Miracle-dz/UniFAR-FTUs huggingface dataset:
Lens-specific deletion of the Msx2 gene increased apoptosis by enhancing the caspase-3/caspase-8 signaling pathway

Objective To investigate the influence of Msx2 conditional gene knockout during lens development in mice. Methods Lens-specific Msx2 knockout mice were generated using the Cre-loxP system. The eyes of Msx2 conditional knockout (Msx2CKO) and wild-type (Msx2WT) mice were examined during embryonic and early postnatal periods using histological, immunofluorescence, in situ hybridization, cell proliferation, apoptosis, and mRNA microarray analyses. Results Msx2CKO mice exhibited small lens formation and microphthalmia after birth, while Msx2CKO embryos exhibited a persistent lens stalk, small lens formation, and microphthalmia. Conditional deletion of Msx2 also led to an increased apoptosis rate, a significant reduction in FoxE3 expression, and an upregulation of Prox1 expression in the lens vesicle during the early embryonic period. Microarray comparison of Msx2CKO and Msx2WT lens transcriptomes identified a large number of differentially expressed genes. Real-time PCR showed that Casp8 and Casp3 expression was upregulated in Msx2CKO mice at post-natal day 1. Conclusion The activation of apoptosis through the caspase-8/caspase-3 signaling pathway, together with the downregulation of FoxE3 expression, appeared to account for the smaller lens formation in Msx2CKO mice.
Data Augmentation in Emotion Classification Using Generative Adversarial Networks

It is a difficult task to classify images with multiple class labels using only a small number of labeled examples, especially when the label (class) distribution is imbalanced. Emotion classification is such an example of imbalanced label distribution, because some classes of emotions like \emph{disgusted} are relatively rare comparing to other labels like {\it happy or sad}. In this paper, we propose a data augmentation method using generative adversarial networks (GAN). It can complement and complete the data manifold and find better margins between neighboring classes. Specifically, we design a framework with a CNN model as the classifier and a cycle-consistent adversarial networks (CycleGAN) as the generator. In order to avoid gradient vanishing problem, we employ the least-squared loss as adversarial loss. We also propose several evaluation methods on three benchmark datasets to validate GAN's performance. Empirical results show that we can obtain 5%~10% increase in the classification accuracy after employing the GAN-based data augmentation techniques.
Trainable Calibration Measures For Neural Networks From Kernel Mean Embeddings

Modern neural networks have recently been found to be poorly calibrated, primarily in the direction of over-conﬁdence. Methods like entropy penalty and temperature smoothing improve calibration by clamping conﬁdence, but in doing so compromise the many legitimately conﬁdent predictions. We propose a more principled ﬁx that minimizes an explicit calibration error during training. We present MMCE, a RKHS kernel based measure of calibration that is efﬁciently trainable alongside the negative likelihood loss without careful hyper-parameter tuning. Theoretically too, MMCE is a sound measure of calibration that is minimized at perfect calibration, and whose ﬁnite sample estimates are consistent and enjoy fast convergence rates. Extensive experiments on several network architectures demonstrate that MMCE is a fast, stable, and accurate method to minimize calibration error metrics while maximally preserving the number of high conﬁdence predictions.
Effects of Intrinsic Factors on the Clinical Pharmacokinetics of Vortioxetine

Vortioxetine is an antidepressant agent with multimodal activity that is approved for the treatment of major depressive disorder at doses of 5 to 20 mg once daily. Vortioxetine is a medium‐clearance drug that undergoes extensive metabolism via several cytochrome P450 isozymes. A series of single‐ and multiple‐dose pharmacokinetic studies were performed to evaluate the impact of intrinsic (ie, subject‐related) factors, such as age, sex, race, and renal and hepatic function, on the pharmacokinetics of vortioxetine. The point estimates on the ratios and their 90% confidence intervals (CIs) for the central values of AUC (area under the concentration‐time curve) and Cmax (maximum plasma concentration) were obtained by taking the antilog of the differences and 90%CIs in the log‐transformed least‐squares means. The results demonstrate that there were no clinically meaningful differences (defined as exposure difference between 50% and 2‐fold change) in the exposure to vortioxetine (as assessed by AUC and Cmax) between elderly and younger subjects, men and women, and blacks and whites and among subjects with varying degrees of renal or hepatic impairment. These results suggest that no dosing adjustments of vortioxetine are required for the intrinsic factors investigated in these studies.
Thermal Sensations During a Partial-Body Cryostimulation Exposure in Elite Basketball Players

