Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibiotic Resistance Among Pediatric-Sourced Ocular Pathogens: 8-Year Findings From the Antibiotic Resistance Monitoring in Ocular Microorganisms (ARMOR) Surveillance Study

Background: The Antibiotic Resistance Monitoring in Ocular Microorganisms (ARMOR) study is a nationwide longitudinal antibiotic resistance surveillance program specific to bacterial pathogens commonly encountered in ocular infections. We evaluated in vitro resistance rates and trends among isolates obtained from pediatric patients (⩽17 years of age). Methods: Clinical centers across the United States were invited to submit ocular isolates of Staphylococcus aureus, coagulase-negative staphylococci (CoNS), Streptococcus pneumoniae, Haemophilus influenzae and Pseudomonas aeruginosa to a central laboratory. Minimum inhibitory concentrations for various antibiotic classes were determined by broth microdilution per Clinical and Laboratory Standards Institute guidelines and interpreted as susceptible, intermediate or resistant based on available breakpoints. Longitudinal trends were analyzed using a Cochran-Armitage test for linear trends in a proportion. Results: Of 4829 isolates collected from January 2009 to December 2016, 995 isolates, sourced primarily from hospitals and referral centers, were obtained from pediatric patients (n = 286 H. influenzae, n = 284 S. aureus, n = 213 CoNS, n = 150 S. pneumoniae and n = 62 P. aeruginosa). With few exceptions, P. aeruginosa and H. influenzae were generally susceptible to the antibiotics tested. Of S. aureus and CoNS isolates, respectively, 56% and 72% were resistant to azithromycin and 24% and 47% were methicillin-resistant (MR); concurrent resistance to other drug classes and multidrug resistance (≥3 drug classes) were prevalent among MR staphylococci. Of S. pneumoniae isolates, 38% and 35% demonstrated resistance to azithromycin and penicillin, respectively. Besifloxacin had the lowest minimum inhibitory concentration against the Gram-positive isolates. Conclusions: These in vitro data suggest antibiotic resistance is common among staphylococcal and pneumococcal isolates collected from pediatric patients with ocular infections. Methicillin resistance was prevalent among staphylococci with many strains demonstrating multidrug resistance. These findings may not be representative of resistance trends in community-based practices.
Comparison of Convolutive Kernel Compensation and Non-Negative Matrix Factorization of Surface Electromyograms

We compared non-negative matrix factorization (NMF) and convolution kernel compensation techniques for high-density electromyogram decomposition. The experimental data were recorded from nine healthy persons during controlled single degree of freedom (DOF) wrist flexion-extension, supination-pronation, and ulnar–radial deviation movements. We assembled the identified motor units and NMF components into three groups. Those active mostly during the first and the second movement direction per DOF were placed in the G1 and G3 groups, respectively. The remaining components were nonspecific for movement direction and were placed in the G2 group. In ulnar and radial deviation, the relative energies of identified cumulative motor unit spike trains (CSTs) and NMF components were similarly distributed among the groups. In other two movement types, the energy of NMF components in the G2 group was significantly larger than the energy of CSTs. We further performed a coherence analysis between CSTs and sums of NMF components in each group. Both decompositions demonstrated a solid match, but only at frequencies <3 Hz. At higher frequencies, the coherence hardly exceeded the value of 0.5. Potential reasons for these discrepancies include the negative impact of motor unit action potential shapes and noise on NMF decomposition.
Stride-to-stride fluctuations in transtibial amputees are not affected by changes in push-off mechanics from using different prostheses

