bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nut consumption and disability-free survival in community-dwelling older adults: a prospective cohort study
Authors: Wild Holly , Nurgozhina Madina , Gasevic Danijela , Coates Alison M , Woods Robyn L , Ryan Joanne , Beilin Lawrence , Govindaraju Thara , McNeil John J , Owen Alice J 
Published: November 2024

Abstract

Objectives
The relationship between nut intake and disability-free survival (healthy lifespan) in later life is unclear. The objective was to evaluate the association between nut intake and disability-free survival in a cohort of adults aged ≥70 years, and whether this varied according to overall diet quality.

Methods
This prospective cohort study involved 9916 participants from the ASPREE Longitudinal Study of Older Persons. Participants completed a 49-item Food Frequency questionnaire from which frequency of nut intake was obtained and were asked to categories usual intake as no/infrequent [never/rarely, 1–2 times/month], weekly [1–2 times/week, often 3–6 times/week] or daily [every day or several times a day]. The outcome measured was a composite of first-event mortality, onset of dementia, or persistent physical disability. Cox proportional hazards regression models, adjusted for socio-demographic factors, health-related and clinical covariates and overall dietary quality were conducted to examine the association between varying levels of nut intake and disability-free survival.

Results
Over a mean of 3.9 years of follow-up, the risk of reaching the DFS endpoint were 23% lower (HR 0.77 [0.61–0.98]) for those who consumed nuts daily, when compared to those with no/infrequent nut consumption. Subgroup analysis demonstrated a significant association between daily nut consumption and healthy lifespan among individuals in the second dietary quality tertile (HR 0.71[0.51–0.98]).

Conclusion
For community-dwelling adults aged 70 years and over with sub-optimal diets, daily nut consumption is associated with the promotion of healthy lifespan (disability-free survival).
A gentle introduction to pangenomics
Authors: Matthews Chelsea A , Watson-Haigh Nathan S , Burton Rachel A , Sheppard Anna E 
Published: November 2024

Abstract
Pangenomes have emerged in response to limitations associated with traditional linear reference genomes. In contrast to a traditional reference that is (usually) assembled from a single individual, pangenomes aim to represent all of the genomic variation found in a group of organisms. The term ‘pangenome’ is currently used to describe multiple different types of genomic information, and limited language is available to differentiate between them. This is frustrating for researchers working in the field and confusing for researchers new to the field. Here, we provide an introduction to pangenomics relevant to both prokaryotic and eukaryotic organisms and propose a formalization of the language used to describe pangenomes (see the Glossary) to improve the specificity of discussion in the field.
Digital annealing optimization for natural product structure elucidation
Authors: Lee Chien , Wang Pei-Hua , Tseng Yufeng Jane 
Published: November 2024

Abstract
The digital annealer (DA) leverages its computational capabilities of up to 100 000 bits to address the complex nondeterministic polynomial-time (NP)-complete challenge inherent in elucidating complex structures of natural products. Conventional computational methods often face limitations with complex mixtures, as they struggle to manage the high dimensionality and intertwined relationships typical in natural products, resulting in inefficiencies and inaccuracies. This study reformulates the challenge into a Quadratic Unconstrained Binary Optimization framework, thereby harnessing the quantum-inspired computing power of the DA. Utilizing mass spectrometry data from three distinct herb species and various potential scaffolds, the DA proficiently locates optimal sidechain combinations that adhere to predefined target molecular weights. This methodology enhances the probability of selecting appropriate sidechains and substituted positions and ensures the generation of solutions within a reasonable 5-min window. The findings underscore the transformative potential of the DA in the realms of analytical chemistry and drug discovery, markedly improving both the precision and practicality of natural product structure elucidation.
Dynamic factor analysis with dependent Gaussian processes for high-dimensional gene expression trajectories
Authors: Cai Jiachen , Goudie Robert J B , Starr Colin , Tom Brian D M 
Published: November 2024