Abstract Partial-body cryostimulation is used to improve recovery after exercise, especially during competitions or heavy training; however, a limited number of studies have been conducted with international-level athletes in situ during competitions. This study was undertaken to assess the thermal sensation ratings during 3 min of cold exposure (at –130°C) in 24 international-level athletes during the European Basketball Championship. The mean thermal sensation score, measured using a perceptive scale, increased significantly (p < 0.05) during partial-body cryostimulation exposure in athletes from 3.0 ± 1.7 at 30 s to 5.7 ± 2.3 at 3 min (maximal observed value = 10.0). The mean value of 5.7 is considered a “cold” sensation on the scale (ranging from 0 = neutral sensation to 10 = very cold). However, we observed a large inter-individual variation in the perceived thermal sensations. The body mass index was significantly and negatively correlated with the thermal sensation value after 2 min 30 s and 3 min of exposure in females (r = –0.61, n = 13, p < 0.05; r = –0.56, n = 13, p = 0.054, respectively). Three participants reported high perceived thermal sensation after 30 s of exposure and their cold-induced discomfort worsened as the exposure continued. In conclusion, a 3-min exposure is globally well tolerated by athletes and can be used during a heavy competition period and/or during a training period. However, special attention should be given to female athletes with a low body mass index as they seem to be much more sensitive to cold.
Neural Code Comprehension: A Learnable Representation of Code Semantics

With the recent success of embeddings in natural language processing, research has been conducted into applying similar methods to code analysis. Most works attempt to process the code directly or use a syntactic tree representation, treating it like sentences written in a natural language. However, none of the existing methods are sufficient to comprehend program semantics robustly, due to structural features such as function calls, branching, and interchangeable order of statements. In this paper, we propose a novel processing technique to learn code semantics, and apply it to a variety of program analysis tasks. In particular, we stipulate that a robust distributional hypothesis of code applies to both human- and machine-generated programs. Following this hypothesis, we define an embedding space, inst2vec, based on an Intermediate Representation (IR) of the code that is independent of the source programming language. We provide a novel definition of contextual flow for this IR, leveraging both the underlying data- and control-flow of the program. We then analyze the embeddings qualitatively using analogies and clustering, and evaluate the learned representation on three different high-level tasks. We show that even without fine-tuning, a single RNN architecture and fixed inst2vec embeddings outperform specialized approaches for performance prediction (compute device mapping, optimal thread coarsening); and algorithm classification from raw code (104 classes), where we set a new state-of-the-art.
Insights From the Geographic Spread of the Lyme Disease Epidemic

Background Lyme disease is the most common reportable zoonotic infection in the United States. Recent data suggest spread of the Ixodes tick vector and increasing incidence of Lyme disease in several states, including Pennsylvania. We sought to determine the clinical presentation and healthcare use patterns for pediatric Lyme disease in western Pennsylvania. Methods The electronic medical records of all patients with an International Classification of Disease, Ninth Revision, diagnosis of Lyme disease between 2003 and 2013 at Children's Hospital of Pittsburgh were individually reviewed to identify confirmed cases of Lyme disease. The records of 773 patients meeting these criteria were retrospectively analyzed for patient demographics, disease manifestations, and healthcare use. Results An Lyme disease increased exponentially in the pediatric population of western Pennsylvania. There was a southwestward migration of Lyme disease cases, with a shift from rural to nonrural zip codes. Healthcare provider involvement evolved from subspecialists to primary care pediatricians and emergency departments (EDs). Patients from nonrural zip codes more commonly presented to the ED, while patients from rural zip codes used primary care pediatricians and EDs equally. Conclusions The current study details the conversion of western Pennsylvania from a Lyme-naive to a Lyme-epidemic area, highlighting changes in clinical presentation and healthcare use over time. Presenting symptoms and provider type differed between those from rural and nonrural zip codes. By elucidating the temporospatial epidemiology and healthcare use for pediatric Lyme disease, the current study may inform public health measures regionally while serving as an archetype for other areas at-risk for Lyme disease epidemics.
Rpp29 regulates histone H3.3 chromatin assembly through transcriptional mechanisms

