Miracle-dz/UniFAR-FTUs huggingface dataset:
High throughput sequencing reveals high specificity of TNFAIP3 mutations in ocular adnexal marginal zone B‐cell lymphomas

The majority of ocular adnexal (OA) lymphomas (OAL) are extranodal marginal zone lymphomas (MZL). First high throughput sequencing (HTS) studies on OA‐MZL showed inconsistent results and the distribution of mutations in reactive lymphoid lesions of this anatomic region has not yet been sufficiently addressed.
Scope of Practice in Speech-Language Pathology

Note. &copy; 1996 by the American Speech-Language-Hearing Association. Reprinted with permission. This document was approved by the ASHA Legislative Council in April 2001 (LC 7-01). Members of the 2000 Ad Hoc Committee on Scope of Practice in Speech-Language Pathology that developed this document are Nicholas Bankson (chair), Allan Diefendorf, Roberta Elman, Susan Forsythe, Elizabeth Gavett, Alex Johnson (vice president for professional practices in speech-language pathology who serves as Executive Board liaison), Lori Lombard, Ninevah Murray, Arlene Pietranton (ex officio), and Carmen Vega-Barachowitz.
Compact Series Visco-Elastic Joint (SVEJ) for Smooth Torque Control

The design and control of a new series-viscous-elastic joint are presented. The proposed joint consists of 3D printed parts compressing nonlinear elastic silicone springs. The use of silicone springs is the main novelty of the system; they exhibit internal damping, which enhances system performance allowing a simpler and more stable control. Their stiffness allows the system to bear a torque of about 4.5 Nm at a deformation angle of about 20 degrees. In this article, the system is modeled using the Neo-Hookean material model and then characterized through experiments to build the joint torque estimator. A proportional torque controller is implemented to evaluate bandwidth, transparency, impedance rendering, and stability, obtaining satisfactory results. The bandwidth ranges from 6.9 to 9.9 Hz depending on chirp input torque amplitude, as the system is nonlinear. The proposed solution is compact and cheap; both the design and the torque controller are suitable for future integration in an exoskeleton, or a cooperative robot, or a haptic device. SVEJ works as a torque sensor and introduces compliance between the motor and the environment, enhancing safety for robotic devices interacting with humans.
A Mobile Health Team Challenge to Promote Stepping and Stair Climbing Activities: Exploratory Feasibility Study

Background Mobile health (mHealth) approaches are growing in popularity as a means of addressing low levels of physical activity (PA). Objective This study aimed to determine the validity of wearables in measuring step count and floor count per day and assess the feasibility and effects of a 6-week team challenge intervention delivered through smartphone apps. Methods Staff and students from a public university were recruited between 2015 and 2016. In phase 1, everyone wore a Fitbit tracker (Charge or Charge HR) and an ActiGraph for 7 days to compare daily step count estimated by the two devices under free-living conditions. They were also asked to climb 4 bouts of floors in an indoor stairwell to measure floor count which was compared against direct observation. In phase 2, participants were allocated to either a control or intervention group and received a Fitbit tracker synced to the Fitbit app. Furthermore, the intervention group participants were randomized to 4 teams and competed in 6 weekly (Monday to Friday) real-time challenges. A valid day was defined as having 1500 steps or more per day. The outcomes were as follows: (1) adherence to wearing the Fitbit (ie, number of days in which all participants in each group were classified as valid users aggregated across the entire study period), (2) mean proportion of valid participants over the study period, and (3) the effects of the intervention on step count and floor count determined using multiple linear regression models and generalized estimating equations (GEEs) for longitudinal data analysis. Results In phase 1, 32 of 40 eligible participants provided valid step count data, whereas all 40 participants provided valid floor count data. The Fitbit trackers demonstrated high correlations (step count: Spearman ρ=0.89; P<.001; floor count: Spearman ρ=0.98; P<.001). The trackers overestimated step count (median absolute error: 17%) but accurately estimated floor count. In phase 2, 20 participants each were allocated to an intervention or control group. Overall, 24 participants provided complete covariates and valid PA data for analyses. Multiple linear regressions revealed that the average daily steps was 15.9% higher for the intervention group (95% CI −8.9 to 47.6; P=.21) during the final two intervention weeks; the average daily floors climbed was 39.4% higher (95% CI 2.4 to 89.7; P=.04). GEE results indicated no significant interaction effects between groups and the intervention week for weekly step count, whereas a significant effect (P<.001) was observed for weekly floor count. Conclusions The consumer wearables used in this study provided acceptable validity in estimating stepping and stair climbing activities, and the mHealth-based team challenge interventions were feasible. Compared with the control group, the participants in the intervention group climbed more stairs, so this can be introduced as an additional PA promotion target in the context of mHealth strategies. Methodologically rigorous studies are warranted to further strengthen this study’s findings.
Nutrients Essential for Cognitive Function Are Typical Problem Nutrients in the Diets of Myanmar Primary School Children: Findings of a Linear Programming Analysis

