CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices.

Over a decade has passed since the development of the Hi-C method for genome-wide analysis of 3D genome organization. Hi-C utilizes next-generation sequencing (NGS) technology to generate large-scale chromatin interaction data, which has accumulated across a diverse range of species and cell types, particularly in eukaryotes. There is thus a growing need to streamline the process of Hi-C data analysis to utilize these data sets effectively. Hi-C generates data that are much larger compared to other NGS techniques such as chromatin immunoprecipitation sequencing (ChIP-seq) or RNA-seq, making the data reanalysis process computationally expensive. In an effort to bridge this resource gap, the 4D Nucleome (4DN) Data Portal has reanalyzed approximately 600 Hi-C data sets, allowing users to access and utilize the analyzed data. In this chapter, we provide detailed instructions for the implementation of the common workflow language (CWL)-based Hi-C analysis pipeline adopted by the 4DN Data Portal ecosystem. This reproducible and portable pipeline generates standard Hi-C contact matrices in formats such as .hic or .mcool from FASTQ files. It enables users to output their own Hi-C data in the same format as those registered in the 4DN Data portal, facilitating comparative analysis using data registered in the portal. Our custom-made scripts are available on GitHub at https://github.com/kuzobuta/4dn_cwl_pipeline .

Three-Dimensional Simulation of Whole-Genome Structuring Through the Transition from Anaphase to Interphase.

In order to analyze the three-dimensional genome architecture, it is important to simulate how the genome is structured through the cell cycle progression. In this chapter, we present the usage of our computation codes for simulating how the human genome is formed as the cell transforms from anaphase to interphase. We do not use the global Hi-C data as an input into the genome simulation but represent all chromosomes as linear polymers annotated by the neighboring region contact index (NCI), which classifies the A/B type of each local chromatin region. The simulated mitotic chromosomes heterogeneously expand upon entry to the G1 phase, which induces phase separation of A and B chromatin regions, establishing chromosome territories, compartments, and lamina and nucleolus associations in the interphase nucleus. When the appropriate one-dimensional chromosomal annotation is possible, using the protocol of this chapter, one can quantitatively simulate the three-dimensional genome structure and dynamics of human cells of interest.

Structural Maintenance of Chromosomes Complexes.

The Structural Maintenance of Chromosomes (SMC) protein complexes are DNA-binding molecular machines required to shape chromosomes into functional units and to safeguard the genome through cell division. These ring-shaped multi-subunit protein complexes, which are present in all kingdoms of life, achieve this by organizing chromosomes in three-dimensional space. Mechanistically, the SMC complexes hydrolyze ATP to either stably entrap DNA molecules within their lumen, or rapidly reel DNA into large loops, which allow them to link two stretches of DNA in cis or trans. In this chapter, the canonical structure of the SMC complexes is first introduced, followed by a description of the composition and general functions of the main types of eukaryotic and prokaryotic SMC complexes. Thereafter, the current model for how SMC complexes perform in vitro DNA loop extrusion is presented. Lastly, chromosome loop formation by SMC complexes is introduced, and how the DNA loop extrusion mechanism contributes to chromosome looping by SMC complexes in cells is discussed.

Forms of resistance, experiences and ethnopolitical organization of a Mapuche community in the province of Buenos Aires, Argentina / Formas de resistencia, experiencias y organización etnopolítica de una comunidad mapuche en provincia de buenos aires, argentina

