Miracle-dz/UniFAR-FTUs huggingface dataset:
A Systematic Review of Epidemiology and Risk Factors Associated With Chinese Inflammatory Bowel Disease

Background: Recent epidemiological data have revealed a dramatically rising prevalence and incidence of inflammatory bowel diseases (IBDs) in Mainland China, a rapidly growing industrialized region, over the last two decades. Objectives: We performed a systematic review to investigate the changing trends in the incidence of IBD in Mainland China and summarized the recent findings in risk factors associated with Chinese IBD. Methods: Relevant references were obtained from an electronic database search via MEDLINE and EMBASE (for English literatures), the China Academic Journals Full-text Database (CJFD) and the China Science Periodical Database (CSPD) in Wanfang Data (for Chinese literatures). Results: Total 1,584 abstracts in Chinese and 171 abstracts in English were collected. Eight full-text with epidemiological data, 25 with risk factor data in Chinese and 7 full-text with epidemiological data, 12 with risk factor data in English were finally identified and included for analysis. Data from included epidemiological studies has showed a striking increase in the incidence rate of IBD in Mainland China over time, and current incidence rates for IBD, UC, and CD were 1.80 (IBD), 1.33 (UC), and 0.46/1,000,000 (CD), though it varies among regions and ethnic minority populations. In addition, several risk factors including environmental factors, diet, intestinal infectious agents, hygiene, stress, and lifestyle have been reported to be associated with the increased incidence of Chinese IBD. Conclusion: This systematic review revealed an increased incidence of IBD in Mainland China. Although it is still lower than that in the Western world, however, China has a huge population; therefore, the total number of IBD patients might not be so little as previously thought and the disease burden of IBD in China is likely underestimated. HIGHLIGHTS Recent epidemiological data have revealed a dramatically rising prevalence and incidence of inflammatory bowel diseases (IBD) in Mainland China, a rapidly growing industrialized region, over the last two decades. This systematic review based on recent epidemiological data has revealed a striking increase in the incidence rate of IBD in Mainland China, though it varies among regions and ethnic minority populations. Several potential risk factors of IBD including environmental factors, diet, intestinal infectious agents, hygiene, stress, and lifestyle have been reported to be associated with the increased incidence of Chinese IBD. This systematic review on epidemiologic and risk factor studies has expanded understanding of the occurrence, distribution, geographic variance and risk factors of Chinese IBD and will provide clinicians important information in understanding current status of IBD in Mainland China.
Synergy in anti-malarial pre-erythrocytic and transmission-blocking antibodies is achieved by reducing parasite density

Anti-malarial pre-erythrocytic vaccines (PEV) target transmission by inhibiting human infection but are currently partially protective. It has been posited, but never demonstrated, that co-administering transmission-blocking vaccines (TBV) would enhance malaria control. We hypothesized a mechanism that TBV could reduce parasite density in the mosquito salivary glands, thereby enhancing PEV efficacy. This was tested using a multigenerational population assay, passaging Plasmodium berghei to Anopheles stephensi mosquitoes. A combined efficacy of 90.8% (86.7-94.2%) was observed in the PEV +TBV antibody group, higher than the estimated efficacy of 83.3% (95% CrI 79.1-87.0%) if the two antibodies acted independently. Higher PEV efficacy at lower mosquito parasite loads was observed, comprising the first direct evidence that co-administering anti-sporozoite and anti-transmission interventions act synergistically, enhancing PEV efficacy across a range of TBV doses and transmission intensities. Combining partially effective vaccines of differing anti-parasitic classes is a pragmatic, powerful way to accelerate malaria elimination efforts.
Enhancing Motion-In-Depth Perception of Random-Dot Stereograms

Random-dot stereograms have been widely used to explore the neural mechanisms underlying binocular vision. Although they are a powerful tool to stimulate motion-in-depth (MID) perception, published results report some difficulties in the capacity to perceive MID generated by random-dot stereograms. The purpose of this study was to investigate whether the performance of MID perception could be improved using an appropriate stimulus design. Sixteen inexperienced observers participated in the experiment. A training session was carried out to improve the accuracy of MID detection before the experiment. Four aspects of stimulus design were investigated: presence of a static reference, background texture, relative disparity, and stimulus contrast. Participants’ performance in MID direction discrimination was recorded and compared to evaluate whether varying these factors helped MID perception. Results showed that only the presence of background texture had a significant effect on MID direction perception. This study provides suggestions for the design of 3D stimuli in order to facilitate MID perception.
On the Use of LoRaWAN for Indoor Industrial IoT Applications

