Nevin Manimala

Phys Rev Lett. 2024 Feb 16;132(7):078402. doi: 10.1103/PhysRevLett.132.078402.

ABSTRACT

Genetic oscillations are generated by delayed transcriptional negative feedback loops, wherein repressor proteins inhibit their own synthesis after a temporal production delay. This delay is distributed because it arises from a sequence of noisy processes, including transcription, translocation, translation, and folding. Because the delay determines repression timing and, therefore, oscillation period, it has been commonly believed that delay noise weakens oscillatory dynamics. Here, we demonstrate that noisy delay can surprisingly denoise genetic oscillators. Specifically, moderate delay noise improves the signal-to-noise ratio and sharpens oscillation peaks, all without impacting period and amplitude. We show that this denoising phenomenon occurs in a variety of well-studied genetic oscillators, and we use queueing theory to uncover the universal mechanisms that produce it.

PMID:38427894 | DOI:10.1103/PhysRevLett.132.078402

Phys Rev Lett. 2024 Feb 16;132(7):073803. doi: 10.1103/PhysRevLett.132.073803.

ABSTRACT

Over the last few years, crystalline topology has been used in photonic crystals to realize edge- and corner-localized states that enhance light-matter interactions for potential device applications. However, the band-theoretic approaches currently used to classify bulk topological crystalline phases cannot predict the existence, localization, or spectral isolation of any resulting boundary-localized modes. While interfaces between materials in different crystalline phases must have topological states at some energy, these states need not appear within the band gap, and thus may not be useful for applications. Here, we derive a class of local markers for identifying material topology due to crystalline symmetries, as well as a corresponding measure of topological protection. As our real-space-based approach is inherently local, it immediately reveals the existence and robustness of topological boundary-localized states, yielding a predictive framework for designing topological crystalline heterostructures. Beyond enabling the optimization of device geometries, we anticipate that our framework will also provide a route forward to deriving local markers for other classes of topology that are reliant upon spatial symmetries.

PMID:38427858 | DOI:10.1103/PhysRevLett.132.073803

Phys Rev Lett. 2024 Feb 16;132(7):078203. doi: 10.1103/PhysRevLett.132.078203.

ABSTRACT

Equilibrium gels provide physically attractive counterparts of nonequilibrium gels, allowing statistical understanding and design of the equilibrium gel structure. Here, we assemble two-dimensional equilibrium gels from limited-valency “patchy” colloidal particles and follow their evolution at the particle scale to elucidate cluster-size distributions and free energies. By finely adjusting the patch attraction with critical Casimir forces, we let a mixture of two-valent and pseudo-three-valent patchy particles approach the percolated network state through a set of equilibrium states. Comparing this equilibrium route with a deep quench, we find that both routes approach the percolated state via the same equilibrium states, revealing that the network topology is uniquely set by the particle bond angles, independent of the formation history. The limited-valency system follows percolation theory remarkably well, approaching the percolation point with the expected universal exponents.

PMID:38427857 | DOI:10.1103/PhysRevLett.132.078203

Phys Rev Lett. 2024 Feb 16;132(7):077301. doi: 10.1103/PhysRevLett.132.077301.

ABSTRACT

Recent generalizations of the Hopfield model of associative memories are able to store a number P of random patterns that grows exponentially with the number N of neurons, P=exp(αN). Besides the huge storage capacity, another interesting feature of these networks is their connection to the attention mechanism which is part of the Transformer architecture widely applied in deep learning. In this work, we study a generic family of pattern ensembles using a statistical mechanics analysis which gives exact asymptotic thresholds for the retrieval of a typical pattern, α_{1}, and lower bounds for the maximum of the load α for which all patterns can be retrieved, α_{c}, as well as sizes of attraction basins. We discuss in detail the cases of Gaussian and spherical patterns, and show that they display rich and qualitatively different phase diagrams.

PMID:38427855 | DOI:10.1103/PhysRevLett.132.077301

J Geriatr Phys Ther. 2024 Feb 27. doi: 10.1519/JPT.0000000000000411. Online ahead of print.

ABSTRACT

BACKGROUND AND PURPOSE: There is a high frequency of frailty in patients with musculoskeletal pain. Pain from osteoarthritis and lower back pain may be associated with frailty. However, the future risk of frailty among older adults with pain remains unclear. Thus, the primary objective of this study was to examine the association between musculoskeletal pain and the risk of becoming prefrail and frail in older adults.

PARTICIPANTS AND METHODS: A secondary analysis was performed using data from baseline and 1-, 2-, 3-, 4-, 6-, and 8-year follow-ups of the Osteoarthritis Initiative (OAI). The OAI recruited participants from 4 clinical sites in the United States, between February 2004 and May 2006. A self-reported questionnaire was used to determine the baseline musculoskeletal pain status in older adults (n = 1780) 65 years and older, including pain in the lower back, hip, knee, and at 2 or more sites. Using the Fried phenotypic criteria, participants were classified as nonfrail, prefrail, and frail at each period over 8 years.

