bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness of Functional or Aerobic Exercise Combined With Breathing Techniques in Telerehabilitation for Patients With Long COVID: A Randomized Controlled Trial
Authors: Espinoza-Bravo Claudia , Arnal-Gómez Anna , Martínez-Arnau Francisco Miguel , Núñez-Cortés Rodrigo , Hernández-Guillén David , Flor-Rufino Cristina , Cortés-Amador Sara 
Published: September 2023

Abstract

Objective
The aim of this study was to compare the short-term clinical effects of 2 telerehabilitation programs, functional versus aerobic exercises (AEs), both combined with breathing techniques, regarding the improvement of long coronavirus disease 2019 (COVID-19) symptoms.

Methods
A randomized controlled trial was conducted. The participants were assigned randomly to either the functional exercise (FE) group or AE group, both including breathing techniques. The interventions lasted for 8 weeks with 3 sessions per week, and they were conducted through the Fisiotrack mobile phone application. Assessments were performed at baseline and after treatment, including testing fatigue (Fatigue Assessment Scale), dyspnea (London Chest Activity of Daily Living Scale), functional performance (30 Seconds Standing Test), perceived stress (Perceived Stress Scale), anxiety and depression (Hospital Anxiety and Depression Questionnaire), and quality of life (European Quality of Life Scale). The perceived change after treatment (Patient Global Impression of Change Scale), the usability of the application (System Usability Scale), and the adherence to treatment were also examined after treatment.

Results
In total, 43 participants (FE group, n = 21; AE group, n = 22; mean age = 42.4 [SD = 6.5] years) completed the study. In the intragroup comparison, the FE group showed improved fatigue (−6.7 points; 95% CI = −11.9 to −1.3), functional capacity (2.6 repetitions; 95% CI = 0.3 to 4.9), and perceived stress (−4.9 points; 95% CI = −9.1 to 0.8), while the AE group showed improved perceived stress (−6.2 points; 95% CI = −10.3 to −2.1). No significant differences in the intergroup effect were identified for the studied variables. Significant differences were observed in the Patient Global Impression of Change Scale in favor of the FE group compared to the AE group, and quality of life reached the minimal clinically important difference for both groups. The ease of use of the telerehabilitation tool was rated excellent in both groups.

Conclusions
Both telerehabilitation exercise modalities are effective at improving stress symptoms and quality of life in patients with long COVID-19. For improving fatigue and functional performance, FE shows more promising results.

Impact
FE or AE may be recommended depending on patients’ symptoms, and both may improve quality of life and stress symptoms in patients with long COVID-19. Telerehabilitation may be an optimal intervention modality for the prescription of physical exercise in patients with long COVID-19.
Effects of Comprehensive Outpatient Cardiac Rehabilitation on Exercise Capacity, Functional Status, and Quality of Life in People With Heart Failure: A Systematic Review and Meta-Analysis
Authors: Gore Shweta , Khanna Hargun , Kumar Amit 
Published: September 2023

Abstract

Purpose
The purpose of this study was to systematically review and conduct a meta-analysis to examine the impact of comprehensive outpatient cardiac rehabilitation on exercise capacity, functional status, and quality of life in patients with heart failure.

Methods
PubMed, Embase, and CINAHL were searched using keywords and MeSH terms on heart failure and cardiac rehabilitation. Randomized clinical trials published in English using outpatient exercise-based cardiac rehabilitation in patients with heart failure were included. The Grading of Recommendations Assessment, Development, and Evaluation was utilized for quality appraisal. Pooled estimates were computed using standardized mean differences (SMDs) and 95% CIs. Primary outcomes were functional status (6-minute walk distance, quality of life, exercise capacity using peak oxygen consumption, muscle strength, and endurance).

Results
Eleven randomized controlled trials including 1523 participants ranging from 45 to 80 years old and an intervention duration ranging from 2 to 26 weeks were analyzed. Pooled results indicated significant improvements with comprehensive cardiac rehabilitation on 6-minute walk distance (SMD = 0.30; 95% CI = 0.06 to 0.54) and oxygen consumption (SMD = 0.23; 95% CI = 0.06 to 0.40). However, there was no additional benefit for the quality of life beyond that seen in the comparison groups.

