bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disease gene prioritization with quantum walks
Authors: Saarinen Harto , Goldsmith Mark , Wang Rui-Sheng , Loscalzo Joseph , Maniscalco Sabrina 
Published: August 2024

Abstract

Motivation
Disease gene prioritization methods assign scores to genes or proteins according to their likely relevance for a given disease based on a provided set of seed genes. This scoring can be used to find new biologically relevant genes or proteins for many diseases. Although methods based on classical random walks have proven to yield competitive results, quantum walk methods have not been explored to this end.

Results
We propose a new algorithm for disease gene prioritization based on continuous-time quantum walks using the adjacency matrix of a protein–protein interaction (PPI) network. We demonstrate the success of our proposed quantum walk method by comparing it to several well-known gene prioritization methods on three disease sets, across seven different PPI networks. In order to compare these methods, we use cross-validation and examine the mean reciprocal ranks of recall and average precision values. We further validate our method by performing an enrichment analysis of the predicted genes for coronary artery disease.

Availability and implementation
The data and code for the methods can be accessed at https://github.com/markgolds/qdgp.
GTAM: A Molecular Pretraining Model with Geometric Triangle Awareness
Authors: Hou Xiaoyang , Zhu Tian , Ren Milong , Duan Bo , Zhang Chunming , Bu Dongbo , Sun Shiwei 
Published: August 2024

Abstract

Motivation
Molecular representation learning is pivotal for advancing deep learning applications in quantum chemistry and drug discovery. Existing methods for molecular representation learning often fall short of fully capturing the intricate interactions within chemical bonds of 2D topological graphs and the multifaceted effects of 3D geometric conformations.

Results
To overcome these challenges, we present a novel contrastive learning strategy for molecular representation learning, named Geometric Triangle Awareness Model (GTAM). This method integrates innovative molecular encoders for both 2D graphs and 3D conformations, enabling the accurate capture of geometric dependencies among edges in graph-based molecular structures. Furthermore, GTAM is bolstered by the development of two contrastive training objectives designed to facilitate the direct transfer of edge information between 2D topological graphs and 3D geometric conformations, enhancing the functionality of the molecular encoders. Through extensive evaluations on a range of 2D and 3D downstream tasks, our model has demonstrated superior performance over existing approaches.

Availability
The test code and data of GTAM are available online at https://github.com/StellaHxy/GTAM.

Supplementary information
Comprehensive implementation details, datasets, and additional experiments can be found in Supplementary Materials A-C.
Interspecific variation in paper wasp body size supports the converse Bergmann’s rule
Authors: de Souza André R , Lopez Vinicius M , Somavilla Alexandre , Nascimento Fábio S , Guillermo Ferreira Rhainer , Yotoko Karla 
Published: August 2024

Abstract
Variation in body size is a conspicuous phenomenon and much scientific interest has been devoted to study the processes affecting this trait. Clines of body size across geographical areas have been detected, supporting ecogeographical rules that describe spatial patterns of phenotypic differences driven by environmental variation. In social insects, the causes of body size variation have been best studied at the within-species level, even though interspecific variation is far more striking. This is the case of Polistes paper wasps, a model genus for sociobiological and ecological studies. Here, we examined whether environmental variation predicts interspecific differences in the body size of New World Polistes, a monophyletic clade widespread through the Americas. Dried museum specimens comprising females from 37 species and males from 28 species were measured. In a phylogenetically controlled analysis, body size was associated with latitude, environmental temperature, and environmental seasonality. Larger species were more likely at low latitudes, in warmer climates, or in environments with mild seasonality. There was no evidence for a phylogenetic signal in body size. These findings support a pattern consistent with the converse Bergmann’s rule, thus suggesting that the limited time for foraging and growth in environments with strong seasonality (or higher latitudes) selects for faster development and maturation at smaller sizes. If so, the evolutionary lability of body size reported here might have contributed to the geographical spread and species diversification in this genus.
Methods in cancer research: Assessing therapy response of spheroid cultures by life cell imaging using a cost-effective live-dead staining protocol
Authors: Phour Jaison , Vassella Erik 
Published: August 2024

