states, we report pluripotent/stem and mature cell state–specific “regulatory transposable elements.” Pluripotent/stem elements are binding sites for pluripotency factors (e.g., NANOG, SOX2, OCT4). Mature cell elements are docking sites for lineage-specific transcription factors, including AR and FOXA1 in prostate epithelium. Expanding the analysis to prostate tumors, we identify a subset of regulatory transposable elements shared with pluripotent/stem cells, including Tigger3a. Using chromatin editing technology, we show how such elements promote prostate cancer growth by regulating AR transcriptional activity. Collectively, our results suggest that oncogenesis arises from lineage-specific transcription factors hijacking pluripotent/stem cell regulatory transposable elements.

Significance:
We show that oncogenesis relies on co-opting transposable elements from pluripotent stem cells as regulatory elements altering the recruitment of lineage-specific transcription factors. We further discover how co-option is dependent on active chromatin states with important implications for developing treatment options against drivers of oncogenesis across the repetitive DNA.
This article is featured in Selected Articles from This Issue, p. 2293
A comunidade de jornalistas LGBTQIA+ e o esforço das ações afirmativas num Brasil conservador
Authors: Assis Francisco de 
Published: September 2023

Este ensaio discute o esforço da comunidade de jornalistas LGBTQIA+ em ações afirmativas no mundo do trabalho, considerando a onda conservadora que tomou conta da cena político-social do Brasil nos últimos anos. São evidenciadas três iniciativas: a criação de uma Comissão LGBT pelo Sindicato dos Jornalistas Profissionais no Estado de São Paulo; uma pesquisa sobre profissionais de jornalismo que se identificam com a referida sigla; e o Manual de Comunicação LGBTI+ destinado a amparar jornalistas em relação às pautas de gênero. Embora significativas, em um contexto marcado por preconceitos e por silenciamentos de minorias, essas ações caminham devagar, justamente porque esbarram em outras questões, resultando em paradoxo semelhante ao que o feminismo identificou, há tempos, sobre a divisão sexual do trabalho: “tudo muda, mas nada muda”.
"Mulheres Fotógrafas Anos 80": narrativas sobre uma exposição dedicada a mulheres
Authors: Nichele Heloisa , Corrêa Ronaldo de Oliveira 
Published: September 2023

Neste artigo, propomos uma reconstrução da mostra “Mulheres fotógrafas anos 80”, promovida pelo Instituto Nacional de Fotografia da Funarte em 1989, no Rio de Janeiro. A partir de uma investigação documental de registros fragmentários e heterogêneos, tais como reportagens, notas de jornais e o catálogo resultante da mostra, criamos narrativas preliminares sobre a produção, circulação e recepção da exposição que coincidem com agendas sociais e políticas coletivas, tais como os movimentos feministas, o processo de institucionalização da fotografia no Brasil e a adesão de mulheres ao campo profissional. Por fim, pretendemos contribuir com a visibilidade de eventos desconsiderados pela historiografia, de forma a ampliar as versões sobre a participação de mulheres na história da fotografia brasileira.
Effective Delivery of Vagus Nerve Stimulation Requires Many Stimulations Per Session and Many Sessions Per Week Over Many Weeks to Improve Recovery of Somatosensation
Authors: Ruiz Andrea D. , Malley Kaitlyn M. , Danaphongse Tanya T. , Ahmad Fatima N. , Mota Beltran Clareth , Rennaker Robert L. , Kilgard Michael P. , Hays Seth A. 
Published: September 2023