Background: Good cognitive function is important for school-age children. Although essential fatty acids play a main role in cognitive functions, their intakes are assumed as inadequate among developing countries including Myanmar. However, there is still lack of evidence to show whether they are problem nutrients. Objective: This study aimed to determine the problem nutrients in the diets of Myanmar primary schoolchildren and to formulate food-based recommendations (FBR) to optimize the intake of these micronutrients. Methods: A cross-sectional study was conducted at 3 primary schools in Nyaungdon Township of Myanmar. A 1-week dietary intake assessment was done on 7- to 9-year-old (n = 100) primary schoolchildren. A linear programming approach using the World Health Organization Optifood software was used to assess the nutrient intake and develop FBRs. Results: The prevalence of stunted growth, wasting, and being underweight in the students were 28%, 18%, and 28%, respectively. The intake of calcium, vitamin B1, folate, iron, omega-3 fatty acids, eicosapentaenoic acid, and docosahexaenoic acid was insufficient. Locally available nutrient-dense foods that include water spinach, carp fish, duck egg, garden pea, and shrimp were selected to develop FBR to increase the intake of problem nutrients. Conclusion: The linear programming analysis showed that the primary schoolchildren have difficulty meeting nutrient recommendations given locally available foods, especially iron and essential fatty acids which are important for cognitive performance of schoolchildren.
Wearable Emotion Recognition Using Heart Rate Data from a Smart Bracelet

Emotion recognition and monitoring based on commonly used wearable devices can play an important role in psychological health monitoring and human-computer interaction. However, the existing methods cannot rely on the common smart bracelets or watches for emotion monitoring in daily life. To address this issue, our study proposes a method for emotional recognition using heart rate data from a wearable smart bracelet. A ‘neutral + target’ pair emotion stimulation experimental paradigm was presented, and a dataset of heart rate from 25 subjects was established, where neutral plus target emotion (neutral, happy, and sad) stimulation video pairs from China’s standard Emotional Video Stimuli materials (CEVS) were applied to the recruited subjects. Normalized features from the data of target emotions normalized by the baseline data of neutral mood were adopted. Emotion recognition experiment results approved the effectiveness of ‘neutral + target’ video pair simulation experimental paradigm, the baseline setting using neutral mood data, and the normalized features, as well as the classifiers of Adaboost and GBDT on this dataset. This method will promote the development of wearable consumer electronic devices for monitoring human emotional moods.
Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas

The introduction of genomics is profoundly changing current bacterial taxonomy. Phylogenomics provides accurate methods for delineating species and allows us to infer the phylogeny of higher taxonomic ranks as well as those at the subspecies level. We present as a model the currently accepted taxonomy of the genus Pseudomonas and how it can be modified when new taxonomic methodologies are applied. A phylogeny of the species in the genus deduced from analyses of gene sequences or by whole genome comparison with different algorithms allows three main conclusions: (i) several named species are synonymous and have to be reorganized in a single genomic species; (ii) many strains assigned to known species have to be proposed as new genomic species within the genus; and (iii) the main phylogenetic groups defined by 4-, 100- and 120-gene multilocus sequence analyses are concordant with the groupings in the whole genome analyses. Moreover, the boundaries of the genus Pseudomonas are also discussed based on phylogenomic analyses in relation to other genera in the family Pseudomonadaceae. The new technologies will result in a substantial increase in the number of species and probably split the current genus into several genera or subgenera, although these classifications have to be supported by a polyphasic taxonomic approach.
Stress of Dialysis Nurses—Analyzing the Buffering Role of Influence at Work and Feedback

Dialysis nurses face complex and demanding working conditions. Due to demographic changes, the number of dialysis patients has increased, while the number of skilled personnel is expected to decrease, leading to tremendous increases in quantitative demands in the near future. Against the background of increasing workload, focusing on the provision of job resources is considered a promising approach because resources can buffer the negative effects of job demands. The aim of this study is to investigate whether different job resources—in particular influence at work and feedback—play a buffering role in the relationship between job demands and employee well-being. The study used a cross-sectional paper–pencil survey design. Data were collected from 951 dialysis nurses working in dialysis facilities in Germany between October 2010 and March 2012 using validated measures of quantitative job demands, job-related resources (influence at work and feedback), and cognitive stress symptoms. To test the moderating role of resources, we applied hierarchical regression analyses. The findings indicate that feedback buffers the relationship between quantitative demands and well-being; that is, the positive relationship between quantitative demands and cognitive stress symptoms was weaker when feedback was high. However, we found no buffering role of influence at work. The results suggest that feedback is a promising resource that may buffer the negative impact of quantitative demands on well-being of dialysis nurses. The findings offer new approaches for training nurses and implementing a feedback culture.
Silicone-Based Fouling-Release Coatings for Marine Antifouling.