Stride-to-stride fluctuations of joint kinematics during walking reflect a highly structured organization that is characteristic of healthy gait. The organization of stride-to-stride fluctuations is disturbed in lower-limb prosthesis users, yet the factors contributing to this difference are unclear. One potential contributor to the changes in stride-to-stride fluctuations is the altered push-off mechanics experienced by passive prosthesis users. The purpose of our study was to determine if changes in push-off mechanics affect stride-to-stride fluctuations in transtibial amputees. Twenty-two unilateral transtibial amputees were enrolled in the 6-week cross-over study, where High and Low Activity (based on the Medicare Functional Classification System) prostheses were worn for three weeks each. Data collection took place at the end of the third week. Participants walked on a treadmill in a motion capture laboratory to quantify stride-to-stride fluctuations of the lower extremity joint angle trajectories using the largest Lyapunov Exponent, and over floor-embedded force platforms to enable calculating push-off work from the prosthesis and the sound limb. Push-off work was 140% greater in the High Activity prosthesis compared to the Low Activity prosthesis (p < 0.001), however no significant change was observed in stride-to-stride fluctuations of the ankle between the two prosthesis types (p = 0.576). There was no significant correlation between changes in prosthesis push-off work and the largest Lyapunov exponent. Though differences in push-off work were observed between the two prosthesis types, stride-to-stride fluctuations remained similar, indicating that prosthesis propulsion mechanics may not be a strong determinant of stride-to-stride fluctuations in unpowered transtibial prosthesis users.
Contracting to a Longest Path in H-Free Graphs

We prove two dichotomy results for detecting long paths as patterns in a given graph. The NP-hard problem Longest Induced Path is to determine the longest induced path in a graph. The NP-hard problem Longest Path Contractibility is to determine the longest path to which a graph can be contracted to. By combining known results with new results we completely classify the computational complexity of both problems for $H$-free graphs. Our main focus is on the second problem, for which we design a general contractibility technique that enables us to reduce the problem to a matching problem.
OTIDS: A Novel Intrusion Detection System for In-vehicle Network by Using Remote Frame

Controller Area Network (CAN) is a bus communication protocol which defines a standard for reliable and efficient transmission between in-vehicle nodes in real-time. Since CAN message is broadcast from a transmitter to the other nodes on a bus, it does not contain information about the source and destination address for validation. Therefore, an attacker can easily inject any message to lead system malfunctions. In this paper, we propose an intrusion detection method based on the analysis of the offset ratio and time interval between request and response messages in CAN. If a remote frame having a particular identifier is transmitted, a receiver node should respond to the remote frame immediately. In attack-free state, each node has a fixed response offset ratio and time interval while these values vary in attack state. Using this property, we can measure the response performance of the existing nodes based on the offset ratio and time interval between request and response messages. As a result, our methodology can detect intrusions by monitoring offset ratio and time interval, and it allows quick intrusion detection with high accuracy.
Staged lower lip reconstruction following gangrenous stomatitis in an immunosuppressed patient

A 70-year-old male with a history of diabetes mellitus, hypertension, and coronary stent insertion visited our hospital 7 days after biting his lower lip. Swelling and inflammation had worsened despite debridement and antibiotic treatment. On the 8th hospital day, fungal infection with Candida albicans and superimposed bacterial infection with Klebsiella pneumoniae were found on tissue culture. Extensive necrosis resulted in a defect of approximately 3/4 of the entire lower lip and a full-layer skin defect from the vermilion to the gingivobuccal sulcus at the right corner of the mouth. To correct drooling, incomplete lip sealing, and trismus, staged reconstruction was performed with consideration of cosmetic and functional features. The treatment process using staged reconstruction and antifungal treatment for an extensive lower lip defect caused by fungal stomatitis is described.
A computational method to characterize the missense mutations in the catalytic domain of GAA protein causing Pompe disease

Pompe disease is an autosomal recessive lysosomal storage disease caused by acid α‐glucosidase (GAA) deficiency, resulting in intralysosomal accumulation of glycogen, including cardiac, skeletal, and smooth muscle cells. The GAA gene is located on chromosome 17 (17q25.3), the GAA protein consists of 952 amino acids; of which 378 amino acids (347‐726) falls within the catalytic domain of the protein and comprises of active sites (518 and 521) and binding sites (404, 600, 616, and 674). In this study, we used several computational tools to classify the missense mutations in the catalytic domain of GAA for their pathogenicity and stability. Eight missense mutations (R437C, G478R, N573H, Y575S, G605D, V642D, L705P, and L712P) were predicted to be pathogenic and destabilizing to the protein structure. These mutations were further subjected to phenotyping analysis using SNPeffect 4.0 to predict the chaperone binding sites and structural stability of the protein. The mutations R437C and G478R were found to compromise the chaperone‐binding activity with GAA. Molecular docking analysis revealed that the G478R mutation to be more significant and hinders binding to the DNJ (Miglustat) compared with the R437C. Further molecular dynamic analysis for the two mutations demonstrated that the G478R mutation was acquired higher deviation, fluctuation, and lower compactness with decreased intramolecular hydrogen bonds compared to the mutant R437C. These data are expected to serve as a platform for drug design against Pompe disease and will serve as an ultimate tool for variant classification and interpretations.
Florbetapir Image Analysis for Alzheimer's Disease Diagnosis

