bluuebunny/crossref_metadata_2025_split huggingface dataset:
High α-SMA expression in the tumor stroma is associated with adverse clinical parameters in mismatch repair–proficient colorectal cancers only
Authors: Sculthorpe Declan J , Denton Amy , Fadhil Wakkas , Rusnita Dewi , Ilyas Mohammad , Mukherjee Abhik 
Published: November 2024

Abstract

Objectives
As mismatch repair status confers differential prognosis in colorectal cancers, this study aimed to determine associations of α–smooth muscle actin (α-SMA) protein expression in mismatch repair–proficient (pMMR) and mismatch repair–deficient (dMMR) colorectal tumors with clinicopathologic and prognostic features.

Methods
Tissue microarrays from patients with colorectal cancer, immunostained with α-SMA, were assessed through digital image analysis. Total (n = 962), pMMR (n = 782), and dMMR (n = 156) stromal H-scores were assessed for associations with clinicopathologic and survival data.

Results
Higher α-SMA expression was correlated with pMMR status (P = 5.2223 × 10–8). In the pMMR subgroup, higher α-SMA stromal expression at the tumor periphery was correlated with higher T stage (P = .002), perineural invasion (P = .038), infiltrative tumor edge (P = .01), involved nodal status (P = .036), metastases (P = .013), synchronous metastases (P = .007), recurrence (P = .004), and both 3-year and 5-year survival (P = .018). dMMR tumors showed no significant correlations with α-SMA staining.

Conclusions
The findings highlight that immunostaining with α-SMA in pMMR colorectal tumors, especially at the tumor periphery, has the potential to identify patients with adverse prognostic features. Digital assessment of α-SMA may offer improved objectivity, accuracy, economy of time, and risk stratification for management.
Bayesian clustering of high-dimensional data via latent repulsive mixtures
Authors: Ghilotti L , Beraha M , Guglielmi A 
Published: November 2024

SUMMARY
Model-based clustering of moderate or large dimensional data is notoriously difficult. We propose a model for simultaneous dimensionality reduction and clustering by assuming a mixture model for a set of latent scores, which are then linked to the observations via a Gaussian latent factor model. This approach was recently investigated by Chandra et al. (2023). The authors use a factor-analytic representation and assume a mixture model for the latent factors. However, performance can deteriorate in the presence of model misspecification. Assuming a repulsive point process prior for the component-specific means of the mixture for the latent scores is shown to yield a more robust model that outperforms the standard mixture model for the latent factors in several simulated scenarios. The repulsive point process must be anisotropic to favour well-separated clusters of data, and its density should be tractable for efficient posterior inference. We address these issues by proposing a general construction for anisotropic determinantal point processes. We illustrate our model in simulations as well as a plant species co-occurrence dataset.
‘A lot of social workers don’t seem to understand or realize the harm that they cause’: Disabled young people’s experiences with sexual well-being in social work practice
Authors: Goulden Ami 
Published: November 2024

Abstract
Young disabled people are disproportionately excluded from equal control, access, and choices concerning their sexual and reproductive rights. While sexual citizenship is founded on a rights-based approach and is closely connected with social work values such as empowerment and entitlement to full participation, many social workers do not include dimensions of sexual well-being in their scope of practice. This phenomenological study explores how social workers address the intersection of sexual well-being and disability from the perspectives of young disabled people. A total of twenty-four semi-structured interviews were carried out with individuals between the ages of 17 and 24 in Ontario, Canada, who identify themselves as disabled and have had prior interactions with a social worker. Social workers adopting risk-averse approaches negatively impacted the trust between young people and their social workers. Young people expressed their discontent with sexual well-being being deprioritized in practice, as participants considered dimensions of sexual well-being to be closely related to their physical, mental, and emotional health. Participants overwhelmingly reported that social workers should discuss sexual well-being with service users using sex-positive perspectives. The findings highlight the importance of holistic and comprehensive social work practices, including sexual well-being and sex-positive perspectives.
Current and Future Strategies for the Prevention and Treatment of Cytomegalovirus Infections in Transplantation
Authors: Heldman Madeleine R , Boeckh Michael J , Limaye Ajit P 
Published: November 2024