RESUMEN Objetivo: Analizar desde una perspectiva etnográfica los procesos étnicos-identitarios y la organización etnopolítica de la población indígena en la localidad de Carhué, provincia de Buenos Aires (Argentina). Para ello fueron atendidas diversas cuestiones, como las estrategias, los reclamos y las formas de resistencia llevadas a cabo por las familias que la componen. En este análisis resulta central atender a la emergencia étnica de la década de 1990 en espacios urbanos y las legislaciones que tienen como principales destinatarios a los pueblos originarios del país. Materiales y métodos: El trabajo con las familias mapuches de Carhué comenzó en 2018 a partir de una demanda específica para colaborar en la tramitación de su personería jurídica y las pautas de trabajo fueron definidas en conjunto. De esta manera, la metodología parte y se sustenta en el trabajo colaborativo. La perspectiva etnográfica se nutrió de entrevistas formales y dirigidas, charlas informales y observación participante, lo cual se trianguló con la búsqueda de fuentes en diversos archivos y la lectura bibliográfica de antecedentes teóricos en el tema. Resultados: En este trabajo hemos mostrado la necesaria movilización y elaboración de estrategias de las comunidades indígenas para hacer cumplir sus derechos como pueblos preexistentes ante la ausencia de respuestas de los diversos niveles del Estado y la falta de implementación de las leyes y normativas concernientes a los pueblos indígenas. Conclusiones: Pudimos observar que, a pesar de la falta de respuesta en relación con los reclamos indígenas, la organización etnopolítica de la comunidad de Carhué sigue creciendo en pos de visibilizar su presencia en el ámbito local, reclamar por el cumplimiento de derechos y por el acceso a la tierra para disponer de espacios propios para su reproducción y fortalecimiento.

ABSTRACT Objective: This paper seeks to contribute, from the perspective of Social Anthropology, to the analysis of the ethnopolitical organization and identity revaluation of indigenous communities in Argentina. For this purpose, we will focus on the organization process of the families of the Mapuche Kalfulafken community in the urban region of Carhué, province of Buenos Aires (Argentina), which has gained momentum in the last decades. In short, the aim is to analyze how indigenous claims in Carhué are constituted around territory, ethnic identity and living conditions by considering resistance strategies and access to resources over time and in relation to the different levels of the State -municipality, province and nation-. Central to this analysis is the indigenous emergence of recent times, which began in the 1990s and is characterized by a growing ethnic awareness and emergence. Additionally, reanalyzing the legislations that principally address the original pueblos of the country and the legal and regulatory advances that, in many cases, are due to the continued mobilization and organization of indigenous groups have been very important in the processes of identity reconstruction. Materials and methods: The approach from which we start this research corresponds to the perspective of Social Anthropology. The fieldwork with the Mapuche families of Carhué began in 2018 from a specific demand to the research/outreach group to collaborate in their request for recognition before the provincial State (through the processing of their legal status). The steps to be followed in the research and the work guidelines were defined together with the community, so that the methodology is based on collaborative work. A bibliographic survey of theoretical antecedents was carried out. The research question focused on the forms of organization of the Mapuche families and their relationship with the processes of ethnic-identity reconfiguration in Carhué, framed in the context of the indigenous emergence and resurgence of ethnic and territorial demands in the area. Returning to the field on several occasions, deepening the topics and reworking the methodological strategies allowed us to construct the objectives and better orient the research. The methodology was ethnographic and a diverse group of actors were interviewed: the members of the indigenous organization, inhabitants of Carhué, governmental and non-governmental officials, and others. Open and in-depth interviews, semi-structured interviews, individual, and group interviews were carried out. The aim was to reconstruct life histories and trajectories in order to try to understand social phenomena from the perspective of the actors. Thus, participant observation was an importantpart of the fieldwork. The perspective was nurtured and triangulated with the search for primary and secondary sources and complementary cases through the work in the local archive at the request of Kalfulafken, given the importance of making an approach with some historical depth to reconstruct the facts of persecution and violence against indigenous peoples in Argentina. Results: The work is framed within the resurgence of the demands and processes of identity reconstruction that have been gaining strength in the country since the 1990s. The large presence of the indigenous population in urban spaces is highlighted in the face of the historically constructed ideas of denial, discrimination and exclusion that have their roots in the colonial period and continued with the formation of the National State. We focus on the history of ethnopolitical organization and the forms of resistance ofthefamilies of Carhué, which has gained momentum in the last decades and seeks to assert their presence in the urban environment. From which, the members appeal to distance themselvesfrom and question the discourses promoted by state institutions that sought to dominate and make the indigenous population in the region invisible. In this way, we address the strategies and activities implemented by the Kalfulafken community that seek to question the 'official history' and demonstrate the subjugation, discrimination and invisibilization suffered and to reaffirm their current presence in Carhué. Such processes have led, on the one hand, to new links with other ethnopolitical groups, universities, national and local institutions, and on the other hand, to the generation of new spaces for participation and networks in the area in order to have greater visibility and strengthen their claims. In addition, we highlight the community's search for support and recognitionfrom local authorities in order to make their claims viable. Conclusions: From the analysis on the organizational processes of a Mapuche community in the province of Buenos Aires we can make several conclusions. On the one hand, in the absence of responses from the various levels of the State and the lack of implementation of laws and regulations concerning indigenous peoples, it is the communities that must mobilize and develop strategies to enforce their rights as pre-existing peoples. Despite the lack of response to the indigenous claims, the ethnopolitical organization of the community of Carhué continues to grow in order to make its presence visible at the local level and to claim the fulfillment of their rights and the recovery of their territories in order to have their own spaces and cultural autonomy for their reproduction. Another issue that was highlighted was the need forgreater access to funds and social projects that would allow these objectives to be carried out and that wouldprovide scholarships for the younger generations to study. That is to say that these requests that have arisen in the organization are linked, since in order to have autonomy they must have territories and funds to sustain it. In summary, the above allows us to account for the local ethnopolitical work and the impact of the productions and materials produced within the framework of university extension to accompany such processes. Likewise, the presence of indigenous movements makes it clear that the state projects of a homogeneous Argentina have not been achieved. In the case of Kalfulafken we have been able to see that in addition to the processing of their legal status, the community seeks to generate new spaces for intervention and networks in the region to achieve greater visibility and strengthen their claims.