The histone H3 variant H3.3 is a highly conserved and dynamic regulator of chromatin organization. Therefore, fully elucidating its nucleosome incorporation mechanisms is essential to understanding its functions in epigenetic inheritance. We previously identified the RNase P protein subunit, Rpp29, as a repressor of H3.3 chromatin assembly. Here, we use a biochemical assay to show that Rpp29 interacts with H3.3 through a sequence element in its own N terminus, and we identify a novel interaction with histone H2B at an adjacent site. The fact that archaeal Rpp29 does not include this N-terminal region suggests that it evolved to regulate eukaryote-specific functions. Oncogenic H3.3 mutations alter the H3.3–Rpp29 interaction, which suggests that they could dysregulate Rpp29 function in chromatin assembly. We also used KNS42 cells, an H3.3(G34V) pediatric high-grade glioma cell line, to show that Rpp29 1) represses H3.3 incorporation into transcriptionally active protein-coding, rRNA, and tRNA genes; 2) represses mRNA, protein expression, and antisense RNA; and 3) represses euchromatic post-translational modifications (PTMs) and promotes heterochromatic PTM deposition (i.e. histone H3 Lys-9 trimethylation (H3K9me3) and H3.1/2/3K27me3). Notably, we also found that K27me2 is increased and K36me1 decreased on H3.3(G34V), which suggests that Gly-34 mutations dysregulate Lys-27 and Lys-36 methylation in cis. The fact that Rpp29 represses H3.3 chromatin assembly and sense and antisense RNA and promotes H3K9me3 and H3K27me3 suggests that Rpp29 regulates H3.3-mediated epigenetic mechanisms by processing a transcribed signal that recruits H3.3 to its incorporation sites.
Down-regulation of microRNA-23b aggravates LPS-induced inflammatory injury in chondrogenic ATDC5 cells by targeting PDCD4

Objective(s): Osteoarthritis (OA), characterized by degradation of articular cartilage, is a leading cause of disability. As the only cell type present in cartilage, chondrocytes play curial roles in the progression of OA. In our study, we aimed to explore the roles of miR-23b in the lipopolysaccharide (LPS)-induced inflammatory injury. Materials and Methods: LPS-induced cell injury of ATDC5 cells was evaluated by the loss of cell viability, enhancement of cell apoptosis, alteration of apoptosis-associated proteins, and release of inflammatory cytokines. Then, miR-23b level after LPS treatment was assessed by qRT-PCR. Next, the effects of aberrantly expressed miR-23b on the LPS-induced inflammatory injury were explored. The possible target genes of miR-23b were virtually screened by informatics and verified by luciferase assay. Subsequently, whether miR-23b functioned through regulating the target gene was validated. The involved signaling pathways were investigated finally. Results: Cell viability was decreased but cell apoptosis, as well as release of inflammatory cytokines, was enhanced by LPS treatment. MiR-23b was down-regulated by LPS and its overexpression alleviated LPS-induced inflammatory injury. PDCD4, negatively regulated by miR-23b expression, was verified as a target gene of miR-23b. Following experiments showed miR-23b alleviated LPS-induced cell injury through down-regulating PDCD4 expression. Phosphorylated levels of key kinases in the NF-κB pathway, as well as expressions of key kinases in the Notch pathways, were increased by PDCD4 overexpression. Conclusion: MiR-23b was down-regulated after LPS treatment, and its overexpression ameliorated LPS-induced inflammatory injury in ATDC5 cells by targeting PDCD4, which could activate the NF-κB/Notch pathways.
Future of 3D printing: How 3D bioprinting technology can revolutionize healthcare?