Abstract
Successful prevention and treatment of cytomegalovirus (CMV) infection remains a central focus of clinical care in solid organ transplantation (SOT) and allogeneic hematopoietic cell transplantation (HCT). Over the past 5 years, pivotal clinical trials have created new paradigms in CMV prevention, including diverging approaches in HCT and SOT. We review recent advances in CMV risk assessment and progress in antiviral and immune-based strategies for CMV prevention and treatment. We highlight approaches to optimize CMV-specific immunity through vaccination, monoclonal antibodies, and virus-specific T cells. Observational studies and interventional trials of commercially available CMV cell-mediated immunity assays for refining preventive and treatment strategies are summarized. Finally, we discuss the importance of enhancing CMV-specific immunity to mitigate the negative impacts of CMV in different transplant settings. CMV infections in recipients of chimeric antigen receptor-T (CAR-T) cell therapies and other immunocompromised populations are growing areas of importance that are beyond the scope of this review.
Left ventricular volume as a predictor of exercise capacity and functional independence in individuals with normal ejection fraction
Authors: Rowe Stephanie , L’Hoyes Wouter , Milani Mauricio , Spencer Luke , Foulkes Stephen , Paratz Elizabeth , Janssens Kristel , Stassen Jan , Delpire Boris , Pauwels Rik , Moura-Ferreira Sara , Falter Maarten , Bekhuis Youri , Herbots Lieven , Haykowsky Mark J , Claessen Guido , La Gerche Andre , Verwerft Jan 
Published: November 2024

Abstract

Aims
Low cardiorespiratory fitness (CRF) is associated with functional disability, heart failure, and mortality. Left ventricular (LV) end-diastolic volume (LVEDV) has been linked with CRF, but its utility as a diagnostic marker of low CRF has not been tested.

Methods and results
This multi-centre international cohort examined the relationship between LV size on echocardiography and CRF [peak oxygen uptake (peak VO2) from cardiopulmonary exercise testing] in individuals with LV ejection fraction ≥50%. Absolute and body surface area–indexed LVEDV (LVEDVi) were tested as predictors of low CRF and functional disability (peak VO2 &lt;1100 mL/min or &lt;18 mL/kg/min) and compared against candidate measures of cardiac structure and function. A total of 2876 individuals (309 endurance athletes, 251 healthy non-athletes, 1969 individuals with unexplained dyspnoea, and 347 individuals with heart failure with preserved ejection fraction) were included. For the entire cohort, LVEDV had the strongest univariable association with peak VO2 [R2 = 0.45, standardized (std) β = 0.67, P &lt; 0.001] and remained the strongest independent predictor of peak VO2 after adjusting for age, sex, and body mass index (std β = 0.30, P &lt; 0.001). Left ventricular end-diastolic volume was better in identifying low CRF than most established echocardiographic measures [LVEDV area under the receiver operating characteristic curve (AUC) 0.72; LVEDVi AUC 0.71], but equivalent to the E/eʹ ratio. The probability of achieving a peak VO2 below the functional independence threshold was highest for smaller ventricular volumes, with LVEDV and LVEDVi of 88 mL and 57 mL/m2 providing the optimal cut-points, respectively.