Low-Power Wide-Area Networks (LPWANs) have recently emerged as appealing communication systems in the context of the Internet of Things (IoT). Particularly, they proved effective in typical IoT applications such as environmental monitoring and smart metering. Such networks, however, have a great potential also in the industrial scenario and, hence, in the context of the Industrial Internet of Things (IIoT), which represents a dramatically growing field of application. In this paper we focus on a specific LPWAN, namely, LoRaWAN, and provide an assessment of its performance for typical IIoT employments such as those represented by indoor industrial monitoring applications. In detail, after a general description of LoRaWAN, we discuss how to set some of its parameters in order to achieve the best performance in the considered industrial scenario. Subsequently we present the outcomes of a performance assessment, based on realistic simulations, aimed at evaluating the behavior of LoRaWAN for industrial monitoring applications. Moreover, the paper proposes a comparison with the IEEE 802.15. 4 network protocol, which is often adopted in similar application contexts. The obtained results confirm that LoRaWAN can be considered as a strongly viable opportunity, since it is able to provide high reliability and timeliness, while ensuring very low energy consumption.
REGISTOR: A Platform for Unstructured Data Processing Inside SSD Storage

This paper presents REGISTOR, a platform for regular expression grabbing inside storage. The main idea of Registor is accelerating regular expression (regex) search inside storage where large data set is stored, eliminating the I/O bottleneck problem. A special hardware engine for regex search is designed and augmented inside flash SSD that processes data on-the-fly during data transmission from NAND flash to host. In order to make the speed of regex search match the internal bus speed of modern SSD, a deep pipeline structure is designed in Registor hardware consisting of file semantics extractor, matching candidates finder, regex matching units (REMUs) and results organizer. Furthermore, each stage of the pipeline makes use of maximal parallelism possible. To make Registor readily usable by high level applications, we have developed a set of APIs and libraries in Linux allowing Registor to process files in SSD by recombining separate data blocks into files efficiently. A working prototype of Registor has been built in our newly designed NVMe-SSD. Extensive experiments and analyses have been carried out to show that Registor achieves high throughput, reduces I/O bandwidth requirement by up to 97% and CPU utilization by as much as 82% for regex search in large data sets.
Variability of longitudinal strain measurements: levelling the playing field*

Abstract Speckle tracking echocardiography offers a unique opportunity to evaluate myocardial function, and global longitudinal strain (GLS) is currently recommended as a measurement of global left ventricular function. To facilitate clinical applicability of the method, collective efforts have been made to standardise strain measurements and to raise awareness of the potential sources of variability. The purpose of this review is to familiarise the reader with the most common sources of variability of longitudinal strain measurements and detail the possible measures to increase the accuracy and reproducibility of strain parameters.
Enhanced oral absorption of pemetrexed by ion-pairing complex formation with deoxycholic acid derivative and multiple nanoemulsion formulations: preparation, characterization, and in vivo oral bioavailability and anticancer effect