RESULTS: After adjusting for age, sex, race, education, marital status, annual income, smoking status, comorbidities, and body mass index, binary logistic regression modeling using generalized estimating equations revealed that in older adults musculoskeletal pain in the lower back and at multiple sites was associated with a slightly but significantly decreased risk of prefrailty over time (adjusted odds ratio [AOR] = 0.98, 95% CI = 0.95-0.99, P = .019; AOR = 0.96, CI = 0.92-0.99, P = .032). The association between musculoskeletal pain and frailty among older adults was not statistically significant (all P > .05).

CONCLUSIONS: Musculoskeletal pain did not independently significantly increase the risk of prefrailty or frailty over time. It remains possible that when musculoskeletal is combined with other factors, the risk of prefrailty and frailty may be heightened. Further research into the combination of characteristics that best predict prefrailty and frailty, including but not limited to musculoskeletal pain, is warranted.

PMID:38427805 | DOI:10.1519/JPT.0000000000000411

Med Phys. 2024 Mar 1. doi: 10.1002/mp.17006. Online ahead of print.

ABSTRACT

BACKGROUND: Lung cancer has the highest morbidity and mortality rate among all types of cancer. Histological subtypes serve as crucial markers for the development of lung cancer and possess significant clinical values for cancer diagnosis, prognosis, and prediction of treatment responses. However, existing studies only dichotomize normal and cancerous tissues, failing to capture the unique characteristics of tissue sections and cancer types.

PURPOSE: Therefore, we have pioneered the classification of lung adenocarcinoma (LAD) cancer tissues into five subtypes (acinar, lepidic, micropapillary, papillary, and solid) based on section data in whole-slide image sections. In addition, a novel model called HybridNet was designed to improve the classification performance.

METHODS: HybridNet primarily consists of two interactive streams: a Transformer and a convolutional neural network (CNN). The Transformer stream captures rich global representations using a self-attention mechanism, while the CNN stream extracts local semantic features to optimize image details. Specifically, during the dual-stream parallelism, the feature maps of the Transformer stream as weights are weighted and summed with those of the CNN stream backbone; at the end of the parallelism, the respective final features are concatenated to obtain more discriminative semantic information.

RESULTS: Experimental results on a private dataset of LAD showed that HybridNet achieved 95.12% classification accuracy, and the accuracy of five histological subtypes (acinar, lepidic, micropapillary, papillary, and solid) reached 94.5%, 97.1%, 94%, 91%, and 99% respectively; the experimental results on the public BreakHis dataset show that HybridNet achieves the best results in three evaluation metrics: accuracy, recall and F1-score, with 92.40%, 90.63%, and 91.43%, respectively.

CONCLUSIONS: The process of classifying LAD into five subtypes assists pathologists in selecting appropriate treatments and enables them to predict tumor mutation burden (TMB) and analyze the spatial distribution of immune checkpoint proteins based on this and other clinical data. In addition, the proposed HybridNet fuses CNN and Transformer information several times and is able to improve the accuracy of subtype classification, and also shows satisfactory performance on public datasets with some generalization ability.

PMID:38427790 | DOI:10.1002/mp.17006

Rev Esc Enferm USP. 2024 Mar 1;58:e20230146. doi: 10.1590/1980-220X-REEUSP-2023-0146en. eCollection 2024.

ABSTRACT

OBJECTIVE: To understand Primary Health Care nurses’ role in treating Lower Urinary Tract Dysfunction.

METHOD: Cross-sectional multi-methodological research, composed of quantitative and qualitative steps, independently and sequentially. Data collected remotely, through a questionnaire and focus group, analyzed using descriptive statistics and thematic analysis by Braun and Clarke, respectively. The project was approved under Opinion 22691119.0.0000.0030.

RESULTS: A total of 145 nurses participated in the study in the quantitative step and 20 in the qualitative step, working in Primary Health Care in Brazil. Of the 93.1% nurses who reported having already cared for people with Urinary Tract Dysfunction, only 54.4% provided guidance, mainly for training the pelvic floor muscles.

CONCLUSION: Even though they have legal support and access to demand, nurses do not have the knowledge to offer conservative treatment for Lower Urinary Tract Dysfunction. Despite this, they were motivated to do so as long as they received specific training.

PMID:38427780 | DOI:10.1590/1980-220X-REEUSP-2023-0146en

Indian J Pathol Microbiol. 2024 Feb 19. doi: 10.4103/ijpm.ijpm_426_23. Online ahead of print.