Abstract
Spheroid cultures of cancer cell lines or primary cells represent a more clinically relevant model for predicting therapy response compared to two-dimensional cell culture. However, current live-dead staining protocols used for treatment response in spheroid cultures are often expensive, toxic to the cells, or limited in their ability to monitor therapy response over an extended period due to reduced stability. In our study, we have developed a cost-effective method utilizing calcein-AM and Helix NP™ Blue for live-dead staining, enabling the monitoring of therapy response of spheroid cultures for up to 10 days. Additionally, we used ICY BioImage Analysis and Z-stacks projection to calculate viability, which is a more accurate method for assessing treatment response compared to traditional methods on spheroid size. Using the example of glioblastoma cell lines and primary glioblastoma cells, we show that spheroid cultures typically exhibit a green outer layer of viable cells, a turquoise mantle of hypoxic quiescent cells, and a blue core of necrotic cells when visualized using confocal microscopy. Upon treatment of spheroids with the alkylating agent temozolomide, we observed a reduction in the viability of glioblastoma cells after an incubation period of 7 days. This method can also be adapted for monitoring therapy response in different cancer systems, offering a versatile and cost-effective approach for assessing therapy efficacy in three-dimensional culture models.
Association of genetic alterations with prognosis in extramammary Paget disease: insights into the involvement of somatic CDKN2A variants in patients with a poor prognosis
Authors: Iwasawa Okuto , Ikegami Masachika , Miyagawa Takuya , Morita Hiromichi , Saito Hinako , Omori Issei , Awaji Kentaro , Omatsu Jun , Yamada Daisuke , Kage Hidenori , Oda Katsutoshi , Sato Shinichi , Sumida Hayakazu 
Published: August 2024

Abstract

Background
Previous studies have reported the mutational landscape in extramammary Paget disease (EMPD); however, the prognostic implications of genetic alterations remain unexplored. While CDKN2A loss is known to be associated with tumour progression or poor prognosis in some types of cancer, its significance in EMPD has not been investigated.

Objectives
To examine the association between common genetic alterations and prognosis in EMPD.

Methods
A retrospective cohort study was carried out to analyse the data of patients with EMPD registered up to January 2024 in the Center for Cancer Genomics and Advanced Therapeutics database, a nationwide database that records clinical data and comprehensive genomic profiling (CGP) test results in Japan.

Results
A total of 167 patients with EMPD were recorded in the database, with CDKN2A loss being the most frequent genetic variant. Survival analysis was conducted on data from 127 patients. Survival from the initiation of chemotherapy was analysed, adjusting for length bias inherent in the database with the Kaplan–Meier estimator, an established method of adjustment. Patients with BRCA2-mutant tumours (n = 18) had a worse prognosis than those with BRCA2 wildtype (WT) tumours [n = 109; hazard ratio (HR) 2.97, 95% confidence interval (CI) 1.46–6.01 (P = 0.003)]. Additionally, patients in the CDKN2A mutant group (n = 72) had a significantly worse prognosis compared with those in the CDKN2A WT group [n = 55; HR 1.81, 95% CI 1.06–3.07 (P = 0.029)]. Most CDKN2A variants were pathogenic, primarily characterized by loss, while most BRCA2 variants were variants of uncertain significance. In the survival analysis of CGP enrolment based on Eastern Cooperative Oncology Group performance status (ECOG-PS), patients with an ECOG-PS of 1 at the time of CGP enrolment had a significantly poorer prognosis compared with those with an ECOG-PS of 0 (P = 0.034; median survival time 531 vs. 259 days).

