Miracle-dz/UniFAR-FTUs huggingface dataset:
Ultrasound Diagnosis of Calf Injuries

Context: The medial head of the gastrocnemius is the third most commonly strained muscle in elite athletes after the biceps femoris and rectus femoris. The differential diagnosis of posterior calf injury includes musculoskeletal and nonmusculoskeletal causes. Classically, delineation of these injuries from one another relied primarily on historical features and physical examination findings. The utilization of musculoskeletal ultrasound (sonography) has augmented the diagnosis of these injuries by providing dynamic, real-time confirmation. Evidence Acquisition: A review of PubMed, OVID, and MD Consult prior to January 2016 was performed using search terms, including soleus ultrasound, gastrocnemius ultrasound, and tennis leg. The references of the pertinent articles were further reviewed for other relevant sources. Study Design: Clinical review. Level of Evidence: Level 4. Results: There have been few reviews to date of calf injuries and the use of sonography in their diagnosis. Prompt diagnosis utilizing ultrasound allows the clinician to focus management on gastrocnemius injury if present. Two-thirds of calf injuries occur at the junction of the fascia between the medial head of the gastrocnemius and the soleus. Injuries to the lateral head of the gastrocnemius occur in up to 14% of patients in some case series, but injury may occur anywhere from the proximal origin to the mid-belly to the fascial junction with the soleus. Numerous injuries to the posterior compartment can mimic gastrocnemius strain, and musculoskeletal ultrasound can aide in their diagnosis by incorporating real-time imaging into the grading of the injury and visual confirmation of physical examination findings. Conclusion: Acute injury to the posterior compartment of the lower extremity can represent a diagnostic challenge. Medial gastrocnemius strain represents the most common injury of the posterior compartment of the lower extremity. Ultrasound is a useful tool to assist the clinician in determining the specific cause of calf injury, estimate the severity of the injury, and monitor progress of healing. The vast majority of calf injuries can be diagnosed and managed without any additional imaging. Serial diagnostic ultrasound of an injured area allows for direct monitoring of tissue healing and may allow the clinician to more confidently assess response to treatment and help guide return-to-play decisions.
Robust inference in summary data Mendelian randomization via the zero modal pleiotropy assumption

Background Mendelian randomisation (MR) is being increasingly used as a strategy to improve causal inference in observational studies. Availability of summary data of genetic associations for a variety of phenotypes from large genome-wide association studies (GWAS) allows straightforward application of MR in a two-sample design. In addition to the conventional inverse variance weighting (IVW) method, recently developed summary data MR methods, such as the MR-Egger and weighted median approaches, allow a relaxation of the instrumental variable assumptions. Methods Here, a new method –the mode estimator – is proposed to obtain a single causal effect estimate from multiple genetic instruments. The mode estimate is consistent when the largest number of similar (identical in infinite samples) individual-instrument causal effect estimates comes from valid instruments, even if the majority of instruments are invalid. We evaluated the performance of the method in simulations designed to mimic the two-sample summary data setting, and demonstrate its use by investigating the causal effect of plasma lipid fractions and urate levels on coronary heart disease risk. Results The mode estimates presented less bias and type-I error rates than other methods under the null in many situations. Its power to detect a causal effect was smaller compared to the IVW and weighted median methods, but was larger than that of MR-Egger regression, with sample size requirements typically smaller than those available from GWAS consortia. Conclusions The mode estimator relaxes the instrumental variable assumptions, and should be used in combination with other approaches in a sensitivity analysis.
pBRIT: gene prioritization by correlating functional and phenotypic annotations through integrative data fusion

