Tag: pubmed

Phys Rev Lett. 2024 Apr 19;132(16):168201. doi: 10.1103/PhysRevLett.132.168201.

ABSTRACT

We study a model chiral fluid in two dimensions composed of Brownian disks interacting via a Lennard-Jones potential and a nonconservative transverse force, mimicking colloids spinning at a given rate. The system exhibits a phase separation between a chiral liquid and a dilute gas phase that can be characterized using a thermodynamic framework. We compute the equations of state and show that the surface tension controls interface corrections to the coexisting pressure predicted from the equal-area construction. Transverse forces increase surface tension and generate edge currents at the liquid-gas interface. The analysis of these currents shows that the rotational viscosity introduced in chiral hydrodynamics is consistent with microscopic bulk mechanical measurements. Chirality can also break the solid phase, giving rise to a dense fluid made of rotating hexatic patches. Our Letter paves the way for the development of the statistical mechanics of chiral particles assemblies.

PMID:38701478 | DOI:10.1103/PhysRevLett.132.168201

Phys Rev Lett. 2024 Apr 19;132(16):160201. doi: 10.1103/PhysRevLett.132.160201.

ABSTRACT

Quantum theory allows information to flow through a single device in a coherent superposition of two opposite directions, resulting into situations where the input-output direction is indefinite. Here we introduce a theoretical method to witness input-output indefiniteness in a single quantum device, and we experimentally demonstrate it by constructing a photonic setup that exhibits input-output indefiniteness with a statistical significance exceeding 69 standard deviations. Our results provide a way to characterize input-output indefiniteness as a resource for quantum information and photonic quantum technologies and enable tabletop simulations of hypothetical scenarios exhibiting quantum indefiniteness in the direction of time.

PMID:38701466 | DOI:10.1103/PhysRevLett.132.160201

JMIR Public Health Surveill. 2024 May 3;10:e52691. doi: 10.2196/52691.

ABSTRACT

BACKGROUND: Structural racism produces mental health disparities. While studies have examined the impact of individual factors such as poverty and education, the collective contribution of these elements, as manifestations of structural racism, has been less explored. Milwaukee County, Wisconsin, with its racial and socioeconomic diversity, provides a unique context for this multifactorial investigation.

OBJECTIVE: This research aimed to delineate the association between structural racism and mental health disparities in Milwaukee County, using a combination of geospatial and deep learning techniques. We used secondary data sets where all data were aggregated and anonymized before being released by federal agencies.

METHODS: We compiled 217 georeferenced explanatory variables across domains, initially deliberately excluding race-based factors to focus on nonracial determinants. This approach was designed to reveal the underlying patterns of risk factors contributing to poor mental health, subsequently reintegrating race to assess the effects of racism quantitatively. The variable selection combined tree-based methods (random forest) and conventional techniques, supported by variance inflation factor and Pearson correlation analysis for multicollinearity mitigation. The geographically weighted random forest model was used to investigate spatial heterogeneity and dependence. Self-organizing maps, combined with K-means clustering, were used to analyze data from Milwaukee communities, focusing on quantifying the impact of structural racism on the prevalence of poor mental health.

RESULTS: While 12 influential factors collectively accounted for 95.11% of the variability in mental health across communities, the top 6 factors-smoking, poverty, insufficient sleep, lack of health insurance, employment, and age-were particularly impactful. Predominantly, African American neighborhoods were disproportionately affected, which is 2.23 times more likely to encounter high-risk clusters for poor mental health.

CONCLUSIONS: The findings demonstrate that structural racism shapes mental health disparities, with Black community members disproportionately impacted. The multifaceted methodological approach underscores the value of integrating geospatial analysis and deep learning to understand complex social determinants of mental health. These insights highlight the need for targeted interventions, addressing both individual and systemic factors to mitigate mental health disparities rooted in structural racism.

PMID:38701436 | DOI:10.2196/52691

Dis Colon Rectum. 2024 May 3. doi: 10.1097/DCR.0000000000003301. Online ahead of print.

ABSTRACT

BACKGROUND: Some guidelines for rectal carcinoma consider 12 cm, measured by rigid endoscopy to be the cutoff tumor height for optional neoadjuvant chemoradiation. Measuring differences of only a few centimeters may therefore predetermine choice of further therapy. However, rigid endoscopy may exhibit similar operator dependence as do most other clinical examination methods.

OBJECTIVES: Evaluation of concordance of rigid rectoscopic tumor height measurements performed by 4 experienced examiners, 2 in lithotomy and 2 in left lateral position. Assessment of tumor palpability and distance of the anal verge to the anocutaneous line were also evaluated.

DESIGN: Prospective observational study.

SETTING: Academic teaching hospital, referral center for colorectal surgery.

PATIENTS: There were 50 patients, of whom were 35 males (70%). The median age was 72.5 years (53-88 years).