Over decades Alzheimer's disease (AD) remains without decent cure, and only disease-modifying methods are available. This paper is devoted to the analysis of amyloid-PET images with florbetapir (18F-AV-45) tracer to detect the presence of AD or Mild Cognitive Impairment (MCI). The first part of the article dedicated to image processing pipeline, specifically, spacial normalisation and feature extraction. The second part is devoted to the development of the multiclass classifier with deep learning methods. In particular, deep neural network was developed to distinguish three stages: health control (HC), MCI and AD. After tuning and training a neural network, the final specificity of 78% and sensitivity of 90% has been achieved.
Obstructive Sleep Apnea Is Closely Related to Cardiovascular Risk Factors, but Not to Clinical Recurrence of Atrial Fibrillation after Catheter Ablation: An Analysis of Atrial Fibrillation Patients

Background: Obstructive sleep apnea (OSA) is a well-known predictor of atrial fibrillation (AF). However, OSA usually accompanies other risk factors of AF. We tried to investigate whether OSA is related to AF recurrence after catheter ablation. Methods: A total of 378 patients (mean age 59.9 ± 10.7 years, 72.5% male) who underwent catheter ablation of AF were enrolled and underwent overnight ambulatory polysomnography before the ablation procedure. These patients were examined once every 3 months at the outpatient clinic to determine AF recurrence. Results: Based on the apnea-hypopnea index (AHI), we divided the study subjects into 3 groups defined as mild (AHI < 10), moderate (10 30) OSA. Patients with severe OSA had a higher prevalence of hypertension, diabetes mellitus, and coronary artery disease (CAD). However, AF recurrence was not different between the three groups. The Kaplan-Meier analysis also showed no significant difference in AF recurrence according to the degree of severity of OSA. Multivariate logistic regression analysis revealed that OSA might be a predictor of CAD; however, Cox regression analysis showed that only early recurrence is closely related to AF recurrence after catheter ablation, rather than the severity of OSA. Conclusion: This study shows that the severity of OSA is not associated with the recurrence of AF after catheter ablation in Korean patients. Treatment of OSA for the sole indication of lowering AF recurrence may need to be reconsidered.
Large Cytoplasmic Vacuoles within Notochordal Nucleus Pulposus Cells: A Possible Regulator of Intracellular Pressure That Shapes the Cytoskeleton and Controls Proliferation

Degeneration of the intervertebral disc, which is closely associated with the loss of vacuolated notochordal nucleus pulposus cells (NNPC), remains a major cause of lower-back pain and motor deficiency. Being the most defining characteristic of NNPC, large cytoplasmic vacuoles not only modulate the cytoskeleton and shape cell morphology but they also respond to the disc microenvironment and regulate the biological behavior of vacuolated cells as a potent reporter of the histocytological changes that occur at the beginning of disc aging and degeneration. Here we hypothesize a model in which large cytoplasmic vacuoles primarily function to maintain a reasonable intracellular pressure (Pv) that facilitates NNPC in resisting the extracellular mechanical loading (Pe), part of which is absorbed by the extracellular matrix (Pm), forming the equation Pe = Pm + Pv. By mimicking a situation of contact-induced growth inhibition, the crowded cytoplasmic vacuoles slow down the proliferation of NNPC and restrain the generation of nonvacuolated chondrocytic nucleus pulposus cells (CNPC), whereas increased mechanical loading (↑Pe) alters cytoskeletons and breaches cytoplasmic vacuoles, which in turn weakens the vacuoles-mediated proliferation check, increases the generation of CNPC that accumulates fibrocartilaginous matrix, and rebalances the increased loading with elevated Pm (↑Pm) and lowered Pv (↓Pv), equating to ↑Pe = ↑Pm + ↓Pv. By depicting the biological function and the disappearance of the cytoplasmic vacuoles, our model highlights a mechanical exhaustion of the notochordal cell resources, which might help to elucidate the histocytological changes that initiate disc aging and degeneration.
How early media exposure may affect cognitive function: A review of results from observations in humans and experiments in mice

