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Objectives: To compare the effect of the use of custom and prefabricated insoles on the behavior of plantar weight load and musculoskeletal symptoms in assembly line workers. Methods; A randomized trial was carried out with 27 women who worked in a static standing position and had musculoskeletal symptoms. The mean age was 30.3 ± 7.09 years and the weight 64.85 ± 13.65 Kg. The Nordic Musculoskeletal Questionnaire was administered, and plantar pressure was determined using a computerized baropodometric system (FootWork). The sample was then divided into control group, which wore pre-fabricated insoles, and intervention group, which wore ethylvinylacetate insoles for eight weeks. Baropodometric data were collected and the questionnaire was administered once again. Results: There was no statistically significant difference in the comparison between groups and baropodometric data. However, a change was noted in the behavior of the load variables between evaluations, with an increase in mean load pressure and maximal plantar pressure (p<0.05). No statistically significant difference was found between groups for any anatomical site in the different evaluations. Within each group, there was a reduction in foot pain and back pain between evaluations (p<0.05). Conclusions: Both types of insole reduced pain symptoms in the lumbar region and feet. After eight weeks of use, there was an increase in maximal and mean plantar pressure and a reduction in plantar surface area with both types of insole. Article registered in the Australian New Zealand Clinical Trials Registry (ANZCTR) under the number ACTRN 12609000922279. [ABSTRACT FROM AUTHOR]

Studying the tumor microenvironment and surrounding lymph nodes is the main focus of current immunological research on soft tissue sarcomas (STS). However, due to the restricted opportunity to examine tumor samples, alternative approaches are required to evaluate immune responses in non-surgical patients. Therefore, the purpose of this study was to evaluate the peripheral immune profile of STS patients, characterize patients accordingly and explore the impact of peripheral immunotypes on patient survival. Blood samples were collected from 55 STS patients and age-matched healthy donors (HD) controls. Deep immunophenotyping and gene expression analysis of whole blood was analyzed using multiparametric flow cytometry and real-time RT-qPCR, respectively. Using xMAP technology, proteomic analysis was also carried out on plasma samples. Unsupervised clustering analysis was used to classify patients based on their immune profiles to further analyze the impact of peripheral immunotypes on patient survival. Significant differences were found between STS patients and HD controls. It was found a contraction of B cells and CD4 T cells compartment, along with decreased expression levels of ICOSLG and CD40LG; a major contribution of suppressor factors, as increased frequency of M-MDSC and memory Tregs, increased expression levels of ARG1, and increased plasma levels of IL-10, soluble VISTA and soluble TIMD-4; and a compromised cytotoxic potential associated with NK and CD8 T cells, namely decreased frequency of CD56 dim NK cells, and decreased levels of PRF1, GZMB, and KLRK1. In addition, the patients were classified into three peripheral immunotype groups: "immune-high," "immune-intermediate," and "immune-low." Furthermore, it was found a correlation between these immunotypes and patient survival. Patients classified as "immune-high" exhibited higher levels of immune-related factors linked to cytotoxic/effector activity and longer survival times, whereas patients classified as "immune-low" displayed higher levels of immune factors associated with immunosuppression and shorter survival times. In conclusion, it can be suggested that STS patients have a compromised systemic immunity, and the correlation between immunotypes and survival emphasizes the importance of studying peripheral blood samples in STS. Assessing the peripheral immune response holds promise as a useful method for monitoring and forecasting outcomes in STS., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Almeida, Sousa, Couceiro, Andrade, Alves, Martinho, Rodrigues, Fonseca, Freitas-Tavares, Santos-Rosa, Casanova and Rodrigues-Santos.)

Background: Few studies have found long-term effects of early musical environmental enrichment in the NICU on preterm infant's development. This study examines how early music enrichment affects emotional development and effortful control abilities in 12- and 24-month-old very preterm (VPT) infants., Methods: One hundred nineteen newborns were recruited, including 83 VPTs and 36 full-term (FT) infants. The VPT infants were randomly assigned to the music intervention (44 VPT-Music) or control (39 VPT-control) groups. VPT-Music infants listened specifically designed music intervention from the 33rd week of gestation until hospital discharge. At 12 and 24 months, children were clinically evaluated using the Bayley-III Scales of Infant and Toddler Development and the Laboratory Temperament Assessment Battery, and at 24 months, with 3 additional episodes of the Effortful Control Battery., Results and Discussion: Our analysis showed that during a fear eliciting task, the VPT-Music group expressed lower level of fear reactivity and higher positive motor actions than VPT-controls and FT infants. At 24 months, the VPT-music group had lower scores for negative motor actions in the joy task, compared to both VPT-control and FT groups. In addition, both FT and VPT-music had higher scores of sustained attention compared to VPT-controls, but the contrasts were not significant. No significant effects on mental, language and motor outcomes were identified and for all three dimensions of the ECBQ., Conclusion: The present study suggests that an early music intervention in the NICU might influence preterm children's emotional processing at 12 and 24 months. Limitations and suggestions for future research are highlighted., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Filippa, Lordier, Lejeune, De Almeida, Hüppi, Barcos-Munoz, Monaci and Borradori-Tolsa.)

