bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strategies to improve implementation of cascade testing in hereditary cancer syndromes: a systematic review
Authors: Chiang Jianbang , Chua Ziyang , Chan Jia Ying , Sule Ashita Ashish , Loke Wan Hsein , Lum Elaine , Ong Marcus Eng Hock , Graves Nicholas , Ngeow Joanne 
Published: April 2024

AbstractHereditary cancer syndromes constitute approximately 10% of all cancers. Cascade testing involves testing of at-risk relatives to determine if they carry the familial pathogenic variant. Despite growing efforts targeted at improving cascade testing uptake, current literature continues to reflect poor rates of uptake, typically below 30%. This study aims to systematically review current literature on intervention strategies to improve cascade testing, assess the quality of intervention descriptions and evaluate the implementation outcomes of listed interventions. We searched major databases using keywords and subject heading of “cascade testing”. Interventions proposed in each study were classified according to the Effective Practice and Organization of Care (EPOC) taxonomy. Quality of intervention description was assessed using the TIDieR checklist, and evaluation of implementation outcomes was performed using Proctor’s Implementation Outcomes Framework. Improvements in rates of genetic testing uptake was seen in interventions across the different EPOC taxonomy strategies. The average TIDieR score was 7.3 out of 12. Items least reported include modifications (18.5%), plans to assess fidelity/adherence (7.4%) and actual assessment of fidelity/adherence (7.4%). An average of 2.9 out of 8 aspects of implementation outcomes were examined. The most poorly reported outcomes were cost, fidelity and sustainability, with only 3.7% of studies reporting them. Most interventions have demonstrated success in improving cascade testing uptake. Uptake of cascade testing was highest with delivery arrangement (68%). However, the quality of description of interventions and assessment of implementation outcomes are often suboptimal, hindering their replication and implementation downstream. Therefore, further adoption of standardized guidelines in reporting of interventions and formal assessment of implementation outcomes may help promote translation of these interventions into routine practice.
Water-based direct photopatterning of stretchable PEDOT:PSS using amphiphilic block copolymers
Authors: Yoon Soon Joo , Ha Jeongdae , Lee Hyeokjun , Park Jin Tae , Lee Bin Hyung , Jang Kyung-In , Yang Anna , Lee Yoon Kyeung 
Published: April 2024

AbstractThe use of water-based chemistry in photolithography during semiconductor fabrication is desirable due to its cost-effectiveness and minimal environmental impact, especially considering the large scale of semiconductor production. Despite these benefits, limited research has reported successful demonstrations of water-based photopatterning, particularly for intrinsically water-soluble materials such as Poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) due to significant challenges in achieving selective dissolution during the developing process. In this paper, we propose a method for the direct patterning of PEDOT:PSS in water by introducing an amphiphilic Poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol) (PEO-PPO-PEO, P123) block copolymer to the PEDOT:PSS film. The addition of the block copolymer enhances the stretchability of the composite film and reduces the hydrophilicity of the film surface, allowing for water absorption only after UV exposure through a photoinitiated reaction with benzophenone. We apply this technique to fabricate tactile and wearable biosensors, both of which benefit from the mechanical stretchability and transparency of PEDOT:PSS. Our method represents a promising solution for water-based photopatterning of hydrophilic materials, with potential for wider applications in semiconductor fabrication.
Association between self-reported METs and other perioperative cardiorespiratory fitness assessment tools in abdominal surgery—a prospective cross-sectional correlation study
Authors: Czajka Szymon , Krzych Łukasz J. 
Published: April 2024