Objective The current study sought to design an oral delivery system of pemetrexed (PMX), a multitargeted antifolate antimetabolite, by enhancing its intestinal membrane permeability. Materials and methods PMX was ionically complexed with a permeation enhancer such as Nα-deoxycholyl-l-lysyl-methylester (DCK) and prepared as an amorphous solid dispersion by mixing with dispersants such as 2-hydroxypropyl-beta-cyclodextrin (HP-beta-CD) and poloxamer 188 (P188), forming an HP-beta-CD/PMX/DCK/P188; the complex was incorporated into multiple water-in-oil-in-water nanoemulsions in a supersaturated state (HP-beta-CD/PMX/DCK/P188-NE). Results After complex formation, the partition coefficient and in vitro membrane permeability of PMX were markedly increased, but it showed similar cytotoxic and inhibitory effects on cancer cell proliferation/migration. Furthermore, the intestinal membrane permeability and epithelial cell uptake of PMX were synergistically improved after HP-beta-CD/PMX/DCK/P188 was incorporated into a nanoemulsion with a size of 14.5±0.45 nm. The in vitro permeability of HP-beta-CD/PMX/DCK/P188-NE across a Caco-2 cell monolayer was 9.82-fold greater than that of free PMX, which might be attributable to the partitioning of PMX to the epithelial cells being facilitated via specific interaction of DCK with bile acid transporters, as well as the enhanced lipophilicity accompanied by surfactant-induced changes in the intestinal membrane structure and fluidity. Therefore, the oral bioavailability of HP-beta-CD/PMX/DCK/P188-NE in rats was evaluated as 26.8%±2.98% which was 223% higher than that of oral PMX. Moreover, oral HP-beta-CD/PMX/DCK/P188-NE significantly suppressed tumor growth in Lewis lung carcinoma cell-bearing mice, and the tumor volume was maximally inhibited by 61% compared with that in the control group. Conclusion These results imply that HP-beta-CD/PMX/DCK/P188-NE is an effective and promising delivery system for enhancing the oral absorption of PMX. Thus, there is the potential for new medical applications, including applications in metronomic cancer treatment.
Prototyping a Web-Scale Multimedia Retrieval Service Using Spark

The world has experienced phenomenal growth in data production and storage in recent years, much of which has taken the form of media files. At the same time, computing power has become abundant with multi-core machines, grids, and clouds. Yet it remains a challenge to harness the available power and move toward gracefully searching and retrieving from web-scale media collections. Several researchers have experimented with using automatically distributed computing frameworks, notably Hadoop and Spark, for processing multimedia material, but mostly using small collections on small computing clusters. In this article, we describe a prototype of a (near) web-scale throughput-oriented MM retrieval service using the Spark framework running on the AWS cloud service. We present retrieval results using up to 43 billion SIFT feature vectors from the public YFCC 100M collection, making this the largest high-dimensional feature vector collection reported in the literature. We also present a publicly available demonstration retrieval system, running on our own servers, where the implementation of the Spark pipelines can be observed in practice using standard image benchmarks, and downloaded for research purposes. Finally, we describe a method to evaluate retrieval quality of the ever-growing high-dimensional index of the prototype, without actually indexing a web-scale media collection.
Real-World Study on Sofosbuvir-based Therapies in Asian Americans With Chronic Hepatitis C

Background: Limited data exist with regard to treatment outcomes in Asian Americans with chronic hepatitis C (CHC). We evaluated sofosbuvir (SOF)-based regimens in a national cohort of Asian Americans. Methods: Eligible Asian Americans patients with CHC who had posttreatment follow-up of 24 weeks for SOF -based therapies from December 2013 to June 2017 were enrolled from 11 sites across the United States. The primary endpoint was sustained virologic response (SVR) rates at posttreatment weeks 12 and 24. Secondary endpoints were to evaluate safety by tolerability and adverse events (AEs). Results: Among 231 patients screened, 186 were enrolled. At baseline, 31% (57/186) patients were cirrhotic, 34% (63/186) were treatment experienced. Most of the subjects (42%, 79/186) received ledispavir/SOF therapy. The overall SVR12 was 95%, ranging from 86% in genotype (GT) 1b on SOF+ribavirin to 100% in GT 1b patients on ledipasvir/SOF at subgroup analyses. SVR12 was significantly lower in cirrhotic than in noncirrhotic patients [88% (50/57) vs. 98% (126/129), P<0.01]. Stratified by GT, SVR12 were: 96% (43/45) in GT 1a; 93% (67/72) in GT 1b; 100% (23/23) in GT 2; 90% (19/21) in GT 3; 100% (1/1) in GT 4; 83% (5/6) in GT 5; and 100% (16/16) in GT 6. Cirrhotic patients with treatment failure were primarily GT 1, (GT 1a, n=2; GT 1b, n=4) with 1 GT 5 (n=1). Patients tolerated the treatment without serious AEs. Late relapse occurred in 1 patient after achieving SVR12. Conclusions: In Asian Americans with CHC, SOF-based regimens were well tolerated without serious AEs and could achieve high SVR12 regardless of hepatitis C viral infection GT.
DyHard-DNN: Even More DNN Acceleration with Dynamic Hardware Reconfiguration