Motivation Computational gene prioritization can aid in disease gene identification. Here, we propose pBRIT (prioritization using Bayesian Ridge regression and Information Theoretic model), a novel adaptive and scalable prioritization tool, integrating Pubmed abstracts, Gene Ontology, Sequence similarities, Mammalian and Human Phenotype Ontology, Pathway, Interactions, Disease Ontology, Gene Association database and Human Genome Epidemiology database, into the prediction model. We explore and address effects of sparsity and inter‐feature dependencies within annotation sources, and the impact of bias towards specific annotations. Results pBRIT models feature dependencies and sparsity by an Information‐Theoretic (data driven) approach and applies intermediate integration based data fusion. Following the hypothesis that genes underlying similar diseases will share functional and phenotype characteristics, it incorporates Bayesian Ridge regression to learn a linear mapping between functional and phenotype annotations. Genes are prioritized on phenotypic concordance to the training genes. We evaluated pBRIT against nine existing methods, and on over 2000 HPO‐gene associations retrieved after construction of pBRIT data sources. We achieve maximum AUC scores ranging from 0.92 to 0.96 against benchmark datasets and of 0.80 against the time‐stamped HPO entries, indicating good performance with high sensitivity and specificity. Our model shows stable performance with regard to changes in the underlying annotation data, is fast and scalable for implementation in routine pipelines. Availability and implementation http://biomina.be/apps/pbrit/; https://bitbucket.org/medgenua/pbrit.
D-Watch: Embracing "bad" Multipaths for Device-Free Localization with COTS RFID Devices

Device-free localization, which does not require any device attached to the target is playing a critical role in many applications such as intrusion detection, elderly monitoring, etc. This paper introduces D-Watch, a device-free system built on top of low cost commodity-off-the-shelf (COTS) RFID hardware. Unlike previous works which consider multipaths detrimental, D-Watch leverages the "bad" multipaths to provide a decimeter level localization accuracy without offline training. D-Watch harnesses the angle-of-arrival (AoA) information from the RFID tags' backscatter signals. The key intuition is that whenever a target blocks a signal's propagation path, the signal power experiences a drop which can be accurately captured by the proposed novel P-MUSIC algorithm. The wireless phase calibration scheme proposed does not interrupt the ongoing communication. Real-world experiments demonstrate the effectiveness of D-Watch. In a rich-multipath library environment, D-Watch can localize a human target at a median accuracy of 16.5 cm. In a table area of 2 m×2 m, D-Watch can track a user's fist at a median accuracy of 5.8 cm. D-Watch is capable of localizing multiple targets which is well known to be challenging in passive localization
Editor’s Highlight: Pregnancy Alters Aflatoxin B1 Metabolism and Increases DNA Damage in Mouse Liver

Abstract Pregnancy is a complex physiological state, in which the metabolism of endogenous as well as exogenous agents is ostensibly altered. One exogenous agent of concern is the hepatocarcinogen aflatoxin B1 (AFB1), a foodborne fungal toxin, that requires phase I metabolic oxidation for conversion to its toxic and carcinogenic form, the AFB1-8,9-exo-epoxide. The epoxide interacts with cellular targets causing toxicity and cell death; these targets include the covalent modification of DNA leading to mutations that can initiate malignant transformation. The main detoxification pathway of the AFB1-epoxide involves phase II metabolic enzymes including the glutathione-S-transferase (GST) family. Pregnancy can modulate both phase I and II metabolism and alter the biological potency of AFB1. The present work investigated the impact of pregnancy on AFB1 exposure in mice. A single IP dose of 6 mg/kg AFB1 was administered to pregnant C57BL/6 J mice at gestation day 14 and matched non-pregnant controls. Pregnant mice accumulated 2-fold higher AFB1-N7-guanine DNA adducts in the liver when compared with nonpregnant controls 6 h post-exposure. Enhanced DNA adduct formation in pregnant animals paralleled elevated hepatic protein expression of mouse CYP1A2 and mouse homologs of human CYP3A4, phase I enzymes capable of bioactivating AFB1. Although phase II enzymes GSTA1/2 showed decreased protein expression, GSTA3, the primary enzymatic protection against the AFB1-epoxide, was unaffected at the protein level. Taken together, our results reveal that pregnancy may constitute a critical window of susceptibility for maternal health, and provide insight into the biochemical factors that could explain the underlying risks.
Some applications of MTMs based on non-Foster active loads

