Miracle-dz/UniFAR-FTUs huggingface dataset:
The Fit fOR The Aged (FORTA) project and its clinical implications

The demographic change of aging societies around the globe [1] is associated with an increasing prevalence of chronic illnesses among older people (65 years and older) rendering the use of multiple drug treatments in this population often inevitable. Unfortunately, evidence on safety and efficacy is still lacking or sparse for the use of many drugs to treat older patients [2]. Yet, treatment has to be applied even in the absence of compelling evidence [from randomized controlled trials (RCT), for example] and, thus strict guidance by evidence-based guidelines. Paying tribute to this problem, several approaches have been developed to increase the appropriateness of drug treatment in older people [3]. A widely applied model is the development of drug lists labeling the appropriateness of drugs for this population; in most cases drug assessment is based on the combination of existing evidence and experts’ opinions in a consensual procedure (Delphi process, for example). The resulting lists are impressively diverse: they may label drugs both positively (should be used) or negatively (to be avoided) (FORTA as an example), or provide both recommendations on drugs and actions (e.g. START criteria), or compile generic questions, but provide no answers regarding the appropriateness of drug treatment (e.g. MAI) [3]. Besides, these approaches may differ regarding recommendations pertaining various aspects of drug therapy such as drug-drug interactions, dosing and kidney function.
Social network intervention to increase pre-exposure prophylaxis (PrEP) awareness, interest, and use among African American men who have sex with men

ABSTRACT In the U.S., HIV incidence is highest among Black men who have sex with men (MSM) but PrEP uptake is low, in part due to lack of normative support for using PrEP. This research pilot tested a social network-level intervention designed to increase PrEP use willingness, interest, and peer supports among Black MSM in Milwaukee. Five community social networks (n = 40 participants) of racial minority MSM were assessed at baseline with measures of PrEP knowledge, interest, attitudes, and action taking. Persons most interconnected with others in each network attended an intervention that provided training to increase knowledge about PrEPbenefits, address PrEP concerns, endorse PrEP use as a symbol of pride and health, and deliver these messages to others in their social networks. All network members were re-administered the same measures at 3-month followup. Significant increases over time were found in network members’ PrEP knowledge, attitudes, norm perceptions, self-efficacy, and willingness to use PrEP. Participants more often talked with friends about HIV and with their health care providers about PrEP. The percentage of participants who reported using PrEP increased from 3% to 11%. Larger-scale evaluations of this intervention model are needed.
Investigation of Presumptive HIV Transmission Associated with Hospitalization Using Nucleotide Sequence Analysis — New York, 2017

Since implementation of Standard Precautions* for the prevention of bloodborne pathogen transmission in 1985, health care-associated transmission of human immunodeficiency virus (HIV) in the United States has been rare (1). In October 2017, the New York City Department of Health and Mental Hygiene (NYCDOHMH) and the New York State Department of Health (NYSDOH) were notified by a clinician of a diagnosis of acute HIV infection in a young adult male (patient A) without recognized risk factors (i.e., he was monogamous, had an HIV-negative partner, and had no injection drug use) who had recently been hospitalized for a chronic medical condition. The low risk coupled with the recent hospitalization and medical procedures prompted NYSDOH, NYCDOHMH, and CDC to investigate this case as possible health care-associated transmission of HIV. Among persons with known HIV infection who had hospitalization dates overlapping those of patient A, one person (patient B) had an HIV strain highly similar to patient A's strain by nucleotide sequence analysis. The sequence relatedness, combined with other investigation findings, indicated a likely health care-associated transmission. Nucleotide sequence analysis, which is increasingly used for detecting HIV clusters (i.e., persons with closely related HIV strains) and to inform public health response (2,3), might also be used to identify possible health care-associated transmission of HIV to someone with health care exposure and no known HIV risk factors (4).
Study of susceptibility to antibiotics and molecular characterization of high virulence Staphylococcus aureus strains isolated from a rural hospital in Ethiopia

