Miracle-dz/UniFAR-FTUs huggingface dataset:
Ultrasound- versus Palpation-Guided Injection of Corticosteroid for Plantar Fasciitis: A Meta-Analysis

Background It is controversial whether ultrasound-guided injection of corticosteroid is superior to palpation-guided injection for plantar fasciitis. This meta-analysis was performed to compare the effectiveness of ultrasound-guided and palpation-guided injection of corticosteroid for the treatment of plantar fasciitis. Methods Databases (MEDLINE, Cochrane library and EMBASE) and reference lists were searched from their establishment to August 30, 2013 for randomized controlled trials (RCTs) comparing ultrasound-guided with palpation-guided injection for plantar fasciitis. The Cochrane risk of bias (ROB) tool was used to assess the methodological quality. Outcome measurements were visual analogue scale (VAS), tenderness threshold (TT), heel tenderness index (HTI), response rate, plantar fascia thickness (PFT), hypoechogenicity and heel pad thickness (HPT). The statistical analysis was performed with software RevMan 5.2 and Stata 12.0. When I2<50%, the fixed-effects model was adopted. Otherwise the randomized-effects model was adopted. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) system was used to assess the quality of evidence. Results Five RCTs with 149 patients were identified and analyzed. Compared with palpation-guided injection, ultrasound-guided injection was superior with regard to VAS, TT, response rate, PFT and hypoechogenicity. However, there was no statistical significance between the two groups for HPT and HTI. Conclusion Ultrasound-guided injection of corticosteroid tends to be more effective than palpation-guided injection. However, it needs to be confirmed by further research.
Model-Based Planning with Discrete and Continuous Actions

Action planning using learned and differentiable forward models of the world is a general approach which has a number of desirable properties, including improved sample complexity over model-free RL methods, reuse of learned models across different tasks, and the ability to perform efficient gradient-based optimization in continuous action spaces. However, this approach does not apply straightforwardly when the action space is discrete. In this work, we show that it is in fact possible to effectively perform planning via backprop in discrete action spaces, using a simple paramaterization of the actions vectors on the simplex combined with input noise when training the forward model. Our experiments show that this approach can match or outperform model-free RL and discrete planning methods on gridworld navigation tasks in terms of performance and/or planning time while using limited environment interactions, and can additionally be used to perform model-based control in a challenging new task where the action space combines discrete and continuous actions. We furthermore propose a policy distillation approach which yields a fast policy network which can be used at inference time, removing the need for an iterative planning procedure.
Exploring the Human-Nipah Virus Protein-Protein Interactome

ABSTRACT Nipah virus is an emerging, highly pathogenic, zoonotic virus of the Paramyxoviridae family. Human transmission occurs by close contact with infected animals, the consumption of contaminated food, or, occasionally, via other infected individuals. Currently, we lack therapeutic or prophylactic treatments for Nipah virus. To develop these agents we must now improve our understanding of the host-virus interactions that underpin a productive infection. This aim led us to perform the present work, in which we identified 101 human-Nipah virus protein-protein interactions (PPIs), most of which (88) are novel. This data set provides a comprehensive view of the host complexes that are manipulated by viral proteins. Host targets include the PRP19 complex and the microRNA (miRNA) processing machinery. Furthermore, we explored the biologic consequences of the interaction with the PRP19 complex and found that the Nipah virus W protein is capable of altering p53 control and gene expression. We anticipate that these data will help in guiding the development of novel interventional strategies to counter this emerging viral threat. IMPORTANCE Nipah virus is a recently discovered virus that infects a wide range of mammals, including humans. Since its discovery there have been yearly outbreaks, and in some of them the mortality rate has reached 100% of the confirmed cases. However, the study of Nipah virus has been largely neglected, and currently we lack treatments for this infection. To develop these agents we must now improve our understanding of the host-virus interactions that underpin a productive infection. In the present work, we identified 101 human-Nipah virus protein-protein interactions using an affinity purification approach coupled with mass spectrometry. Additionally, we explored the cellular consequences of some of these interactions. Globally, this data set offers a comprehensive and detailed view of the host machinery's contribution to the Nipah virus's life cycle. Furthermore, our data present a large number of putative drug targets that could be exploited for the treatment of this infection.
Metabolomic Biomarkers in Serum and Urine in Women with Preeclampsia