Background Chronic sensory loss is a common and undertreated consequence of many forms of neurological injury. Emerging evidence indicates that vagus nerve stimulation (VNS) delivered during tactile rehabilitation promotes recovery of somatosensation. Objective Here, we characterize the amount, intensity, frequency, and duration of VNS therapy paradigms to determine the optimal dosage for VNS-dependent enhancement of recovery in a model of peripheral nerve injury (PNI). Methods Rats underwent transection of the medial and ulnar nerves in the forelimb, resulting in chronic sensory loss in the paw. Eight weeks after injury, rats were implanted with a VNS cuff and received tactile rehabilitation sessions consisting of repeated mechanical stimulation of the previously denervated forepaw paired with short bursts of VNS. Rats received VNS therapy in 1 of 6 systematically varied dosing schedules to identify a paradigm that balanced therapy effectiveness with a shorter regimen. Results Delivering 200 VNS pairings a day 4 days a week for 4 weeks produced the greatest percent improvement in somatosensory function compared to any of the 6 other groups (One Way analysis of variance at the end of therapy, F[4 70] P = .005). Conclusions Our findings demonstrate that an effective VNS therapy dosage delivers many stimulations per session, with many sessions per week, over many weeks. These results provide a framework to inform the development of VNS-based therapies for sensory restoration.
Pedestrian gaze pattern before crossing road in a naturalistic traffic setting
Authors: Zhao Qingxian , Zhuang Xiangling , Zhang Tong , He Yunqi , Ma Guojie 
Published: September 2023

Abstract
Background
Gaze is the primary way for pedestrians to obtain clues from traffic scenes before making decisions. Therefore, understanding pedestrian gaze pattern is vital for traffic safety in general and for the design of autonomous vehicles.

Methods
In this study, participants made road-crossing decisions in a naturalistic traffic scene, with an eye-tracker recording their gaze behaviors. We manually encoded the recorded videos with 14,898 fixations, and then analyzed the gaze pattern at three levels from general to specific: gaze towards overall scenes, gaze towards vehicles and gaze towards components of vehicles.

Findings
At the first level, our findings indicate that frequent fixations began to appear at the distance of 100 m and peaked around 5–30 m away from pedestrians. Transversely pedestrians mainly gazed at the two lanes adjacent to themselves. Pedestrians allocated 53% gaze duration to motor vehicles. For a specific vehicle, which is the second level, the gaze duration varied with vehicles' attributes such as distances, sizes, and types. Finally, at the third level, we discovered that pedestrians’ gaze duration on different vehicle components varied with the longitudinal distance. As vehicles approach, the main area of fixation expanded from the near side headlight to the whole front and near side, and finally shift to the near side of a vehicle.

Implications
The distribution of fixations in space and vehicle components before pedestrian crossing can provide fundamental information for understanding and modeling of pedestrian's road-crossing behaviors. In practice, our findings can guide the timing and position of information displays on autonomous vehicles to facilitate friendly interaction with pedestrians.
HMCDA: a novel method based on the heterogeneous graph neural network and metapath for circRNA-disease associations prediction
Authors: Liang Shiyang , Liu Siwei , Song Junliang , Lin Qiang , Zhao Shihong , Li Shuaixin , Li Jiahui , Liang Shangsong , Wang Jingjie 
Published: September 2023

AbstractCircular RNA (CircRNA) is a type of non-coding RNAs in which both ends are covalently linked. Researchers have demonstrated that many circRNAs can act as biomarkers of diseases. However, traditional experimental methods for circRNA-disease associations identification are labor-intensive. In this work, we propose a novel method based on the heterogeneous graph neural network and metapaths for circRNA-disease associations prediction termed as HMCDA. First, a heterogeneous graph consisting of circRNA-disease associations, circRNA-miRNA associations, miRNA-disease associations and disease-disease associations are constructed. Then, six metapaths are defined and generated according to the biomedical pathways. Afterwards, the entity content transformation, intra-metapath and inter-metapath aggregation are implemented to learn the embeddings of circRNA and disease entities. Finally, the learned embeddings are used to predict novel circRNA-disase associations. In particular, the result of extensive experiments demonstrates that HMCDA outperforms four state-of-the-art models in fivefold cross validation. In addition, our case study indicates that HMCDA has the ability to identify novel circRNA-disease associations.
Purifying selection leads to low protein diversity of the mitochondrial cyt b gene in avian malaria parasites
Authors: Wang Xinyi , Bensch Staffan , Huang Xi , Dong Lu 
Published: September 2023