Health outcomes reported by healthcare providers and clients of a community-based medically tailored meal program.

BACKGROUND: Medically tailored meal (MTM) programs provide home-delivered meals to people living with serious illness and poor nutritional status. Client outcome studies have found evidence of decreased healthcare utilization and cost savings associated with MTM program participation, and inconclusive evidence of change in health measures. The purpose of this study was to use a novel observational framework to describe the client profile and change in health outcomes using routinely collected health and program data from a community-based MTM program at MANNA (Philadelphia, PA). METHODS: Clients reported their self-rated health and experiences of food insecurity and malnutrition. Healthcare providers reported clients' body mass index, systolic blood pressure, and hemoglobin A1C. These health outcomes, measured at program intake and 3-6 months later, were linked with administrative data for 1,959 clients who completed at least two months of MTM services in 2020, 2021, and 2022. RESULTS: Clients exhibited substantial heterogeneity in demographics and health status at intake. Self-reported malnutrition risk decreased significantly over program duration (p < .001). Nearly one-third of clients with poor health reported improvement over time. Over 60% of clients with obesity experienced stable BMI. Clients with hypertension experienced significant improvements in systolic blood pressure (p < .001). Clients with diabetes and available data (n = 45) demonstrated significant reduction in hemoglobin A1C (p = .005). CONCLUSION: We found evidence that participation in MANNA's MTM program was associated with favorable health outcomes for clients with serious illness and nutritional risk. Community-based organizations can maximize the completeness of their data by focusing on routinely collected internal data like validated health screeners and surveys.

Inclusive leadership, self-efficacy, organization-based self-esteem, and intensive care nurses' job performance: A cross-sectional study using structural equation modeling.

