bluuebunny/crossref_metadata_2025_split huggingface dataset:
SCSMD: Single Cell Consistent Clustering based on Spectral Matrix Decomposition
Authors: Jia Ran , Ren Ying-Zan , Li Po-Nian , Gao Rui , Zhang Yu-Sen 
Published: June 2024

AbstractCluster analysis, a pivotal step in single-cell sequencing data analysis, presents substantial opportunities to effectively unveil the molecular mechanisms underlying cellular heterogeneity and intercellular phenotypic variations. However, the inherent imperfections arise as different clustering algorithms yield diverse estimates of cluster numbers and cluster assignments. This study introduces Single Cell Consistent Clustering based on Spectral Matrix Decomposition (SCSMD), a comprehensive clustering approach that integrates the strengths of multiple methods to determine the optimal clustering scheme. Testing the performance of SCSMD across different distances and employing the bespoke evaluation metric, the methodological selection undergoes validation to ensure the optimal efficacy of the SCSMD. A consistent clustering test is conducted on 15 authentic scRNA-seq datasets. The application of SCSMD to human embryonic stem cell scRNA-seq data successfully identifies known cell types and delineates their developmental trajectories. Similarly, when applied to glioblastoma cells, SCSMD accurately detects pre-existing cell types and provides finer sub-division within one of the original clusters. The results affirm the robust performance of our SCSMD method in terms of both the number of clusters and cluster assignments. Moreover, we have broadened the application scope of SCSMD to encompass larger datasets, thereby furnishing additional evidence of its superiority. The findings suggest that SCSMD is poised for application to additional scRNA-seq datasets and for further downstream analyses.
HiCDiff: single-cell Hi-C data denoising with diffusion models
Authors: Wang Yanli , Cheng Jianlin 
Published: June 2024

Abstract
The genome-wide single-cell chromosome conformation capture technique, i.e. single-cell Hi-C (ScHi-C), was recently developed to interrogate the conformation of the genome of individual cells. However, single-cell Hi-C data are much sparser than bulk Hi-C data of a population of cells, and noise in single-cell Hi-C makes it difficult to apply and analyze them in biological research. Here, we developed the first generative diffusion models (HiCDiff) to denoise single-cell Hi-C data in the form of chromosomal contact matrices. HiCDiff uses a deep residual network to remove the noise in the reverse process of diffusion and can be trained in both unsupervised and supervised learning modes. Benchmarked on several single-cell Hi-C test datasets, the diffusion models substantially remove the noise in single-cell Hi-C data. The unsupervised HiCDiff outperforms most supervised non-diffusion deep learning methods and achieves the performance comparable to the state-of-the-art supervised deep learning method in terms of multiple metrics, demonstrating that diffusion models are a useful approach to denoising single-cell Hi-C data. Moreover, its good performance holds on denoising bulk Hi-C data.
Obese mice have decreased uterine contractility and altered energy metabolism in the uterus at term gestation
Authors: Prifti Kevin K , McCarthy Ronald , Ma Xiaofeng , Finck Brian N , England Sarah K , Frolova Antonina I 
Published: June 2024

Abstract
Over 35% of reproductive-age women in the USA have obesity, putting them at increased risk for numerous obstetric complications due to abnormal labor. While the association between maternal obesity and abnormal labor has been well documented, the mechanisms responsible for this remain understudied. The uterine smooth muscle, myometrium, has high energy needs in order to fuel regular uterine contractions during parturition. However, the precise mechanisms by which the myometrium meets its energy demands has not been defined. Here, our objective was to define the effects of obesity on energy utilization in the myometrium during labor. We generated a mouse model of maternal diet-induced obesity and found that these mice had a higher rate of dystocia than control chow-fed mice. Moreover, compared to control chow-fed mice, DIO mice at term, both before and during labor had lower in vivo spontaneous uterine contractility. Untargeted transcriptomic and metabolomic analyses suggest that diet-induced obesity is associated with elevated long-chain fatty acid uptake and utilization in the uterus, but also an accumulation of medium-chain fatty acids. Diet-induced obesity uteri also had an increase in the abundance of long chain-specific beta-oxidation enzymes, which may be responsible for the observed increase in long-chain fatty acid utilization. This altered energy substrate utilization may be a contributor to the observed contractile dysfunction.
The phase coherence of the neurovascular unit is reduced in Huntington’s disease
Authors: Bjerkan Juliane , Kobal Jan , Lancaster Gemma , Šešok Sanja , Meglič Bernard , McClintock Peter V E , Budohoski Karol P , Kirkpatrick Peter J , Stefanovska Aneta 
Published: June 2024