Conclusion
Small resting ventricular size is associated with a higher probability of low CRF and functional disability. Left ventricular size is the strongest independent echocardiographic predictor of CRF across the health–disease continuum.
Current Challenges, Solutions, and Novel Directions in Research and Clinical Care: Proceedings From the 14th Annual International Workshop on HIV and Aging
Authors: Baim-Lance Abigail , Cooley Sarah , Yoo-Jeong Moka , Ances Beau , Duque Gustavo , Ellis Ronald J , Flexner Charles , Pence Brian W , Plankey Michael , Mullins John David , Sun Jing , Thames April D , Margolick Joseph B , Moore David J , Erlandson Kristine M 
Published: November 2024

Abstract
Integrating antiretroviral therapy into HIV care dramatically extended the lifespan for people living with HIV. Improving the health span requires understanding aging, HIV, associated comorbid conditions, and concurrent treatments. The 14th annual International Workshop on HIV and Aging on October 26–27, 2023 included podium presentations on: Sarcopenia: Biology, Pathophysiology, Prevention and Treatment; Long-acting ART; Central Nervous System (CNS) complications; Asymptomatic Neurocognitive Impairment (ANI); Mental Health; Loneliness; and Resilience. Presentations highlighted persistent concerns for people living with HIV including sarcopenia and frailty, mental health, loneliness, and cognition. Presenters encouraged prioritizing mental health treatment, reducing social isolation, and research on resiliency.
The Evolution in Dementia Caregiving Research: NIA’s Catalyst Role
Authors: Ory Marcia G , Stevens Alan B 
Published: November 2024

Abstract
This article celebrates the National Institute on Aging (NIA)’s successes over the past 50 years in advancing the science base and informing the need for and response to dementia caregiving. In parallel with other public and private efforts, insightful NIA leadership supported by funding initiatives established the field of dementia caregiving research. In support of the health and well-being of family caregivers, NIA was a catalyst of innovation that led to numerous evidence-based caregiving interventions informed by basic research on care tasks and consequences. As evidence of the impending burden of dementia care on US families mounted, NIA-funded multidisciplinary collaboratives of researchers generated comprehensive models of family caregiving across diverse populations. Today, the dementia caregiving evidence base is shaping public policy and making possible dementia caregiving support services in health systems and community-based organizations. NIA continues to support the scientific study of dementia caregiving with a collaboration of leading scientists and by making available state-of-the-art datasets and encouraging standardized research methodologies. NIA’s leadership in the field of dementia caregiving research has never been more significant, as the number of persons living with dementia in the United States approaches 7 million and the value of family caregiving is estimated to be $350 billion.
Digital recognition: cybersecurity and internet infrastructure in UAE–Israel diplomacy
Authors: Hassib Bassant , Shires James 
Published: November 2024

Abstract
The 2020 Israel–UAE Abraham Accords normalized these states' relations, with heavy emphasis on digital technologies. International Relations theories of recognition, however, hardly consider the role digital technologies play in establishing recognition between states. What role, then, did digital technologies play in this landmark shift in UAE–Israel recognition? This article uses three aspects of digital technologies in the UAE–Israel case—cybersecurity cooperation, cloud computing, and subsea cables—to inductively develop three propositions regarding the role of digital technologies in state recognition. First, states use digital technologies—and private sector companies that own and operate them—as diplomatic lubrication: a means to navigate around and overcome difficult diplomatic relationships, building momentum towards recognition. Second, digital competition between states leads them to conform their national economic structures towards global technology companies in similar ways, thereby recognizing each other as equal participants in a global market—which we term market-oriented homogenization. Third, states involved in transnational internet infrastructure projects together develop technical working practices, interests, and dependencies that facilitate diplomatic recognition—which we term infrastructural integration. Building on these three propositions, we put forward an overall concept of ‘digital recognition’ to capture their common theme: the influence of digital technologies, their owners or their operators on state recognition.
The influence of human and marine wildlife presence on white shark behaviour in nearshore areas
Authors: Monteforte Kim I , Butcher Paul A , Morris Stephen G , Tucker James P , Griffin Kingsley J , Kelaher Brendan P 
Published: November 2024