Spinal cord injury (SCI) is one of the most serious conditions of the central nervous system, causing motor and sensory deficits that lead to a significant impairment in the quality of life. Previous studies have indicated that inosine can promote regeneration after SCI. Here we investigated the effects of inosine on the behavioral and morphological recovery after a compressive injury. Adult female C57BL/6 mice were subjected to laminectomy and spinal cord compression using a vascular clip. Inosine or saline injections were administered intraperitoneally, with the first dose performed 24 h after injury and daily for 7 days after injury. The mice were evaluated using Basso Mouse Scale (BMS), locomotor rating scale, and pinprick test for 8 weeks. At the end, the animals were anesthetized and euthanized, and the spinal cords were collected for morphological evaluation. Inosine-treated animals presented better results in the immunostaining for oligodendrocytes and in the number of myelinated fibers through semithin sections compared to saline-treated animals, showing that there was a greater preservation of the white matter. Analysis of the immunoreactivity of astrocytes and evaluation of the inflammatory profile with macrophage labeling revealed that the animals of the inosine group had a lower immunoreactivity when compared to control, which suggests a reduction of the glial scar and less inflammation, respectively, leading to a more favorable microenvironment for spinal cord regeneration. Indeed, inosine-treated animals scored higher on the BMS scale and presented better results on the pinprick test, indicating that the treatment contributed to motor and sensory recovery. After the animals were sacrificed, we obtained the electroneuromyography, where the inosine group showed a greater amplitude of the compound muscle action potential. These results indicate that inosine contributed to the regeneration process in the spinal cord of mice submitted to compressive injury and should be further investigated as a candidate for SCI therapy., (© The Author(s) 2024. Published by Mary Ann Liebert, Inc.)

Music is ubiquitous, both in its instrumental and vocal forms. While speech perception at birth has been at the core of an extensive corpus of research, the origins of the ability to discriminate instrumental or vocal melodies is still not well investigated. In previous studies comparing vocal and musical perception, the vocal stimuli were mainly related to speaking, including language, and not to the non-language singing voice. In the present study, to better compare a melodic instrumental line with the voice, we used singing as a comparison stimulus, to reduce the dissimilarities between the two stimuli as much as possible, separating language perception from vocal musical perception. In the present study, 45 newborns were scanned, 10 full-term born infants and 35 preterm infants at term-equivalent age (mean gestational age at test = 40.17 weeks, SD = 0.44) using functional magnetic resonance imaging while listening to five melodies played by a musical instrument (flute) or sung by a female voice. To examine the dynamic task-based effective connectivity, we employed a psychophysiological interaction of co-activation patterns (PPI-CAPs) analysis, using the auditory cortices as seed region, to investigate moment-to-moment changes in task-driven modulation of cortical activity during an fMRI task. Our findings reveal condition-specific, dynamically occurring patterns of co-activation (PPI-CAPs). During the vocal condition, the auditory cortex co-activates with the sensorimotor and salience networks, while during the instrumental condition, it co-activates with the visual cortex and the superior frontal cortex. Our results show that the vocal stimulus elicits sensorimotor aspects of the auditory perception and is processed as a more salient stimulus while the instrumental condition activated higher-order cognitive and visuo-spatial networks. Common neural signatures for both auditory stimuli were found in the precuneus and posterior cingulate gyrus. Finally, this study adds knowledge on the dynamic brain connectivity underlying the newborns capability of early and specialized auditory processing, highlighting the relevance of dynamic approaches to study brain function in newborn populations., (© 2024 The Author(s). Human Brain Mapping published by Wiley Periodicals LLC.)