AbstractCardiovascular complications represent a significant proportion of adverse events during the perioperative period, necessitating accurate preoperative risk assessment. This study aimed to investigate the association between well-established risk assessment tools and self-reported preoperative physical performance, quantified by metabolic equivalent (MET) equivalents, in high-risk patients scheduled for elective abdominal surgery. A prospective cross-sectional correlation study was conducted, involving 184 patients admitted to a Gastrointestinal Surgery Department. Various risk assessment tools, including the Revised Cardiac Risk Index (RCRI), Surgical Mortality Probability Model (S-MPM), American University of Beirut (AUB)-HAS2 Cardiovascular Risk Index, and Surgical Risk Calculator (NSQIP-MICA), were utilized to evaluate perioperative risk. Patients self-reported their physical performance using the MET-REPAIR questionnaire. The findings demonstrated weak or negligible correlations between the risk assessment tools and self-reported MET equivalents (Spearman’s ρ = − 0.1 to − 0.3). However, a statistically significant relationship was observed between the ability to ascend two flights of stairs and the risk assessment scores. Good correlations were identified among ASA-PS, S-MPM, NSQIP-MICA, and AUB-HAS2 scores (Spearman’s ρ = 0.3–0.8). Although risk assessment tools exhibited limited correlation with self-reported MET equivalents, simple questions regarding physical fitness, such as the ability to climb stairs, showed better associations. A comprehensive preoperative risk assessment should incorporate both objective and subjective measures to enhance accuracy. Further research with larger cohorts is needed to validate these findings and develop a comprehensive screening tool for high-risk patients undergoing elective abdominal surgery.
Trail pheromone identification in the ant Crematogaster scutellaris
Authors: Scarano Florencia , Giannetti Daniele , Trenti Francesco , Giacomazzi Federico , Vigna Jacopo , Guella Graziano , Grasso Donato A. , Haase Albrecht 
Published: April 2024

AbstractIn this work, we identified the trail pheromone of the ant Crematogaster scutellaris. We combined gas chromatography–mass spectrometry analysis of extracts from the hind tibia, the location of the respective glands, with automated trail following assays. The study found tridecan-2-ol to be the strongest discriminator between hind tibia and other body part extracts. Tridecan-2-ol elicited trail-following behaviour at concentrations of 1 ng/µL. A separation of the enantiomers showed responses to (R)-tridecan-2-ol already at 0.001 ng/µL and only at a 1000-fold higher concentration for (S)-tridecan-2-ol, suggesting that only the R enantiomer is used by C. scutellaris in its natural environment. We also found strong behavioural responses to 2-dodecanol, a substance that was not detectable in the hind tibia extract of C. scutellaris, but which has been reported to be the trail pheromone of the related species C. castanea. We discuss the contribution of these results to the 'dissection and reconstruction' of strategies and mechanisms underlying the social organization of ants.
Aldosterone levels do not predict 28-day mortality in patients treated for COVID-19 in the intensive care unit
Authors: Janc Jarosław , Janc Jędrzej Jerzy , Suchański Michał , Fidut Miłosz , Leśnik Patrycja 
Published: April 2024

AbstractThe immunotropic effects of aldosterone might play a role in COVID-19, as SARS-CoV-2 reportedly uses angiotensin-converting enzyme 2 receptors as an entry point into cells. Aldosterone function is closely linked to its action on mineralocorticoid receptors in kidneys; it increases the renal retention of sodium and the excretion of potassium, which increases blood pressure. Despite the large number of studies examining the effect of Ang-II and its blockers on the course of COVID-19 infection, there is still uncertainty about the role of aldosterone. The aim of the study was to assess the correlation of aldosterone, urea, creatinine, C-reactive protein (CRP), and procalcitonin (PCT) levels with 28 days of mortality in patients treated for COVID19 in an intensive care unit (ICU). This cross-selection study involved 115 adult patients who were divided into two groups: those who died within a 28-day period (n = 82) and those who survived (n = 33). The correlation of aldosterone, urea, creatinine, C-reactive protein (CRP), and procalcitonin (PCT) levels with 28 days of mortality in patients treated for COVID-19 were performed. The patients’ age, sex, scores from the APACHE II, SAPS II, and SOFA scales and comorbidities like HA, IHD and DM were also analyzed. Remarkably, the individuals who survived for 28 days were of significantly lower mean age and achieved notably lower scores on the APACHE II, SAPS II, and SOFA assessment scales. Statistically significantly higher CRP levels were observed on days 3, 5, and 7 in individuals who survived for 28 days. Creatinine levels in the same group were also statistically significantly lower on days 1, 3, and 5 than those of individuals who died within 28 days. The investigation employed both univariate and multivariate Cox proportional hazard regression models to explore factors related to mortality. In the univariate analysis, variables with a p value of less than 0.50 were included in the multivariate model. Age, APACHE II, SAPS II, and SOFA demonstrated significance in univariate analysis and were considered to be associated with mortality. The outcomes of the multivariate analysis indicated that age (HR = 1.03, p = 0.033) served as a robust predictor of mortality in the entire study population. In conclusion the plasma aldosterone level is not associated with ICU mortality in patients with COVID-19. Other factors, including the patient’s age, creatinine or CRP contribute to the severity and prognosis of the disease. This study was retrospectively registered in the Australian New Zealand Clinical Trials Registry (ANZCTR) with registration no. ACTRN12621001300864 (27/09/2021: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=382563&isReview=true).
Declining incidence and improving survival of ocular and orbital lymphomas in the US between 1995 and 2018
Authors: Alfaar Ahmad Samir , Yousef Yacoub A. , W. Wilson Matthew , Hassanain Omneya , Kakkassery Vinodh , Moustafa Mohanad , Kunbaz Ahmad , Esmael Amanne , Strauß Olaf 
Published: April 2024

