Miracle-dz/UniFAR-FTUs huggingface dataset:
Effectiveness of the computerized balance rehabilitation after hip fracture surgery

Introduction: Although balance problems in older populations are directly correlated with hip fractures, the overall physical gain afforded by balance rehabilitation itself has not yet been fully investigated. Here we describe a protocol for an open-label clinical trial to evaluate the effectiveness of computer-based balance-specific exercise (BSE) on the performance and balance of elderly women who underwent hip fracture surgery (HFS). Methods and analysis: Elderly female patients (≥65 years old) who underwent surgery for femoral neck, intertrochanteric, or subtrochanteric fracture regardless of surgery type will be included. The BSE will be conducted using a computed posturographic system for a 2-week intervention period following HFS. The primary outcome of this study is Berg balance scale score. All functional outcomes will be measured at 1 and 3 weeks and at 3 and 6 months after the surgical intervention. The data will be analyzed using the intention-to-treat principle.
Evolution of Human Respiratory Syncytial Virus (RSV) over Multiple Seasons in New South Wales, Australia

There is an ongoing global pandemic of human respiratory syncytial virus (RSV) infection that results in substantial annual morbidity and mortality. In Australia, RSV is a major cause of acute lower respiratory tract infections (ALRI). Nevertheless, little is known about the extent and origins of the genetic diversity of RSV in Australia, nor the factors that shape this diversity. We have conducted a genome-scale analysis of RSV infections in New South Wales (NSW). RSV genomes were successfully sequenced for 144 specimens collected between 2010–2016. Of these, 64 belonged to the RSVA and 80 to the RSVB subtype. Phylogenetic analysis revealed a wide diversity of RSV lineages within NSW and that both subtypes evolved rapidly in a strongly clock-like manner, with mean rates of approximately 6–8 × 10−4 nucleotide substitutions per site per year. There was only weak evidence for geographic clustering of sequences, indicative of fluid patterns of transmission within the infected population and no evidence of any clustering by patient age such that viruses in the same lineages circulate through the entire host population. Importantly, we show that both subtypes circulated concurrently in NSW with multiple introductions into the Australian population in each year and only limited evidence for multi-year persistence.
Towards Automated Knowledge Discovery of Hepatocellular Carcinoma: Extract Patient Information from Chinese Clinical Reports

Objectives: To accurately determine significant prognostic risk factors, patient information must be quantified accurately according to their extent of disease. An essential step for prediction of prognostic risk factors requires the determination of patient features which are typically hidden in electronic medical record(EMR). The goal of this study is to extract clinical entities of Chinese clinical reports, enabling automated hepatocellular carcinoma knowledge extraction. Materials and Methods: In this paper, we annotated hepatocellular carcinoma corpora with patient records from EMR database. We present an information extraction solution based on assembled method. Our evaluation dataset contains 3996 training sentences and 1570 test sentences. The evaluation metrics are precision, recall, F1 of extract matching. Results and Conclusions: NER of admission reports, radiology reports and discharge summaries with F1 of 0.8449, 0.5935 and 0.7320 respectively. RE of overall F1 is 0.9129. This study prepares a foundation for larger population studies to identify clinical features of hepatocellular carcinoma.
Tunable Multipolar Fano Resonances and Electric Field Enhancements in Au Ring-Disk Plasmonic Nanostructures

We theoretically research the characteristics of tunable multipolar Fano resonances in novel-designed Au ring-disk plasmonic nanostructures. We systematically study some structural parameters that influence the multipolar Fano resonances of the nanostructures. Adjustment of the radius (R1 and R2) of the Au ring, the radius (R3) of the Au disk and the thickness (H) of the Au ring-disk can effectively adjust the multipolar Fano resonances. The complex field distributions excited by a Au ring-disk can produce dark resonance modes. At the frequency of the multipolar Fano resonances, strong localized field distributions can be obtained. The Fano resonances exhibit strong light-extinction properties in Au ring-disk nanostructures, which can be applied to an optical tunable filter and optical switch.
Toward a computational history of universities: Evaluating text mining methods for interdisciplinarity detection from PhD dissertation abstracts

For the first time, historians of higher education have large data sets of primary sources that reflect the complete output of academic institutions at their disposal. To analyze this unprecedented abundance of digital materials, scholars have access to a large suite of computational methods developed in the field of Natural Language Processing. However, when the intention is to move beyond exploratory studies and use the results of such analyses as quantitative evidences, historians need to take into account the reliability of these techniques. The main goal of this article is to investigate the performance of different text mining methods for a specific task: the automatic identification of interdisciplinary works from a corpus of PhD dissertation abstracts. Based on the output of our study, we provide the research community of a new data set for analyzing recent changes in interdisciplinary practices in a large sample of European universities. We show the potential of this collection by tracking the growth in adoption of computational approaches across different research fields, during the past 30 years.
Acute flaccid myelitis associated with enterovirus D68 infection