BACKGROUND: The job performance of intensive care nurses is critical to the treatment and recovery of critically ill patients. Inclusive leadership, self-efficacy and organization-based self-esteem (OBSE) are important psychosocial factors affecting job performance. However, few studies have explored the relationships among these factors in critical care nurses. AIMS: To examine the impact of inclusive leadership on the job performance of intensive care nurses and to explore the potential mediation through self-efficacy and OBSE. METHODS: A cross-sectional survey design was employed. Between November and December 2023, a total of 460 intensive care nurses from China completed the survey, which included standard assessments on inclusive leadership, self-efficacy, OBSE, and job performance. Mediation analysis was conducted using structural equation modeling. Indirect effects were evaluated through bootstrapping. RESULTS: The results indicated significant positive correlations among inclusive leadership, self-efficacy, OBSE, and job performance (all P < 0.01). Inclusive leadership not only directly affected the job performance of intensive care nurses but also influenced it through the partial mediating roles of self-efficacy and OBSE, with the mediating effects accounting for 14.29 % and 30.61 % of the total effect, respectively. Additionally, the analysis found that self-efficacy and OBSE played a chain mediating role in the relationship between inclusive leadership and the job performance, with the mediating effect accounting for 22.45 % of the total effect. CONCLUSIONS: Inclusive leadership positively predict the job performance of intensive care nurses. Self-efficacy and OBSE act as mediating factors, further explaining how inclusive leadership improves the job performance of intensive care nurses. IMPLICATIONS FOR CLINICAL PRACTICE: Enhancing inclusive leadership can be achieved through targeted training programs that emphasize open communication, team collaboration, and recognition of diverse perspectives. For example, leadership workshops can include role-playing scenarios that promote active listening and constructive feedback. Furthermore, boosting self-efficacy and OBSE is essential, as these variables significantly mediate the relationship between inclusive leadership and job performance. Encouraging mentorship and providing opportunities for professional development can help nurses build their confidence and organizational identity, ultimately leading to improved performance and patient care outcomes.

Investigation and evaluation of risk of pathogen transfer by ballast water in Shahid Rajaee Port, Hormozgan Province, Iran.

Ballast water is essential for ship operations, but can also transport harmful organisms between ports, threatening local environments. The Ballast Water Management (BWM) Convention, established by the International Maritime Organization (IMO), requires ships to implement ballast water management measures to address this issue. In this study, ballast water samples were collected from ships entering Shahid Rajaee Port in Iran before and after the Ballast Water Management Convention came into force in 2017. The sampling was conducted in coordination with Iranian authorities, following IMO guidelines. Vibrio cholerae, Escherichia coli, and Enterococci were identified in 97 ships, and physical parameters such as temperature, salinity, and pH were measured in 15 ships. To prevent sample contamination, rigorous protocols were followed, including using sterile equipment, appropriate storage, and immediate transfer to the lab. The results showed that before the BWM Convention, V. cholerae was found in 6 out of 14 ships (42%), with ballast water retention times of 2-58 days. After the convention, V. cholerae was found in only 2 out of 83 ships (2.4%), with ballast water retention of 2-3 days. This indicates a significant reduction in the risk of pathogen transfer through ballast water. Further analysis after the Convention showed that V. cholerae was initially detected in 4 out of 15 ships, but only 1 ship (6.6%) had levels above the standard. E. coli and Enterococci were also detected in multiple ships, but their levels were below the standard. The study investigated the relationship between the bacterial levels and the physical parameters. While some correlations were found between E. coli/Enterococci and parameters like pH, temperature, salinity, and water retention time, no significant impact of physical parameters on V. cholerae levels was observed. T-tests revealed significant relationships between the bacterial levels and the physical parameters, as well as the ballast water retention time. Ships were found to have followed the ballast water exchange guidelines of exchanging at least 200 or 50 nautical miles from shore and at depths over 200 m, as mapped out for the Persian Gulf region. The results indicate that the implementation of the BWM Convention has been effective in reducing the risk of pathogen transfer through ballast water. However, the study emphasizes the importance of ongoing monitoring and enforcement to ensure continued compliance with the convention's requirements.