Abstract
Huntington’s disease is a neurodegenerative disorder in which neuronal death leads to chorea and cognitive decline. Individuals with ≥40 cytosine–adenine–guanine repeats on the interesting transcript 15 gene develop Huntington’s disease due to a mutated huntingtin protein. While the associated structural and molecular changes are well characterized, the alterations in neurovascular function that lead to the symptoms are not yet fully understood. Recently, the neurovascular unit has gained attention as a key player in neurodegenerative diseases. The mutant huntingtin protein is known to be present in the major parts of the neurovascular unit in individuals with Huntington’s disease. However, a non-invasive assessment of neurovascular unit function in Huntington’s disease has not yet been performed. Here, we investigate neurovascular interactions in presymptomatic (N = 13) and symptomatic (N = 15) Huntington’s disease participants compared to healthy controls (N = 36). To assess the dynamics of oxygen transport to the brain, functional near-infrared spectroscopy, ECG and respiration effort were recorded. Simultaneously, neuronal activity was assessed using EEG. The resultant time series were analysed using methods for discerning time-resolved multiscale dynamics, such as wavelet transform power and wavelet phase coherence. Neurovascular phase coherence in the interval around 0.1 Hz is significantly reduced in both Huntington’s disease groups. The presymptomatic Huntington’s disease group has a lower power of oxygenation oscillations compared to controls. The spatial coherence of the oxygenation oscillations is lower in the symptomatic Huntington’s disease group compared to the controls. The EEG phase coherence, especially in the α band, is reduced in both Huntington’s disease groups and, to a significantly greater extent, in the symptomatic group. Our results show a reduced efficiency of the neurovascular unit in Huntington’s disease both in the presymptomatic and symptomatic stages of the disease. The vasculature is already significantly impaired in the presymptomatic stage of the disease, resulting in reduced cerebral blood flow control. The results indicate vascular remodelling, which is most likely a compensatory mechanism. In contrast, the declines in α and γ coherence indicate a gradual deterioration of neuronal activity. The results raise the question of whether functional changes in the vasculature precede the functional changes in neuronal activity, which requires further investigation. The observation of altered dynamics paves the way for a simple method to monitor the progression of Huntington’s disease non-invasively and evaluate the efficacy of treatments.
Structure-optimized and microenvironment-inspired nanocomposite biomaterials in bone tissue engineering
Authors: Lv Zheng , Ji Ying , Wen Guoliang , Liang Xiayi , Zhang Kun , Zhang Wei 
Published: June 2024

Abstract
Critical-sized bone defects represent a significant clinical challenge due to their inability to undergo spontaneous regeneration, necessitating graft interventions for effective treatment. The development of tissue-engineered scaffolds and regenerative medicine has made bone tissue engineering a highly viable treatment for bone defects. The physical and biological properties of nanocomposite biomaterials, which have optimized structures and the ability to simulate the regenerative microenvironment of bone, are promising for application in the field of tissue engineering. These biomaterials offer distinct advantages over traditional materials by facilitating cellular adhesion and proliferation, maintaining excellent osteoconductivity and biocompatibility, enabling precise control of degradation rates, and enhancing mechanical properties. Importantly, they can simulate the natural structure of bone tissue, including the specific microenvironment, which is crucial for promoting the repair and regeneration of bone defects. This manuscript provides a comprehensive review of the recent research developments and applications of structure-optimized and microenvironment-inspired nanocomposite biomaterials in bone tissue engineering. This review focuses on the properties and advantages these materials offer for bone repair and tissue regeneration, summarizing the latest progress in the application of nanocomposite biomaterials for bone tissue engineering and highlighting the challenges and future perspectives in the field. Through this analysis, the paper aims to underscore the promising potential of nanocomposite biomaterials in bone tissue engineering, contributing to the informed design and strategic planning of next-generation biomaterials for regenerative medicine.
Lifeways of families in coffee-growing territories: vulnerability and response capacity
Authors: Herrera Obeimar B , Parra Manuel , Guerrero Cristina , Soto-Pinto Lorena 
Published: June 2024