Spinal cord injury (SCI) results from various mechanisms that damage the nervous tissue and the blood-brain barrier, leading to sensory and motor function loss below the injury site. Unfortunately, current therapeutic approaches for SCI have limited efficacy in improving patients outcomes. Galectin-3, a protein whose expression increases after SCI, influences the neuroinflammatory response by favoring pro-inflammatory M1 macrophages and microglia, while inhibiting pro-regenerative M2 macrophages and microglia, which are crucial for inflammation resolution and tissue regeneration. Previous studies with Galectin-3 knock-out mice demonstrated enhanced motor recovery after SCI. The M1/M2 balance is strongly influenced by the predominant lymphocytic profiles (Th1, Th2, T Reg, Th17) and cytokines and chemokines released at the lesion site. The present study aimed to investigate how the absence of galectin-3 impacts the adaptive immune system cell population dynamics in various lymphoid spaces following a low thoracic spinal cord compression injury (T9-T10) using a 30 g vascular clip for one minute. It also aimed to assess its influence on the functional outcome in wild-type (WT)and Galectin-3 knock-out (GALNEG) mice. Histological analysis with hematoxylin-eosin and Luxol Fast Blue staining revealed that WT and GALNEG animals exhibit similar spinal cord morphology. The absence of galectin-3 does not affect the common neuroanatomy shared between the groups prompting us to analyze outcomes between both groups. Following our crush model, both groups lost motor and sensory functions below the lesion level. During a 42-day period, GALNEG mice demonstrated superior locomotor recovery in the Basso Mouse Scale (BMS) gait analysis and enhanced motor coordination performance in the ladder rung walk test (LRW) compared to WT mice. GALNEG mice also exhibited better sensory recovery, and their electrophysiological parameters suggested a higher number of functional axons with faster nerve conduction. Seven days after injury, flow cytometry of thymus, spleen, and blood revealed an increased number of T Reg and Th2 cells, accompanied by a decrease in Th1 and Th17 cells in GALNEG mice. Immunohistochemistry conducted on the same day exhibited an increased number of Th2 and T Reg cells around the GALNEG's spinal cord lesion site. At 42-day dpi immunohistochemistry analyses displayed reduced astrogliosis and greater axon preservation in GALNEG's spinal cord seem as a reduction of GFAP immunostaining and an increase in NFH immunostaining, respectively. In conclusion, GALNEG mice exhibited better functional recovery attributed to the milder pro-inflammatory influence, compensated by a higher quantity of T Reg and Th2 cells. These findings suggest that galectin-3 plays a crucial role in the immune response after spinal cord injury and could be a potential target for clinical therapeutic interventions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Inc.)

Objectives: Absolute risk models estimate an individual's future disease risk over a specified time interval. Applications utilizing server-side risk tooling, the R-based iCARE (R-iCARE), to build, validate, and apply absolute risk models, face limitations in portability and privacy due to their need for circulating user data in remote servers for operation. We overcome this by porting iCARE to the web platform., Materials and Methods: We refactored R-iCARE into a Python package (Py-iCARE) and then compiled it to WebAssembly (Wasm-iCARE)-a portable web module, which operates within the privacy of the user's device., Results: We showcase the portability and privacy of Wasm-iCARE through 2 applications: for researchers to statistically validate risk models and to deliver them to end-users. Both applications run entirely on the client side, requiring no downloads or installations, and keep user data on-device during risk calculation., Conclusions: Wasm-iCARE fosters accessible and privacy-preserving risk tools, accelerating their validation and delivery., Competing Interests: None declared., (Published by Oxford University Press on behalf of the American Medical Informatics Association 2024.)

Motivation : The proliferation of genetic testing and consumer genomics represents a logistic challenge to the personalized use of GWAS data in VCF format. Specifically, the challenge of retrieving target genetic variation from large compressed files filled with unrelated variation information. Compounding the data traversal challenge, privacy-sensitive VCF files are typically managed as large stand-alone single files (no companion index file) composed of variable-sized compressed chunks, hosted in consumer-facing environments with no native support for hosted execution. Results : A portable JavaScript module was developed to support in-browser fetching of partial content using byte-range requests. This includes on-the-fly decompressing irregularly positioned compressed chunks, coupled with a binary search algorithm iteratively identifying chromosome-position ranges. The in-browser zero-footprint solution (no downloads, no installations) enables the interoperability, reusability, and user-facing governance advanced by the FAIR principles for stewardship of scientific data. Availability - https://episphere.github.io/vcf, including supplementary material., (©2024 AMIA - All rights reserved.)

Whole Slide Images (WSI), obtained by high-resolution digital scanning of microscope slides at multiple scales, are the cornerstone of modern Digital Pathology. However, they represent a particular challenge to AI-based/AI-mediated analysis because pathology labeling is typically done at slide-level, instead of tile-level. It is not just that medical diagnostics is recorded at the specimen level, the detection of oncogene mutation is also experimentally obtained, and recorded by initiatives like The Cancer Genome Atlas (TCGA), at the slide level. This configures a dual challenge: a) accurately predicting the overall cancer phenotype and b) finding out what cellular morphologies are associated with it at the tile level. To address these challenges, a weakly supervised Multiple Instance Learning (MIL) approach was explored for two prevalent cancer types, Invasive Breast Carcinoma (TCGA-BRCA) and Lung Squamous Cell Carcinoma (TCGA-LUSC). This approach was explored for tumor detection at low magnification levels and TP53 mutations at various levels. Our results show that a novel additive implementation of MIL matched the performance of reference implementation (AUC 0.96), and was only slightly outperformed by Attention MIL (AUC 0.97). More interestingly from the perspective of the molecular pathologist, these different AI architectures identify distinct sensitivities to morphological features (through the detection of Regions of Interest, RoI) at different amplification levels. Tellingly, TP53 mutation was most sensitive to features at the higher applications where cellular morphology is resolved., Competing Interests: 7.Author Declaration There is no conflict of interest to report.