Marine biofouling profoundly influences marine industries and activities. It slows the speed and increases the fuel consumption of ships, corrodes the offshore platforms and blocks the seawater pipelines. The most effective and economic antifouling approach is using coatings. Fouling release coatings (FRCs) with low surface free energy and high elasticity weakly adhere to marine organisms so they can be readily removed by the water shear force. FRCs have received increasing interest because they are biocide-free and hence eco-friendly. Yet, traditional silicone based FRCs have weak adhesion to substrate, low mechanical strength and low fouling resistance, limiting their applications. In recent years, many attempts have been made to improve their mechanical properties and fouling resistance. The review deals with the progress in construction of high-performance silicone based fouling release surfaces.
Outer membrane protein OmpV mediates Salmonella enterica serovar typhimurium adhesion to intestinal epithelial cells via fibronectin and α1β1 integrin

Salmonella typhimurium is an invasive Gram‐negative enteric bacterium, which causes salmonellosis, a type of gastroenteritis in humans and typhoid‐like symptoms in mice. Upon entering through the contaminated food and water, S. typhimurium adheres, colonises, and invades intestinal epithelial cells (IECs) of the small intestine. In this study, we have shown that upon deletion of the outer membrane protein OmpV, there is a significant decrease in adherence of S. typhimurium to the IECs, indicating that OmpV is an important adhesin of S. typhimurium. Further, our study showed that OmpV binds to the extracellular matrix component fibronectin and signals through α1β1 integrin receptor on the IECs and OmpV‐mediated activation of α1β1, resulting in the activation of focal adhesion kinase and F‐actin modulation. Actin modulation is crucial for bacterial invasion. To the best of our knowledge, this is the first report of an adhesin mediated its effect through integrin in S. typhimurium. Further, we have observed a decrease in pathogenicity in terms of increased LD50 dose, lesser bacterial numbers in stool, and less colonisation of bacteria in different organs of mice infected with Δompv mutant compared with the wild‐type bacteria, thus confirming the crucial role of OmpV in the pathogenesis of S. typhimurium.
Opportunities and Challenges in the Delivery of mRNA-Based Vaccines

In the past few years, there has been increasing focus on the use of messenger RNA (mRNA) as a new therapeutic modality. Current clinical efforts encompassing mRNA-based drugs are directed toward infectious disease vaccines, cancer immunotherapies, therapeutic protein replacement therapies, and treatment of genetic diseases. However, challenges that impede the successful translation of these molecules into drugs are that (i) mRNA is a very large molecule, (ii) it is intrinsically unstable and prone to degradation by nucleases, and (iii) it activates the immune system. Although some of these challenges have been partially solved by means of chemical modification of the mRNA, intracellular delivery of mRNA still represents a major hurdle. The clinical translation of mRNA-based therapeutics requires delivery technologies that can ensure stabilization of mRNA under physiological conditions. Here, we (i) review opportunities and challenges in the delivery of mRNA-based therapeutics with a focus on non-viral delivery systems, (ii) present the clinical status of mRNA vaccines, and (iii) highlight perspectives on the future of this promising new type of medicine.
Understanding Patient- and Hospital-Level Factors Leading to Differences, and Disparities, in Critical Care

(the mean exposure was just 4 pack-years). To truly reduce the burden of COPD, we will need to understand the complexities of its natural history, profile of risk factors, and phenotypic manifestations across the entire lifespan. The study by Çolak and colleagues is an important starting point to characterize COPD in the first 50 years of life. Although the importance of smoking cessation cannot be overemphasized, we argue that understanding the interplay among smoking, early life risk factors, and developmental processes in age spans that have been traditionally left out of COPD research will be key to fully advance prevention strategies for stages when the natural history of the disease can still be substantially modified. n
Before it catches the eye….

Epithelial ovarian cancer (EOC) is a relatively rare but lethal disease. While the lifetime risk in the general population is 1.3% with a median age of 65 years, women with a BRCA1 and BRCA2 mutation have a lifetime risk up to 40% and 18% respectively and develop EOC at a younger age (1,2).
BRCA Mutational Status is a Promising Predictive Biomarker for Platinum-based Chemotherapy in Triple-Negative Breast Cancer.

