bluuebunny/crossref_metadata_2025_split huggingface dataset:
A CAG repeat threshold for therapeutics targeting somatic instability in Huntington's disease
Authors: Aldous Sarah G , Smith Edward J , Landles Christian , Osborne Georgina F , Cañibano-Pico Maria , Nita Iulia M , Phillips Jemima , Zhang Yongwei , Jin Bo , Hirst Marissa B , Benn Caroline L , Bond Brian C , Edelmann Winfried , Greene Jonathan R , Bates Gillian P 
Published: February 2024

Abstract
The Huntington's disease mutation is a CAG repeat expansion in the huntingtin gene that results in an expanded polyglutamine tract in the huntingtin protein. The CAG repeat is unstable and expansions of hundreds of CAGs have been detected in Huntington's disease post-mortem brains. The age of disease onset can be predicted partially from the length of the CAG repeat as measured in blood. Onset age is also determined by genetic modifiers, which in six cases involve variation in DNA mismatch repair pathways genes. Knocking-out specific mismatch repair genes in mouse models of Huntington's disease prevents somatic CAG repeat expansion. Taken together, these results have led to the hypothesis that somatic CAG repeat expansion in Huntington's disease brains is required for pathogenesis. Therefore, the pathogenic repeat threshold in brain is longer than (CAG)40, as measured in blood, and is currently unknown.
The mismatch repair gene MSH3 has become a major focus for therapeutic development, as unlike other mismatch repair genes, nullizygosity for MSH3 does not cause malignancies associated with mismatch repair deficiency. Potential treatments targeting MSH3 currently under development include gene therapy, biologics and small molecules, which will be assessed for efficacy in mouse models of Huntington's disease. The zQ175 knock-in model carries a mutation of approximately (CAG)185 and develops early molecular and pathological phenotypes that have been extensively characterized. Therefore, we crossed the mutant huntingtin allele onto heterozygous and homozygous Msh3 knockout backgrounds to determine the maximum benefit of targeting Msh3 in this model.
Ablation of Msh3 prevented somatic expansion throughout the brain and periphery, and reduction of Msh3 by 50% decreased the rate of expansion. This had no effect on the deposition of huntingtin aggregation in the nuclei of striatal neurons, nor on the dysregulated striatal transcriptional profile. This contrasts with ablating Msh3 in knock-in models with shorter CAG repeat expansions. Therefore, further expansion of a (CAG)185 repeat in striatal neurons does not accelerate the onset of molecular and neuropathological phenotypes. It is striking that highly expanded CAG repeats of a similar size in humans cause disease onset before 2 years of age, indicating that somatic CAG repeat expansion in the brain is not required for pathogenesis.
Given that the trajectory for somatic CAG expansion in the brains of Huntington's disease mutation carriers is unknown, our study underlines the importance of administering treatments targeting somatic instability as early as possible.
Regulatory T-cell frequency and function in acute myocardial infarction patients and its correlation with ventricular dysfunction
Authors: Martínez-Shio Elena Berenice , Marín-Jáuregui Laura Sherell , Rodríguez-Ortega Alma Celeste , Doníz-Padilla Lesly Marsol , González-Amaro Roberto , Escobedo-Uribe Carlos David , Monsiváis-Urenda Adriana Elizabeth 
Published: February 2024

Abstract
A high percentage of patients with acute coronary syndrome develop heart failure due to the ischemic event. Regulatory T (Treg) cells are lymphocytes with suppressive capacity that control the immune response and include the conventional CD4+ CD25hi Foxp3+ cells and the CD4+ CD25var CD69+ LAP+ Foxp3− IL-10+ cells. No human follow-up studies focus on Treg cells’ behavior after infarction and their possible relationship with ventricular function as a sign of postischemic cardiac remodeling. This study aimed to analyze, by flow cytometry, the circulating levels of CD69+ Treg cells and CD4+ CD25hi Foxp3+ cells, their IL-10+ production as well as their function in patients with acute myocardial infarction (AMI), and its possible relation with ventricular dysfunction. We found a significant difference in the percentage of CD4+ CD25hi Foxp3+ cells and IL-10+ MFI in patients with AMI at 72 hours compared with the healthy control group, and the levels of these cells were reduced 6 months post-AMI. Regarding the suppressive function of CD4+ CD25+ regulatory cells, they were dysfunctional at 3 and 6 months post-AMI. The frequency of CD69+ Treg cells was similar between patients with AMI at 72 hours postinfarction and the control groups. Moreover, the frequency of CD69+ Treg cells at 3 and 6 months postischemic event did not vary over time. Treg cells play a role in regulating inflammation after an AMI, and its function may be compromised in this pathology. This work is the first report to evaluate CD69+ Foxp3− Treg cells in AMI patients.
Altered CD226/TIGIT expressions were associated with NK phenotypes in primary antiphospholipid syndrome and affected by IL-4/JAK pathway
Authors: Long Yan , Lu Ke-Jia , Xia Chang-Sheng , Feng Jing-Hong , Li Wen-Yi , Ma Yin-Ting , Sun Yuan-Yuan , Fan Chun-Hong , Li Chun 
Published: February 2024