Conclusions
A somatic CDKN2A variant, mainly exhibiting loss, may be associated with a poor prognosis in EMPD. Patients with EMPD with BRCA2-mutant disease might also have a worse prognosis. In addition, CGP testing before ECOG-PS deteriorates is preferable, considering that the observed median survival of individuals undergoing CGP tests in an ECOG-PS 1 condition was &lt; 9 months.
Frailty using the Clinical Frailty Scale to predict short- and long-term adverse outcomes following emergency laparotomy: meta-analysis
Authors: Park Brittany , Alani Zena , Sulistio Edrick , Barazanchi Ahmed W H , Koea Jonathan , Vandal Alain , Hill Andrew G , MacCormick Andrew D 
Published: August 2024

Abstract

Background
Emergency laparotomy has high morbidity and mortality rates. Frailty assessment remains underutilized in this setting, in part due to time constraints and feasibility. The Clinical Frailty Scale has been identified as the most appropriate tool for frailty assessment in emergency laparotomy patients and is recommended for all older patients undergoing emergency laparotomy. The prognostic impact of measured frailty using the Clinical Frailty Scale on short- and long-term mortality and morbidity rates remains to be determined.

Methods
Observational cohort studies were identified by systematically searching Medline, Embase, Scopus and CENTRAL databases up to February 2024, comparing outcomes following emergency laparotomy for frail and non-frail participants defined according to the Clinical Frailty Scale. The primary outcomes were short- and long-term mortality rates. A random-effects model was created with pooling of effect estimates and a separate narrative synthesis was created. Risk of bias was assessed.

Results
Twelve articles comprising 5704 patients were included. Frailty prevalence was 25% in all patients and 32% in older adults (age ≥55 years). Older patients with frailty had a significantly greater risk of postoperative death (30-day mortality rate OR 3.84, 95% c.i. 2.90 to 5.09, 1-year mortality rate OR 3.03, 95% c.i. 2.17 to 4.23). Meta-regression revealed that variations in cut-off values to define frailty did not significantly affect the association with frailty and 30-day mortality rate. Frailty was associated with higher rates of major complications (OR 1.93, 95% c.i. 1.27 to 2.93) and discharge to an increased level of care.

Conclusion
Frailty is significantly correlated with short- and long-term mortality rates following emergency laparotomy, as well as an adverse morbidity rate and functional outcomes. Identifying frailty using the Clinical Frailty Scale may aid in patient-centred decision-making and implementation of tailored care strategies for these ‘high-risk’ patients, with the aim of reducing adverse outcomes following emergency laparotomy.
Social Entrepreneurship in Social Work in Multicultural Societies: A Majority and Minority Lens
Authors: Nouman Hani , Choi Daniel Y 
Published: August 2024

Abstract
Despite the growing interest in social entrepreneurship in social work, the concept has not been examined from the perspective of majority and minority groups in multicultural societies. This study presents empirical evidence concerning factors that explain the entrepreneurial intention of social workers based on data from an extensive survey of social workers from the Jewish majority and the Arab minority in Israel. The findings revealed high levels of entrepreneurial intention amongst all the social workers, although it is lower amongst those from the minority group. Social workers from the majority group reported higher levels of openness to experience in the context of entrepreneurial intention and in extraversion compared to the minority group. Training for social entrepreneurship was identified as a key factor driving entrepreneurial intention.
Serum and CSF biomarkers in asymptomatic patients during primary HIV infection: a randomized study
Authors: Calcagno Andrea , Cusato Jessica , Cinque Paola , Marchetti Giulia , Bernasconi Davide , Trunfio Mattia , Bruzzesi Elena , Rusconi Stefano , Gabrieli Arianna , Muscatello Antonio , Antinori Andrea , Ripamonti Diego , Gulminetti Roberto , Antonucci Miriam , Nozza Silvia 
Published: August 2024