Abstract
The increasing availability of high-dimensional, longitudinal measures of gene expression can facilitate understanding of biological mechanisms, as required for precision medicine. Biological knowledge suggests that it may be best to describe complex diseases at the level of underlying pathways, which may interact with one another. We propose a Bayesian approach that allows for characterizing such correlation among different pathways through dependent Gaussian processes (DGP) and mapping the observed high-dimensional gene expression trajectories into unobserved low-dimensional pathway expression trajectories via Bayesian sparse factor analysis. Our proposal is the first attempt to relax the classical assumption of independent factors for longitudinal data and has demonstrated a superior performance in recovering the shape of pathway expression trajectories, revealing the relationships between genes and pathways, and predicting gene expressions (closer point estimates and narrower predictive intervals), as demonstrated through simulations and real data analysis. To fit the model, we propose a Monte Carlo expectation maximization (MCEM) scheme that can be implemented conveniently by combining a standard Markov Chain Monte Carlo sampler and an R package GPFDA,which returns the maximum likelihood estimates of DGP hyperparameters. The modular structure of MCEM makes it generalizable to other complex models involving the DGP model component. Our R package DGP4LCF that implements the proposed approach is available on the Comprehensive R Archive Network (CRAN).
Recoverability of causal effects under presence of missing data: a longitudinal case study
Authors: Holovchak Anastasiia , McIlleron Helen , Denti Paolo , Schomaker Michael 
Published: November 2024

Summary
Missing data in multiple variables is a common issue. We investigate the applicability of the framework of graphical models for handling missing data to a complex longitudinal pharmacological study of children with HIV treated with an efavirenz-based regimen as part of the CHAPAS-3 trial. Specifically, we examine whether the causal effects of interest, defined through static interventions on multiple continuous variables, can be recovered (estimated consistently) from the available data only. So far, no general algorithms are available to decide on recoverability, and decisions have to be made on a case-by-case basis. We emphasize the sensitivity of recoverability to even the smallest changes in the graph structure, and present recoverability results for three plausible missingness-directed acyclic graphs (m-DAGs) in the CHAPAS-3 study, informed by clinical knowledge. Furthermore, we propose the concept of a “closed missingness mechanism”: if missing data are generated based on this mechanism, an available case analysis is admissible for consistent estimation of any statistical or causal estimand, even if data are missing not at random. Both simulations and theoretical considerations demonstrate how, in the assumed MNAR setting of our study, a complete or available case analysis can be superior to multiple imputation, and estimation results vary depending on the assumed missingness DAG. Our analyses demonstrate an innovative application of missingness DAGs to complex longitudinal real-world data, while highlighting the sensitivity of the results with respect to the assumed causal model.
Risk factors and protective measures for desmoid tumours in familial adenomatous polyposis: retrospective cohort study
Authors: Rausa Emanuele , Duroni Valeria , Ferrari Davide , Signoroni Stefano , Ciniselli Chiara M , Lauricella Sara , Brignola Clorinda , Ricci Maria T , Gronchi Alessandro , Verderio Paolo , Vitellaro Marco 
Published: November 2024

Abstract

Background
Familial adenomatous polyposis is a cancer-predisposing syndrome caused by germline pathogenic variants of the adenomatous polyposis coli gene, leading to numerous colorectal polyps and a high risk of colorectal cancer. Desmoid tumours have become significant in the management of familial adenomatous polyposis after a colectomy, yet the exact incidence remains undetermined due to a lack of dedicated surveillance.

Methods
This retrospective study accessed data from the prospectively maintained Hereditary Digestive Tumours Registry from 2000 to 2023. Desmoid-free survival was analysed using Cox regression and Kaplan–Meier curves.

Results
A total of 202 patients with familial adenomatous polyposis who underwent colorectal surgery were enrolled. Of the patients, 21 (10.4%) developed intra-abdominal desmoid tumours after surgery. Desmoid tumours were associated with surgical procedure, histology of cancer at the time of surgery, and family history of intra-abdominal desmoid tumours. The overall desmoid-free survival probability at a median follow-up of 84 months was 90%. Histology of cancer at the time of surgery (HR 0.25 (95% c.i. 0.10 to 0.59)), family history of intra-abdominal desmoid tumours (HR 2.92 (95% c.i. 1.22 to 6.97)), an open approach compared with a laparoscopic approach (HR 2.43 (95% c.i. 1.03 to 5.73)), and a proctocolectomy compared with a rectal-sparing total colectomy (HR 3.01 (95% c.i. 1.28 to 7.10)) emerged as significant prognostic factors affecting desmoid-free survival.