Study Objectives: To examine the associations between sleep duration, continuity, timing, and mortality using actigraphy among adults., Methods: Data were from a cohort of 88 282 adults (40-69 years) in UK Biobank that wore a wrist-worn triaxial accelerometer for 7 days. Actigraphy data were processed to generate estimates of sleep duration and other sleep characteristics including wake after sleep onset (WASO), number of 5-minute awakenings, and midpoint for sleep onset/wake-up and the least active 5 hours (L5). Data were linked to mortality outcomes with follow-up to October 31, 2021. We implemented Cox models (hazard ratio, confidence intervals [HR, 95% CI]) to quantify sleep associations with mortality. Models were adjusted for demographics, lifestyle factors, and medical conditions., Results: Over an average of 6.8 years 2973 deaths occurred (1700 cancer, 586 CVD deaths). Overall sleep duration was significantly associated with risk for all-cause (p < 0.01), cancer (p < 0.01), and CVD (p = 0.03) mortality. For example, when compared to sleep durations of 7.0 hrs/d, durations of 5 hrs/d were associated with a 29% higher risk for all-cause mortality (HR: 1.29 [1.09, 1.52]). WASO and number of awakenings were not associated with mortality. Individuals with L5 early or late midpoints (<2:30 or ≥ 3:30) had a ~20% higher risk for all-cause mortality, compared to those with intermediate L5 midpoints (3:00-3:29; p ≤ 0.01; e.g. HR ≥ 3:30: 1.19 [1.07, 1.32])., Conclusions: Shorter sleep duration and both early and late sleep timing were associated with a higher mortality risk. These findings reinforce the importance of public health efforts to promote healthy sleep patterns in adults., (Published by Oxford University Press on behalf of Sleep Research Society (SRS) 2023.)

Background: Studies of sleep and prostate cancer are almost entirely based on self-report, with limited research using actigraphy. Our goal was to evaluate actigraphy-measured sleep and prostate cancer and to expand on findings from prior studies of self-reported sleep., Methods: We prospectively examined 34 260 men without a history of prostate cancer in the UK Biobank. Sleep characteristics were measured over 7 days using actigraphy. We calculated sleep duration, onset, midpoint, wake-up time, social jetlag (difference in weekend-weekday sleep midpoints), sleep efficiency (percentage of time spent asleep between onset and wake-up time), and wakefulness after sleep onset. Cox proportional hazards models were used to estimate covariate-adjusted hazards ratios (HRs) and 95% confidence intervals (CIs)., Results: Over 7.6 years, 1152 men were diagnosed with prostate cancer. Sleep duration was not associated with prostate cancer risk. Sleep midpoint earlier than 4:00 am was not associated with prostate cancer risk, though sleep midpoint of 5:00 am or later was suggestively associated with lower prostate cancer risk but had limited precision (earlier than 4:00 am vs 4:00-4:59 am HR = 1.00, 95% CI = 0.87 to 1.16; 5:00 am or later vs 4:00-4:59 am HR = 0.79, 95% CI = 0.57 to 1.10). Social jetlag was not associated with greater prostate cancer risk (1 to <2 hours vs <1 hour HR = 1.06, 95% CI = 0.89 to 1.25; ≥2 hours vs <1 hour HR = 0.90, 95% CI = 0.65 to 1.26). Compared with men who averaged less than 30 minutes of wakefulness after sleep onset per day, men with 60 minutes or more had a higher risk of prostate cancer (HR = 1.20, 95% CI = 1.00 to 1.43)., Conclusions: Of the sleep characteristics studied, higher wakefulness after sleep onset-a measure of poor sleep quality-was associated with greater prostate cancer risk. Replication of our findings between wakefulness after sleep onset and prostate cancer are warranted., (Published by Oxford University Press 2023.)