ABSTRACT

INTRODUCTION: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide with 878,348 new cases. Cancer-associated fibroblasts (CAFs) are the predominant cell type in tumor stroma and are important promoters of tumor progression.

OBJECTIVE: The aim of the study was to evaluate the pattern of desmoplastic stromal reaction and peri-tumoral inflammatory infiltrate with the histological grade and clinical data.

MATERIALS AND METHODS: A total of 60 cases of HNSCC were included in the study. The hematoxylin and eosin (H and E)-stained sections from all cases were examined by two experienced pathologists for the grade, nature of stomal reaction (SR), peri-tumoral inflammatory infiltration, Yamamoto-Kohama classification grade, worst pattern of invasion (WPOI), depth of invasion (DOI), and other histopathological parameters. Correlation analysis was conducted using the Chi-square test. P-value less than 0.05 was considered statistically significant.

RESULTS: Immature SR was not observed in any of the well-differentiated squamous cell carcinoma (SCC) cases. However, one (3.7%) case of moderately differentiated SCC and two (28.6%) cases of poorly differentiated SCC showed signs of immature SR. In the case of the higher grades of the YK classification, specifically grades 4C and 4D, a more profound depth of tumor cell invasion, equal to or exceeding 10 mm, was evident in six (66.67%) and two (28.57%) cases, respectively. Additionally, among the seven (11.7%) cases classified as poorly differentiated carcinoma, three (42.85%) displayed a WPOI score of 5.

CONCLUSION: SR and the tumor invasive pattern in HNSCC are related to prognosis and may indicate tumor aggressiveness.

PMID:38427768 | DOI:10.4103/ijpm.ijpm_426_23

Indian J Pathol Microbiol. 2024 Feb 19. doi: 10.4103/ijpm.ijpm_582_23. Online ahead of print.

ABSTRACT

BACKGROUND: Coronavirus disease 2019 (COVID-19) emerged as a global pandemic, threatening millions of lives worldwide. Everyone was overwhelmed by the plethora of information from different sources, creating confusion, misconceptions, and panic in the community.

AIMS: This study aimed to estimate the knowledge, attitudes, and practices (KAP) among medical and dental students toward COVID-19 and to identify factors influencing them.

MATERIALS AND METHODS: A cross-sectional study was conducted among undergraduate students enrolled in MBBS and BDS courses, and KAP scores were calculated using a self-administered questionnaire. The statistical analysis was done by unpaired t test and one-way analysis of variance.

RESULTS: MBBS students had higher KAP scores when compared with BDS students. Knowledge gaps were discovered in the areas of COVID-19 transmission through blood, World Health Organization (WHO)-designated variants of concern, disinfectant usage, and mandatory vaccination. A majority (91.33%) of the students had a positive attitude toward COVID-19. Better knowledge and practice scores were significantly associated with vaccinated students and those who trusted government website resources.

CONCLUSION: Curriculum modifications and creative teaching strategies can fill the lacunae in the KAP scores. Medical and dental students, as torchbearers of the healthcare fraternity, can play a critical role in raising awareness during public health emergencies.

PMID:38427767 | DOI:10.4103/ijpm.ijpm_582_23

Indian J Pathol Microbiol. 2024 Feb 19. doi: 10.4103/ijpm.ijpm_361_23. Online ahead of print.

ABSTRACT

BACKGROUND: Prostate cancer is a common cancer in males, frequently leading to mortality. Multiple genetic factors play roles in prostate cancer pathogenesis. Demonstration of pathological pathways and customised treatment options have been possible with next-generation sequencing.

AIM: In this study, we aimed to evaluate the relationships of the changes in the prostate cancer pathways genes with the pathological, immunohistochemical and the clinical parameters.

STUDY DESIGN: Retrospective cross-sectional study. Materials and Methods: Among the prostate needle biopsy materials investigated in Adnan Menderes University Faculty of Medicine, Department of Pathology, thirty-one cases, who had been analysed using the next-generation sequencing system, were included in this study.

RESULTS: As a result of statistical analysis, a significant relationship was found between the pathogenic mutation detected in androgen receptor and Breast Cancer Gene 2 genes and tumour volume. In all cases with a pathogenic mutation in the androgen receptor gene, a pathogenic mutation in the Protein Tyrosine Phosphatase and Tensin Homolog gene was also observed and a significant relationship was found between them. Castration resistance was observed in cases with high tumour volume, and a statistically significant difference was found. A statistically significant relationship was found between tumour volume and Ki-67 expression. In addition, a significant relationship was observed between the castration resistance and Ki-67, c-erbB2 expressions. A statistically significant relationship was found between Ki-67 and c-erbB2.

CONCLUSION: Regarding prognosis prediction and treatment, identifying the molecular changes in genes playing roles in prostate cancer with next-generation sequencing is very important.

PMID:38427749 | DOI:10.4103/ijpm.ijpm_361_23