Abstract
It is debated whether CNS involvement begins during acute human immunodeficiency virus (HIV) infection in persons without meningitis/encephalitis and whether specific antiretroviral drugs or combinations would be beneficial.
Neurologically asymptomatic participants enrolled in a randomized and controlled study comparing three combination antiretroviral regimens (tenofovir alafenamide/emtricitabine plus dolutegravir; darunavir; or both) during primary HIV infection were enrolled. Serum and CSF were collected at baseline and at 12 and 48 (serum only) weeks after treatment initiation. Single molecule array was used to measure neurofilament light chain (NFL), total tau protein (Tau), brain-derived neurotrophic factor, glial fibrillary acidic protein (GFAP) and ubiquitin C-terminal hydrolase. We assessed the longitudinal change in biomarkers over time, in addition to the change in the prevalence of serum NFL concentrations above previously published age-adjusted cut-offs (7 pg/ml if 5–18 years, 10 pg/ml if 18–51 years, 15 pg/ml if 51–61 years, 20 pg/ml if 61–70 years and 35 pg/ml if &gt;70 years).
Serum was available from 47 participants at all time points, and CSF was available from 13 participants at baseline and 7 at Week 12. We observed a significant direct serum-to-CSF correlation for NFL (ρ = 0.692, P = 0.009), GFAP (ρ = 0.659, P = 0.014) and brain-derived neurotrophic factor (ρ = 0.587, P = 0.045). Serum (ρ = 0.560, P = 0.046) and CSF NFL (ρ = 0.582, P = 0.037) concentrations were directly associated with CSF HIV RNA levels. We observed a significant decrease over time in serum NFL (P = 0.006) and GFAP (P = 0.006) but not in the other biomarkers. No significant difference was observed among the treatment arms. At baseline, serum and CSF age-adjusted NFL levels were above age-adjusted cut-offs in 23 (48.9%) and four participants (30.8%), respectively; considering serum NFL, this proportion was lower at Weeks 12 (31.9%, P = 0.057) and 48 (27.7%, P = 0.13).
A relevant proportion of neurologically asymptomatic participants had abnormal CSF and serum NFL levels during primary HIV infection. NFL and GFAP decreased in serum following combination antiretroviral therapy without significant differences among the treatment arms.
What does it mean to be queer in Wikidata? Practices of gender representation within a transnational online community
Authors: Melis Beatrice , Paolini Chiara , Fioravanti Marta , Metilli Daniele 
Published: August 2024

Abstract
The continuing digitization and datafication that our society is undergoing are having a significant impact on our daily lives, giving rise to new possibilities but also entailing significant risks for people who are discriminated against or marginalized. Queer communities are particularly affected by these processes; therefore, it is crucially relevant to research transnational digital projects that involve them. In the Wikidata Gender Diversity (WiGeDi) project, we are looking at practices of gender representation in the Wikidata knowledge base, a collaborative online project managed by a worldwide community. Working from the idea that gender is a complex social construct, we investigate how the Wikidata community has approached the complex issue of modeling and populating gender data, progressing from a very narrow interpretation of gender as a binary to a representation that is more inclusive of a multiplicity of gender identities.
Reproducing poverty through participation: examining the constraints of community development strategies in fostering empowerment and social change
Authors: Khan Shahzad , Eversole Robyn 
Published: August 2024