The African buffalo, Syncerus caffer, is a key species in African ecosystems. Like other large herbivores, it plays a fundamental role in its habitat acting as an ecosystem engineer. Over the last few centuries, African buffalo populations have declined because of range contraction and demographic decline caused by direct or indirect human activities. In Mozambique, historically home to large buffalo herds, the combined effect of colonialism and subsequent civil wars has created a critical situation that urgently needs to be addressed. In this study, we focused on the analysis of genetic diversity of Syncerus caffer caffer populations from six areas of Mozambique. Using genome-wide SNPs obtained from ddRAD sequencing, we examined the population structure across the country, estimated gene flow between areas under conservation management, including national reserves, and assessed the inbreeding coefficients. Our results indicate that all studied populations of Syncerus caffer caffer are genetically depauperate, with a high level of inbreeding. Moreover, buffaloes in Mozambique present a significant population differentiation between southern and central areas. We found an unexpected genotype in the Gorongosa National Park, where buffaloes experienced a dramatic population size reduction, that shares a common ancestry with southern populations of Catuane and Namaacha. This could suggest the past occurrence of a connection between southern and central Mozambique and that the observed population structuring could reflect recent events of anthropogenic origin. All the populations analysed showed high levels of homozygosity, likely due to extensive inbreeding over the last few decades, which could have increased the frequency of recessive deleterious alleles. Improving the resilience of Syncerus caffer caffer in Mozambique is essential for preserving the ecosystem integrity. The most viable approach appears to be facilitating translocations and re-establishing connectivity between isolated herds. However, our results also highlight the importance of assessing intraspecific genetic diversity when considering interventions aimed at enhancing population viability such as selecting suitable source populations., (© 2024. The Author(s).)

Recent advances in the field of immuno-oncology have brought transformative changes in the management of cancer patients. The immune profile of tumours has been found to have key value in predicting disease prognosis and treatment response in various cancers. Multiplex immunohistochemistry and immunofluorescence have emerged as potent tools for the simultaneous detection of multiple protein biomarkers in a single tissue section, thereby expanding opportunities for molecular and immune profiling while preserving tissue samples. By establishing the phenotype of individual tumour cells when distributed within a mixed cell population, the identification of clinically relevant biomarkers with high-throughput multiplex immunophenotyping of tumour samples has great potential to guide appropriate treatment choices. Moreover, the emergence of novel multi-marker imaging approaches can now provide unprecedented insights into the tumour microenvironment, including the potential interplay between various cell types. However, there are significant challenges to widespread integration of these technologies in daily research and clinical practice. This review addresses the challenges and potential solutions within a structured framework of action from a regulatory and clinical trial perspective. New developments within the field of immunophenotyping using multiplexed tissue imaging platforms and associated digital pathology are also described, with a specific focus on translational implications across different subtypes of cancer. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland., (© 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.)

Introduction: Scorpionism is a public health problem, especially in tropical regions. In Brazil, the prevalence of envenomation by scorpions is high, and the average national lethality is around 0.16 percent. The Tityus serrulatus scorpion is the primary species of medical importance. However, objective tools to predict and define the severity of these envenomations are lacking., Materials and Methods: This was an observational study conducted among patients aged 0-19 years with scorpionism. Patients were admitted to a reference hospital between December 2020 and May 2022. Point-of-care ultrasound was performed within 24 hours of the scorpion sting., Results: Forty-nine patients were included, with a median age of 3.6 (interquartile range 2.3-5.3) years and a predominance of females (51 percent). Fifteen patients (30.6 percent) presented major life-threatening signs, 32 (65.3 percent) minor systemic manifestations, and two (4.1 percent) only local manifestations. Left ventricular dysfunction was identified in 13 patients (26.5 percent). Ten patients (20.4 percent) presented pattern B (visualization of three or more B lines in the evaluated quadrant) in at least one lung window. The sensitivity and specificity of cardiac and pulmonary ultrasound to identify the most severely ill patients were 86 percent and 94 percent, respectively., Discussion: The changes found on point-of-care ultrasound were associated with life-threatening signs. All patients with class III envenomation were referred to the intensive care unit, showing the importance of early identification of this subgroup. The main limitations were the small sample size and the fact that admission to intensive care was not based on systematic criteria., Conclusions: Point-of-care ultrasound is able to identify early signs of pulmonary congestion and heart failure in scorpionism. It can be useful for the objective selection of patients who are at a higher risk of complications and death and who require intensive support; it may also be valuable for periodic reassessments. Point-of-care ultrasound is a valuable tool for identifying and monitoring severe cases of scorpionism.

Coffee is a beverage consumed globally. Although few studies have indicated adverse effects, it is typically a beneficial health-promoting agent in a range of diseases, including depression, diabetes, cardiovascular disease, and obesity. Coffee is rich in caffeine, antioxidants, and phenolic compounds, which can modulate the composition of the gut microbiota and mitigate both inflammation and oxidative stress, common features of the burden of lifestyle diseases. This review will discuss the possible benefits of coffee on complications present in patients with diabetes, cardiovascular disease and chronic kidney disease, outwith the social and emotional benefits attributed to caffeine consumption.