Triple-negative breast cancer (TNBC) can be distinguished from other breast malignancies by the lack of expression of estrogen receptors (ER), progesterone receptors (RP) as well as Human Epidermal Growth Factor Receptor 2 (HER2). TNBC is associated with adverse clinical outcomes and high risk of metastasis. Currently, several clinical and translational reports are focusing on developing targeted therapies for this aggressive cancer. In addition to approved targeted drugs such as poly(ADP-ribose) polymerase inhibitors (PARPi) and immune-checkpoint inhibitors, platinum-based chemotherapy is still a cornerstone therapeutic option in TNBC. However, despite the observed improved outcomes with platinum-based chemotherapy in TNBC, there is still a large proportion of patients who do not respond to this treatment, hence, the need for predictive biomarkers to stratify TNBC patients and therefore, avoiding unwanted toxicities of these agents. With the emergence of genetic testing, several recent studies suggested mutations in breast cancer susceptibility gene (BRCA) in TNBC patients as important predictors of outcomes. These mutations alter the homologous recombination repair (HRR) mechanisms leading to genomic instability. Consequently, sensitivity to platinum-based treatments in this subpopulation of TNBC patients may be explained by cell death enhanced by DNA damage induced by these potent anticancer drugs. Through this paper, we review a number of recent studies on this topic to better understand the mechanisms and discuss the potential of BRCA mutational status as a predictive biomarker of platinum-based chemotherapy in TNBC.
Total physical activity and risk of chronic low back and knee pain in middle‐aged and elderly Japanese people: The Murakami cohort study

Specific components of physical activity, such as vigorous exercise and heavy occupational work, are known to increase the risk of chronic low back pain (CLBP) and chronic knee pain (CKP), but impacts of other components are less known. This study aimed to assess the relationship between total physical activity and risk of CLBP and CKP from a public health perspective.
Non-standard AGE4 epitopes that predict polyneuropathy independently of obesity can be detected by slot dot-blot immunoassay.

BACKGROUND Advanced glycation end-products (AGEs) are formed during cascade reactions between reducing sugars or reactive aldehydes and proteins, lipids or DNA molecules. They constitute a group of various stable compounds. Advanced glycation end-products are considered potential biomarkers of metabolic disorders. However, so far only a few methods to determine the level of individual AGEs have been developed. OBJECTIVES The aim of the study was to compare the efficiency of the slot-dot blot method and direct enzyme-linked immunosorbent assay (ELISA) in detecting non-standard epitopes of methylglyoxal (MGO)-modified proteins (AGE4) found in diabetes serum in trace amounts, and to assess AGE4 in diabetes and associated metabolic abnormalities. MATERIAL AND METHODS The presence of AGE4 was detected using 2 methods: direct ELISA and the slot-dot blot method - a newly developed immunoassay based on monoclonal, commercially available antibody detection of non-standard AGE epitopes. AGE4 quantification, expressed as median AGE4 in arbitrary units (AU) and AGE4 positivity (the percent of samples with detectable AGE4) was related to diabetes-associated metabolic abnormalities, complications and treatment. RESULTS Slot-dot blot was significantly more efficient than ELISA in detecting non-standard AGE4 epitopes. AGE4 positivity was less frequent in patients with microangiopathy and in those with polyneuropathy. In patients with abnormal glucose metabolism, metformin treatment was associated with higher AGE4. AGE4 positivity was significantly lower in gliptin-treated patients. Multivariate analysis showed that polyneuropathy and obesity were independently associated with AGE4 positivity, with odds ratios (ORs) of 0.21 and 3.02, respectively. Moreover, logistic regression showed that AGE4 positivity and HbA1c are independent predictors of polyneuropathy. Considering both indicators allows correct classification of 70.4% of cases with a general accuracy of 76%. CONCLUSIONS The slot dot-blot method detects compounds found in serum in trace amounts. Accumulation of AGE4 was associated with glucose metabolism abnormalities. A tendency toward AGE4 positivity was less frequent in patients with microangiopathy and in non-treated and gliptin-treated diabetes patients.
An examination of citation-based impact of the computational biology conferences

The importance of scientific conferences, symposia, workshops and satellite meetings is often discussed in scientific circles. When deciding where to submit a manuscript and present new findings, the quality of science and the opportunity to network with top researchers are of significant concern. To explore the question of the quality of science, we are interested in assessing the impact of primary research presented in the meetings in the field of bioinformatics and computational biology. We looked at five conferences with good reputation: Intelligent Systems for Molecular Biology (ISMB), Pacific Symposium on Biocomputing (PSB), Research in Computational Molecular Biology (RECOMB), European Conference on Computational Biology (ECCB) and the ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB). We collected all research papers published in these venues and extracted their citations. We then summarized these citations to quantify the long-term performance of an average paper, median paper, and median of the top 10 papers for each meeting in each year. Our results suggest that the original research presented in all conferences is influential, with ISMB being more impactful than ECCB and RECOMB, that themselves have comparable statistics. Despite some outstanding years and strong top papers, PSB ranked next, and ahead of BCB. Although citation-based measures of impact are imperfect, we submit that the results of our analyses provide a useful characterization of these venues. AVAILABILITY https://github.com/predragradivojac/conferences. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.