AbstractMultilateral and research organizations have developed studies in coffee-growing zones that are focused on sustainable livelihoods; however, the origin of this research and its emphasis on capital limits the explanatory capacity of this approach. To overcome this gap in knowledge and analysis, we developed the lifeways and territorial innovation approach that has been used in research in Chiapas, Mexico, through quantitative and qualitative methodology: workshops and interviews, with the aim of analysing complementarity between capital, strategy, expected results and values of the lifeways of coffee-growing families that facilitate or limit their capacity of response to problems. Our study identified that generational change, coffee pests and diseases, the effects of climate change and the volatility of coffee prices and staple crops are the principal problems that, depending on the typology of the coffee-growing territory (the dynamics of the regime, transition to local initiatives, identity appropriation, appropriation and autonomy), affect each family differently.
Diagnostic differences in high-resolution esophageal motility in a large Mexican cohort based on geographic distribution
Authors: Vázquez-Elizondo Genaro , Remes-Troche José María , Valdovinos-Díaz Miguel Ángel , Coss-Adame Enrique , Morán Edgardo Suárez , Achem Sami R 
Published: June 2024

SummaryHigh-resolution esophageal manometry [HRM] has become the gold standard for the evaluation of esophageal motility disorders. It is unclear whether there are HRM differences in diagnostic outcome based on regional or geographic distribution. The diagnostic outcome of HRM in a diverse geographical population of Mexico was compared and determined if there is variability in diagnostic results among referral centers. Consecutive patients referred for HRM during 2016–2020 were included. Four major referral centers in Mexico participated in the study: northeastern, southeastern, and central (Mexico City, two centers). All studies were interpreted by experienced investigators using Chicago Classification 3 and the same technology. A total of 2293 consecutive patients were included. More abnormal studies were found in the center (61.3%) versus south (45.8%) or north (45.2%) P &lt; 0.001. Higher prevalence of achalasia was noted in the south (21.5%) versus center (12.4%) versus north (9.5%) P &lt; 0.001. Hypercontractile disorders were more common in the north (11.0%) versus the south (5.2%) or the center (3.6%) P.001. A higher frequency of weak peristalsis occurred in the center (76.8%) versus the north (74.2%) or the south (69.2%) P &lt; 0.033. Gastroesophageal junction obstruction was diagnosed in (7.2%) in the center versus the (5.3%) in the north and (4.2%) in the south p.141 (ns). This is the first study to address the diagnostic outcome of HRM in diverse geographical regions of Mexico. We identified several significant diagnostic differences across geographical centers. Our study provides the basis for further analysis of the causes contributing to these differences.
Case report: three ways to mitigate the risk of embolization during left atrial appendage closure in a patient with a massive and proximal left atrial appendage thrombus
Authors: Zendjebil Sandra , Horvilleur Jérôme , Boilève Victor , Millien Vincent , Garot Philippe 
Published: June 2024

Abstract

Background
Left atrial appendage (LAA) thrombus is a contraindication for LAA closure (LAAC). However, in selected cases, oral anticoagulants are strictly contraindicated because of a history of life-threatening bleeding, and LAAC remains the only possible therapy to avoid systemic and especially cerebral embolization.

Case summary
We report a case of LAAC despite a massive proximal thrombus in a patient who had an absolute contraindication to anticoagulant therapy, with thorough pre-planning using CT scan, device modelling and thrombus trapping techniques to reduce the risk of systemic embolic events and perform LAAC safely.