Objective To explore the potential of magnetic resonance (MR) metabolomics for study of preeclampsia, for improved phenotyping and elucidating potential clues to etiology and pathogenesis. Methods Urine and serum samples from pregnant women with preeclampsia (n = 10), normal pregnancies (n = 10) and non-pregnant women (n = 10) matched by age and gestational age were analyzed with MR spectroscopy and subjected to multivariate analysis. Metabolites were then quantified and compared between groups. Results Urine and serum samples revealed clear differences between women with preeclampsia and both control groups (normal pregnant and non-pregnant women). Nine urine metabolites were significantly different between preeclampsia and the normal pregnant group. Urine samples from women with early onset preeclampsia clustered together in the multivariate analysis. The preeclampsia serum spectra showed higher levels of low and very-low density lipoproteins and lower levels of high-density lipoproteins when compared to both non-pregnant and normal pregnant women. Conclusion The MR determined metabolic profiles in urine and serum from women with preeclampsia are clearly different from normal pregnant women. The observed differences represent a potential to examine mechanisms underlying different preeclampsia phenotypes in urine and serum samples in larger studies. In addition, similarities between preeclampsia and cardiovascular disease in metabolomics are demonstrated.
Polyurethane damping material

The mechanical and damping properties of thermoplastic polyurethanes (TPUs) prepared by polyether–aromatic polyester polyols were studied. Dynamic viscoelastic properties (E′ and tan δ) were mainly investigated using a dynamical mechanical analysis. By increasing the content of the aromatic ester component of soft segment in each segmented PU, the value of tan δ increased, and the width of the peak narrowed with the same hard segment contents. It was desired that interaction between hard and soft segment in U-Fine (UF)-A and UF-B is uniform, and the degree of phase separation between hard and soft segment in UF-A and UF-B advanced in comparison with TPU-A. Tensile strength and abrasion resistance of UF-B (ester component content of polyether–ester polyol = 20.3 mol%) showed superior data compared with other commercial damping materials.
No Evidence for the Effect of MHC on Male Mating Success in the Brown Bear

Mate choice is thought to contribute to the maintenance of the spectacularly high polymorphism of the Major Histocompatibility Complex (MHC) genes, along with balancing selection from parasites, but the relative contribution of the former mechanism is debated. Here, we investigated the association between male MHC genotype and mating success in the brown bear. We analysed fragments of sequences coding for the peptide-binding region of the highly polymorphic MHC class I and class II DRB genes, while controlling for genome-wide effects using a panel of 18 microsatellite markers. Male mating success did not depend on the number of alleles shared with the female or amino-acid distance between potential mates at either locus. Furthermore, we found no indication of female mating preferences for MHC similarity being contingent on the number of alleles the females carried. Finally, we found no significant association between the number of MHC alleles a male carried and his mating success. Thus, our results provided no support for the role of mate choice in shaping MHC polymorphism in the brown bear.
Crotoxin stimulates an M1 activation profile in murine macrophages during Leishmania amazonensis infection