Conclusion
A minimally invasive rectal-sparing total colectomy appears protective against the development of desmoid tumours. Early surgery does not seem to increase desmoid tumour risk. A dedicated surveillance regimen for desmoid tumours in patients with familial adenomatous polyposis is needed to improve outcomes and quality of life.
Strengths-Based Screeners for K–8 Students: A Scoping Review
Authors: Nelson Tiffany , Raines James C 
Published: November 2024

Abstract
Students are increasingly experiencing social–emotional, behavioral, and mental health challenges. Although it is necessary to pinpoint students’ academic, social–emotional, and behavioral deficits, it is essential to focus on assessing the student’s strengths as a central component in intervention planning to improve student outcomes. A scoping review was conducted to identify rating scales recognized as strengths-based screeners in the literature for K–8 students and examine those scales based on 12 rating scale criteria. Four online databases and standard reference books were used to identify screeners in the literature from 1997 to 2024 that met the eligibility criteria. The RAND Education Assessment Finder was used to identify gray literature. The screeners found in the literature were examined using the 12 rating scale criteria. Research of the literature resulted in 110 sources reviewed. Twenty screeners were identified from the 46 sources screened for evidence, resulting in three scales that best met the criteria for a strengths-based screener: Social–Emotional Assets and Resilience Scales, Devereux Student Strengths Assessment-Mini, and Social Skills Improvement System Social and Emotional Learning Brief Scales. Many screeners are referred to as strengths-based but focus on student deficits. This scoping review synthesizes the literature, discusses gaps in knowledge, and highlights 12 rating scale criteria as one approach to identifying strengths-based brief screening tools. As a vital member of the school-based team, school social workers can assist in selecting strength-based screeners to enhance Tier 2 interventions and student outcomes.
C–C Motif chemokine receptor-2 blockade ameliorates pulmonary hypertension in rats and synergizes with a pulmonary vasodilator
Authors: Tsuboya Naoki , Sawada Hirofumi , Mitani Yoshihide , Oshita Hironori , Ohya Kazunobu , Takeoka Mami , Kabwe Jane Chanda , Miyasaka Yoshiki , Ito Hiromasa , Yodoya Noriko , Ohashi Hiroyuki , Maruyama Junko , Okamoto Ryuji , Mashimo Tomoji , Dohi Kaoru , Nishimura Yuhei , Maruyama Kazuo , Hirayama Masahiro 
Published: November 2024

Abstract

Aims
We investigated whether the disruption of C–C motif chemokine receptor (CCR) 2 may attenuate the development of pulmonary arterial hypertension (PAH) in any rat models with the reversal of the associated pro-inflammatory state and vascular dysfunction, and synergize with a conventional pulmonary vasodilator.

Methods and results
Using Ccr2(−/−) rats generated by CRISPR/Cas9, we investigated pulmonary hypertension (PH) in Ccr2(+/+) or Ccr2(−/−) rats treated with monocrotaline (MCT), SU5416/hypoxia (SuHx) and chronic hypoxia (CH). Ccr2(−/−) decreased the right ventricular systolic pressure, an index of right ventricular hypertrophy and mortality rate, and reversed increased expression of inflammatory cytokines/chemokines [interleukin-6, tumour necrosis factor-α, C–C motif chemokine receptor (CCL)-2, interleukin-1β, transforming growth factor-β] in rats 3weeks after MCT injection, but not in SuHx or CH models. Consistently, Ccr2(−/−) decreased indices of pulmonary vascular diseases (PVDs) and perivascular macrophage infiltration, as well as reversed impaired bone morphogenetic protein receptor type 2 signalling, increased endothelial apoptosis and impaired nitric oxide signalling and decreased phosphodiesterase-5 (PDE5) expression in lungs in MCT-treated rats. Gene expression of receptors for prostaglandin I2 and endothelin was not changed by Ccr2(−/−) in MCT-treated rats. In cultured pulmonary arterial smooth muscle cells (PASMCs), Ccr2(−/−) suppressed CCL2-induced hyperproliferation and dedifferentiation as well as reversed CCL2-induced decrease in PDE5 expression. The whole-genome RNA sequencing analysis identified differentially expressed genes in CCL2-stimulated Ccr2(−/−) PASMCs, which are related to the regulation of cellular differentiation and contraction. Based on studies in rats and cultured PASMCs, we investigated whether a PDE5 inhibitor, tadalafil, synergizes with Ccr2(−/−). Tadalafil administration ameliorated PH and PVDs in MCT-treated Ccr2(−/−) rats but not in Ccr2(+/+) rats. Tadalafil further improved survival in MCT-treated Ccr2(−/−) rats.