Discussion
Although LAAC remains at high risk in this setting, the use of cautious techniques and tools, from pre-procedure planning to systemic embolization prevention systems associated to a precise transoesopheageal echocardiography guiding throughout the procedure, allows it to be performed as safely as possible when no other option is available.
Catheter ablation for patients with anomalous pulmonary venous return and atrial fibrillation: a case report and literature review
Authors: Wei Zhaoyang , Li Minghua , Wang Zhenggui , Zhang Zhiguo 
Published: June 2024

Abstract

Background
Anomalous pulmonary venous return involves the partial or complete absence of a connection between the pulmonary veins and the left atrium. The pulmonary vein potential plays a vital role in atrial fibrillation, and catheter ablation to isolate the pulmonary vein is crucial for treating this condition. However, when anomalous pulmonary venous return is present, it makes ablation more challenging and increases the risk of atrial fibrillation recurrence after the procedure.

Case summary
A 49-year-old man was hospitalized because he had been experiencing occasional palpitations for 2 months. He had previously undergone surgery to repair an atrial septal defect when he was 11 years old, during which an issue with the right inferior pulmonary vein was identified but left unaddressed. Electrocardiography upon admission showed atrial fibrillation. Left atrial computed tomography angiography revealed that following atrial septal repair surgery, the right inferior pulmonary vein drained into the right atrium. The patient underwent transcatheter radiofrequency ablation to electrically isolate the pulmonary vein with anomalous return. After 12 months of follow-up, there was no atrial fibrillation recurrence.

Discussion
When performing catheter ablation for anomalous pulmonary venous return and atrial fibrillation, it is essential to consider ablating the irregular pulmonary vein before surgery. This helps to reduce surgical complications and the likelihood of atrial fibrillation recurrence. This case report highlights the challenges encountered during ablation in patients with atrial fibrillation and anomalous pulmonary venous return. In addition, we have reviewed the literature to offer insights into the development of ablation strategies for similar patients.
Effects of prime-boost strategies on the protective efficacy and immunogenicity of a PLGA (85:15)-encapsulated Chlamydia recombinant MOMP nanovaccine
Authors: Sahu Rajnish , Verma Richa , Egbo Timothy E , Giambartolomei Guillermo H , Singh Shree R , Dennis Vida A 
Published: June 2024

Abstract
To begin to optimize the immunization routes for our reported PLGA-rMOMP nanovaccine [PLGA-encapsulated Chlamydia muridarum (Cm) recombinant major outer membrane protein (rMOMP)], we compared two prime-boost immunization strategies [subcutaneous (SC) and intramuscular (IM-p) prime routes followed by two SC-boosts)] to evaluate the nanovaccine-induced protective efficacy and immunogenicity in female BALB/c mice. Our results showed that mice immunized via the SC and IM-p routes were protected against a Cm genital challenge by a reduction in bacterial burden and with fewer bacteria in the SC mice. Protection of mice correlated with rMOMP-specific Th1 (IL-2 and IFN-γ) and not Th2 (IL-4, IL-9, and IL-13) cytokines, and CD4+ memory (CD44highCD62Lhigh) T-cells, especially in the SC mice. We also observed higher levels of IL-1α, IL-6, IL-17, CCL-2, and G-CSF in SC-immunized mice. Notably, an increase of cytokines/chemokines was seen after the challenge in the SC, IM-p, and control mice (rMOMP and PBS), suggesting a Cm stimulation. In parallel, rMOMP-specific Th1 (IgG2a and IgG2b) and Th2 (IgG1) serum, mucosal, serum avidity, and neutralizing antibodies were more elevated in SC than in IM-p mice. Overall, the homologous SC prime-boost immunization of mice induced enhanced cellular and antibody responses with better protection against a genital challenge compared to the heterologous IM-p.
PAR1-mediated Non-periodical Synchronized Calcium Oscillations in Human Mesangial Cells
Authors: Stefanenko Mariia , Fedoriuk Mykhailo , Mamenko Mykola , Semenikhina Marharyta , Nowling Tamara K , Lipschutz Joshua H , Maximyuk Oleksandr , Staruschenko Alexander , Palygin Oleg 
Published: June 2024