Conclusion
Results of this study suggest that comprehensive outpatient cardiac rehabilitation is associated with significantly better clinical outcomes than single-component exercise programs in cardiac rehabilitation settings, multicomponent exercise in noncardiac rehabilitation settings, or no exercise.

Impact
Heart failure is significantly associated with an increased risk of poor exercise tolerance. Despite the proven benefit of cardiac rehabilitation on exercise tolerance and physical activities from individual randomized clinical trials, questions regarding its impact on clinical outcomes such as exercise capacity, functional status, and quality of life remain inadequate. This systematic review and meta-analysis provides strong evidence supporting comprehensive outpatient cardiac rehabilitation for improving clinical outcomes in heart failure.
A set of codes for numerical convection and geodynamo calculations
Authors: Gibbons Steven J , Willis Ashley P , Davies Chris , Gubbins David 
Published: September 2023

Abstract
We present a set of codes for calculating and displaying solutions to diverse problems within thermal convection and magnetic field generation in rotating fluid-filled spheres and spherical shells. There are diverse programs for the kinematic dynamo problem, the onset of thermal convection, and boundary-locked thermal convection, and time-stepping codes for non-magnetic convection and the dynamo with either homogeneous or spatially varying thermal boundary conditions. Where possible, all programs have been benchmarked against other codes and tested by reproducing previously published results. Each program comes with the complete source code, a pdf instruction manual, and at least one example run with a sample input file and all necessary files for describing an initial condition. The only prerequisite for running most of the codes is a FORTRAN compiler. The plotting programs require in addition the PGPLOT graphics library. All source code, examples, input files, solutions, and instructions are available for download from github and Zenodo.
Scalp and hippocampal sleep correlates of memory function in drug-resistant temporal lobe epilepsy
Authors: Latreille Véronique , Avigdor Tamir , Thomas John , Crane Joelle , Sziklas Viviane , Jones-Gotman Marilyn , Frauscher Birgit 
Published: September 2023

AbstractSeminal animal studies demonstrated the role of sleep oscillations such as cortical slow waves, thalamocortical spindles, and hippocampal ripples in memory consolidation. In humans, whether ripples are involved in sleep-related memory processes is less clear. Here, we explored the interactions between sleep oscillations (measured as traits) and general episodic memory abilities in 26 adults with drug-resistant temporal lobe epilepsy who performed scalp-intracranial electroencephalographic recordings and neuropsychological testing, including two analogous hippocampal-dependent verbal and nonverbal memory tasks. We explored the relationships between hemispheric scalp (spindles, slow waves) and hippocampal physiological and pathological oscillations (spindles, slow waves, ripples, and epileptic spikes) and material-specific memory function. To differentiate physiological from pathological ripples, we used multiple unbiased data-driven clustering approaches. At the individual level, we found material-specific cerebral lateralization effects (left-verbal memory, right-nonverbal memory) for all scalp spindles (rs &gt; 0.51, ps &lt; 0.01) and fast spindles (rs &gt; 0.61, ps &lt; 0.002). Hippocampal epileptic spikes and short pathological ripples, but not physiological oscillations, were negatively (rs &gt; −0.59, ps &lt; 0.01) associated with verbal learning and retention scores, with left lateralizing and antero-posterior effects. However, data-driven clustering failed to separate the ripple events into defined clusters. Correlation analyses with the resulting clusters revealed no meaningful or significant associations with the memory scores. Our results corroborate the role of scalp spindles in memory processes in patients with drug-resistant temporal lobe epilepsy. Yet, physiological and pathological ripples were not separable when using data-driven clustering, and thus our findings do not provide support for a role of sleep ripples as trait-like characteristics of general memory abilities in epilepsy.
Altered sleep architecture in diabetes and prediabetes: findings from the Baependi Heart Study
Authors: Chen Daniel M , Taporoski Tâmara P , Alexandria Shaina J , Aaby David A , Beijamini Felipe , Krieger José E , von Schantz Malcolm , Pereira Alexandre C , Knutson Kristen L 
Published: September 2023

Abstract

Study Objectives
People with diabetes and prediabetes are more likely to have sleep-disordered breathing (SDB), but few studies examined sleep architecture in people with diabetes or prediabetes in the absence of moderate-severe SDB, which was the aim of our cross-sectional study.