AbstractThis epidemiological study examined ocular and orbital lymphomas in the United States from 1995 to 2018, using data from the North American Association of Central Cancer Registries database of 87,543 patients with ocular and adnexal malignancies. We identified 17,878 patients (20.4%) with ocular and orbital lymphomas, with an age-standardized incidence rate (ASIR) of 2.6 persons per million (ppm). The incidence was the highest in the orbit (ASIR = 1.24), followed by the conjunctiva (ASIR = 0.57). Non-Hodgkin B-cell lymphoma was the most prevalent subtype (85.4%), particularly marginal-zone lymphoma (45.7%). Racial disparities were noted, with Asia–Pacific Islanders showing the highest incidence (orbit, 1.3 ppm). The incidence increased significantly from 1995 to 2003 (Average Percent Change, APC = 2.1%) but declined thereafter until 2018 (APC = − 0.7%). 5-year relative survival (RS) rates varied, with the highest rate for conjunctival lymphoma (100%) and the lowest for intraocular lymphoma (70.6%). Survival rates have generally improved, with an annual increase in the 5-year RS of 0.45%. This study highlights the changing epidemiological landscape, pointing to initial increases and subsequent decreases in incidence until 2003, with survival improvements likely due to advancements in treatment. These findings underscore the need for further research to investigate the root causes of these shifts and the declining incidence of ocular lymphoma.
Haplotype-resolved assembly of auto-polyploid genomes via combining Hi-C and gametic data
Authors: Zhang Xiaohui , Li Dongxi , Pan Weihua 
Published: April 2024

AbstractHaplotype-resolved genome assembly plays a crucial role in understanding allele-specific functions. However, obtaining haplotype-resolved assembly for auto-polyploid genomes remains challenging. Existing methods can be classified into reference-based phasing, assembly-based phasing, and gamete binning. Nevertheless, there is a lack of cost-effective and efficient methods for haplotyping auto-polyploid genomes. In this study, we propose a novel phasing algorithm called PolyGH, which combines Hi-C and gametic data. We conducted experiments on tetraploid potato cultivars and divided the method into three steps. Firstly, gametic data was utilized to bin non-collapsed contigs, followed by merging adjacent fragments of the same type within the same contig. Secondly, accurate Hi-C signals related to differential genomic regions were acquired using unique k-mers. Finally, collapsed fragments were assigned to haplotigs based on combined Hi-C and gametic signals. Comparing PolyGH with Hi-C-based and gametic data-based methods, we found that PolyGH exhibited superior performance in haplotyping auto-polyploid genomes when integrating both data types. This approach has the potential to enhance haplotype-resolved assembly for auto-polyploid genomes.
Multi-Attribute Subset Selection enables prediction of representative phenotypes across microbial populations
Authors: Herbst Konrad , Wang Taiyao , Forchielli Elena J. , Thommes Meghan , Paschalidis Ioannis Ch. , Segrè Daniel 
Published: April 2024