In this contribution, we propose a novel approach to dramatically improve the operation bandwidth of a Split Ring Resonator (SRR) by loading its external gap with an active non-Foster circuit. The theoretical aspects, as well as some applications in the field of electrically small microwave antennas, enhanced microwave transmission, and microwave absorbers are presented.
Somatic symptoms and internalizing problems in urban youth: a cross-cultural comparison of Czech and Russian adolescents

Background Although the association between somatic complaints and internalizing problems (anxiety, somatic anxiety and depression) is well established, it remains unclear whether the pattern of this relationship differs by gender and in different cultures. The aim of this study was to examine cross-cultural and gender-specific differences in the association between somatic complaints and internalizing problems in youth from the Czech Republic and Russia. Methods The Social and Health Assessment, a self-report survey, was completed by representative community samples of adolescents, age 12-17 years, from the Czech Republic (N = 4770) and Russia (N = 2728). Results A strong association was observed between somatic complaints and internalizing psychopathology. Although the levels of internalizing problems differed by country and gender, they increased together with and largely in a similar way to somatic complaints for boys and girls in both countries. Conclusion The association between somatic symptoms and internalizing problems seems to be similar for boys and girls across cultures.
Weekly Standard Kt/Vurea and Clinical Outcomes in Home and In-Center Hemodialysis.

BACKGROUND AND OBJECTIVES Patients undergoing hemodialysis with a frequency other than thrice weekly are not included in current clinical performance metrics for dialysis adequacy. The weekly standard Kt/Vurea incorporates treatment frequency, but there are limited data on its association with clinical outcomes. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We used multivariable regression to examine the association of dialysis standard Kt/Vurea with BP and metabolic control (serum potassium, calcium, bicarbonate, and phosphorus) in patients incidental to dialysis treated with home (n=2373) or in-center hemodialysis (n=109,273). We further used Cox survival models to examine the association of dialysis standard Kt/Vurea with mortality, hospitalization, and among patients on home hemodialysis, transfer to in-center hemodialysis. RESULTS After adjustment for potential confounders, patients with dialysis standard Kt/Vurea <2.1 had higher BPs compared with patients with standard Kt/Vurea 2.1 to <2.3 (3.4 mm Hg higher [P<0.001] for home hemodialysis and 0.9 mm Hg higher [P<0.001] for in-center hemodialysis). There were no clinically meaningful associations between dialysis standard Kt/Vurea and markers of metabolic control, irrespective of dialysis modality. There was no association between dialysis standard Kt/Vurea and risk for mortality, hospitalization, or transfer to in-center hemodialysis among patients undergoing home hemodialysis. Among patients on in-center hemodialysis, dialysis standard Kt/Vurea <2.1 was associated with higher risk (adjusted hazard ratio, 1.11; 95% confidence interval, 1.07 to 1.14) and standard Kt/Vurea ≥2.3 was associated with lower risk (adjusted hazard ratio, 0.97; 95% confidence interval, 0.94 to 0.99) for death compared with standard Kt/Vurea 2.1 to <2.3. Additional analyses limited to patients with available data on residual kidney function showed similar relationships of dialysis and total (dialysis plus kidney) standard Kt/Vurea with outcomes. CONCLUSIONS Current targets for standard Kt/Vurea have limited utility in identifying individuals at increased risk for adverse clinical outcomes for those undergoing home hemodialysis but may enhance risk stratification for in-center hemodialysis.
Characterizing cognitive aging in humans with links to animal models