Objective: to understand feelings about birth among a group of high-risk pregnant women., Method: a descriptive and qualitative study, using Alfred Schütz's social phenomenology as a philosophical theoretical framework. The study included 25 pregnant women undergoing high-risk prenatal care. The interview had the following guiding questions: tell me about your feelings regarding the moment of birth/childbirth; How do you deal with the high-risk diagnosis? What are your expectations for birth/childbirth?, Results: five categories emerged: Fear of obstetric care; Fear of complications with the baby; Fear of cesarean section; Resilience in the face of high-risk pregnancy; and Expectations for birth., Considerations: high-risk pregnant women are afraid of the care they will receive, the risks and concern about the baby's vitality at birth. The importance of care is emphasized, with a welcoming environment, bonding and communication between health team and pregnant woman.

The analysis of data over space and time is a core part of descriptive epidemiology, but the complexity of spatiotemporal data makes this challenging. There is a need for methods that simplify the exploration of such data for tasks such as surveillance and hypothesis generation. In this paper, we use combined clustering and dimensionality reduction methods (hereafter referred to as 'cluster embedding' methods) to spatially visualize patterns in epidemiological time-series data. We compare several cluster embedding techniques to see which performs best along a variety of internal cluster validation metrics. We find that methods based on k-means clustering generally perform better than self-organizing maps on real world epidemiological data, with some minor exceptions. We also introduce EpiVECS, a tool which allows the user to perform cluster embedding and explore the results using interactive visualization. EpiVECS is available as a privacy preserving, in-browser open source web application at https://episphere.github.io/epivecs ., (© 2023. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Motivation: As prescription drug prices have drastically risen over the past decade, so has the need for real-time drug tracking resources. In spite of increased public availability to raw data sources, individual drug metrics remain concealed behind intricate nomenclature and complex data models. Some web applications, such as GoodRX, provide insight into real-time drug prices but offer limited interoperability. To overcome both obstacles we pursued the direct programmatic operation of the stateless Application Programming interfaces (HTTP REST APIs) maintained by the Food and Drug Administration (FDA), Medicaid, and National Library of Medicine. These data-intensive resources represent an opportunity to develop Software Development Kits (SDK) to streamline drug metrics without downloads or installations, in a manner that addresses the FAIR principles for stewardship in scientific data-Findability, Accessibility, Interoperability, and Reusability. These principles provide a guideline for continual stewardship of scientific data., Results: MedicaidJS SDK was developed to orchestrate API calls to three complementary data resources: Medicaid (data.medicaid.gov), Food and Drug Administration (open.fda.gov), and the National Library of Medicine RxNorm (lhncbc.nlm.nih.gov/RxNav). MedicaidJS synthesizes response data from each platform into a zero-footprint JavaScript modular library that provides data wrangling, analysis, and generation of embeddable interactive visualizations. The SDK is served on github with live examples on observableHQ notebooks. It is freely available and can be embedded into web applications as modules returning structured JSON data with standardized identifiers., Availability and Implementation: Open source code publicly available at https://github.com/episphere/medicaid, live at episphere.github.io/medicaid, supplementary interactive Observable Notebooks at observablehq.com/@medicaidsdk/medicaidsdk., Competing Interests: None declared., (Published by Oxford University Press 2023.)

Background: Online questionnaires are commonly used to collect information from participants in epidemiological studies. This requires building questionnaires using machine-readable formats that can be delivered to study participants using web-based technologies such as progressive web applications. However, the paucity of open-source markup standards with support for complex logic make collaborative development of web-based questionnaire modules difficult. This often prevents interoperability and reusability of questionnaire modules across epidemiological studies., Results: We developed an open-source markup language for presentation of questionnaire content and logic, Quest, within a real-time renderer that enables the user to test logic (e.g., skip patterns) and view the structure of data collection. We provide the Quest markup language, an in-browser markup rendering tool, questionnaire development tool and an example web application that embeds the renderer, developed for The Connect for Cancer Prevention Study., Conclusion: A markup language can specify both the content and logic of a questionnaire as plain text. Questionnaire markup, such as Quest, can become a standard format for storing questionnaires or sharing questionnaires across the web. Quest is a step towards generation of FAIR data in epidemiological studies by facilitating reusability of questionnaires and data interoperability using open-source tools., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Motivation: Currently, the Polygenic Score (PGS) Catalog curates over 400 publications on over 500 traits corresponding to over 3000 polygenic risk scores (PRSs). To assess the feasibility of privately calculating the underlying multivariate relative risk for individuals with consumer genomics data, we developed an in-browserPRS calculator for genomic data that does not circulate any data or engage in any computation outside of the user's personal device., Results: A prototype personal risk score calculator, created for research purposes, was developed to demonstrate how the PGS Catalog can be privately and readily applied to readily available direct-to-consumer genetic testing services, such as 23andMe. No software download, installation, or configuration is needed. The PRS web calculator matches individual PGS catalog entries with an individual's 23andMe genome data composed of 600k to 1.4 M single-nucleotide polymorphisms (SNPs). Beta coefficients provide researchers with a convenient assessment of risk associated with matched SNPs. This in-browser application was tested in a variety of personal devices, including smartphones, establishing the feasibility of privately calculating personal risk scores with up to a few thousand reference genetic variations and from the full 23andMe SNP data file (compressed or not)., Availability and Implementation: The PRScalc web application is developed in JavaScript, HTML, and CSS and is available at GitHub repository (https://episphere.github.io/prs) under an MIT license. The datasets were derived from sources in the public domain: [PGS Catalog, Personal Genome Project]., Competing Interests: None declared., (Published by Oxford University Press 2023.)