Abstract
Natural killer (NK) cells were reported to be involved in the pathogenesis of primary antiphospholipid syndrome (pAPS). Immunosuppressive receptor T-cell immunoreceptor with Ig and ITIM domains (TIGIT) and activating receptor cluster of differentiation 226 (CD226) are specifically expressed on NK cells with competitive functions. This study aims to investigate the expression diversities of CD226/TIGIT on NK subsets and their associations with NK subsets activation phenotypes and potential clinical significance, furthermore, to explore potential cause for CD226/TIGIT expression diversities in pAPS. We comparatively assessed the changes of CD56brightNK, CD56dimNK, and NK-like cells in 70 pAPS patients compared with control groups, including systemic lupus erythematosus, asymptomatic antiphospholipid antibodies carriers (asymp-aPLs carriers), and healthy controls and their expression diversities of CD226/TIGIT by flow cytometry. CD25, CD69, CD107α expression, and interferon gamma (IFN-γ) secretion levels of NK subsets were detected to determine the potential association of CD226/TIGIT expression with NK subsets phenotypes. CD226/TIGIT expression levels were compared among different subgroups divided by aPLs status. Moreover, in vitro cultures were conducted to explore the potential mechanisms of CD226/TIGIT expression imbalance. CD56brightNK and CD3+CD56+NK-like cells were significantly increased while CD56dimNK cells were obviously decreased in pAPS, and CD56brightNK and NK-like cells exhibited significantly higher CD226 but lower TIGIT expressions. CD226+CD56brightNK and TIGIT-CD56brightNK cells show higher CD69 expression and IFN-γ secretion capacity, and CD226+NK-like and TIGIT-NK-like cells showed higher expressions of CD25 and CD69 but lower apoptosis rate than CD226− and TIGIT+CD56brightNK/NK-like cells, respectively. The imbalanced CD226/TIGIT expressions were most significant in aPLs triple-positive group. Imbalanced expressions of CD226/TIGIT on CD56brightNK and NK-like cells were aggravated after interleukin-4 (IL-4) stimulation and recovered after tofacitinib blocking. Our data revealed significant imbalanced CD226/TIGIT expressions on NK subsets in pAPS, which closely associated with NK subsets phenotypes and more complicated autoantibody status. CD226/TIGIT imbalanced may be affected by IL-4/Janus Kinase (JAK) pathway activation.
Measures of resting-state brain network segregation and integration vary in relation to data quantity: implications for within and between subject comparisons of functional brain network organization
Authors: Han Liang , Chan Micaela Y , Agres Phillip F , Winter-Nelson Ezra , Zhang Ziwei , Wig Gagan S 
Published: February 2024

Abstract
Measures of functional brain network segregation and integration vary with an individual’s age, cognitive ability, and health status. Based on these relationships, these measures are frequently examined to study and quantify large-scale patterns of network organization in both basic and applied research settings. However, there is limited information on the stability and reliability of the network measures as applied to functional time-series; these measurement properties are critical to understand if the measures are to be used for individualized characterization of brain networks. We examine measurement reliability using several human datasets (Midnight Scan Club and Human Connectome Project [both Young Adult and Aging]). These datasets include participants with multiple scanning sessions, and collectively include individuals spanning a broad age range of the adult lifespan. The measurement and reliability of measures of resting-state network segregation and integration vary in relation to data quantity for a given participant’s scan session; notably, both properties asymptote when estimated using adequate amounts of clean data. We demonstrate how this source of variability can systematically bias interpretation of differences and changes in brain network organization if appropriate safeguards are not included. These observations have important implications for cross-sectional, longitudinal, and interventional comparisons of functional brain network organization.
Caudally pronounced deficiencies in preplate splitting and migration underly a rostro-caudal progression of cortical lamination defects in the reeler brain
Authors: Mingo-Moreno Nieves , Truschow Pavel , Staiger Jochen F , Wagener Robin J 
Published: February 2024