Technology adaptation in sugarcane supply chain based on a novel p, q Quasirung Orthopair Fuzzy decision making framework.

The present paper contributes to the literature in two ways. First, it develops a novel p, q Quasirung Orthopair Fuzzy (p, q QOF) based group decision making framework to modify a recently developed multi-criteria decision making (MCDM) model such as Comparisons between Ranked Criteria (COBRAC). Second, the paper ruminates on the Strength-Weakness-Opportunity-Threat (SWOT) of the sugarcane supply chain (SSC) in India vis-à-vis adaptation of the advanced technologies featuring Industry 4.0. To set the sub-factors of various dimensions of SWOT, the theoretical ground of Technology-Organization-Environment (TOE) framework has been used. The sub-factors of SWOT have been derived through an informal in-depth discussion with the experts of the sugar industry. Then using a Likert five-point linguistic scale the experts rated the sub-factors based on their relative importance. To determine the weights the modified COBRAC method has been applied. In subsequent stages the reliability of the model has been tested and sensitivity analysis has been carried out to check the stability of the result. The analysis reveals that while experience, by-product utilization and high demand provides strength and create opportunities for SSC, the areas of concern are lack of variety, fragmented nature of supply chains, shortage of next-gen talent and inadequate infrastructure. However, there are enough promises for SSC. The paper shall provide impetus to strategic decision makers for the sugar industry and puts forth a new decision-making framework for the analysts.

High levels of consanguinity in a child from Paquimé, Chihuahua, Mexico.

This study reports results from the ancient DNA analysis of a unique child burial at Paquimé, northern Chihuahua, Mexico. Located between Mesoamerican and Ancestral Puebloan groups, Paquimé (also known as Casas Grandes) was a vibrant multicultural centre during the 13th-14th centuries AD. Archaeologists have long debated Paquimé's social organization. Our analysis of Burial 23-8 has revealed that this child, placed under the centre post of an important room, had parents who were close genetic relatives. We argue that this child's consanguinity and special depositional context resulted from an elite family's practice of aggrandizing social status.

Accentuation, Boolean maps and perception of (dis)similarity in a neural model of visual segmentation.

We developed an interactive cortical circuit for visual segmentation that integrates bottom-up and top-down processing to segregate or group visual elements. A bottom-up pathway incorporates stimulus-driven saliency computation, top-down feature-based weighting by relevance and winner-take-all selection. A top-down pathway encompasses multiscale feedback projections, an object-based attention network and a visual segmentation network. Computer simulations have shown that a salient element in the stimulus guides spatial attention and further influences the decomposition of the nearby object into its parts, as postulated by the principle of accentuation. By contrast, when no single salient element is present, top-down feature-based attention highlights all locations occupied by the attended feature and the model forms a Boolean map, i.e., a spatial representation that makes the feature-based grouping explicit. The same distinction between bottom-up and top-down influences in perceptual organization can also be applied to texture perception. The model suggests that the principle of accentuation and feature-based similarity grouping are two manifestations of the same cortical circuit designed to detect similarities and dissimilarities of visual elements in a stimulus.

Type II topoisomerases shape multi-scale 3D chromatin folding in regions of positive supercoils.

Type II topoisomerases (TOP2s) resolve torsional stress accumulated during various cellular processes and are enriched at chromatin loop anchors and topologically associated domain (TAD) boundaries, where, when trapped, can lead to genomic instability promoting the formation of oncogenic fusions. Whether TOP2s relieve topological constraints at these positions and/or participate in 3D chromosome folding remains unclear. Here, we combine 3D genomics, imaging, and GapRUN, a method for the genome-wide profiling of positive supercoiling, to assess the role of TOP2s in shaping chromosome organization in human cells. Acute TOP2 depletion led to the emergence of new, large-scale contacts at the boundaries between active, positively supercoiled, and lamina-associated domains. TOP2-dependent changes at the higher-order chromatin folding were accompanied by remodeling of chromatin-nuclear lamina interactions and of gene expression, while at the chromatin loop level, TOP2 depletion predominantly remodeled transcriptionally anchored, positively supercoiled loops. We propose that TOP2s act as a fine regulator of chromosome folding at multiple scales.