We characterised 80 Staphylococcus aureus strains isolated from human patients with SSTIs at a rural hospital in Ethiopia. Susceptibility to antibiotic of all strains was tested. The MLST method was used to type and a phylogenetic analysis was conducted employing the sequences of 7 housekeeping genes. PCR amplification was used to investigate the presence of the following virulence genes in all strains: hla (α-haemolysin), tstH (toxic shock syndrome toxin), luk PV (Panton-Valentine leukocidin), fnbA (fibronectin binding protein A) and mecA (methicillin resistance). Most of the strains were resistant to penicillin and ampicillin, but only 3 strains were resistant to oxacillin, and 1 of them was a true MRSA. The MLST results showed a high diversity of sequence types (ST), 55% of which were new, and ST152 was the most prevalent. A phylogeny study showed that many of the new STs were phylogenetically related to other previously described STs, but bore little relationship to the only ST from Ethiopia described in the database. Virulence gene detection showed a high prevalence of strains encoding the hla, fnbA and pvl genes (98.77%, 96.3% and 72.84%, respectively), a low prevalence of the tst gene (13.58%) and a markedly low prevalence of MRSA (1.25%). S. aureus strains isolated from patients in a rural area in Ethiopia showed low levels of antibiotic resistance, except to penicillin. Moreover, this study reveals new STs in Eastern Africa that are phylogenetically related to other previously described STs, and confirm the high prevalence of the pvl gene and the low prevalence of MRSA on the continent.
Institutional experience of healthy pediatric patients presenting with atrial fibrillation who had an electrophysiology study

Atrial fibrillation (AF) is a very common tachyarrhythmia with increasing prevalence with age, but uncommon in the pediatric population. Understanding that AF increases comorbidities make the need for investigation and potential elimination of alternate etiologies in pediatric AF patients critical. The objective of this study was to review our institutional data and compare our findings with previously documented adult AF risk factors to pediatric patients while also identifying which patients had alternate electrophysiology diagnoses amenable to transcatheter ablation.
Convolutional Networks for Historic Text Recognition

The aim of this work is to create a tool for automatic transcription of historical documents. The work is mainly focused on the recognition of texts from the period of early modern times written primarily using font called Fraktur. The problem is solved using convolutional neural networks with addition of Spatial Transformer Network. The solution also includes implemented generator of artiﬁcial historical texts. The proposed neural network was trained on a dataset created by this generator and for evaluation real historical texts were used. On the real historical dataset, the network achieved 81.8 % of correctly recognized characters. The beneﬁt of this work is the ﬁnding that it is possible to train the neural network on artiﬁcial data to be able to recognize real historical texts.
Learning to learn from data: Using deep adversarial learning to construct optimal statistical procedures

Optimal statistical procedures are constructed using deep adversarial learning to optimize play in a two-player game. Traditionally, statistical procedures have been derived via analytic calculations whose validity often relies on sample size growing to infinity. We use tools from deep learning to develop a new approach, adversarial Monte Carlo meta-learning, for constructing optimal statistical procedures. Statistical problems are framed as two-player games in which Nature adversarially selects a distribution that makes it difficult for a statistician to answer the scientific question using data drawn from this distribution. The players’ strategies are parameterized via neural networks, and optimal play is learned by modifying the network weights over many repetitions of the game. Given sufficient computing time, the statistician’s strategy is (nearly) optimal at the finite observed sample size, rather than in the hypothetical scenario where sample size grows to infinity. In numerical experiments and data examples, this approach performs favorably compared to standard practice in point estimation, individual-level predictions, and interval estimation.
Training Load, Neuromuscular Readiness, and Perceptual Fatigue Profile in Youth Elite Long-Jump Athletes.

PURPOSE To describe and identify individual trends and changes in training load, neuromuscular readiness, and perceptual fatigue measures in 2 youth elite long jumpers, finalists at the European Athletics U18 (Under 18) Championships (athlete A, female, age 16.5 y, long-jump record 6.25 m; athlete B, male, age 16.0 y, long-jump record 7.28 m). METHODS Data were collected from both training sessions and athletics competitions during a 16-week period, divided into a preparation (weeks 1-8) and a competitive phase (weeks 9-16). Training load was computed through training diaries (training time, sprint, jumping, and weights volume). The countermovement jump and the 10-to-5 repeated-jump test were executed on a weekly basis to assess neuromuscular readiness, and perceptual fatigue measures were collected through a wellness questionnaire. Statistical analysis was conducted using a magnitude-based decisions approach. RESULTS The results highlighted a decrease in training load during the competitive period with moderate to large differences for training time, sprint, and jump volume. Moreover, data showed an upward trend and very likely higher scores in vertical-jump performance across the competitive phase together with a very likely lower perceptual fatigue. CONCLUSIONS This scenario seemed to be favorable to achieve competition performance very close to the personal record during the competitive season. This study provided an example of application of a comprehensive monitoring system with young athletes involved in track-and-field jumping events.
Electronic Health Literacy in Swiss-German Parents: Cross-Sectional Study of eHealth Literacy Scale Unidimensionality