Attention deficit hyperactivity disorder (ADHD) is now among the most commonly diagnosed chronic psychological dysfunctions of childhood. By varying estimates, it has increased by 30% in the past 20 years. Environmental factors that might explain this increase have been explored. One such factor may be audiovisual media exposure during early childhood. Observational studies in humans have linked exposure to fast-paced television in the first 3 years of life with subsequent attentional deficits in later childhood. Although longitudinal and well controlled, the observational nature of these studies precludes definitive conclusions regarding a causal relationship. As experimental studies in humans are neither ethical nor practical, mouse models of excessive sensory stimulation (ESS) during childhood, akin to the enrichment studies that have previously shown benefits of stimulation in rodents, have been developed. Experimental studies using this model have corroborated that ESS leads to cognitive and behavioral deficits, some of which may be potentially detrimental. Given the ubiquity of media during childhood, these findings in humansand rodents perhaps have important implications for public health.
Percutaneous drainage of iliopsoas abscess: an effective option in cases not suitable for surgery

ABSTRACT The aim of this study were to describe the technique of percutaneous drainage of iliopsoas abscess, and to discuss the benefits of using this minimally-invasive tool. A single center study with retrospective analysis of patients with psoas abscess confirmed by imaging scans, sent to the interventional medicine center and submitted to computed tomography and ultrasound-guided percutaneous drainage, from November 2013 to August 2016. Seven patients underwent percutaneous drainage of psoas abscess in this period. The mean initial drained volume was 61.4±50.7mL (ranging from 10 to 130mL), and the mean drainage duration was 8.3±2.8 days (ranging from 4 to 12 days). The success rate of the percutaneous procedures was 71.5%, and two patients required re-intervention. Image-guided percutaneous drainage of iliopsoas abscess is a minimally invasive, efficient and safe procedure, and an extremely valuable technique, especially for patients who are not suitable for surgical repair.
Linking speciation to extinction: Diversification raises contemporary extinction risk in amphibians

Many of the traits associated with elevated rates of speciation, including niche specialization and having small and isolated populations, are similarly linked with an elevated risk of extinction. This suggests that rapidly speciating lineages may also be more extinction prone. Empirical tests of a speciation‐extinction correlation are rare because assessing paleontological extinction rates is difficult. However, the modern biodiversity crisis allows us to observe patterns of extinction in real time, and if this hypothesis is true then we would expect young clades that have recently diversified to have high contemporary extinction risk. Here, we examine evolutionary patterns of modern extinction risk across over 300 genera within one of the most threatened vertebrate classes, the Amphibia. Consistent with predictions, rapidly diversifying amphibian clades also had a greater share of threatened species. Curiously, this pattern is not reflected in other tetrapod classes and may reflect a greater propensity to speciate through peripheral isolation in amphibians, which is partly supported by a negative correlation between diversification rate and mean geographic range size. This clustered threat in rapidly diversifying amphibian genera means that protecting a small number of species can achieve large gains in preserving amphibian phylogenetic diversity. Nonindependence between speciation and extinction rates has many consequences for patterns of biodiversity and how we may choose to conserve it.
Mosquito (Diptera: Culicidae) Species Composition in Ovitraps From a Mesoamerican Tropical Montane Cloud Forest