STAG2 loss in Ewing sarcoma alters enhancer-promoter contacts dependent and independent of EWS::FLI1.

Cohesin complexes carrying STAG1 or STAG2 organize the genome into chromatin loops. STAG2 loss-of-function mutations promote metastasis in Ewing sarcoma, a pediatric cancer driven by the fusion transcription factor EWS::FLI1. We integrated transcriptomic data from patients and cellular models to identify a STAG2-dependent gene signature associated with worse prognosis. Subsequent genomic profiling and high-resolution chromatin interaction data from Capture Hi-C indicated that cohesin-STAG2 facilitates communication between EWS::FLI1-bound long GGAA repeats, presumably acting as neoenhancers, and their target promoters. Changes in CTCF-dependent chromatin contacts involving signature genes, unrelated to EWS::FLI1 binding, were also identified. STAG1 is unable to compensate for STAG2 loss and chromatin-bound cohesin is severely decreased, while levels of the processivity factor NIPBL remain unchanged, likely affecting DNA looping dynamics. These results illuminate how STAG2 loss modifies the chromatin interactome of Ewing sarcoma cells and provide a list of potential biomarkers and therapeutic targets.

Fibrin-associated diffuse large B-cell lymphoma in the aortic valve and ascending aorta.

Primary cardiac lymphoma is an extremely rare disease, with the most common being diffuse large B-cell lymphoma (DLBCL). Fibrin-associated diffuse large B-cell lymphoma (FA-DLBCL) has been classified as a rare and unusual type of lymphoma and is included in the category of DLBCL associated with chronic inflammation (DLBCL-CI). In this study, we report a case of FA-DLBCL in the aortic valve and ascending aorta of a 51-year-old-woman. Learning objective: In this rare case of FA-DLBCL in the aortic valve and ascending aorta, we highlight the features of FA-DLBCL and its differences from DLBCL-CI.

The Value of Work: The Gendered Outcomes of Organizational Wage Reforms.

This study explores the influence of organizational practices on gender in/equality in a unique setting: the reformed Israeli kibbutz. The transition of the kibbutz from all members receiving an allowance to waged labor provides an opportunity to explore the impact of wage determination systems on gender pay inequality. The study uses a mixed-method approach: descriptive statistics of administrative data, in-depth interviews, and a focus group with kibbutz management. The findings demonstrate that a "market-based logic," embedded with gendered preconceptions of "women's work," can seep into an organization through a shift in the wage determination system, and increase gender inequality. The findings also highlight the lack of organizational awareness about the gendered consequences of this shift, or even their uncritical acceptance of the "value hierarchy" as ordained by the market. The study thus supports the theory positing gender as a hidden but integral aspect of reward systems in contemporary labor markets. HIGHLIGHTS The choice of a wage determination system is critical for gender inequality."Women's work" is valued higher by analytical job evaluation systems, which reduce gender biases.Market-based wage determinations introduce biases and increase organizational gender inequality.Management prefers market-based wage determinations due to competition and costs.The "free market" not only obscures gender hierarchies but also legitimizes them.

Psychometric Properties of the Danish International Trauma Questionnaire-Child and Adolescent Version (ITQ-CA).