Background Parents often use digital media to search for information related to their children’s health. As the quantity and quality of digital sources meant specifically for parents expand, parents’ digital health literacy is increasingly important to process the information they retrieve. One of the earliest developed and widely used instruments to assess digital health literacy is the self-reported eHealth Literacy Scale (eHEALS). However, the eHEALS has not been psychometrically validated in a sample of parents. Given the inconsistency of the eHEALS underlying factor structure across previous reports, it is particularly important for validation to occur. Objective This study aimed to determine the factor structure of the German eHEALS measure in a sample of parents by adopting classic and modern psychometric approaches. In particular, this study sought to identify the eHEALS validity as a unidimensional index as well as the viability for potential subscales. Methods A cross-sectional design was used across two purposive sampling frames: online and paper administrations. Responses were collected between January 2018 and May 2018 from 703 Swiss-German parents. In addition to determining the sampling characteristics, we conducted exploratory factor analysis of the eHEALS by considering its ordinal structure using polychoric correlations. This analysis was performed separately for online–based and paper–based responses to examine the general factor strength of the eHEALS as a unidimensional index. Furthermore, item response theory (IRT) analyses were conducted by fitting eHEALS to a bifactor model to further inspect its unidimensionality and subscale viability. Results Parents in both samples were predominantly mothers (622/703, 88.5%), highly educated (538/703, 76.9%), of Swiss nationality (489/703, 71.8%), and living with a partner (692/703, 98.4%). Factor analyses of the eHEALS indicated the presence of a strong general factor across both paper and online samples, and the Wilcoxon rank-sum test indicated that the eHEALS total sum score was not significantly different between the paper and online samples (P=.12). Finally, the IRT analyses indicated negligible multidimensionality, insufficient subscale reliability after accounting for the eHEALS general factor, and a reduced subset of items that could serve as a unidimensional index of the eHEALS across the paper and online samples. Conclusions The German eHEALS evidenced good psychometric properties in a parent-specific study sample. Factor analyses indicated a strong general factor across purposively distinct sample frames (online and paper). IRT analyses validated the eHEALS as a unidimensional index while failing to find support for subscale usage.
Neurogenesis in the inner ear: the zebrafish statoacoustic ganglion provides new neurons from a Neurod/Nestin-positive progenitor pool well into adulthood

ABSTRACT The vertebrate inner ear employs sensory hair cells and neurons to mediate hearing and balance. In mammals, damaged hair cells and neurons are not regenerated. In contrast, hair cells in the inner ear of zebrafish are produced throughout life and regenerate after trauma. However, it is unknown whether new sensory neurons are also formed in the adult zebrafish statoacoustic ganglion (SAG), the sensory ganglion connecting the inner ear to the brain. Using transgenic lines and marker analysis, we identify distinct cell populations and anatomical landmarks in the juvenile and adult SAG. In particular, we analyze a Neurod/Nestin-positive progenitor pool that produces large amounts of new neurons at juvenile stages, which transitions to a quiescent state in the adult SAG. Moreover, BrdU pulse chase experiments reveal the existence of a proliferative but otherwise marker-negative cell population that replenishes the Neurod/Nestin-positive progenitor pool at adult stages. Taken together, our study represents the first comprehensive characterization of the adult zebrafish SAG showing that zebrafish, in sharp contrast to mammals, display continued neurogenesis in the SAG well beyond embryonic and larval stages. Summary: This study provides the first comprehensive characterization of the zebrafish statoacoustic ganglion showing that, in sharp contrast to mammals, zebrafish display continued neurogenesis in the inner ear into adult stages.
Consequences of being phenotypically mismatched with the environment: no evidence of oxidative stress in cold- and warm-acclimated birds facing a cold spell

ABSTRACT Seasonal changes in maximal thermogenic capacity (Msum) in wild black-capped chickadees suggests that adjustments in metabolic performance are slow and begin to take place before winter peaks. However, when mean minimal ambient temperature (Ta) reaches −10°C, the chickadee phenotype appears to provide enough spare capacity to endure days with colder Ta, down to −20°C or below. This suggests that birds could also maintain a higher antioxidant capacity as part of their cold-acclimated phenotype to deal with sudden decreases in temperature. Here, we tested how environmental mismatch affected oxidative stress by comparing cold-acclimated (−5°C) and transition (20°C) phenotypes in chickadees exposed to an acute 15°C drop in temperature with that of control individuals. We measured superoxide dismutase, catalase and glutathione peroxidase activities, as well as lipid peroxidation damage and antioxidant scavenging capacity in pectoralis muscle, brain, intestine and liver. We generally found differences between seasonal phenotypes and across tissues, but no differences with respect to an acute cold drop treatment. Our data suggest oxidative stress is closely matched to whole-animal physiology in cold-acclimated birds compared with transition birds, implying that changes to the oxidative stress system happen slowly. Summary: Oxidative stress appears to be closely matched to whole-animal physiology in cold-acclimated birds compared with transition birds, implying that changes to the oxidative stress system happen slowly.
Draft Genome Sequences of 30 Salmonella enterica Serovar Enteritidis Isolates Associated with Multiple Outbreaks in Brazil