AbstractThe interpretation of complex biological datasets requires the identification of representative variables that describe the data without critical information loss. This is particularly important in the analysis of large phenotypic datasets (phenomics). Here we introduce Multi-Attribute Subset Selection (MASS), an algorithm which separates a matrix of phenotypes (e.g., yield across microbial species and environmental conditions) into predictor and response sets of conditions. Using mixed integer linear programming, MASS expresses the response conditions as a linear combination of the predictor conditions, while simultaneously searching for the optimally descriptive set of predictors. We apply the algorithm to three microbial datasets and identify environmental conditions that predict phenotypes under other conditions, providing biologically interpretable axes for strain discrimination. MASS could be used to reduce the number of experiments needed to identify species or to map their metabolic capabilities. The generality of the algorithm allows addressing subset selection problems in areas beyond biology.
Boreal forest cover was reduced in the mid-Holocene with warming and recurring wildfires
Authors: Girardin Martin P. , Gaboriau Dorian M. , Ali Adam A. , Gajewski Konrad , Briere Michelle D. , Bergeron Yves , Paillard Jordan , Waito Justin , Tardif Jacques C. 
Published: April 2024

AbstractThe hemi-boreal zone, marking North America’s southern boreal forest boundary, has evolved post-glaciation, hosting diverse ecosystems including mixed forests with savannas, grasslands, and wetlands. While human, climate, and fire interactions shape vegetation dynamics therein, specific influences remain unclear. Here we unveil 12,000 years of hemi-boreal zone dynamics, exploring wildfire, vegetation, climate, and human population size interactions at such long time scales. Postglacial biomass burning exhibited episodes of persistent elevated activity, and a pivotal shift around 7000 years ago saw the boreal forest transition to an oak-pine barren ecosystem for about 2000 years before reverting. This mid-Holocene shift occurred during a period of more frequent burning and a sudden uptick in mean annual temperatures. Population size of Indigenous peoples mirrored wildfire fluctuations, decreasing with more frequent burning. Anticipated increases of fire activity with climate change are expected to echo transformations observed 7000 years ago, reducing boreal forest extent, and impacting land use.
Genomic profiling and clinical utility of circulating tumor DNA in metastatic prostate cancer: SCRUM-Japan MONSTAR SCREEN project
Authors: Shiota Masaki , Matsubara Nobuaki , Kato Taigo , Eto Masatoshi , Osawa Takahiro , Abe Takashige , Shinohara Nobuo , Nishimoto Koshiro , Yasumizu Yota , Tanaka Nobuyuki , Oya Mototsugu , Fujisawa Takao , Horasawa Satoshi , Nakamura Yoshiaki , Yoshino Takayuki , Nonomura Norio 
Published: April 2024

Abstract
Background
Circulating tumor DNA (ctDNA) testing has emerged as a novel tool for cancer precision medicine. This study investigated the genomic profiling and clinical utility of ctDNA in metastatic prostate cancer.

Methods
This is a nation-wide prospective observational study. Patients treated with systemic treatment for metastatic castration-sensitive prostate cancer (mCSPC) and metastatic castration-resistant prostate cancer (mCRPC) were included. ctDNA was analyzed using FoundationOne Liquid®CDx at enrollment. In a subset of patients, ctDNA after disease progression and tissue prior to the initiation of treatment were examined using FoundationOne Liquid®CDx and FoundationOne®CDx, respectively.

Results
The frequency of AR alterations and homologous recombination repair (HRR) defect was higher in mCRPC compared with mCSPC. Tumor mutational burden was correlated between tissue and ctDNA at pre-treatment, as well as ctDNA between at pre-treatment and at post-treatment. Patients with HRR defect were associated with shorter time to castration resistance in androgen deprivation therapy/combined androgen blockade, but not in androgen receptor pathway inhibitor, compared with patients without HRR defect in mCSPC. Time to treatment failure in patients with AR amplification or AR mutation was shorter compared with patients without AR alterations in mCRPC.