Abstract
In mammalian neocortex development, every cohort of newborn neurons is guided toward the marginal zone, leading to an “inside-out” organization of the 6 neocortical layers. This migratory pattern is regulated by the extracellular glycoprotein Reelin. The reeler mouse shows a homozygous mutation of the reelin gene. Using RNA in situ hybridization we could demonstrate that the Reelin-deficient mouse cortex (male and female) displays an increasing lamination defect along the rostro-caudal axis that is characterized by strong cellular intermingling, but roughly reproduces the “inside-out” pattern in rostral cortex, while caudal cortex shows a relative inversion of neuronal positioning (“outside-in”). We found that in development of the reeler cortex, preplate-splitting is also defective with an increasing severity along the rostro-caudal axis. This leads to a misplacement of subplate neurons that are crucial for a switch in migration mode within the cortical plate. Using Flash Tag labeling and nucleoside analog pulse-chasing, we found an according migration defect within the cortical plate, again with a progressive severity along the rostro-caudal axis. Thus, loss of one key player in neocortical development leads to highly area-specific (caudally pronounced) developmental deficiencies that result in multiple roughly opposite rostral versus caudal adult neocortical phenotypes.
Distribution of initial caries lesions in relation to fixed orthodontic therapy. A systematic review and meta-analysis
Authors: Salerno Claudia , Grazia Cagetti Maria , Cirio Silvia , Esteves-Oliveira Marcella , Wierichs Richard J , Kloukos Dimitrios , Campus Guglielmo 
Published: February 2024

Abstract

Background
Initial caries lesion (ICLs) adjacent to orthodontic brackets are the most common side effect of orthodontic treatment with fixed appliances. The reported prevalence is uncertain and varies considerably across studies, from 27% to 97%.

Objectives
This paper was designed to evaluate and synthesize the available evidence on the prevalence and incidence rates of ICLs in relation to orthodontic treatment. Selection criteria: The review (Prospero protocol CRD42023412952) included randomized and non-randomized clinical trials of interventions, cohort studies, and cross-sectional studies, published after 1990 on the prevalence or incidence of ICLs during or after orthodontic treatment with fixed appliances. Search methods: Pubmed, Scopus, and Embase databases were searched from 1990 until 01 May 2023. The risk of bias assessment was performed with RoB 2 and ROBINS-I tool and the Joanna Briggs Institute Critical Appraisal Checklist. Data collection and analysis: The proportion of individuals with ICLs, reported as the number/percentage of individuals/teeth with ICLs or mean number of ICLs per subject, were used to synthesize results.

Results
The search yielded a total of 468 papers; 21 studies were included in the systematic review, 2 of which were not included in the meta-analysis. The prevalence rate [95%CI] of ICLs was 0.57% [0.48; 0.65] in 1448 patients, 0.22% [0.14; 0.33] in 11583 teeth, with a mean number of lesions equal to 2.24 [1.79; 2.70] in 484 patients evaluated. The incidence rate of new carious lesions developed during orthodontic treatment was 0.48% [0.33; 0.63] in 533 patients, 0.15% [0.08; 0.26] in 1890 teeth with a mean number of ICLs equal to 2.29 [1.12; 3.46] in 208 patients evaluated.

Limitations
Although the high number of included studies and the overall good quality, there was a significant heterogeneity in the collected data.