Abstract
Mesangial cells offer structural support to the glomerular tuft and regulate glomerular capillary flow through their contractile capabilities. These cells undergo phenotypic changes, such as proliferation and mesangial expansion, resulting in abnormal glomerular tuft formation and reduced capillary loops. Such adaptation to the changing environment is commonly associated with various glomerular diseases, including diabetic nephropathy and glomerulonephritis. Thrombin-induced mesangial remodeling was found in diabetic patients, and expression of the corresponding protease-activated receptors (PARs) in the renal mesangium was reported. However, the functional PAR-mediated signaling in mesangial cells was not examined. This study investigated protease-activated mechanisms regulating mesangial cell calcium waves that may play an essential role in the mesangial proliferation or constriction of the arteriolar cells. Our results indicate that coagulation proteases such as thrombin induce synchronized oscillations in cytoplasmic Ca2+ concentration of mesangial cells. The oscillations required PAR1 G-protein coupled receptors-related activation, but not a PAR4, and were further mediated presumably through store-operated calcium entry and transient receptor potential canonical 3 (TRPC3) channel activity. Understanding thrombin signaling pathways and their relation to mesangial cells, contractile or synthetic (proliferative) phenotype may play a role in the development of chronic kidney disease and requires further investigation.
Telomere-to-telomere Genome Assembly of the Clubroot Pathogen Plasmodiophora Brassicae
Authors: Javed Muhammad Asim , Mukhopadhyay Soham , Normandeau Eric , Brochu Anne-Sophie , Pérez-López Edel 
Published: June 2024

Abstract
Plasmodiophora brassicae (Woronin, 1877), a biotrophic, obligate parasite, is the causal agent of clubroot disease in brassicas. The clubroot pathogen has been reported in more than 80 countries worldwide, causing economic losses of hundreds of millions every year. Despite its widespread impact, very little is known about the molecular strategies it employs to induce the characteristic clubs in the roots of susceptible hosts during infection, nor about the mechanisms it uses to overcome genetic resistance. Here, we provide the first telomere-to-telomere complete genome of P. brassicae. We generated ∼27 Gb of Illumina, Oxford Nanopore, and PacBio HiFi data from resting spores of strain Pb3A and produced a 25.3 Mb assembly comprising 20 chromosomes, with an N50 of 1.37 Mb. The BUSCO score, the highest reported for any member of the group Rhizaria (Eukaryota: 88.2%), highlights the limitations within the Eukaryota database for members of this lineage. Using available transcriptomic data and protein evidence, we annotated the Pb3A genome, identifying 10,521 protein-coding gene models. This high-quality, complete genome of P. brassicae will serve as a crucial resource for the plant pathology community to advance the much-needed understanding of the evolution of the clubroot pathogen.
Self-Directed Home- and Community-Based Services Improve Outcomes for Family Caregivers: A Systematic Review
Authors: Kueakomoldej Supakorn , Dinelli Emily , Beestrum Molly , Sadler Tonie , Caldwell Joseph , McHugh Megan , Heinemann Allen W 
Published: June 2024

Abstract

Background and Objectives
Self-direction is an approach that allows older adults and people with disabilities to determine the home- and community-based services they receive, including the ability to hire caregivers of their choice. Self-direction has been shown to improve outcomes for the service recipients. The promotion of choice and control in self-direction may also affect family caregivers. We conducted a systematic review examining the impact of self-direction on a broad range of caregiver outcomes.

Research Design and Methods
We conducted a systematic review guided by PRISMA guidelines. Literature search was conducted in 8 databases. We appraised risk of bias using the Joanna Briggs Institute critical appraisal checklists and assessed certainty of evidence using the GRADE framework.

Results
Sixteen studies meeting inclusion criteria were included. We found, with moderate certainty, that self-direction is associated with improved caregivers’ personal and social well-being. Caregivers also reported reduced unmet needs and increased access to care for the care recipients under self-direction. Self-direction did not appear to reduce caregiving hours. With less certainty, self-direction was also positively associated with increased respite care use, perception of choice, and intention to continue caregiving by caregivers.

Discussion and Implications
Beyond delivering person-centered services that improve recipient outcomes, self-direction may also improve the outcomes of family caregivers.