Conclusion
The present findings demonstrated that CCR2 disruption ameliorated PAH in MCT-treated rats, which was associated with the reversal of dysregulated inflammatory pathways and vascular dysfunction and synergized with tadalafil. These findings suggest that CCR2 may be a therapeutic target in intractable PAH patients with a certain CCR2-related inflammatory phenotype and refractory to conventional pulmonary vasodilators.
An infusion port for recurrent massive pericardial effusion: a case report
Authors: Zhao Yuechen , He Ying , Zou Fengwei , Hou Xiaofeng 
Published: November 2024

Abstract

Background
Patients with recurrent massive pericardial effusion are at risk of recurrent cardiac tamponade. The current standard of care includes repeat pericardiocentesis or pericardial window when recurrent effusions cause haemodynamic compromise. Here, we report a case of a patient in whom an infusion port was used for drainage of recurrent pericardial effusion. Patient was followed up for 10 months demonstrating convenience and safety of use without evidence of cardiac tamponade.

Case summary
We present a patient with recurrent massive pericardial effusion after previously undergoing two difficult pericardiocenteses of posteriorly located pericardial effusion causing tamponade. An infusion port was implanted and periodical follow-up and drainage through the port were performed. During follow-up, there was no evidence of tamponade caused by recurrence of pericardial effusion and no complications from the port.

Discussion
Pericardiocentesis can be challenging in certain circumstances such as loculated or posteriorly located pericardial effusion. For patients with recurrent effusion, there is an incremental risk of serious complications with every pericardiocentesis. This case illustrates the feasibility of using an infusion port in recurrent pericardial effusion. After subcutaneous implantation of the infusion port, repeat pericardiocentesis and its related complications were avoided. Later pericardial decompression and intrapericardial administration of medications were simple and safe by accessing the port top.
Influence of smoking on cardiometabolic profile and surgical outcomes in patients with primary aldosteronism: a cohort study
Authors: Araujo-Castro Marta , Paja Fano Miguel , González-Boillos Marga , Pascual-Corrales Eider , Parra Ramírez Paola , Martín Rojas-Marcos Patricia , García-Cano Ana , Ruiz-Sanchez Jorge Gabriel , Vicente Almudena , Gómez-Hoyos Emilia , Casterás Ana , Puig-Perez Albert , García Sanz Iñigo , Recasens Mònica , Barahona San Millan Rebeca , Picón César María José , Díaz Guardiola Patricia , Perdomo Carolina , Manjón-Miguélez Laura , Rebollo Román Ángel , Robles Lázaro Cristina , María Recio José , Morales-Ruiz Manuel , Calatayud María , Jiménez López Noemi , Meneses Diego , Sampedro Nuñez Miguel , Ribas Elena Mena , Sanmartín Sánchez Alicia , Gonzalvo Diaz Cesar , Lamas Cristina , del Castillo Tous María , Serrano Joaquín , Michalopoulou Theodora , Tenes Rodrigo Susana , Roa Chamorro Ricardo , Jaén Aguila Fernando , Moya Mateo Eva María , Gutiérrez-Medina Sonsoles , Hanzu Felicia Alexandra 
Published: November 2024

Abstract

Aim
To evaluate the influence of smoking on cardiometabolic profile and surgical outcomes in patients with primary aldosteronism (PA).

Methods
Multicentre retrospective study of patients with PA evaluated in 36 Spanish tertiary hospitals with available information on smoking habits [smokers and non-smokers (never smokers and ex-smokers)].

Results
A total of 881 patients were included, of whom 180 (20.4%) were classified as smokers and 701 as non-smokers. At diagnosis, smokers and non-smokers did not differ in blood pressure or serum potassium levels between. However, smokers had a higher prevalence of left ventricular hypertrophy (LVH) than non-smokers [odds ratio (OR) 2.0, 95% confidence interval (CI) 1.23-3.25], and smokers were more likely to have severe LVH than non-smokers (12.5% vs 6.6%, P = .164). A larger mean tumour size of the adrenal nodule/s was observed in the smoking group (18.6 ± 9.66 vs 15.8 ± 8.66 mm, P = .002). In addition, the odds of mild autonomous cortisol secretion (MACS) was greater in smokers than in non-smokers (OR 2.1, 95% CI 1.14-4.06), but these differences disappeared when adjusted for the size of the adrenal nodule/s (adjusted OR 1.6, 95% CI 0.76-3.37). The rate of biochemical and hypertension cure was similar in both groups; however, hypertension cure tended to be more frequent in the non-smoker group (41.2% vs 29.9%, P = .076).