Rationale: We present the first case of enterovirus (EV) D68, lineage B3 infection, associated with acute flaccid myelitis (AFM) in Taiwan. AFM caused by EV D68 is relatively rare. This report highlights the importance of clinical recognition of the disease and discusses treatments that can benefit such patients. Patient concerns: A 5-year-old boy experienced sudden onset of acute flaccid paralysis (AFP) involving left arm after fever and respiratory symptoms for 3 days. Diagnoses: Magnetic resonance imaging (MRI) of the spinal cord revealed signal changes over segments C1 to T5 on a T2-weighted image (T2WI), compatible with the diagnosis of AFM. The EV D68 strain, cultured from the throat of the patient was identified. Interventions: We administered intravenous immunoglobulin (IVIG, 1g/kg, twice), pulse steroid therapy (methylprednisolone, 30 mg/kg, twice) and oral prednisolone (1mg/kg/day). Rehabilitation was also arranged. Outcomes: The patient still had mild muscle atrophy over left arm after following-up for 1 year. Lessons: Early diagnosis and prompt management are essential for managing this kind of patient. IVIG, pulse therapy, and oral prednisolone may play crucial roles in controlling its clinical course.
On Finding a First-Order Sentence Consistent with a Sample of Strings

We investigate the following problem: given a sample of classified strings, find a first-order sentence of minimal quantifier rank that is consistent with the sample. We represent strings as successor string structures, that is, finite structures with unary predicates to denote symbols in an alphabet, and a successor relation. We use results of the Ehrenfeucht-Fra\"iss\'e game over successor string structures in order to design an algorithm to find such sentence. We use conditions characterizing the winning strategies for the Spoiler on successor strings structures in order to define formulas which distinguish two strings. Our algorithm returns a boolean combination of such formulas.
Uremic Toxins Activates Na/K-ATPase Oxidant Amplification Loop Causing Phenotypic Changes in Adipocytes in In Vitro Models

Background: Oxidant stress plays a key role in the development of chronic kidney disease (CKD). Experimental CKD leads to accumulation of uremic toxins (UT) in the circulation resulting in increased ROS production, which in turn, is known to activate the Na/K-ATPase/ROS amplification loop. Studies in a murine model of obesity have shown that increased oxidative stress in plasma is due to increased ROS and cytokine production from dysfunctional adipocytes. Therefore, we hypothesized that adipocytes exposed to UTs will activate the Na/K-ATPase oxidant amplification loop causing redox imbalance and phenotypic alterations in adipocytes. We also aimed to demonstrate that the Na/K-ATPase signaling antagonist, pNaKtide, attenuates these pathophysiological consequences. Methods: In the first set of experiments, 3T3-L1 murine pre-adipocytes were treated with varying concentrations of UTs, indoxyl sulfate (IS) (50, 100 and 250 µM) and p-cresol (50, 100 and 200 µM), with or without pNaKtide (0.7 µM) for five days in adipogenic media, followed by Oil Red O staining to study adipogenesis. RT-PCR analysis was performed to study expression of adipogenic, apoptotic and inflammatory markers, while DHE staining evaluated the superoxide levels in UT treated cells. In a second set of experiments, visceral fat was obtained from the West Virginian population. MSCs were isolated and cultured in adipogenic media for 14 days, which was treated with indoxyl sulfate (0, 25, 50 and 100 µM) with or without pNaKtide (1 µM). MSC-derived adipocytes were evaluated for morphological and molecular analysis of the above markers. Results: Our results demonstrated that 3T3-L1 cells and MSCs-derived adipocytes, treated with UTs, exhibited a significant decrease in adipogenesis and apoptosis through activation of the Na/K-ATPase/ROS amplification loop. The treatment with pNaKtide in 3T3-L1 cells and MSC-derived adipocytes negated the effects of UTs and restored cellular redox in adipocytes. We noted a varying effect of pNaKtide, in adipocytes treated with UTs, on inflammatory markers, adipogenic marker and superoxide levels in 3T3-L1 cells and MSC-derived adipocytes. Conclusions: This study demonstrates for the first time that the Na/K-ATPase/ROS amplification loop activated by elevated levels of UTs has varying effect on phenotypic alterations in adipocytes in various in vitro models. Thus, we propose that, if proven in humans, inhibition of Na/K-ATPase amplification of oxidant stress in CKD patients may ultimately be a novel way to combat adipocyte dysfunction and metabolic imbalance in these patients.
Identifying Attributes That Influence In Vitro-to-In Vivo Concordance by Comparing In Vitro Tox21 Bioactivity Versus In Vivo DrugMatrix Transcriptomic Responses Across 130 Chemicals