Conclusions
This study revealed valuable findings for the clinical care of metastatic prostate cancer. Especially, predictive factors such as HRR defect in mCSPC should be validated in the future.
Full orbital solutions in pre-main sequence high-order multiple systems: GG Tau Ab and UX Tau B
Authors: Duchêne Gaspard , LeBouquin Jean-Baptiste , Ménard François , Cuello Nicolás , Toci Claudia , Langlois Maud 
Published: April 2024

Context. High-order multiple (triple and beyond) systems are relatively common. Their interaction with circumstellar and circumbinary material can have a large impact on the formation and evolution of planetary systems and depends on their orbital properties.
Aims. GG Tau and UX Tau are two pre-main sequence high-order multiple systems in which the tightest pair has a projected separation of ≈5–20 au. Characterizing precisely their orbits is crucial to establish their long-term stability, to predict the dynamics and evolution of circumstellar matter, and to evaluate the potential for planet formation in such systems.
Methods. We combine existing astrometric measurements with previously unpublished high-resolution observations of the GG Tau Ab and UX Tau B pairs and perform Keplerian orbital fits.
Results. For GG Tau Ab the data presented here represent the first detection of orbital motion. For both systems they yield dramatic increases in orbital coverage (≳60% and ≈100% for UX Tau B and GG Tau Ab, for orbital periods of ≈32 and ≈8 yr, respectively) and allow us to obtain well-constrained orbital fits, including dynamical masses with ≲10% and ≲7% random and systematic uncertainties. We find that both GG Tau A and UX Tau A–B likely form stable hierarchical systems, although one possible deprojection solution for GG Tau is strongly misaligned and could experience von Zeipel-Lidov-Kozai oscillations. We further find that the UX Tau B orbit is much more eccentric than the GG Tau Ab one, possibly explaining the lack of circumstellar material in the former.
Conclusions. The newly-determined orbits revive the question of the dynamical fate of gas and dust in these two hierarchical systems and should spur new dedicated simulations to assess the long-term evolution of the systems and the dynamical perturbations imposed by the close binaries they host.
ChatGPT and the digitisation of writing
Authors: Zhao Xin , Cox Andrew , Cai Liang 
Published: April 2024

AbstractThe aim of this study is to uncover how students’ practices of writing in higher education are being impacted by ChatGPT. The use of ChatGPT and other generative AI needs to be set in the context of a longer-term process of the digitisation of writing, where many tools are being employed by students to support writing because it is a complex iterative process. Generative AI appears to have had a large impact on how students write, and we propose a model of generative AI literacy to assess their capabilities in doing so. Semi-structured interviews and observation data were collected at a British University with 23 students from diverse backgrounds, including the UK, USA, China, Japan, and Saudi Arabia. The data was analysed thematically. It was found that students used ChatGPT alongside many other tools, and in rather individualistic ways often to address specific challenges they felt they had with writing. Their main concerns were around plagiarism, information inaccuracy and technology dependence. There was a relatively weak understanding or interest in the ethical issues around the exploitative and environmental impacts of generative AI. The social controversy around ChatGPT can be seen as a useful opportunity to engage students in a discussion about the digitisation of writing and promote AI literacy in this context.
Subtitling Saudi Arabic slang into English: the case of “The Book of the Sun” on Netflix
Authors: Ali Sukayna , Al-Jabri Hanan , AL-Adwan Amer , Eliza Abdul Rahman Wan Rose 
Published: April 2024

AbstractThe aim of this study is to analyze Saudi Arabic slang expressions and examine their subtitling into English. The data utilized in this research consists of slang terms identified in the film titled “The Book of the Sun”, available on the streaming platform Netflix, along with their corresponding English translations. This study primarily examines three key dimensions of slang expressions: originality, conciseness, and humor. It also explores the subtitling strategies used to render these slangs and the effectiveness of such strategies. The study’s findings indicate that all identified slangs (100%) are created by assigning new meanings to pre-existing established words in a creative way. Some of them are made concise by mapping them into faʕʕala verb template. Additionally, the subtitler has employed specific strategies to convey the intended meaning of these slangs, namely generalization, paraphrase, official equivalent, direct translation, and cultural substitution. However, the study posits that the strategies employed are ineffective in conveying the intended meaning of slang expressions.