Currently there are more than 2,000 children on the transplant waiting list—and more than 100,000 Americans nationwide—awaiting a matching organ. Most children aged one through 10 are awaiting a kidney, liver, or heart. As with any transplant, there are two ways to find an organ—someone can donate or someone can die. Unfortunately, the supply falls far short of the demand, leaving people to die every day waiting for a second chance at life. Scientific and medical experts, however, continue to develop promising technology like 3D bioprinting that could save thousands of lives without the need of a donor.
Which Plants Used in Ethnomedicine Are Characterized? Phylogenetic Patterns in Traditional Use Related to Research Effort

Plants are important resources in healthcare and for producing pharmaceutical drugs. Pharmacological and phytochemical characterization contributes to both the safe use of herbal medicines and the identification of leads for drug development. However, there is no recent assessment of the proportion of plants used in ethnomedicine that are characterized in this way. Further, although it is increasingly apparent that plants used in ethnomedicine belong to preferred phylogenetic lineages, it is not known how this relates to the focusing of research effort. Here we identify species and lineages rich in ethnomedicinal use and develop methods to describe how well they are known pharmacologically and/or phytochemically. We find 50% of plant species of the family Leguminosae used in ethnomedicine in Brazil, a geographical area where plants are an important part of healthcare, have been the focus of either phytochemical screening or testing for biological activity. Plant species which have more use reports are studied significantly more often (p < 0.05). Considering the taxonomic distribution of use, 70% of genera that include species with ethnomedicinal use have been studied, compared to 19% of genera with no reported use. Using a novel phylogenetic framework, we show that lineages with significantly greater numbers of ethnomedicinal species are phylogenetically over-dispersed within the family, highlighting the diversity of species used. “Hotnode clades” contain 16% of species but 46% of ethnomedicinally-used species. The ethnomedicinal species in hotnode clades have more use reports per species (p < 0.05), suggesting they are more frequently used. They are also more likely to be characterized pharmacologically and/or phytochemically. Research focus has followed traditional use by these measures, at least for these Brazilian plants, yet ethnomedicinal species yielding candidate drugs, raising public health concerns and more intensively studied lie outside of the hotnode clades.
A Proposed Propagation-Based Methodology with Which to Address the Hidden Node Problem and Security/Reliability Issues in Cognitive Radio

A highly accurate, fast and robust integral equation-based propagation method is presented here. It is explained how this method, in conjunction with a radio environment mapping server can be used to address the dasiahidden node problempsila and salient security/reliability issues in cognitive radio (CR) by accurately quantifying the effects or CR transmissions in realtime thus allaying the legitimate concerns of primary users regarding the deployment of CR technology. A roadmap for the development of the propagation method is given such that sufficient accuracy and execution times can be achieved.
Learning from Chunk-based Feedback in Neural Machine Translation

We empirically investigate learning from partial feedback in neural machine translation (NMT), when partial feedback is collected by asking users to highlight a correct chunk of a translation. We propose a simple and effective way of utilizing such feedback in NMT training. We demonstrate how the common machine translation problem of domain mismatch between training and deployment can be reduced solely based on chunk-level user feedback. We conduct a series of simulation experiments to test the effectiveness of the proposed method. Our results show that chunk-level feedback outperforms sentence based feedback by up to 2.61% BLEU absolute.
Whole-body 18F-fluorodeoxyglucose positron emission tomography-computed tomography (18F-FDG PET/CT) for staging locally advanced breast cancer: A prospective study from a tertiary cancer centre in south India