Abstract Knowledge about mosquito species diversity at tropical montane cloud forests (TMCFs) in Mesoamerica is scarce. Here, we present data on mosquito species richness from samples biweekly collected, from January to December 2017, in ovitraps installed in aTMCF patch at Vázquez de Coronado County, Costa Rica. Ovitraps were placed at 2.25, 1.50 and 0.75 m at 16 sampling points. During the study period we measured relative humidity and air temperature at each sampling point, and water temperature, volume and pH in each ovitrap. We collected a total of 431 mosquito larvae belonging to five taxonomic units, one identified to the genus level and four to the species level. The most common mosquito species was Culex bihaicolus Dyar & Nuñez Tovar (Diptera: Culicidae), which accounted for nearly 80% (n = 344) of the collected mosquitoes. Culex nigripalpus Theobald (Diptera: Culicidae) was the only medically important species we found and it was collected both in the dry (January to March) and rainy season (April to December). Over 95% (n = 411) of the mosquitoes were collected during the rainy season and 60% (n = 257) at 0.75 m. Among the environmental variables that we measured, only water volume and pH were significantly (P < 0.05) different between the dry and rainy season, the former increasing and the later decreasing during the rainy season. These results suggest that rainfall plays a major role regulating the phenology of the sampled mosquito species and highlight the need to screen for pathogens in Cx. nigripalpus at the study area.
Updates in the Clinical Development of Epacadostat and Other Indoleamine 2,3-Dioxygenase 1 Inhibitors (IDO1) for Human Cancers

Recent application of immunotherapy in clinical oncology revolutionized our management of advanced human cancers. Check point inhibitors targeting CTLA4 and PD-1/PD-L1 axis are immunotherapeutic agents currently available to treat a variety of cancers. However, a novel therapeutic approach is needed to further improve patient outcome with these agents. Indoleamine 2,3-dioxygenase 1 (IDO1) is a rate-limiting enzyme in the metabolism of essential amino acid tryptophan in the peripheral tissue. IDO1 is overexpressed in human cancer cells and suppresses effector T cell function and promotes regulatory T cells (Tregs). Overexpression of IDO1 is associated with poor patient survival in several types of human cancer. These findings indicate that IDO1 is a promising target that can improve the treatment outcome in the field of Immuno-oncology. Several orally available IDO1 inhibitors including Epacadostat have entered human clinical trials over the last few years without a major safety concern. Although there is no objective response in single-agent trials, combination regimens with PD-1 inhibitors appear to exceed the activity of PD-1 inhibitors alone. Recent phase III ECHO 301 trial testing the combination of Epacadostat with Pembrolizumab in melanoma did not show superior outcome compared to Pembrolizumab alone. This lead to halting of other phase III trials using IDO1 inhibitors. In this minireview, we will discuss the recent clinical development of Epacadostat and other IDO1 inhibitors.
Changes in Implicit Alcohol Attitudes Across Adolescence, and Associations With Emerging Alcohol Use: Testing the Reciprocal Determinism Hypothesis

Implicit alcohol-related cognitions develop during adolescence and are thought to play an important role in the etiology of adolescent alcohol use. Rooted in reciprocal determinism, a developmental theory of alcohol-related cognitions, the current study sought to enhance our understanding of the development of automatic alcohol associations and their relationship with alcohol use. To provide a theoretically aligned test of reciprocal determinism, we used latent change score models to examine whether growth in automatic alcohol associations and alcohol use was related to each other (between-person effects) and whether each construct led to changes in the other over time (within-person effects). Adolescents (N = 378) completed 4 annual assessments, spanning early to middle adolescence. Automatic alcohol associations were assessed with a Single Category Implicit Association Test, and we used a quadruple processing tree model to extract a more “process pure” index of these associations. Alcohol use increased from early to middle adolescence, as negative automatic alcohol associations weakened over that same time period. Although there was no support for between-person associations, on the within-person level, weak negative automatic alcohol associations at Waves 2 and 3 were associated with increases in drinking at subsequent waves. Alcohol use did not significantly predict changes in automatic alcohol associations. Findings suggest the utility of distinguishing within- and between-person associations to understand the development of automatic alcohol associations and that automatic alcohol associations are prospectively associated with alcohol use and a potential target for intervention, one that becomes an increasingly salient influence on drinking as adolescence progresses.