Abstract
The co-occurrence of people and sharks within nearshore areas raises concerns about human safety. Unprovoked shark bites are one of the most renowned negative human–wildlife encounters. White sharks (Carcharodon carcharias) are implicated in most fatal unprovoked shark bites globally, but there is limited knowledge of white shark behaviour in the presence of people. We used drone-based methods to analyse human–shark and wildlife–shark interactions. We found a higher probability of a white shark interaction with a nearby person (0.81) in comparison to an animal (0.65). Fishers had the highest, and swimmers had the lowest probability of a white shark interaction. White sharks exhibited investigative behaviour in most interactions, with directional changes towards a nearby person or animal in 85.9% and 94.0% of interactions, respectively. There was a higher probability for white sharks to increase their speed towards animals (0.16) than people (0.01). The likelihood of white sharks altering their speed or direction when people were present depended on human activity. Overall, our study highlighted the value of drone technology in providing insights into white shark behaviour. It also supported the contention that, while people and white sharks coexist within nearshore areas, the probability of a negative human–wildlife encounter remains low.
Sex, sexual orientation, and gender identity data collection across electronic health record platforms: a national cross-sectional survey
Authors: Streed Carl G , Navarra Maylene , Beach Lauren B , Phillips Gregory , Hackenberger Paige N , Jordan Sumanas 
Published: November 2024

Abstract

Objectives
To assess the current state of sex, sexual orientation, and gender identity (SSOGI) data collection options in US electronic health record (EHR) platforms.

Materials and Methods
We utilized an anonymous survey distributed via purposive snowball sampling to assess EHR platforms across the United States.

Results
Of 90 surveys started, 41 (45.6%) were completed and used for data analysis. Respondents represented a geographically diverse sample of health care centers across the United States. EPIC was the most used EHR platform (70.7%) followed by Cerner (9.8%). Across reported platforms, a majority utilized structured fields to collect and document patient SSOGI data (n = 25, 61.0%). There was variability across platforms regarding SSOGI data elements collected. No platform collected all recommended SSOGI data elements.

Discussion
Significant variation exists across EHR platforms and across health care settings using the same EHR platform.

Conclusion
National standards need to be followed for SSOGI data collection in EHR platforms.
Validation of an LC–MS–MS method for analysis of 58 drugs of abuse in oral fluid and method comparison with an established LC–HRMS method
Authors: Zheng Yufang , Axelsson Magnus A.B , Andresen Bergström Moa 
Published: November 2024

Abstract
Liquid chromatography–mass spectrometry (LC–MS) methods for detection of multiple drugs of abuse (DoA) in oral fluid (OF) samples are being implemented in many clinical routine laboratories. Therefore, there is a need to develop new multianalyte methods with simple sample pretreatment and short analysis times. The purpose of this work was to validate a method detecting 58 DoA to be used with two different OF sampling kits, the saliva collection system (SCS) from Greiner Bio-One and Quantisal from Immunalysis, using the same sample pretreatment and analytical method. A set of 110 samples collected with the SCS kit was further compared to an high-resolution mass spectrometry (LC–HRMS) method in another laboratory. The method was successfully validated, with precision and accuracy of ≤15% and z-scores of &lt;2 for external controls. Using a sensitive LC–MS–MS instrument, the detection limits were &lt;1 µg/l in neat oral fluid. In the comparative study between the LC–MS–MS and LC–HRMS methods using SCS samples, a good agreement was observed. Discrepancies were limited to lower concentration ranges, attributable to differences in cut-off thresholds between the methods. This work contributes to the development of LC–MS multianalyte methods for OF samples, which are suitable for clinical routine laboratories.
On probabilistic and causal reasoning with summation operators
Authors: Ibeling Duligur , Icard Thomas , Mossé Milan 
Published: November 2024