With the population of older adults expected to grow rapidly over the next two decades, it has become increasingly important to advance research efforts to elucidate the mechanisms associated with cognitive aging, with the ultimate goal of developing effective interventions and prevention therapies. Although there has been a vast research literature on the use of cognitive tests to evaluate the effects of aging and age-related neurodegenerative disease, the need for a set of standardized measures to characterize the cognitive profiles specific to healthy aging has been widely recognized. Here we present a review of selected methods and approaches that have been applied in human research studies to evaluate the effects of aging on cognition, including executive function, memory, processing speed, language, and visuospatial function. The effects of healthy aging on each of these cognitive domains are discussed with examples from cognitive/experimental and clinical/neuropsychological approaches. Further, we consider those measures that have clear conceptual and methodological links to tasks currently in use for non-human animal studies of aging, as well as those that have the potential for translation to animal aging research. Having a complementary set of measures to assess the cognitive profiles of healthy aging across species provides a unique opportunity to enhance research efforts for cross-sectional, longitudinal, and intervention studies of cognitive aging. Taking a cross-species, translational approach will help to advance cognitive aging research, leading to a greater understanding of associated neurobiological mechanisms with the potential for developing effective interventions and prevention therapies for age-related cognitive decline.
Infectious complications after hematopoietic stem cell transplantation: current status and future perspectives in Korea

Hematopoietic stem cell transplantation (HSCT) is a treatment for hematologic malignancies, immune deficiencies, or genetic diseases, ect. Recently, the number of HSCTs performed in Korea has increased and the outcomes have improved. However, infectious complications account for most of the morbidity and mortality after HSCT. Post-HSCT infectious complications are usually classified according to the time after HSCT: pre-engraftment, immediate post-engraftment, and late post-engraftment period. In addition, the types and risk factors of infectious complications differ according to the stem cell source, donor type, conditioning intensity, region, prophylaxis strategy, and comorbidities, such as graft-versushost disease and invasive fungal infection. In this review, we summarize infectious complications after HSCT, focusing on the Korean perspectives.
Trends in Lifetime Cannabis Use among Czech School-aged Children from 2002 to 2014.

OBJECTIVE The aim of the study was to examine trends in the prevalence of lifetime cannabis use among the Czech 15-year old students. METHODS Data from the nationally representative Health Behaviour in School-aged Children Survey, conducted in the Czech Republic in 2002, 2006, 2010 and 2014, were used. Trends in cannabis use among both boys and girls were modelled through binary logistic regression with period as a predictor of the lifetime cannabis use. RESULTS The prevalence of lifetime cannabis use has significantly decreased among young Czechs, particularly among boys. Gender differences in cannabis use have been also gradually decreasing since 2002, with no significant differences between genders in recent period. CONCLUSIONS Although there are positive changes in the prevalence of adolescent cannabis use, from the European perspective, Czech students still belong to those with significantly higher rates in this respect. Thus, alongside with the use of other substances, adolescent cannabis consumption remains an important challenge for the national public health policy.
A novel optical mesh network-on-chip for gigascale systems-on-chip

Nanoscale CMOS technologies are posing new network-on-chip (NoC) concepts to gigascale system-on-chip (SoCs). However, electronic network on chip designs face several problems like energy consumption, bandwidth and latency. Optical NoC (ONoC) promises to solve these problems. The advances in nanoscale photonic technology make ONoCs possible. This paper proposes a new non-blocking optical router, OXY, and uses it to build a 2D mesh ONoC. OXY based optical mesh NoC fully utilizes the properties of XY routing in 2D networks, and significantly reduce the number of microring resonators required for ONoCs. We compared OXY based optical mesh NoC with three other schemes in number of microring resonators, loss and energy consumption. The results show that OXY based optical mesh NoC achieves the best in all the comparisons. We simulated 2D optical mesh ONoC based on OXY, and showed the end-to-end delay and throughput under different traffic loads and network sizes.
Fault Diagnosis in Partially Observed Petri Nets Using Redundancies