MAIN OUTCOME MEASURES: Interrater agreement of tumor height assessment and tumor allocation beneath or beyond the 12-cm height limit.

RESULTS: With an intraclass correlation coefficient of 0.947 (95% CI: 0.918-0.967, p < 0.001), interrater reliability of tumor height assessment was statistically rated “excellent.” Despite this, in 26% of patients, there was no agreement regarding the allocation of the tumor beneath or beyond the 12-cm height limit. Furthermore there was also considerable disagreement concerning tumor palpability and the distance of the anal verge to the anocutaneous line. Patient positioning was not found to influence results.

LIMITATIONS: Single center study.

CONCLUSIONS: Rigid rectal endoscopy may not be a sound pivotal basis for the consideration of optional chemoradiation in rectal carcinoma. Application of a universally valid height limit obviously ignores biological variability in body frame, gender, and acquired pelvic descent. Eligibility for neoadjuvant therapy should not rely on height measurements alone. Uniform MRI or CT imaging protocols, based on agreed terminology, including factors such as tumor height relative to pelvic frame and peritoneal reflection, may be an important diagnostic addition for such decision. See Video Abstract.

CLINICAL TRIAL REGISTRATION: DRKS00012758 (German National Study Registry), ST-D 406 (German Cancer Society).

PMID:38701433 | DOI:10.1097/DCR.0000000000003301

Brief Bioinform. 2024 Mar 27;25(3):bbae197. doi: 10.1093/bib/bbae197.

ABSTRACT

Coverage quantification is required in many sequencing datasets within the field of genomics research. However, most existing tools fail to provide comprehensive statistical results and exhibit limited performance gains from multithreading. Here, we present PanDepth, an ultra-fast and efficient tool for calculating coverage and depth from sequencing alignments. PanDepth outperforms other tools in computation time and memory efficiency for both BAM and CRAM-format alignment files from sequencing data, regardless of read length. It employs chromosome parallel computation and optimized data structures, resulting in ultrafast computation speeds and memory efficiency. It accepts sorted or unsorted BAM and CRAM-format alignment files as well as GTF, GFF and BED-formatted interval files or a specific window size. When provided with a reference genome sequence and the option to enable GC content calculation, PanDepth includes GC content statistics, enhancing the accuracy and reliability of copy number variation analysis. Overall, PanDepth is a powerful tool that accelerates scientific discovery in genomics research.

PMID:38701418 | DOI:10.1093/bib/bbae197

Brief Bioinform. 2024 Mar 27;25(3):bbae200. doi: 10.1093/bib/bbae200.

ABSTRACT

N4-acetylcytidine (ac4C) is a modification found in ribonucleic acid (RNA) related to diseases. Expensive and labor-intensive methods hindered the exploration of ac4C mechanisms and the development of specific anti-ac4C drugs. Therefore, an advanced prediction model for ac4C in RNA is urgently needed. Despite the construction of various prediction models, several limitations exist: (1) insufficient resolution at base level for ac4C sites; (2) lack of information on species other than Homo sapiens; (3) lack of information on RNA other than mRNA; and (4) lack of interpretation for each prediction. In light of these limitations, we have reconstructed the previous benchmark dataset and introduced a new dataset including balanced RNA sequences from multiple species and RNA types, while also providing base-level resolution for ac4C sites. Additionally, we have proposed a novel transformer-based architecture and pipeline for predicting ac4C sites, allowing for highly accurate predictions, visually interpretable results and no restrictions on the length of input RNA sequences. Statistically, our work has improved the accuracy of predicting specific ac4C sites in multiple species from less than 40% to around 85%, achieving a high AUC > 0.9. These results significantly surpass the performance of all existing models.

PMID:38701415 | DOI:10.1093/bib/bbae200

Brief Bioinform. 2024 Mar 27;25(3):bbae205. doi: 10.1093/bib/bbae205.

ABSTRACT

Potentially pathogenic or probiotic microbes can be identified by comparing their abundance levels between healthy and diseased populations, or more broadly, by linking microbiome composition with clinical phenotypes or environmental factors. However, in microbiome studies, feature tables provide relative rather than absolute abundance of each feature in each sample, as the microbial loads of the samples and the ratios of sequencing depth to microbial load are both unknown and subject to considerable variation. Moreover, microbiome abundance data are count-valued, often over-dispersed and contain a substantial proportion of zeros. To carry out differential abundance analysis while addressing these challenges, we introduce mbDecoda, a model-based approach for debiased analysis of sparse compositions of microbiomes. mbDecoda employs a zero-inflated negative binomial model, linking mean abundance to the variable of interest through a log link function, and it accommodates the adjustment for confounding factors. To efficiently obtain maximum likelihood estimates of model parameters, an Expectation Maximization algorithm is developed. A minimum coverage interval approach is then proposed to rectify compositional bias, enabling accurate and reliable absolute abundance analysis. Through extensive simulation studies and analysis of real-world microbiome datasets, we demonstrate that mbDecoda compares favorably with state-of-the-art methods in terms of effectiveness, robustness and reproducibility.