Salmonella enterica subsp. enterica serovar Enteritidis has been the prevalent serovar isolated from gastroenteritis cases in Brazil since the 1990s. Here, we report the draft genomes of 30 S. Enteritidis isolates originating from a variety of patients and implicated foods during outbreaks between 1999 and 2006 in Brazil. ABSTRACT Salmonella enterica subsp. enterica serovar Enteritidis has been the prevalent serovar isolated from gastroenteritis cases in Brazil since the 1990s. Here, we report the draft genomes of 30 S. Enteritidis isolates originating from a variety of patients and implicated foods during outbreaks between 1999 and 2006 in Brazil.
How I curate: applying American Society of Hematology-Clinical Genome Resource Myeloid Malignancy Variant Curation Expert Panel rules for RUNX1 variant curation for germline predisposition to myeloid malignancies

The broad use of next-generation sequencing and microarray platforms in research and clinical laboratories has led to an increasing appreciation of the role of germline mutations in genes involved in hematopoiesis and lineage differentiation that contribute to myeloid neoplasms. Despite implementation of the American College of Medical Genetics and Genomics and Association for Molecular Pathology 2015 guidelines for sequence variant interpretation, the number of variants deposited in ClinVar, a genomic repository of genotype and phenotype data, and classified as having uncertain significance or being discordantly classified among clinical laboratories remains elevated and contributes to indeterminate or inconsistent patient care. In 2018, the American Society of Hematology and the Clinical Genome Resource co-sponsored the Myeloid Malignancy Variant Curation Expert Panel to develop rules for classifying gene variants associated with germline predisposition to myeloid neoplasia. Herein, we demonstrate application of our rules developed for the RUNX1 gene to variants in six examples to show how we would classify them within the proposed framework.
Characterization of the prohormone complement in Amphiprion and related fish species integrating genome and transcriptome assemblies

The Amphiprion (anemonefish or clownfish) family of teleost fish, which is not a common model species, exhibits multiple unique characteristics, including social control of body size and protandrous sex change. The social changes in sex and body size are modulated by neuropeptide signaling pathways. These neuropeptides are formed from complex processing from larger prohormone proteins; understanding the neuropeptide complement requires information on complete prohormones sequences. Genome and transcriptome information within and across 22 teleost fish species, including 11 Amphiprion species, were assembled and integrated to achieve the first comprehensive survey of their prohormone genes. This information enabled the identification of 175 prohormone isoforms from 159 prohormone proteins across all species. This included identification of 9 CART prepropeptide genes and the loss of insulin-like 5B and tachykinin precursor 1B genes in Pomacentridae species. Transcriptome assemblies generally detected most prohormone genes but provided fewer prohormone genes than genome assemblies due to the lack of expression of prohormone genes or specific isoforms and tissue sampled. Comparisons between duplicate genes indicated that subfunctionalization, degradation, and neofunctionalization may be occurring between all copies. Characterization of the prohormone complement lays the foundation for future peptidomic investigation of the molecular basis of social physiology and behavior in the teleost fish.
Ion Channels Controlling Circadian Rhythms in Suprachiasmatic Nucleus Excitability.

Animals synchronize to the environmental day-night cycle by means of an internal circadian clock in the brain. In mammals, this timekeeping mechanism is housed in the suprachiasmatic nucleus (SCN) of the hypothalamus and is entrained by light input from the retina. The output of the SCN is a neural code for circadian time, which arises from the collective activity of neurons within the SCN circuit and is comprised of two fundamental components: 1) periodic alterations in the spontaneous excitability of individual neurons that result in higher firing rates during the day and lower firing rates at night, and 2) synchronization of these cellular oscillations throughout the SCN. In this review, we summarize current evidence for the identity of ion channels in SCN neurons and the mechanisms by which they set the rhythmic parameters of the time code. During the day, voltage-dependent and independent Na+ and Ca2+ currents, as well as several K+ currents, contribute to increased membrane excitability and therefore higher firing frequency. At night, an increase in different K+ currents, including Ca2+-activated BK currents, contribute to membrane hyperpolarization and decreased firing. Layered on top of these intrinsically-regulated changes in membrane excitability, more than a dozen neuromodulators influence action potential activity and rhythmicity in SCN neurons, facilitating both synchronization and plasticity of the neural code.