This paper is devoted to the development of an approach to the diagnosability of a system described in the framework of partially observed Petri nets (POPNs) such that the developed fault diagnosis technique can be widely applicable to systems with mutable initial states and partial observations. Existing studies show that the diagnosability of a discrete event system (DES) can be improved by suitable sensor selections or redundancies. This paper proposes a redundancy-building method for a POPN with a certain sensor selection such that no matter how the POPN is initially marked, it achieves maximally structural diagnosability, i.e., the diagnosability of a system cannot be further improved based on the given sensor selection and knowledge of the plant model, which is critical and fundamental in fault recovery capabilities for operating large and complex DESs. To make the proposed method practically applicable, we do not require prior knowledge of faults or special structure of a system, instead we model faults as abnormal events occurring on transitions or places in the plant but not special transitions. Necessary and sufficient conditions for maximally structural diagnosability of a system are established. Redundancies (externally observable places) that guarantee behavior permissiveness and maximally structural diagnosability are built by solving integer linear programming problems.
Norepinephrine Augments Salmonella enterica-Induced Enteritis in a Manner Associated with Increased Net Replication but Independent of the Putative Adrenergic Sensor Kinases QseC and QseE

ABSTRACT Stress has long been correlated with susceptibility to microbial infection. One explanation for this phenomenon is the ability of pathogens to sense and respond to host stress-related catecholamines, such as norepinephrine (NE). In Gram-negative enteric pathogens, it has been proposed that NE may facilitate growth by mediating iron supply, or it may alter gene expression by activating adrenergic sensor kinases. The aim of this work was to investigate the relative importance of these processes in a model in which NE alters the outcome of Salmonella enterica serovar Typhimurium infection. A bovine ligated ileal loop model was used to study the effect of NE on enteritis induced by S. Typhimurium and on the bacterial in vivo replication rate. Mutants lacking putative adrenergic receptor genes were assessed in the loop model, in a calf intestinal colonization model, and in vitro. S. Typhimurium-induced enteritis was significantly enhanced by addition of 5 mM NE. This effect was associated with increased net bacterial replication in the same model. Exogenous ferric iron also stimulated bacterial replication in the medium used but not transcription of enteritis-associated loci. The putative adrenergic sensors QseC and QseE were not required for NE-enhanced enteritis, intestinal colonization of calves, or NE-dependent growth in iron-restricted medium and did not influence expression or secretion of enteritis-associated virulence factors. Our findings support a role for stress-related catecholamines in modulating the virulence of enteric bacterial pathogens in vivo but suggest that bacterial adrenergic sensors may not be the vital link in such interkingdom signaling in Salmonella.
Planning the trajectories of multiple mobile sinks in large-scale, time-sensitive WSNs

Controlled sink mobility has been shown to be very beneficial in lifetime prolongation of wireless sensor networks (WSNs) by avoiding the typical hot-spot problem near the sink. Besides striving for elongated lifetimes, many applications of WSNs are time-sensitive, i.e., they strongly benefit from bounds on the message transfer delay. Further, large WSNs require multiple sinks in order to scale well with respect to delay and lifetime. Therefore, it becomes very interesting to investigate how to plan the trajectories of multiple mobile sinks such that lifetime and delay goals are met simultaneously. To that end, we propose a geometrically principled heuristic for finding good trajectories of multiple mobile sinks in large-scale, time-sensitive WSNs. First, we discuss the high analytical challenges of optimally planning the trajectories of multiple mobile sinks. Based on this, we relax the problem by transforming it into a geometric design problem, which, subsequently, is solved in closed form. In simulations, we investigate how well this geometric heuristic for sink trajectories of multiple mobile sinks performs with respect to delay and lifetime. We find that it excels especially in large-scale WSNs, for example in a WSN with 500 nodes and 20 sinks, it roughly cuts delay bounds by 50% while tripling the lifetime compared to the sinks following random walks. Hence planning the sink trajectories carefully really pays off.