Abstract
Background
Mitochondrial respiration plays a central role in the survival of many eukaryotes, including apicomplexan parasites. A 479-bp fragment from the mitochondrial cytochrome b gene is widely used as a barcode to identify genetic lineages of avian malaria parasites Plasmodium and related haemosporidians. Here we looked for evidence of selection in the avian Plasmodium cyt b gene, using tests of selection and protein structure modeling. We also tested for the association between cyt b polymorphism and the host specificity of these parasites.

Results
Based on 1,089 lineages retrieved from the Malavi database, we found that the frequency of the most conserved amino acids in most sites was more than 90%, indicating that the protein diversity of the avian Plasmodium cyt b barcode was low. The exceptions were four amino acid sites that were highly polymorphic, though the substitutions had only slight functional impacts on the encoded proteins. The selection analyses revealed that avian Plasmodium cyt b was under strong purifying selection, and no positively selected sites were detected. Besides, lineages with a wide host range tend to share cyt b protein haplotypes.

Conclusions
Our research indicates that purifying selection is the dominant force in the evolution of the avian Plasmodium cyt b lineages and leads to its low diversity at the protein level. Host specificity may also play a role in shaping the low mitochondrial diversity in the evolution of avian malaria parasites. Our results highlight the importance of considering selection pressure on the cyt b barcode region and lay a foundation for further understanding the evolutionary pattern of mitochondrial genes in avian malaria.
Codon usage pattern of the ancestor of green plants revealed through Rhodophyta
Authors: Yao Huipeng , Li Tingting , Ma Zheng , Wang Xiyuan , Xu Lixiao , Zhang Yuxin , Cai Yi , Tang Zizhong 
Published: September 2023

AbstractRhodophyta are among the closest known relatives of green plants. Studying the codons of their genomes can help us understand the codon usage pattern and characteristics of the ancestor of green plants. By studying the codon usage pattern of all available red algae, it was found that although there are some differences among species, high-bias genes in most red algae prefer codons ending with GC. Correlation analysis, Nc-GC3s plots, parity rule 2 plots, neutrality plot analysis, differential protein region analysis and comparison of the nucleotide content of introns and flanking sequences showed that the bias phenomenon is likely to be influenced by local mutation pressure and natural selection, the latter of which is the dominant factor in terms of translation accuracy and efficiency. It is worth noting that selection on translation accuracy could even be detected in the low-bias genes of individual species. In addition, we identified 15 common optimal codons in seven red algae except for G. sulphuraria for the first time, most of which were found to be complementary and bound to the tRNA genes with the highest copy number. Interestingly, tRNA modification was found for the highly degenerate amino acids of all multicellular red algae and individual unicellular red algae, which indicates that highly biased genes tend to use modified tRNA in translation. Our research not only lays a foundation for exploring the characteristics of codon usage of the red algae as green plant ancestors, but will also facilitate the design and performance of transgenic work in some economic red algae in the future.
Genome-wide identification of GhRLCK-VII subfamily genes in Gossypium hirsutum and investigation of their functions in resistance to Verticillium wilt
Authors: Liu Xiuyan , Lei Zhongping , Yang Yuzhen , Wang Zhenkai , Ha Shengying , Lei Zhangying , He Daohua 
Published: September 2023

Abstract
Background
The receptor-like cytoplasmic kinases subfamily VII (RLCK-VII) is critical in regulating plant growth, development, and pattern-triggered immunity. However, a comprehensive exploration of these genes in the allotetraploid Gossypium hirsutum is still lacking. This study aimed to identify RLCK-VII genes in G. hirsutum and investigate their evolutionary history, structural features, expression patterns, and role in plant defense.