With the introduction of the ICD-11 diagnostic manual, the need for developing and validating new assessment instruments has become urgent. The International Trauma Questionnaire-Child and Adolescent version (ITQ-CA) assesses posttraumatic stress disorder (PTSD) and complex PTSD (CPTSD) based on the ICD-11 diagnostic definition. This study examines the psychometric properties of the Danish version of the ITQ-CA in a non-clinical sample of 226 adolescents. Hierarchical multiple regression analyses were performed to study the effects of gender, age, trauma exposure, family dysfunction, and SDQ variables on PTSD and Disturbances in Self-Organization (DSO). Results showed that 16 participants (7%) met the ITQ-CA criteria for CPTSD and 11 (5.7%) for PTSD. The full model of gender, age, family dysfunction, trauma exposure, and SDQ variables was found to predict PTSD and DSO. The present study supports the validity of the Danish version of the ITQ-CA and represents an important step of establishing and applying validated tools for assessing  PTSD and CPTSD in children and adolescents. The results also underscore the need for a broader trauma definition. Future research should examine the sensitivity of the ITQ-CA.

TP53 Mutation Status in Myelodysplastic Neoplasm and Acute Myeloid Leukemia: Impact of Reclassification Based on the 5th WHO and International Consensus Classification Criteria: A Korean Multicenter Study.

Background: TP53 mutations are associated with poor prognosis in myelodysplastic neoplasm (MDS) and AML. The updated 5th WHO classification and International Consensus Classification (ICC) categorize TP53-mutated MDS and AML as unique entities. We conducted a multicenter study in Korea to investigate the characteristics of TP53-mutated MDS and AML, focusing on diagnostic aspects based on updated classifications. Methods: This study included patients aged ≥ 18 yrs who were diagnosed as having MDS (N=1,244) or AML (N=2,115) at six institutions. The results of bone marrow examination, cytogenetic studies, and targeted next-generation sequencing, including TP53, were collected and analyzed. Results: TP53 mutations were detected in 9.3% and 9.2% of patients with MDS and AML, respectively. Missense mutation was the most common, with hotspot codons R248/R273/G245/Y220/R175/C238 accounting for 25.4% of TP53 mutations. Ten percent of patients had multiple TP53 mutations, and 78.4% had a complex karyotype. The median variant allele frequency (VAF) of TP53 mutations was 41.5%, with a notable difference according to the presence of a complex karyotype. According to the 5th WHO classification and ICC, the multi-hit TP53 mutation criteria were met in 58.6% and 75% of MDS patients, respectively, and the primary determinants were a TP53 VAF >50% for the 5th WHO classification and the presence of a complex karyotype for the ICC. Conclusions: Collectively, we elucidated the molecular genetic characteristics of patients with TP53-mutated MDS and AML, highlighting key factors in applying TP53 mutation-related criteria in updated classifications, which will aid in establishing diagnostic strategies.

Sex Differences in Hierarchical and Modular Organization of Functional Brain Networks: Insights from Hierarchical Entropy and Modularity Analysis.

Existing studies have demonstrated significant sex differences in the neural mechanisms of daily life and neuropsychiatric disorders. The hierarchical organization of the functional brain network is a critical feature for assessing these neural mechanisms. But the sex differences in hierarchical organization have not been fully investigated. Here, we explore whether the hierarchical structure of the brain network differs between females and males using resting-state fMRI data. We measure the hierarchical entropy and the maximum modularity of each individual, and identify a significant negative correlation between the complexity of hierarchy and modularity in brain networks. At the mean level, females show higher modularity, whereas males exhibit a more complex hierarchy. At the consensus level, we use a co-classification matrix to perform a detailed investigation of the differences in the hierarchical organization between sexes and observe that the female group and the male group exhibit different interaction patterns of brain regions in the dorsal attention network (DAN) and visual network (VIN). Our findings suggest that the brains of females and males employ different network topologies to carry out brain functions. In addition, the negative correlation between hierarchy and modularity implies a need to balance the complexity in the hierarchical organization of the brain network, which sheds light on future studies of brain functions.

When Benchmarks Fail Us: A Case Study in Cytoreductive Surgery.