Conclusions
Patients with PA who smoke have a higher prevalence of LVH and MACS and larger adrenal nodule/s than non-smokers. Smoking has no significant effect on the probability of hypertension response after adrenalectomy in patients with PA; however, a tendency to a lower probability of hypertension cure is observed in smokers compared to non-smokers.
Secretin infusion decreases food intake in healthy men—a randomized, placebo-controlled, double-blind, crossover study
Authors: Heimbürger Sebastian M N , Bentzen Maria J , Kizilkaya Hüsün S , Hartmann Bolette , Holst Jens J , Rosenkilde Mette M , Dela Flemming , Hansen Svend H , Rehfeld Jens F , Christensen Mikkel B , Knop Filip K 
Published: November 2024

Abstract

Design
The hormone secretin, best known for regulating pH in the duodenum, has anorectic properties in mice proposedly mediated via secretin-induced brown adipose tissue (BAT) activation. We investigated the effects of exogenous secretin on ad libitum food intake, BAT activity, and postprandial physiology in healthy male volunteers.

Methods
In a randomized, placebo-controlled, double-blind, crossover study, 25 healthy men underwent two 5-h i.v. infusions of secretin (1 pmol/kg/min) and placebo (saline), respectively, with an interposed 2-month wash-out period. After 30 min of infusion, a standardized liquid-mixed meal was ingested, and after 5 h, food intake and meal duration were assessed during an ad libitum meal test. Brown adipose tissue activity was assessed regularly by thermal imaging-measured supraclavicular skin temperature.

Results
Compared with placebo, secretin significantly decreased ad libitum food intake by 173 ± 88 kcal (95% CI, 0.76-0.99, P = .039) but did not alter ad libitum meal duration. Secretin acutely decreased BAT activity but increased it postprandially compared with placebo. Acetaminophen-assessed gastric emptying was not affected by exogenous secretin, but secretin increased gallbladder volume, bile acid synthesis, and circulating levels of lipase, amylase, and triglycerides, while decreasing plasma Na+. Compared with placebo, secretin infusion was associated with 24.0 ± 10.8% (95% CI, 0.3-1, P = .025) more adverse events (headache, nausea, diarrhea, and vomiting).

Conclusions
In healthy men, secretin infusion decreased ad libitum food intake concomitantly with a postprandial increase in BAT activity as assessed by thermal imaging-measured supraclavicular skin temperature.

Clinical trial registration number
Clinicaltrials.gov, NCT04613700
Productivity and growth decomposition: a novel single-index smooth-coefficient stochastic frontier approach
Authors: Sun Kai , Kumbhakar Subal C , Lien Gudbrand 
Published: November 2024

Abstract
Our paper investigates productivity, output growth and total factor productivity (TFP) growth using a novel single-index smooth-coefficient stochastic frontier approach and two firm-level datasets respectively from the high technology (high-tech) manufacturing and Knowledge Intensive Business Services (KIBS) sectors in Norway. The approach considers input productivity and technical inefficiency to be flexible functions of production environmental variables indexed with unknown parameters for more precise estimation of marginal effects of these variables on the frontier and inefficiency. Output growth is decomposed into technical change (TC), input-driven component (IDC) and efficiency change (EC), while TFP growth is decomposed into TC, scale component and EC. The primary objective is to (i) maximise output through the frontier and efficiency channels and (ii) enhance productivity growth through such channels as technical progress and efficiency improvement, specifically tailored for the manufacturing and services industries. The empirical results reveal substantial heterogeneity in technology across firms. Overall speaking, geographical industrial concentration, export intensity and urbanisation positively influence output in both sectors. Technical progress contributes to TFP growth in both sectors; however, TC is biased towards capital in the high-tech sector and driven by labour in the KIBS sector. In addition to TC, TFP growth in the high-tech and KIBS sectors also benefits from EC and IDC, respectively.