Conclusion
The prevalence and incidence rates of ICLs in subjects undergoing orthodontic treatment are quite high and raise some concerns in terms of risk assessment of orthodontic treatment. ICLs represent an alarming challenge for both patients and professionals. Effective caries prevention strategies during treatment need to be considered and implemented where appropriate.
Long-term outcomes of the pentaspline pulsed-field ablation catheter for the treatment of paroxysmal atrial fibrillation: results of the prospective, multicentre FARA-Freedom Study
Authors: Metzner Andreas , Fiala Martin , Vijgen Johan , Ouss Alexandre , Gunawardene Melanie , Hansen Jim , Kautzner Josef , Schmidt Boris , Duytschaever Mattias , Reichlin Tobias , Blaauw Yuri , Sommer Philipp , Vanderper Annelies , Achyutha Anitha B , Johnson Madeline , Raybuck Jonathan D , Neuzil Petr 
Published: February 2024

Abstract

Aims
Pulmonary vein isolation (PVI) is a well-established strategy for the treatment of paroxysmal atrial fibrillation (PAF). Despite randomized controlled trials and real-world data showing the promise of pulsed-field ablation (PFA) for this treatment, long-term efficacy and safety data demonstrating single-procedure outcomes off antiarrhythmic drugs remain limited. The aim of the FARA-Freedom Study was to evaluate the long-term efficacy and safety of PFA using the pentaspline catheter for PAF.

Methods and results
FARA-Freedom, a prospective, non-randomized, multicentre study, enrolled patients with PAF undergoing de novo PVI with PFA, who were followed for 12 months with weekly transtelephonic monitoring and a 72-h Holter ECG at 6 and 12 months. The primary safety endpoint was a composite of device- or procedure-related serious adverse events out to 7 days post-ablation and PV stenosis or atrioesophageal (AE) fistula out to 12 months. Treatment success is a composite of acute PVI and chronic success, which includes freedom from any documented atrial tachyarrhythmia longer than 30 s, use of antiarrhythmic drugs or cardioversion after a 3-month blanking period, or use of amiodarone or repeat ablation at any time. The study enrolled 179 PAF patients (62 ± 10 years, 39% female) at 13 centres. At the index procedure, all PVs were successfully isolated with the pentaspline PFA catheter. Procedure and left atrial dwell times, with a 20-min waiting period, were 71.9 ± 17.6 and 41.0 ± 13.3 min, respectively. Fluoroscopy time was 11.5 ± 7.4 min. Notably, monitoring compliance was high, with 88.4 and 90.3% with weekly events and 72-h Holter monitors, respectively. Freedom from the composite primary effectiveness endpoint was 66.6%, and 41 patients had atrial tachyarrhythmia recurrence, mostly recurrent atrial fibrillation (31 patients). The composite safety endpoint occurred in two patients (1.1%), one tamponade and one transient ischaemic attack. There was no coronary spasm, PV stenosis, or AE fistula. There were four cases of transient phrenic nerve palsy, but all resolved during the index procedure.

Conclusion
In this prospective, non-randomized, multicentre study, PVI using a pentaspline PFA catheter was effective in treating PAF patients despite rigourous endpoint definitions and high monitoring compliance and demonstrated favourable safety.

Registration
Clinical Trials.gov Identifier: NCT05072964 (sponsor: Boston Scientific Corporation).
The Warburg Effect Reinterpreted 100 yr on: A First-Principles Stoichiometric Analysis and Interpretation from the Perspective of ATP Metabolism in Cancer Cells
Authors: Nath Sunil , Balling Rudi 
Published: February 2024

Abstract
The Warburg Effect is a longstanding enigma in cancer biology. Despite the passage of 100 yr since its discovery, and the accumulation of a vast body of research on the subject, no convincing biochemical explanation has been given for the original observations of aerobic glycolysis in cancer cell metabolism. Here, we have worked out a first-principles quantitative analysis of the problem from the principles of stoichiometry and available electron balance. The results have been interpreted using Nath’s unified theory of energy coupling and adenosine triphosphate (ATP) synthesis, and the original data of Warburg and colleagues have been analyzed from this new perspective. Use of the biomass yield based on ATP per unit substrate consumed, ${{Y}_{X/S}}\ ATP$, or the Nath-Warburg number, NaWa has been shown to excellently model the original data on the Warburg Effect with very small standard deviation values, and without employing additional fitted or adjustable parameters. Based on the results of the quantitative analysis, a novel conservative mechanism of synthesis, utilization, and recycling of ATP and other key metabolites (eg, lactate) is proposed. The mechanism offers fresh insights into metabolic symbiosis and coupling within and/or among proliferating cells. The fundamental understanding gained using our approach should help in catalyzing the development of more efficient metabolism-targeting anticancer drugs.
Bursts of coalescence within population pedigrees whenever big families occur
Authors: Diamantidis Dimitrios , Fan Wai-Tong (Louis) , Birkner Matthias , Wakeley John 
Published: February 2024