Methods
This cross-sectional sample is from the Baependi Heart Study, a family-based cohort of adults in Brazil. About 1074 participants underwent at-home polysomnography (PSG). Diabetes was defined as fasting glucose &gt;125 mg/dL or HbA1c &gt; 6.4 mmol/mol or taking diabetic medication, and prediabetes was defined as HbA1c ≥ 5.7 & &lt;6.5 mmol/mol or fasting glucose ≥ 100 & ≤125 mg/dl. We excluded participants with an apnea-hypopnea index (AHI) ≥ 30 in primary analyses and ≥ 15 in secondary analysis. We compared sleep stages among the 3 diabetes groups (prediabetes, diabetes, neither).

Results
Compared to those without diabetes, we found shorter REM duration for participants with diabetes (−6.7 min, 95%CI −13.2, −0.1) and prediabetes (−5.9 min, 95%CI −10.5, −1.3), even after adjusting for age, gender, BMI, and AHI. Diabetes was also associated with lower total sleep time (−13.7 min, 95%CI −26.8, −0.6), longer slow-wave sleep (N3) duration (+7.6 min, 95%CI 0.6, 14.6) and higher N3 percentage (+2.4%, 95%CI 0.6, 4.2), compared to those without diabetes. Results were similar when restricting to AHI &lt; 15.

Conclusions
People with diabetes and prediabetes had less REM sleep than people without either condition. People with diabetes also had more N3 sleep. These results suggest that diabetes and prediabetes are associated with differences in sleep architecture, even in the absence of moderate-severe sleep apnea.
Mesenchymal Stem Cells Promote Polarization of M2 Macrophages in Mice with Acute-On-Chronic Liver Failure via Mertk/JAK1/STAT6 Signaling
Authors: Li Zhi-Hui , Chen Jun-Feng , Zhang Jing , Lei Zi-Ying , Wu Li-Li , Meng Shi-Bo , Wang Jia-Lei , Xiong Jing , Lin Deng-Na , Wang Jun-Yi , Gao Zhi-Liang , Lin Bing-Liang 
Published: September 2023

Abstract
Acute-on-chronic liver failure (ACLF) is a severe disease with a high mortality. Macrophage-related inflammation plays a crucial role in ACLF development. Mesenchymal stem cells (MSCs) treatment was demonstrated to be beneficial in ACLF in our previous study; however, the underlying mechanisms remain unknown. Therefore, mouse bone marrow-derived MSCs were used to treat an ACLF mouse model or cocultured with RAW264.7/J774A.1 macrophages that were stimulated with LPS. Histological and serological parameters and survival were analyzed to evaluate efficacy. We detected changes of Mer tyrosine kinase (Mertk), JAK1/STAT6, inflammatory cytokines, and markers of macrophage polarization in vitro and in vivo. In ACLF mice, MSCs improved liver function and 48-h survival of ACLF mice and alleviated inflammatory injury by promoting M2 macrophage polarization and elevated Mertk expression levels in macrophages. This is significant, as Mertk regulates M2 macrophage polarization via the JAK1/STAT6 signaling pathway.
Detection and characterization of resting state functional networks in squirrel monkey brain
Authors: Sengupta Anirban , Wang Feng , Mishra Arabinda , Reed Jamie L , Chen Li Min , Gore John C 
Published: September 2023

AbstractResting-state fMRI based on analyzing BOLD signals is widely used to derive functional networks in the brain and how they alter during disease or injury conditions. Resting-state networks can also be used to study brain functional connectomes across species, which provides insights into brain evolution. The squirrel monkey (SM) is a non-human primate (NHP) that is widely used as a preclinical model for experimental manipulations to understand the organization and functioning of the brain. We derived resting-state networks from the whole brain of anesthetized SMs using Independent Component Analysis of BOLD acquisitions. We detected 15 anatomically constrained resting-state networks localized in the cortical and subcortical regions as well as in the white-matter. Networks encompassing visual, somatosensory, executive control, sensorimotor, salience and default mode regions, and subcortical networks including the Hippocampus-Amygdala, thalamus, basal-ganglia and brainstem region correspond well with previously detected networks in humans and NHPs. The connectivity pattern between the networks also agrees well with previously reported seed-based resting-state connectivity of SM brain. This study demonstrates that SMs share remarkable homologous network organization with humans and other NHPs, thereby providing strong support for their suitability as a translational animal model for research and additional insight into brain evolution across species.
VData: Temporally annotated data manipulation and storage
Authors: Bouvier Matteo , Bonnaffoux Arnaud 
Published: September 2023