Abstract Recent efforts aimed at integrating in vitro high-throughput screening (HTS) data into chemical toxicity assessments are necessitating increased understanding of concordance between chemical-induced responses observed in vitro versus in vivo. This investigation set out to (1) measure concordance between in vitro HTS data and transcriptomic responses observed in vivo, focusing on the liver, and (2) identify attributes that can influence concordance. Signal response profiles from 130 substances were compared between in vitro data produced through Tox21 and liver transcriptomic data through DrugMatrix, collected from rats exposed to a chemical for ≤5 days. A global in vitro-to-in vivo comparative analysis based on pathway-level responses resulted in an overall average percent agreement of 79%, ranging on a per-chemical basis between 41% and 100%. Whereas concordance amongst inactive chemicals was high (89%), concordance amongst chemicals showing in vitro activity was only 13%, suggesting that follow-up in vivo and/or orthogonal in vitro assays would improve interpretations of in vitro activity. Attributes identified to influence concordance included experimental design attributes (eg, cell type), target pathways, and physicochemical properties (eg, logP). The attribute that most consistently increased concordance was dose applicability, evaluated by filtering for experimental doses administered to rats that were within 10-fold of those related to likely bioactivity, derived using Tox21 data and high-throughput toxicokinetic modeling. Together, findings suggest that in vitro screening approaches to predict in vivo toxicity are viable particularly when certain attributes are considered, including whether activity versus inactivity is observed, experimental design, chemical properties, and dose applicability.
Gut Bacterial Communities of Dendroctonus valens and D. mexicanus (Curculionidae: Scolytinae): A Metagenomic Analysis across Different Geographical Locations in Mexico

Dendroctonus bark beetles are a worldwide significant pest of conifers. This genus comprises 20 species found in North and Central America, and Eurasia. Several studies have documented the microbiota associated with these bark beetles, but little is known regarding how the gut bacterial communities change across host range distribution. We use pyrosequencing to characterize the gut bacterial communities associated with six populations of Dendroctonus valens and D. mexicanus each across Mexico, determine the core bacteriome of both insects and infer the metabolic pathways of these communities with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to evaluate whether these routes are conserved across geographical locations. Our results show that the β-diversity with UniFrac unweighted varies among locations of both bark beetles mainly due to absence/presence of some rare taxa. No association is found between the pairwise phylogenetic distance of bacterial communities and geographic distance. A strict intraspecific core bacteriome is determined for each bark beetle species, but these cores are different in composition and abundance. However, both bark beetles share the interspecific core bacteriome recorded previously for the Dendroctonus genus consisting of Enterobacter, Pantoea, Providencia, Pseudomonas, Rahnella, and Serratia. The predictions of metabolic pathways are the same in the different localities, suggesting that they are conserved through the geographical locations.
Fast Gradient Attack on Network Embedding

Network embedding maps a network into a low-dimensional Euclidean space, and thus facilitate many network analysis tasks, such as node classification, link prediction and community detection etc, by utilizing machine learning methods. In social networks, we may pay special attention to user privacy, and would like to prevent some target nodes from being identified by such network analysis methods in certain cases. Inspired by successful adversarial attack on deep learning models, we propose a framework to generate adversarial networks based on the gradient information in Graph Convolutional Network (GCN). In particular, we extract the gradient of pairwise nodes based on the adversarial network, and select the pair of nodes with maximum absolute gradient to realize the Fast Gradient Attack (FGA) and update the adversarial network. This process is implemented iteratively and terminated until certain condition is satisfied, i.e., the number of modified links reaches certain predefined value. Comprehensive attacks, including unlimited attack, direct attack and indirect attack, are performed on six well-known network embedding methods. The experiments on real-world networks suggest that our proposed FGA behaves better than some baseline methods, i.e., the network embedding can be easily disturbed using FGA by only rewiring few links, achieving state-of-the-art attack performance.
CLASENTI

Arabic text sentiment analysis suffers from low accuracy due to Arabic-specific challenges (e.g., limited resources, morphological complexity, and dialects) and general linguistic issues (e.g., fuzziness, implicit sentiment, sarcasm, and spam). The limited resources problem requires efforts to build new and improved Arabic corpora and lexica. We propose a class-specific sentiment analysis (CLASENTI) framework. The framework includes a new annotation approach to build multi-faceted Arabic corpus and lexicon allowing for simultaneous annotation of different facets, including domains, dialects, linguistic issues, and polarity strengths. Each of these facets has multiple classes (e.g., the nine classes representing dialects found in the Arab world). The new corpus and lexicon annotations facilitate the development of new class-specific classification models and polarity strength calculation. For the new sentiment classification models, we propose a hybrid model combining corpus-based and lexicon-based models. The corpus-based model has two interrelated phases to build; (1) full-corpus classification models for all facets; and (2) class-specific models trained on filtered subsets of the corpus according to the performances of the full-corpus models. To calculate polarity strengths, the lexicon-based model filters the annotated lexicon based on the specific classes of the domain and dialect. As a case study, we collect and annotate 15274 reviews from various sources, including surveys, Facebook comments, and Twitter posts, pertaining to governmental services. In addition, we develop a new web-based application to apply the proposed framework on the case study. CLASENTI framework reaches up to 95% accuracy and 93% F1-Score surpassing the best-known sentiment classifiers implemented in Scikit-learn library that achieve 82% accuracy and 81% F1-Score for Arabic when tested on the same dataset.
A Magnetically-Triggered Soft Capsule for On-Demand Mucus Collection