PMID:38701410 | DOI:10.1093/bib/bbae205

ACS Appl Bio Mater. 2024 May 3. doi: 10.1021/acsabm.4c00241. Online ahead of print.

ABSTRACT

Physicochemical properties of nanoparticles, such as particle size, surface charge, and particle shape, have a significant impact on cell activities. However, the effects of surface functionalization of nanoparticles with small chemical groups on stem cell behavior and function remain understudied. Herein, we incorporated different chemical functional groups (amino, DETA, hydroxyl, phosphate, and sulfonate with charges of +9.5, + 21.7, -14.1, -25.6, and -37.7, respectively) to the surface of inorganic silica nanoparticles. To trace their effects on mesenchymal stem cells (MSCs) of rat bone marrow, these functionalized silica nanoparticles were used to encapsulate Rhodamine B fluorophore dye. We found that surface functionalization with positively charged and short-chain chemical groups facilitates cell internalization and retention of nanoparticles in MSCs. The endocytic pathway differed among functionalized nanoparticles when tested with ion-channel inhibitors. Negatively charged nanoparticles mainly use lysosomal exocytosis to exit cells, while positively charged nanoparticles can undergo endosomal escape to avoid scavenging. The cytotoxic profiles of these functionalized silica nanoparticles are still within acceptable limits and tolerable. They exerted subtle effects on the actin cytoskeleton and migration ability. Last, phosphate-functionalized nanoparticles upregulate osteogenesis-related genes and induce osteoblast-like morphology, implying that it can direct MSCs lineage specification for bone tissue engineering. Our study provides insights into the rational design of biomaterials for effective drug delivery and regenerative medicine.

PMID:38701399 | DOI:10.1021/acsabm.4c00241

Int J Neurosci. 2024 May 3:1-10. doi: 10.1080/00207454.2024.2352023. Online ahead of print.

ABSTRACT

Objective: To explore the improvement effect of probiotics combined with dietary fiber on constipation in patients with schizophrenia.Methods: To compare the improvement scores of constipation, constipation symptoms, quality of life, neurotrophic factors-related indicators, and clinical efficacy between the two groups.Results: There was no statistically significant difference in Cleveland Constipation Scoring System (CCS) scores in the control group before and after treatment (P > 0.05), while the CCS scores in the observation group decreased significantly after treatment (P < 0.05); Patient Assessment of Constipation Symptoms scores significantly decreased in the observation group compared to the control group (P < 0.05), with no significant difference in Patient Assessment of Constipation Quality of Life scores between the two groups pre- and post-treatment; Neuron-specific enolase levels decreased significantly in both groups post-treatment, while brain-derived neurotrophic factor, neuregulin-1, and nerve growth factor levels increased significantly, with a more pronounced rise in the observation group (P < 0.05). Additionally, the total effective rate of clinical treatment in the observation group was higher than that in the control group (P < 0.05).Conclusion: Probiotics combined with dietary fiber can improve constipation symptoms in patients with schizophrenia accompanied by constipation, effectively maintain the balance of intestinal microbiota, and improve the quality of life of patients. Additionally, levels of neurotrophic factors associated with bowel function and neurological health increased significantly, with a higher total effective rate of clinical treatment observed in the probiotics and dietary fiber group. These findings suggest the potential efficacy of probiotics and dietary fiber in managing constipation in this patient population.

PMID:38701375 | DOI:10.1080/00207454.2024.2352023

Blood Adv. 2024 May 3:bloodadvances.2023011458. doi: 10.1182/bloodadvances.2023011458. Online ahead of print.

ABSTRACT

Low levels of vitamin D are associated with a shorter time to first treatment (TTFT) and inferior overall survival in patients with Chronic Lymphocytic leukemia. But whether vitamin D supplement affects the clinical course of CLL patients, remains an open question. In the current study, we aimed to retrospectively explore the clinical benefit of Vitamin D supplement, or one of its analogues, on TTFT and treatment-free survival (TFS) in a large cohort of patients with asymptomatic CLL, who were under watch and wait approach. Among the 3,474 patients included in the study, 931 patients (26.8%) received either vitamin D supplement or its analogue, for a minimum of 6 months. We found that vitamin D supplement was statistically significant for longer TTFT in the young cohort (age<=65) and was associated with a longer TFS for all ages (p-value=0.004). Among non-vitamin D users, the median TFS was found to be 84 months, while among vitamin D supplement users the median TFS extended to 169 months. In conclusion, our long-term retrospective study demonstrates that the administration of vitamin D to patients with CLL in a watch and wait active surveillance is significantly associated with a longer treatment free survival (in any age) and a longer time to first treatment among young patients (age<=65). A prospective clinical trial is needed to validate results.

PMID:38701347 | DOI:10.1182/bloodadvances.2023011458