Abstract
We consider a simple diploid population-genetic model with potentially high variability of offspring numbers among individuals. Specifically, against a backdrop of Wright–Fisher reproduction and no selection, there is an additional probability that a big family occurs, meaning that a pair of individuals has a number of offspring on the order of the population size. We study how the pedigree of the population generated under this model affects the ancestral genetic process of a sample of size two at a single autosomal locus without recombination. Our population model is of the type for which multiple-merger coalescent processes have been described. We prove that the conditional distribution of the pairwise coalescence time given the random pedigree converges to a limit law as the population size tends to infinity. This limit law may or may not be the usual exponential distribution of the Kingman coalescent, depending on the frequency of big families. But because it includes the number and times of big families, it differs from the usual multiple-merger coalescent models. The usual multiple-merger coalescent models are seen as describing the ancestral process marginal to, or averaging over, the pedigree. In the limiting ancestral process conditional on the pedigree, the intervals between big families can be modeled using the Kingman coalescent but each big family causes a discrete jump in the probability of coalescence. Analogous results should hold for larger samples and other population models. We illustrate these results with simulations and additional analysis, highlighting their implications for inference and understanding of multilocus data.
First referral hospitals in low- and middle-income countries: the need for a renewed focus
Authors: Jeffries Mazhar Rosanna , Willows Tamara Mulenga , Bhattarai Suraj , Tinn Chit-Su , Misago Nadine , English Mike 
Published: February 2024

Abstract
First referral hospitals (FRHs) are the hospitals closest to the community, which offer expertise or technologies to complement more widely available ‘basic’ ambulatory care or inpatient care. Despite having been a subject of interest in global health policy in the latter half of the 20th century, in more recent decades, they appear to have been overshadowed. This paper reviews what is understood by FRH, drawing on both academic and policy literature, complemented by specific country case studies. We undertook three reviews: a grey literature review of global and regional policy reports and documents, a structured review of the academic literature on FRH and a review of FRH-related policies in eight countries. Our findings indicate that there is confusion regarding the definitions and roles of FRH; they have fallen off the policy agenda globally and they suffer from lack of advocates in part related to the absence of cohesive definition. Meanwhile, these facilities continue to fulfil important functions in health systems in low- and middle-income countries, and expectations for service delivery remain high. In light of these findings, this paper calls for renewed interest and investment in FRH from the global health academic and policy-making community.
A guide for a student-led doctoral-level qualitative methods short course in epidemiology: faculty and student perspectives
Authors: Gille Felix , Frei Anja , Kaufmann Marco , Lehmann Anja , Muñoz Laguna Javier , Papadopoulos Kimon , Spörri Angela , Stanikić Mina , Tušl Martin , Zavattaro Federica , Puhan Milo Alan 
Published: February 2024

Abstract
Qualitative research and mixed methods are core competencies for epidemiologists. In response to the shortage of guidance on graduate course development, we wrote a course development guide aimed at faculty and students designing similar courses in epidemiology curricula. The guide combines established educational theory with faculty and student experiences from a recent introductory course for epidemiology and biostatistics doctoral students at the University of Zurich and Swiss Federal Institute of Technology, Zurich. We propose a student-centred course with inverse classroom teaching and practice exercises with faculty input. Integration of student input during the course development process helps align the course syllabus with student needs. The proposed course comprises six sessions that cover learning outcomes in comprehension, knowledge, application, analysis, synthesis and evaluation. Following an introductory session, the students engage in face-to-face interviews, focus group interviews, observational methods, analysis and how qualitative and quantitative methods are integrated in mixed methods. Furthermore, the course covers interviewer safety, research ethics, quality in qualitative research and a practice session focused on the use of interview hardware, including video and audio recorders. The student-led teaching characteristic of the course allows for an immersive and reflective teaching-learning environment. After implementation of the course and learning from faculty and student perspectives, we propose these additional foci: a student project to apply learned knowledge to a case study; integration in mixed-methods; and providing faculty a larger space to cover theory and field anecdotes.