INTRODUCTION: Relative Value Units (RVUs) are utilized to measure physician work effort and create national benchmarks. Physicians are often measured against national benchmarks to determine compensation. Using a case study in cytoreductive surgery, we explored variability in coding that can impact national benchmarks. METHODS: A survey was conducted amongst surgeons in the peritoneal surface malignancies consortium (PSM). Data was collected on clinical experience, clinical full time equivalent, wRVUS and institutional coding practice. RESULTS: Coding of the same procedure resulted in significantly varying RVUs (IQR 60-101) across institutions. Higher volume (> 50% practice) appeared to have better coding practices with higher wRVU/case (Median 102 vs 62, p = 0.04). CONCLUSIONS: There is significant variability in the measurement of similar effort across institutions due to coding variability. Such variability creates flaws in measurement necessary for benchmarks.

Diagnostic accuracy of active pulmonary tuberculosis screening during detention admission: a systematic review.

Individuals entering incarceration are at high risk for infectious diseases, other ill conditions, and risky behavior. Typically, the status of active pulmonary tuberculosis (PTB) is not known at the time of admission. Early detection and treatment are essential for effective TB control. So far, no study has compared the diagnostic accuracy of various TB screening tools in detention using a network meta-analysis (NMA). We aimed to investigate the diagnostic accuracy of active PTB screening tests upon detention admission. We searched PubMed, Global Index Medicus, the Cochrane Library electronic databases, and grey literature for publications reporting detention TB entry screening in March 2022 and January 2024. Inclusion was non-restrictive regarding time, language, location, reference standards, or screening tests. Eligible study designs comprised comparative, observational, and diagnostic studies. Publications had to report TB screening of individuals entering confinement and provide data for diagnostic accuracy calculations. The QUADAS-2 tool was designed to assess the quality of primary diagnostic accuracy studies. This systematic review was registered with PROSPERO (CRD42022307863) and conducted without external funding. We screened a total of 2,455 records. Despite extensive searching, no studies met our inclusion criteria. However, we identified evidence revealing key differences in screening algorithm application. In conclusion, more diagnostic accuracy data on TB screening algorithms for detention admission worldwide needs to be collected. We recommend that global TB initiatives set up multi-site studies to investigate the diagnostic accuracy of TB screening on admission in low- and high-prevalence criminal justice systems. Further network meta-analyses of these studies could inform policymakers and public health experts to establish or fine-tune TB control in detention settings.

Awareness and Knowledge of Adverse Drug Reactions and Pharmacovigilance Among Medical and Nursing Students and Staff in a Tertiary Care Hospital.

Background Pharmacovigilance is defined as the science and activities related to the detection, assessment, understanding, and prevention of adverse effects or other drug-related problems. Underreporting of adverse drug reactions (ADRs) is a global issue, and adequate knowledge among healthcare professionals is essential. Engaging young doctors and nursing professionals in pharmacovigilance is crucial for promoting ADR reporting. Objectives The objective of this study is to evaluate the knowledge and awareness of ADRs and pharmacovigilance among medical and nursing students and staff in a tertiary care hospital in Vijayapura, India. Methods A cross-sectional, observational, questionnaire-based study was carried out using a validated questionnaire that included a total of 19 questions related to knowledge and awareness aspects. This was distributed electronically using Google Forms. By using the convenience sampling method, a sample size of 96 participants was calculated for each group (medical and nursing), and this was rounded to 100 participants per group to account for potential dropouts and to ensure the strength of this study. All the questions were peer-reviewed by expert faculties from the Department of Pharmacology. Results The data analysis showed that medical students and staff had superior knowledge of ADRs and pharmacovigilance. Nursing students and staff exhibited greater awareness of the nearest pharmacovigilance center and ADR monitoring centers in India. Nursing students and staff were more active in ADR and pharmacovigilance awareness programs. Conclusions This study clearly shows the importance of flexible attitudes and robust education in pharmacovigilance and ADR reporting among healthcare professionals. Executing simulation-based training can strengthen the skills and confidence of both medical and nursing professionals in ADR reporting and pharmacovigilance.