AbstractBackgroundRecent advances in both single-cell sequencing technologies and gene expression simulation algorithms have led to the production of increasingly large datasets. Larger datasets (tens or hundreds of Gigabytes) can no longer fit on regular computers’ RAM and thus pose important challenges for storage and manipulation. Existing solutions offer partial solutions but do not explicitly handle the temporal dimension of simulated data and still require large amounts of RAM to run.ResultsVData is a Python extension to the widely used AnnData format that solves these issues by extending 2D dataframes to 3 dimensions (cells, genes and time). VData is built on top of Ch5mpy, a custom built Python library for easily working with hdf5 files and which allows to reduce the memory footprint to the minimum.ConclusionsVData allows to store and manipulate very large datasets of (empirical or simulated) time-stamped data. Since it follows the original Ann-Data format, it is compatible with the scverse tools and AnnData users will find it easy to use.
Dual role of Vascular Endothelial Growth Factor-C (VEGF-C) in post-stroke recovery
Authors: Choi Yun Hwa , Hsu Martin , Laaker Collin , Herbath Melinda , Yang Heeyoon , Cismaru Peter , Johnson Alexis M. , Spellman Bailey , Wigand Kelsey , Sandor Matyas , Fabry Zsuzsanna 
Published: September 2023

SummaryUsing a mouse model of ischemic stroke, this study characterizes stroke-induced lymphangiogenesis at the cribriform plate (CP). While blocking CP lymphangiogenesis with a VEGFR-3 inhibitor improves stroke outcome, administration of VEGF-C induced larger brain infarcts.AbstractCerebrospinal fluid (CSF), antigens, and antigen-presenting cells drain from the central nervous system (CNS) into lymphatic vessels near the cribriform plate and dural meningeal lymphatics. However, the pathological roles of these lymphatic vessels surrounding the CNS during stroke are not well understood. Using a mouse model of ischemic stroke, transient middle cerebral artery occlusion (tMCAO), we show that stroke induces lymphangiogenesis near the cribriform plate. Interestingly, lymphangiogenesis is restricted to lymphatic vessels at the cribriform plate and downstream cervical lymph nodes, without affecting the conserved network of lymphatic vessels in the dura. Cribriform plate lymphangiogenesis peaks at day 7 and regresses by day 14 following tMCAO and is regulated by VEGF-C/VEGFR-3. These newly developed lymphangiogenic vessels transport CSF and immune cells to the cervical lymph nodes. Inhibition of VEGF-C/VEGFR-3 signaling using a blocker of VEGFR-3 prevented lymphangiogenesis and led to improved stroke outcomes at earlier time points but had no effects at later time points following stroke. Administration of VEGF-C after tMCAO did not further increase post-stroke lymphangiogenesis, but instead induced larger brain infarcts. The differential roles for VEGFR-3 inhibition and VEGF-C in regulating stroke pathology call into question recent suggestions to use VEGF-C therapeutically for stroke.
Effects of optogenetic silencing the Anterior Cingulate Cortex in a delayed non-match to trajectory task
Authors: Cruz Ana S , Cruz Sara , Remondes Miguel 
Published: September 2023