Background & objectives: Locally advanced breast cancer (LABC) is associated with substantial risk of occult metastases. The patients with LABC have high rate of systemic relapse, suggesting inadequacy of the current conventional staging in detecting the occult metastatic spread. 18F-fluorodeoxyglucose (FDG) positron emission tomography-computed tomography (PET/CT) is a new modality in the staging of breast cancer patients. Hence, this study was conducted to evaluate the role of 18F-FDG PET/CT in initial staging of LABC and to compare it with conventional methods. Methods: This prospective study included biopsy-confirmed female patients diagnosed with LABC meeting the selection criteria and attending surgical, medical and radiation oncology departments of a tertiary care centre in south India, from April 2013 to December 2014. Conventional workup included serum chemistry, mammogram, bone scan, contrast-enhanced CT (CECT) chest and upper abdomen and ultrasound abdomen and pelvis. All patients following conventional workup underwent 18F-FDG PET/CT. Results: In this study, 61 women with LABC underwent both conventional workup and 18F-FGD PET/CT. The 18F-FDG PET/CT, in comparison to conventional workup, revealed unsuspected N3 nodal disease in 11 more patients, revealed distant metastasis in seven more patients and also detected extra sites of metastasis in five patients. The sensitivity, specificity, positive predictive value, negative predictive value and accuracy of PET/CT to detect distant metastasis were 95, 98, 95, 98 and 97 per cent, respectively, whereas the sensitivity, specificity, positive predictive value, negative predictive value and accuracy of conventional imaging to detect distant metastasis were 65, 93, 81, 84 and 84 per cent, respectively. Interpretation & conclusions: The 18F-FDG PET/CT was found to be more accurate than conventional imaging for staging and modified stage and treatment in 30 and 38 per cent of patients, respectively. It was particularly useful in detecting occult distant metastasis and N3 nodal disease with an added advantage of examining whole body in single session. However, CECT chest was superior over 18F-FDG PET/CT for detecting pulmonary metastasis.
Threshold Models of Collective Behavior

Models of collective behavior are developed for situations where actors have two alternatives and the costs and/or benefits of each depend on how many other actors choose which alternative. The key concept is that of "threshold": the number or proportion of others who must make one decision before a given actor does so; this is the point where net benefits begin to exceed net costs for that particular actor. Beginning with a frequency distribution of thresholds, the models allow calculation of the ultimate or "equilibrium" number making each decision. The stability of equilibrium results against various possible changes in threshold distributions is considered. Stress is placed on the importance of exact distributions distributions for outcomes. Groups with similar average preferences may generate very different results; hence it is hazardous to infer individual dispositions from aggregate outcomes or to assume that behavior was directed by ultimately agreed-upon norms. Suggested applications are to riot behavior, innovation and rumor diffusion, strikes, voting, and migration. Issues of measurement, falsification, and verification are discussed.
Fluid Sketching―Immersive Sketching Based on Fluid Flow

Fluid artwork refers to works of art based on the aesthetics of fluid motion, such as smoke photography, ink injection into water, and paper marbling. Inspired by such types of art, we created Fluid Sketching as a novel medium for creating 3D fluid artwork in immersive virtual environments. It allows artists to draw 3D fluid-like sketches and manipulate them via six degrees of freedom input devices. Different brush stroke settings are available, varying the characteristics of the fluid. Because of fluids' nature, the diffusion of the drawn fluid sketch is animated, and artists have control over altering the fluid properties and stopping the diffusion process whenever they are satisfied with the current result. Furthermore, they can shape the drawn sketch by directly interacting with it, either with their hand or by blowing into the fluid. We rely on particle advection via curl-noise as a fast procedural method for animating the fluid flow.
Changes in Injury Risk Mechanisms after Soccer-Specific Fatigue in Male Youth Soccer Players

Abstract The aim of this study was to examine the acute effects of soccer specific fatigue on muscular and neuromuscular function in male youth soccer players. Elite soccer players (n = 20; age 15.7 ± 0.5 y; body height 177.75 ± 6.61 cm; body mass 67.28 ± 8.29 kg) were measured before and after soccer specific exercise (SAFT90). The reactive strength index (RSI) was determined by a drop jump test, leg stiffness (LS) by a 20 sub-maximal two-legged hopping test, and a functional hamstring to quadriceps strength ratio from isokinetic concentric and eccentric strength of the dominant and non-dominant leg (measured at angular velocities of 1.05 rad · s−1 and 3.14 rad · s−1). Metabolic response to the SAFT90 was determined by blood lactate and perceived exertion was assessed by the Borg scale. After simulated match play, a significant decrease in absolute LS (t = 4.411; p < 0.001; ω2 = 0.48) and relative LS (t = 4.326; p < 0.001; ω2 = 0.49) was observed and the RSI increased significantly (t = 3.806; p = 0.001; ω2 = 0.40). A reduction in LS found after the SAFT90 indicates possible reduction in dynamic knee stabilization. However, if we consider the changes in other observed variables, the present study did not clearly confirm that fatigue induced by a soccer specific protocol increased the risk of ACL and hamstring injury. This may be attributed to the simulated rather than actual match play used in the present study.