SUMMARY American tegumentary leishmaniasis is caused by different species of Leishmania. This protozoan employs several mechanisms to subvert the microbicidal activity of macrophages and, given the limited efficacy of current therapies, the development of alternative treatments is essential. Animal venoms are known to exhibit a variety of pharmacological activities, including antiparasitic effects. Crotoxin (CTX) is the main component of Crotalus durissus terrificus venom, and it has several biological effects. Nevertheless, there is no report of CTX activity during macrophage – Leishmania interactions. Thus, the main objective of this study was to evaluate whether CTX has a role in macrophage M1 polarization during Leishmania infection murine macrophages, Leishmania amazonensis promastigotes and L. amazonensis-infected macrophages were challenged with CTX. MTT [3-(4,5dimethylthiazol-2-yl)-2,5-diphenyl tetrasodium bromide] toxicity assays were performed on murine macrophages, and no damage was observed in these cells. Promastigotes, however, were affected by treatment with CTX (IC50 = 22·86 µg mL−1) as were intracellular amastigotes. Macrophages treated with CTX also demonstrated increased reactive oxygen species production. After they were infected with Leishmania, macrophages exhibited an increase in nitric oxide production that converged into an M1 activation profile, as suggested by their elevated production of the cytokines interleukin-6 and tumour necrosis factor-α and changes in their morphology. CTX was able to reverse the L. amazonensis-mediated inhibition of macrophage immune responses and is capable of polarizing macrophages to the M1 profile, which is associated with a better prognosis for cutaneous leishmaniasis treatment.
Computer Vision and Image Understanding

Removing the inﬂuence of occlusion on the depth estimation for light ﬁeld images has always been a diﬃcult problem, especially for highly noisy and aliased images captured by plenoptic cameras. In this paper, a spinning parallelogram operator (SPO) is integrated into a depth estimation framework to solve these problems. Utilizing the regions divided by the operator in an Epipolar Plane Image (EPI), the lines that indicate depth information are located by maximizing the distribution distances of the regions. Unlike traditional multi-view stereo matching methods, the distance measure is able to keep the correct depth information even if they are occluded or noisy. We further choose the relative reliable information among the rich structures in the light ﬁeld to reduce the inﬂuences of occlusion and ambiguity. The discrete labeling problem is then solved by a ﬁlter-based algorithm to fast approximate the optimal solution. The major advantage of the proposed method is that it is insensitive to occlusion, noise, and aliasing, and has no requirement for depth range and angular resolution. It therefore can be used in various light ﬁeld images, especially in plenoptic camera images. Experimental results demonstrate that the proposed method outperforms state-of-the-art depth estimation methods on light ﬁeld images, including both real world images and synthetic images, especially near occlusion boundaries.
A middle school instructional unit for size and scale contextualized in nanotechnology

Abstract Size and scale is a “big idea” in nanoscale science and engineering and is poorly understood by secondary students. This paper describes the design process, implementation, and evaluation of a 12-h instructional unit for size and scale, in a summer science camp for middle school students from a low SES public school district. Instructional activities were designed following a construct-centered design approach and included the use of microscopes, custom-made computer simulations, and 2-D and 3-D scale models. The unit followed a project-based instructional approach and was contextualized with the driving question, “How can nanotechnology keep me from getting sick? ” Pre- and post-intervention interviews revealed that students significantly increased their qualitative and quantitative knowledge of the size of objects including atom, viruses, and cells, with an effect size of 0.8 for an overall metric. The campers closed the gap with private middle school students and on some measures surpassed high school students from the same district. The principle of “broad spectrum” curriculum and instruction – activities that target specific advanced understandings but simultaneously scaffold or support the learning of more fundamental, prerequisite ideas – was inductively generated from an analysis of the learning activities.
Treatment Effect of Balloon Pulmonary Angioplasty in Chronic Thromboembolic Pulmonary Hypertension Quantified by Automatic Comparative Imaging in Computed Tomography Pulmonary Angiography