Results
Seventy-two RLCK-VII genes in the G. hirsutum genome were unveiled and classified into nine groups following their phylogenetic analysis with Arabidopsis thaliana. Group VII-1 was the largest, accounting for 28%, while Groups VII-2 and VII-3 had only one member each. The analysis using MCScanX revealed that these 72 genes formed 166 collinear gene pairs and were resided on 26 chromosomes of G. hirsutum, suggesting that they were derived from whole genome segmental duplication events. Their calculated Ka/Ks values were below one, implying the occurrence of purification selection during the evolution and inhibition of gene function differentiation/loss. All members of the RLCK-VII subfamily possessed two conserved domains, PKinase-Tyr and PKinase, and several conserved PBS1 kinase subdomains, individually included in one of the ten motifs identified using MEME. The RNA-Seq results showed that RLCK-VII genes exhibited different spatiotemporal expression, indicating their involvement in cotton growth, development, and defense responses to Verticillium dahliae. The transcription patterns of RLCK-VII genes found by RNA-Seq were further validated using qRT-PCR assays after inoculating “20B12” (cotton cultivar) with “V991” (V. dahliae). The virus-induced gene silencing (VIGS) assays uncovered that two RLCK-VII genes (Gohir.A13G227248 and Gohir.A10G219900) were essential to G. hirsutum resistance to Verticillium wilt.

Conclusions
These observations offer valuable insight into the attributes and roles of RLCK-VII genes in G. hirsutum, potentially enable the breeding of new cotton cultivars with enhanced resistance to Verticillium wilt.
Effect of Colchicine in reducing MMP-9, NOX2, and TGF- β1 after myocardial infarction
Authors: Suryono Suryono , Rohman Mohammad Saifur , Widjajanto Edi , Prayitnaningsih Seskoati , Wihastuti Titin Andri , Oktaviono Yudi Her 
Published: September 2023

Abstract
Background
According to WHO 2020, CAD is the second leading cause of death in Indonesia with death cases reaching 259,297 or 15.33% of total deaths. Unfortunately, most of the patients of CAD in Indonesia did not match the golden period or decline to be treated with Percutaneous Coronary Intervention (PCI). Based on the recent study, there were increases in MMP-9, NOX2, and TGF-β1 in STEMI patients which contribute to cardiac remodeling. Moreover, there is controversy regarding the benefit of late PCI (12-48 hours after onset of STEMI) in stable patients. Lately, colchicine is widely used in cardiovascular disease. This study was conducted to explore the effect of colchicine to reduce MMP- 9, NOX2, and TGF-β1 levels after myocardial infarction in stable patients.

Method
In this clinical trial study, we assessed 129 STEMI patients, about 102 patients who met inclusion criteria were randomized into four groups. Around 25 patients received late PCI (12–48 h after the onset of chest pain), optimal medical treatment (OMT) for STEMI, and colchicine; 24 patients received late PCI and OMT; 22 patients didn’t get the revascularization (No Revas), OMT, and colchicine; and 31 patients received No Revas and OMT only. The laboratory test for MMP-9, NOX2, and TGF-β1 were tested in Day-1 and Day-5. The data were analyzed using Mann-Whitney.

Results
A total of 102 patients with mean age of 56 ± 9.9, were assigned into four groups. The data analysis showed significant results within No Revas + OMT + Colchicine group versus No Revas + OMT + Placebo in MMP-9 (Day-1: p = 0.001; Day-5: p = 0.022), NOX2 (Day-1: p = 0.02; Day-5: p = 0.026), and TGF-β1 (Day-1: p = 0.00; Day-5: p = 0.00) with the less three markers in OMT + Colchicine group than OMT + Placebo group. There were no significant differences within the late PCI + OMT + colchicine group and PCI + OMT + Placebo group.

Conclusions
Colchicine could significantly reduce MMP-9, NOX2, and TGF-β1 levels in stable STEMI patients. So that, colchicine could be a potential agent in STEMI patients and prevent cardiac remodeling events.