In this work, we present a soft capsule for mucus collection in human intestine for diagnostic purpose, with reduced risk of tissue damage compared with other biopsy methods. The capsule implements passive locomotion and the sampling process is triggered by magnetic field using a permanent magnet, which is placed on the skin above the region of interest (ROI). The capsule contains a soft vacuum chamber which is sealed with wax. When magnetic field and mucus are present simultaneously, the circuit inside the capsule will be closed and nichrome wire will start to generate heat to melt the wax, and mucus will be collected into the vacuum chamber due to air pressure. Experiments on heating capability of nichrome wire, mucus collection and reliability of the capsule are conducted to validate this design.
Using PageRank for Characterizing Topic Quality in LDA

Topic models based on Latent Dirichlet Allocation (LDA) are employed effectively in various information retrieval and data mining tasks. Despite their popularity and wide-spread application, the question of assessing the quality of topics extracted by LDA models is still not completely resolved. While various measures have been proposed to quantify the thematic coherence and interpretability of a topic extracted by LDA, they do not address this problem sufficiently. We observe that existing quality measures select top topic words based on their topic-word co-occurrence without considering word co-occurrences within the same context. We incorporate precisely this information by constructing topic-specific graphs capturing neighborhood of words in an LDA modeled corpus. Next, the PageRank algorithm is applied on these graphs to assign word importance scores based on centrality. We propose two measures to compute topic quality: (1) the Aggregate PageRank of Top-words of a topic and (2) the PageRank Centralization Index of a topic-specific word graph. Our experiments across three datasets show that unlike existing quality measures, our proposed measures are able to identify topics that are discriminative as well as interpretable and yield superior performance on both classification and intruder word identification tasks.
Suppressing Interferon-γ Stimulates Microglial Responses and Repair of Microbleeds in the Diabetic Brain

Microcirculatory damage is a common complication for those with vascular risk factors, such as diabetes. To resolve vascular insults, the brain's immune cells (microglia) must rapidly envelop the site of injury. Currently, it is unknown whether Type 1 diabetes, a condition associated with chronic immune system dysfunction, alters microglial responses to damage and what mechanisms are responsible. Using in vivo two-photon microscopy in adult male mice, we show that microglial envelopment of laser-induced cerebral microbleeds is diminished in a hyperglycemic mouse model of Type 1 diabetes, which could not be fully rescued with chronic insulin treatment. Microglia were important for vessel repair because reduced microglial accumulation in diabetic mice or near-complete depletion in healthy controls was associated with greater secondary leakage of the damaged vessel. Broadly suppressing inflammation with dexamethasone in diabetic mice but not healthy controls, significantly enhanced microglial responses to microbleeds and attenuated secondary vessel leakage. These enhancements were associated with changes in IFN-γ signaling because dexamethasone suppressed abnormally high levels of IFN-γ protein levels in brain and blood serum of diabetic mice. Further, blocking IFN-γ in diabetic mice with neutralizing antibodies restored normal microglial chemotaxic responses and purinoceptor P2ry12 gene expression, as well as mitigated secondary leakage. These results suggest that abnormal IFN-γ signaling disrupts microglial function in the diabetic brain, and that immunotherapies targeting IFN-γ can stimulate microglial repair of damaged vessels. SIGNIFICANCE STATEMENT Although Type 1 diabetes is an established risk factor for vascular complications, such as microbleeds, and is known to hinder wound healing in the body, no study has examined how diabetes impacts the brain's innate immune reparative response (involving cells called microglia) to vascular injury. Here we show that microglial responses to brain microbleeds were diminished in diabetic animals, which also exacerbated secondary leakage from damaged vessels. These impairments were related to abnormally high levels of the proinflammatory cytokine IFN-γ because reducing IFN-γ with immunosuppressant drugs or blocking antibodies helped restore normal microglial responses and repair of damaged vessels. These data highlight the use of IFN-γ modulating therapeutics to enhance vascular repair in at-risk populations.