Objectives Balloon pulmonary angioplasty (BPA) in patients with inoperable chronic thromboembolic pulmonary hypertension (CTEPH) can have variable outcomes. To gain more insight into this variation, we designed a method for visualizing and quantifying changes in pulmonary perfusion by automatically comparing computed tomography (CT) pulmonary angiography before and after BPA treatment. We validated these quantifications of perfusion changes against hemodynamic changes measured with right-sided heart catheterization. Materials and Methods We studied 14 consecutive CTEPH patients (12 women; age, 70.5 ± 24), who underwent CT pulmonary angiography and right-sided heart catheterization, before and after BPA. Posttreatment images were registered to pretreatment CT scans (using the Elastix toolbox) to obtain corresponding locations. Pulmonary vascular trees and their centerlines were detected using a graph cuts method and a distance transform method, respectively. Areas distal from vessels were defined as pulmonary parenchyma. Subsequently, the density changes within the vascular centerlines and parenchymal areas were calculated and corrected for inspiration level differences. For visualization, the densitometric changes were displayed in color-coded overlays. For quantification, the median and interquartile range of the density changes in the vascular and parenchymal areas (&Dgr;VD and &Dgr;PD) were calculated. The recorded changes in hemodynamic parameters, including changes in systolic, diastolic, and mean pulmonary artery pressure (&Dgr;sPAP, &Dgr;dPAP, and &Dgr;mPAP, respectively) and vascular resistance (&Dgr;PVR), were used as reference assessments of the treatment effect. Spearman correlation coefficients were employed to investigate the correlations between changes in perfusion and hemodynamic changes. Results Comparative imaging maps showed distinct patterns in perfusion changes among patients. Within pulmonary vessels, the interquartile range of &Dgr;VD correlated significantly with &Dgr;sPAP (R = −0.58, P = 0.03), &Dgr;dPAP (R = −0.71, P = 0.005), &Dgr;mPAP (R = −0.71, P = 0.005), and &Dgr;PVR (R = −0.77, P = 0.001). In the parenchyma, the median of &Dgr;PD had significant correlations with &Dgr;dPAP (R = −0.58, P = 0.030) and &Dgr;mPAP (R = −0.59, P = 0.025). Conclusions Comparative imaging analysis in CTEPH patients offers insight into differences in BPA treatment effect. Quantification of perfusion changes provides noninvasive measures that reflect hemodynamic changes.
Regulation of Cardiac Expression of the Diabetic Marker MicroRNA miR-29

Diabetes mellitus (DM) is an independent risk factor for heart disease and its underlying mechanisms are unclear. Increased expression of diabetic marker miR-29 family miRNAs (miR-29a, b and c) that suppress the pro-survival protein Myeloid Cell Leukemia 1(MCL-1) is reported in pancreatic β-cells in Type 1 DM. Whether an up-regulation of miR-29 family miRNAs and suppression of MCL-1 (dysregulation of miR-29-MCL-1 axis) occurs in diabetic heart is not known. This study tested the hypothesis that insulin regulates cardiac miR-29-MCL-1 axis and its dysregulation correlates with DM progression. In vitro studies with mouse cardiomyocyte HL-1 cells showed that insulin suppressed the expression of miR-29a, b and c and increased MCL-1 mRNA. Conversely, Rapamycin (Rap), a drug implicated in the new onset DM, increased the expression of miR-29a, b and c and suppressed MCL-1 and this effect was reversed by transfection with miR-29 inhibitors. Rap inhibited mammalian target of rapamycin complex 1 (mTORC1) signaling in HL-1 cells. Moreover, inhibition of either mTORC1 substrate S6K1 by PF-4708671, or eIF4E-induced translation by 4E1RCat suppressed MCL-1. We used Zucker diabetic fatty (ZDF) rat, a rodent model for DM, to test whether dysregulation of cardiac miR-29-MCL-1 axis correlates with DM progression. 11-week old ZDF rats exhibited significantly increased body weight, plasma glucose, insulin, cholesterol, triglycerides, body fat, heart weight, and decreased lean muscle mass compared to age-matched lean rats. Rap treatment (1.2 mg/kg/day, from 9-weeks to 15-weeks) significantly reduced plasma insulin, body weight and heart weight, and severely dysregulated cardiac miR-29-MCL1 axis in ZDF rats. Importantly, dysregulation of cardiac miR-29-MCL-1 axis in ZDF rat heart correlated with cardiac structural damage (disorganization or loss of myofibril bundles). We conclude that insulin and mTORC1 regulate cardiac miR-29-MCL-1 axis and its dysregulation caused by reduced insulin and mTORC1 inhibition increases the vulnerability of a diabetic heart to structural damage.
Early changes in CSF sTREM2 in dominantly inherited Alzheimer’s disease occur after amyloid deposition and neuronal injury