Modern histologic imaging platforms coupled with machine learning methods have provided new opportunities to map the spatial distribution of immune cells in the tumor microenvironment. However, there exists no standardized method for describing or analyzing spatial immune cell data, and most reported spatial analyses are rudimentary. In this review, we provide an overview of two approaches for reporting and analyzing spatial data (raster versus vector-based). We then provide a compendium of spatial immune cell metrics that have been reported in the literature, summarizing prognostic associations in the context of a variety of cancers. We conclude by discussing two well-described clinical biomarkers, the breast cancer stromal tumor infiltrating lymphocytes score and the colon cancer Immunoscore, and describe investigative opportunities to improve clinical utility of these spatial biomarkers. © 2023 The Pathological Society of Great Britain and Ireland., (© 2023 The Pathological Society of Great Britain and Ireland.)

The clinical significance of the tumor-immune interaction in breast cancer is now established, and tumor-infiltrating lymphocytes (TILs) have emerged as predictive and prognostic biomarkers for patients with triple-negative (estrogen receptor, progesterone receptor, and HER2-negative) breast cancer and HER2-positive breast cancer. How computational assessments of TILs might complement manual TIL assessment in trial and daily practices is currently debated. Recent efforts to use machine learning (ML) to automatically evaluate TILs have shown promising results. We review state-of-the-art approaches and identify pitfalls and challenges of automated TIL evaluation by studying the root cause of ML discordances in comparison to manual TIL quantification. We categorize our findings into four main topics: (1) technical slide issues, (2) ML and image analysis aspects, (3) data challenges, and (4) validation issues. The main reason for discordant assessments is the inclusion of false-positive areas or cells identified by performance on certain tissue patterns or design choices in the computational implementation. To aid the adoption of ML for TIL assessment, we provide an in-depth discussion of ML and image analysis, including validation issues that need to be considered before reliable computational reporting of TILs can be incorporated into the trial and routine clinical management of patients with triple-negative breast cancer. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland., (© 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.)

Starch's crystalline structure and gelatinization temperature might facilitate or hinder its use. Ball milling has frequently been mentioned in the literature as a method for reducing starch size and as a more environmentally friendly way to change starch, such as by increasing surface area and reactivity, which has an impact on other starch properties. In this study, starch samples were milled for varying durations (1, 5, 10, 20, and 30 h) and at different starch-to-ball mass ratios (1:6 and 1:20). Microscopy and XRD revealed that prolonged milling resulted in effective fragmentation and a decrease in crystallinity of the starch granules. Increasing milling times resulted in an increase in amylose content. Rheology and thermal studies revealed that gelatinization temperatures dropped with milling duration and that viscosity and thixotropy were directly influenced. The samples milled for 10, 20, and 30 h at a ratio of 1:20 were the most fragmented and upon drying formed a transparent film at ambient temperature, because of the lower gelatinization temperature. Starch ball milling could lead to the use of this material in thermosensitive systems., Competing Interests: The authors declare no conflicts of interest.