Abstract
Ibeling et al. (2023, Annals of Pure and Applied Logic, 103339) axiomatize increasingly expressive languages of causation and probability, and Mossé et al. (2024, The Review of Symbolic Logic, 17, 106–131) show that reasoning (specifically the satisfiability problem) in each causal language is as difficult, from a computational complexity perspective, as reasoning in its merely probabilistic or ‘correlational’ counterpart. Introducing a summation operator to capture common devices that appear in applications—such as the $do$-calculus of Pearl (Causality. Cambridge University Press, 2009) for causal inference, which makes ample use of marginalization—van der Zander et al. (The hardness of reasoning about probabilities and causality. In Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence, IJCAI-23, E. Elkind, ed., pp. 5730–5738. International Joint Conferences on Artificial Intelligence Organization. Main Track. 2023) extend these earlier complexity results to causal and probabilistic languages with marginalization. We complete this extension, fully characterizing the complexity of probabilistic and causal reasoning with summation, demonstrating that these again remain equally difficult. Surprisingly, allowing free variables for random variable values results in a system that is undecidable, so long as the ranges of these random variables are unrestricted. We finally axiomatize these languages featuring marginalization (or more generally summation), resolving open questions posed by Ibeling et al. (2023, Annals of Pure and Applied Logic, 103339).
The Characterization of Ancient Methanococcales Malate Dehydrogenases Reveals That Strong Thermal Stability Prevents Unfolding Under Intense γ-Irradiation
Authors: Madern Dominique , Halgand Frédéric , Houée-Levin Chantal , Dufour Anne-Béatrice , Coquille Sandrine , Ansanay-Alex Salomé , Sacquin-Mora Sophie , Brochier-Armanet Céline 
Published: November 2024

Abstract
Malate dehydrogenases (MalDHs) (EC.1.1.1.37), which are involved in the conversion of oxaloacetate to pyruvate in the tricarboxylic acid cycle, are a relevant model for the study of enzyme evolution and adaptation. Likewise, a recent study showed that Methanococcales, a major lineage of Archaea, is a good model to study the molecular processes of proteome thermoadaptation in prokaryotes. Here, we use ancestral sequence reconstruction and paleoenzymology to characterize both ancient and extant MalDHs. We observe a good correlation between inferred optimal growth temperatures and experimental optimal temperatures for activity (A-Topt). In particular, we show that the MalDH present in the ancestor of Methanococcales was hyperthermostable and had an A-Topt of 80 °C, consistent with a hyperthermophilic lifestyle. This ancestor gave rise to two lineages with different thermal constraints: one remained hyperthermophilic, while the other underwent several independent adaptations to colder environments. Surprisingly, the enzymes of the first lineage have retained a thermoresistant behavior (i.e. strong thermostability and high A-Topt), whereas the ancestor of the second lineage shows a strong thermostability, but a reduced A-Topt. Using mutants, we mimic the adaptation trajectory toward mesophily and show that it is possible to significantly reduce the A-Topt without altering the thermostability of the enzyme by introducing a few mutations. Finally, we reveal an unexpected link between thermostability and the ability to resist γ-irradiation-induced unfolding.
COG database update 2024
Authors: Galperin Michael Y , Vera Alvarez Roberto , Karamycheva Svetlana , Makarova Kira S , Wolf Yuri I , Landsman David , Koonin Eugene V 
Published: November 2024

Abstract
The Clusters of Orthologous Genes (COG) database, originally created in 1997, has been updated to reflect the constantly growing collection of completely sequenced prokaryotic genomes. This update increased the genome coverage from 1309 to 2296 species, including 2103 bacteria and 193 archaea, in most cases, with a single representative genome per genus. This set covers all genera of bacteria and archaea that included organisms with ‘complete genomes’ as per NCBI databases in November 2023. The number of COGs has been expanded from 4877 to 4981, primarily by including protein families involved in bacterial protein secretion. Accordingly, COG pathways and functional groups now include secretion systems of types II through X, as well as Flp/Tad and type IV pili. These groupings allow straightforward identification and examination of the prokaryotic lineages that encompass—or lack—a particular secretion system. Other developments include improved annotations for the rRNA and tRNA modification proteins, multi-domain signal transduction proteins, and some previously uncharacterized protein families. The new version of COGs is available at https://www.ncbi.nlm.nih.gov/research/COG, as well as on the NCBI FTP site https://ftp.ncbi.nlm.nih.gov/pub/COG/, which also provides archived data from previous COG releases.