CSF sTREM2 increases in early stages of autosomal dominant Alzheimer’s disease, but the increase occurs after changes in Aβ and tau. Microglial activation in AD Little is known about the role of microglia in Alzheimer’s disease (AD). TREM2 is a protein expressed by microglia. Mutations in TREM2 increase the risk for neurodegenerative diseases including AD. Suárez-Calvet and colleagues have measured the amount of a secreted form of TREM2 (sTREM2) as a surrogate marker for microglial activation. They measured sTREM2 in the cerebrospinal fluid (CSF) of a unique cohort of 127 subjects with autosomal dominant AD and 91 healthy siblings. CSF sTREM2 was abnormally increased 5 years before the expected onset of symptoms in the AD patients. This increase occurred after alterations in markers for brain amyloidosis and neuronal injury. Emerging evidence supports a role for innate immunity and microglia in Alzheimer’s disease (AD) pathophysiology. However, no marker related to microglia has been included in the temporal evolution models of AD. TREM2 is a transmembrane protein involved in innate immunity and is selectively expressed by microglia and genetically linked to AD and other neurodegenerative disorders. Its ectodomain is released by proteolysis as a soluble variant (sTREM2) and can be detected in the cerebrospinal fluid (CSF). In patients with autosomal dominant AD, we tested how many years before the expected symptom onset did CSF sTREM2 increase in mutation carriers (MCs) compared to noncarriers (NCs). We also determined the temporal sequence of changes in CSF sTREM2 and markers for amyloid deposition and neurodegeneration as well as cognitive performance. We included 218 participants consisting of 127 MC and 91 NC siblings from the Dominantly Inherited Alzheimer Network. We observed that CSF sTREM2 increased in MCs compared to NCs 5 years before the expected symptom onset and this difference remained significant until 5 years after the expected symptom onset. Changes in CSF sTREM2 occurred after alterations were observed in markers for brain amyloidosis and neuronal injury. We propose that microglial activation occurs several years before the expected symptom onset, but after amyloidosis and neuronal injury have already occurred.
Succinct progress measures for solving parity games

The recent breakthrough paper by Calude et al. has given the first algorithm for solving parity games in quasi-polynomial time, where previously the best algorithms were mildly subexponential. We devise an alternative quasi-polynomial time algorithm based on progress measures, which allows us to reduce the space required from quasi-polynomial to nearly linear. Our key technical tools are a novel concept of ordered tree coding, and a succinct tree coding result that we prove using bounded adaptive multi-counters, both of which are interesting in their own right.
Cracking-Resistant Password Vaults Using Natural Language Encoders

Password vaults are increasingly popular applications that store multiple passwords encrypted under a single master password that the user memorizes. A password vault can greatly reduce the burden on a user of remembering passwords, but introduces a single point of failure. An attacker that obtains a user's encrypted vault can mount offline brute-force attacks and, if successful, compromise all of the passwords in the vault. In this paper, we investigate the construction of encrypted vaults that resist such offline cracking attacks and force attackers instead to mount online attacks. Our contributions are as follows. We present an attack and supporting analysis showing that a previous design for cracking-resistant vaults -- the only one of which we are aware -- actually degrades security relative to conventional password-based approaches. We then introduce a new type of secure encoding scheme that we call a natural language encoder (NLE). An NLE permits the construction of vaults which, when decrypted with the wrong master password, produce plausible-looking decoy passwords. We show how to build NLEs using existing tools from natural language processing, such as n-gram models and probabilistic context-free grammars, and evaluate their ability to generate plausible decoys. Finally, we present, implement, and evaluate a full, NLE-based cracking-resistant vault system called NoCrack.