The industrial residue of cashew apple juice processing (MRC) was evaluated as an alternative medium for bacterial cellulose (BC) production by Komagataeibacter xylinus ATCC 53582 and Komagataeibacter xylinus ARS B42. The synthetic Hestrin-Schramm medium (MHS) was used as a control for growing and BC production. First, BC production was assessed after 4, 6, 8, 10, and 12 days under static culture. After 12 days of cultivation, K. xylinus ATCC 53582 produced the highest BC titer in MHS (3.1 g·L -1 ) and MRC (3 g·L -1 ), while significant productivity was attained at 6 days of fermentation. To understand the effect of culture medium and fermentation time on the properties of the obtained films, BC produced at 4, 6, or 8 days were submitted to infrared spectroscopy with Fourier transform, thermogravimetry, mechanical tests, water absorption capacity, scanning electron microscopy, degree of polymerization and X-ray diffraction. The properties of BC synthesized in MRC were identical to those of BC from MHS, according to structural, physical, and thermal studies. MRC, on the other hand, allows the production of BC with a high water absorption capacity when compared to MHS. Despite the lower titer (0.88 g·L -1 ) achieved in MRC, the BC from K. xylinus ARS B42 presented a high thermal resistance and a remarkable absorption capacity (14664 %), suggesting that it might be used as a superabsorbent biomaterial., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Motivation: Epidemiological studies face two important challenges: the need to ingest ever more complex data types, and mounting concerns about participant privacy and data governance. These two challenges are compounded by the expectation that data infrastructure will eventually need to facilitate cross-registration of participants by multiple epidemiological studies. Implementation: The portable web-service epiDonate was developed using the serverless model known as FaaS (Function-as-a-Service). The reference implementation uses nodejs. The implementation relies on a simple tokenization scheme, mediated by a public API, that a) distinguishes admin from participant roles, with b) extensible permission configuration operating a read/write structure. General Features: The critical design feature of epiDonate is the absence of business logic on the server-side (the web service). The simplicity removes the need to customize virtual machines and enables ecosystems of multiple web Applications backed by one or more data donation deployments. Availability: https://episphere.github.io/donate., (©2023 AMIA - All rights reserved.)

Data sharing is essential for reproducibility of epidemiologic research, replication of findings, pooled analyses in consortia efforts, and maximizing study value to address multiple research questions. However, barriers related to confidentiality, costs, and incentives often limit the extent and speed of data sharing. Epidemiological practices that follow Findable, Accessible, Interoperable, Reusable (FAIR) principles can address these barriers by making data resources findable with the necessary metadata, accessible to authorized users, and interoperable with other data, to optimize the reuse of resources with appropriate credit to its creators. We provide an overview of these principles and describe approaches for implementation in epidemiology. Increasing degrees of FAIRness can be achieved by moving data and code from on-site locations to remote, accessible ("Cloud") data servers, using machine-readable and nonproprietary files, and developing open-source code. Adoption of these practices will improve daily work and collaborative analyses and facilitate compliance with data sharing policies from funders and scientific journals. Achieving a high degree of FAIRness will require funding, training, organizational support, recognition, and incentives for sharing research resources, both data and code. However, these costs are outweighed by the benefits of making research more reproducible, impactful, and equitable by facilitating the reuse of precious research resources by the scientific community., (Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health 2023.)

This work aimed to develop a phosphorous-based biorefinery process for obtaining phosphorylated lignocellulosic fractions in a one-pot protocol from coconut fiber. Natural coconut fiber (NCF) was mixed with 85 % m/m H 3 PO 4 at 70 °C for 1 h to yield the modified coconut fiber (MCF), aqueous phase (AP), and coconut fiber lignin (CFL). MCF was characterized by its TAPPI, FTIR, SEM, EDX, TGA, WCA, and P content. AP was characterized regarding its pH, conductivity, glucose, furfural, HMF, total sugars and ASL contents. CFL structure was evaluated by FTIR, 1 H, 31 P and 1 H- 13 C HSQC NMR, TGA and P content and was compared to that of milled wood lignin (MWL). It was observed that MCF and CFL were phosphorylated during the pulping (0.54 and 0.23 % wt., respectively), while AP has shown high sugar levels, low inhibitor content, and some remaining phosphorous. The phosphorylation of MCF and CFL also showed an enhancement of their thermal and thermo-oxidative properties. The results show that a platform of functional materials such as biosorbents, biofuels, flame retardants, and biocomposites can be created through an eco-friendly, simple, fast, and novel biorefinery process., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Forecasting methods are notoriously difficult to interpret, particularly when the relationship between the data and the resulting forecasts is not obvious. Interpretability is an important property of a forecasting method because it allows the user to complement the forecasts with their own knowledge, a process which leads to more applicable results. In general, mechanistic methods are more interpretable than non-mechanistic methods, but they require explicit knowledge of the underlying dynamics. In this paper, we introduce EpiForecast, a tool which performs interpretable, non-mechanistic forecasts using interactive visualization and a simple, data-focused forecasting technique based on empirical dynamic modelling. EpiForecast's primary feature is a four-plot interactive dashboard which displays a variety of information to help the user understand how the forecasts are generated. In addition to point forecasts, the tool produces distributional forecasts using a kernel density estimation method-these are visualized using color gradients to produce a quick, intuitive visual summary of the estimated future. To ensure the work is FAIR and privacy is ensured, we have released the tool as an entirely in-browser web-application., Competing Interests: The authors have declared that no competing interests exist., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)