Abstract
Community participation is often heralded as a remedy to the disadvantages faced by marginalized people, with the assumption that it catalyses empowerment and social change. However, in development practice, this view may overlook the intricate power dynamics that reinforce marginalization and how they interplay within local communities and with external developers. This paper seeks to examine how power relations in and beyond the local level influence participatory community development initiatives and their potential to challenge or reinforce disadvantage. It focuses on the Rural Support Programmes Network’s much-touted ‘three-tier social mobilization strategy’ in Northwest Pakistan as a qualitative case study, using participant and non-participant observation, document analysis and semi-structured interviews.
Findings indicate that active participation by local people in community development processes does not always catalyse empowerment and social change. Without a deliberate reconfiguration of traditional exclusionary power relations, participation in community initiatives may simply perpetuate social exclusion for disadvantaged groups. Existing social structures allow traditionally powerful people to use participatory processes to reproduce and/or further reinforce their power and control via ‘strategic compliance’. The study concludes that community development programmes require a nuanced understanding of power dynamics and a deliberate effort to reconfigure those dynamics to foster meaningful engagement and empowerment of disadvantaged groups.
Timing of Influenza Antiviral Therapy and Risk of Death in Adults Hospitalized With Influenza-Associated Pneumonia, Influenza Hospitalization Surveillance Network (FluSurv-NET), 2012–2019
Authors: Tenforde Mark W , Noah Kameela P , O’Halloran Alissa C , Kirley Pam Daily , Hoover Cora , Alden Nisha B , Armistead Isaac , Meek James , Yousey-Hindes Kimberly , Openo Kyle P , Witt Lucy S , Monroe Maya L , Ryan Patricia A , Falkowski Anna , Reeg Libby , Lynfield Ruth , McMahon Melissa , Hancock Emily B , Hoffman Marisa R , McGuire Suzanne , Spina Nancy L , Felsen Christina B , Gaitan Maria A , Lung Krista , Shiltz Eli , Thomas Ann , Schaffner William , Talbot H Keipp , Crossland Melanie T , Price Andrea , Masalovich Svetlana , Adams Katherine , Holstein Rachel , Sundaresan Devi , Uyeki Timothy M , Reed Carrie , Bozio Catherine H , Garg Shikha 
Published: August 2024

Abstract

Background
Pneumonia is common in adults hospitalized with laboratory-confirmed influenza, but the association between timeliness of influenza antiviral treatment and severe clinical outcomes in patients with influenza-associated pneumonia is not well characterized.

Methods
We included adults aged ≥18 years hospitalized with laboratory-confirmed influenza and a discharge diagnosis of pneumonia over 7 influenza seasons (2012–2019) sampled from a multistate population-based surveillance network. We evaluated 3 treatment groups based on timing of influenza antiviral initiation relative to admission date (day 0, day 1, days 2–5). Baseline characteristics and clinical outcomes were compared across groups using unweighted counts and weighted percentages accounting for the complex survey design. Logistic regression models were generated to evaluate the association between delayed treatment and 30-day all-cause mortality.

Results
A total of 26 233 adults were sampled in the analysis. Median age was 71 years and most (92.2%) had ≥1 non-immunocompromising condition. Overall, 60.9% started antiviral treatment on day 0, 29.5% on day 1, and 9.7% on days 2–5 (median, 2 days). Baseline characteristics were similar across groups. Thirty-day mortality occurred in 7.5%, 8.5%, and 10.2% of patients who started treatment on day 0, day 1, and days 2–5, respectively. Compared to those treated on day 0, adjusted odds ratio for death was 1.14 (95% confidence interval [CI], 1.01–1.27) in those starting treatment on day 1 and 1.40 (95% CI, 1.17–1.66) in those starting on days 2–5.

Conclusions
Delayed initiation of antiviral treatment in patients hospitalized with influenza-associated pneumonia was associated with higher risk of death, highlighting the importance of timely initiation of antiviral treatment at admission.
Conspicuous consumption for social parity
Authors: Srikanth Chinmayi , Dey Shubhasis 
Published: August 2024

Abstract
Extant literature on status signalling primarily adopts Veblen’s theory of class to caste and racial identities. This study aimed at adopting a more suitable theoretical lens to examine status signalling that is more relevant not only for class identities, but also for other identities such as caste and racial identities. By viewing conspicuous consumption within the framework of the stigma-identity-threat model, the study analyses how socially disadvantaged groups in India respond to stigma through their consumption behaviour. Using data from two rounds of the India Human Development Survey, we study whether disadvantaged social groups embrace or distance themselves from their stigmatised identity. For the periods 2004–05 and 2011–12, we find that households from scheduled castes, scheduled tribes and other backward classes among caste groups, and Muslims among religious groups, tend to move away from their devalued identity. However, the manner in which this is done not only varies across these social groups but also across time. The study also finds that the material threshold that a social group needs to surpass in order to stop signalling status varies based on their position in the social hierarchy.