SummaryWorking memory is a fundamental cognitive ability, allowing us to keep information in memory for the time needed to perform a given task. A complex neural circuit fulfills these functions, among which is the anterior cingulate cortex (CG). Functionally and anatomically connected to the medial prefrontal, retrosplenial, midcingulate and hippocampus, as well as motor cortices, CG has been implicated in retrieving appropriate information when needed to select and control appropriate behavior. The role of cingulate cortex in working memory-guided behaviors remains unclear due to the lack of studies reversibly interfering with its activity during specific epochs of working memory. We used light to activate eNpHR3.0 and thus silence cingulate neurons while animals perform a standard delayed non-match to trajectory task. We found that, while not causing an impairment in eNpHR3.0+ animals when compared to eNpHR3.0-CTRL animals, silencing cingulate neurons during retrieval decreases the mean performance if compared to silencing during encoding. Such retrieval-associated changes are accompanied by longer delays in control animals, consistent with an adaptive recruitment of additional cognitive resources.
Vitamin D promotes DNase1L3 to degrade ecDNA and inhibit the malignant progression of hepatocellular carcinoma
Authors: Zhang Heng , Qin Lu-ning , Li Qing-qing , Wu Ting , Zhang Lei , Wang Kai-wen , Cheng Shan-bin , Shi Yue , Feng Yi-qian , Han Jing-xia , Li Yi-nan , Li Zhi-yang , Liu Hui-juan , Sun Tao 
Published: September 2023

AbstractExtrachromosomal DNA (ecDNA) is an important carrier of oncogene amplification. However, the degradation mechanism of ecDNA is not well understood. We found that endogenous natural molecular vitamin D (VD) reduces ecDNA and inhibits the progression of hepatocellular carcinoma (HCC). VD reduces ecDNA depending on its transporter GC, which interacts with the endonuclease DNase1L3 and stabilize its protein level. DNase1L3 with its lipophilic region on N-terminus exhibiting an affinity towards lipid droplets (LDs) demonstrates direct degradation effect on ecDNA. Intranuclear LDs are abundantly distributed around ecDNA, DNase1L3 therefore shows an affinity for ecDNA owing to its lipophilic region. VD, as a lipid-soluble molecule, can increase the size of LDs and improve the degradation of DNase1L3 on ecDNA. Consequently, we designed two mRNA-based therapeutics, DNase1L3 and GC-DNase, both of which had an anti-tumor effect on PDX models. The above results showed that treatments targeting ecDNA in cancer are prospective in clinical practice.
Discovering optimal kinetic pathways for self-assembly using automatic differentiation
Authors: Jhaveri Adip , Loggia Spencer , Qian Yian , Johnson Margaret E. 
Published: September 2023

AbstractDuring self-assembly of macromolecules ranging from ribosomes to viral capsids, the formation of long-lived intermediates or kinetic traps can dramatically reduce yield of the functional products. Understanding biological mechanisms for avoiding traps and efficiently assembling is essential for designing synthetic assembly systems, but learning optimal solutions requires numerical searches in high-dimensional parameter spaces. Here, we exploit powerful automatic differentiation algorithms commonly employed by deep learning frameworks to optimize physical models of reversible self-assembly, discovering diverse solutions in the space of rate constants for 3-7 subunit complexes. We define two biologically-inspired protocols that prevent kinetic trapping through either internal design of subunit binding kinetics or external design of subunit titration in time. Our third protocol acts to recycle intermediates, mimicking energy-consuming enzymes. Preventative solutions via interface design are the most efficient and scale better with more subunits, but external control via titration or recycling are effective even for poorly evolved binding kinetics. Whilst all protocols can produce good solutions, diverse subunits always helps; these complexes access more efficient solutions when following external control protocols, and are simpler to design for internal control, as molecular interfaces do not need modification during assembly given sufficient variation in dimerization rates. Our results identify universal scaling in the cost of kinetic trapping, and provide multiple strategies for eliminating trapping and maximizing assembly yield across large parameter spaces.SIGNIFICANCEMacromolecular complexes are frequently composed of diverse subunits. While evolution may favor repeated subunits and symmetry, we show how diversity in subunits generates an expansive parameter space that naturally improves the ‘expressivity’ of self-assembly, much like a deeper neural network. By using automatic differentiation algorithms commonly used in deep learning, we searched these parameter spaces to identify classes of kinetic protocols that mimic biological solutions for productive self-assembly. Our results reveal how high-yield complexes that easily become kinetically trapped in incomplete intermediates can instead be steered by internal design of rate constants or external and active control of subunits to efficiently assemble, exploiting nonequilibrium control of these ubiquitous dynamical systems.