Deep Neural Networks (DNNs) have demonstrated their utility across a wide range of input data types, usable across diverse computing substrates, from edge devices to datacenters. This broad utility has resulted in myriad hardware accelerator architectures. However, DNNs exhibit significant heterogeneity in their computational characteristics, e.g., feature and kernel dimensions, and dramatic variances in computational intensity, even between adjacent layers in one DNN. Consequently, accelerators with static hardware parameters run sub-optimally and leave energy-efficiency margins unclaimed. We propose DyHard-DNNs, where accelerator microarchitectural parameters are dynamically reconfigured during DNN execution to significantly improve metrics of interest. We demonstrate the effectiveness of this approach on a configurable SIMD 2D systolic array and show a 15–65% performance improvement (at iso-power) and 25–90% energy improvement (at iso-latency) over the best static configuration in six mainstream DNN workloads.
Identification of a New Antimicrobial Resistance Gene Provides Fresh Insights Into Pleuromutilin Resistance in Brachyspira hyodysenteriae, Aetiological Agent of Swine Dysentery

Brachyspira hyodysenteriae is the aetiological agent of swine dysentery, a globally distributed disease that causes profound economic loss, impedes the free trade and movement of animals, and has significant impact on pig health. Infection is generally treated with antibiotics of which pleuromutilins, such as tiamulin, are widely used for this purpose, but reports of resistance worldwide threaten continued effective control. In Brachyspira hyodysenteriae pleuromutilin resistance has been associated with mutations in chromosomal genes encoding ribosome-associated functions, however the dynamics of resistance acquisition are poorly understood, compromising stewardship efforts to preserve pleuromutilin effectiveness. In this study we undertook whole genome sequencing (WGS) and phenotypic susceptibility testing of 34 UK field isolates and 3 control strains to investigate pleuromutilin resistance in Brachyspira hyodysenteriae. Genome-wide association studies identified a new pleuromutilin resistance gene, tva(A) (tiamulin valnemulin antibiotic resistance), encoding a predicted ABC-F transporter. In vitro culture of isolates in the presence of inhibitory or sub-inhibitory concentrations of tiamulin showed that tva(A) confers reduced pleuromutilin susceptibility that does not lead to clinical resistance but facilitates the development of higher-level resistance via mutations in genes encoding ribosome-associated functions. Genome sequencing of antibiotic-exposed isolates identified both new and previously described mutations in chromosomal genes associated with reduced pleuromutilin susceptibility, including the 23S rRNA gene and rplC, which encodes the L3 ribosomal protein. Interesting three antibiotic-exposed isolates harboured mutations in fusA, encoding Elongation Factor G, a gene not previously associated with pleuromutilin resistance. A longitudinal molecular epidemiological examination of two episodes of swine dysentery at the same farm indicated that tva(A) contributed to development of tiamulin resistance in vivo in a manner consistent with that seen experimentally in vitro. The in vitro studies further showed that tva(A) broadened the mutant selection window and raised the mutant prevention concentration above reported in vivo antibiotic concentrations obtained when administered at certain doses. We show how the identification and characterisation of tva(A), a new marker for pleuromutilin resistance, provides evidence to inform treatment regimes and reduce the development of resistance to this class of highly important antimicrobial agents.
The Role of Low-Density Lipoprotein Receptor-Related Protein 1 in Lipid Metabolism, Glucose Homeostasis and Inflammation

Metabolic syndrome (MetS) is a highly prevalent disorder which can be used to identify individuals with a higher risk for cardiovascular disease and type 2 diabetes. This metabolic syndrome is characterized by a combination of physiological, metabolic, and molecular alterations such as insulin resistance, dyslipidemia, and central obesity. The low-density lipoprotein receptor-related protein 1 (LRP1—A member of the LDL receptor family) is an endocytic and signaling receptor that is expressed in several tissues. It is involved in the clearance of chylomicron remnants from circulation, and has been demonstrated to play a key role in the lipid metabolism at the hepatic level. Recent studies have shown that LRP1 is involved in insulin receptor (IR) trafficking and intracellular signaling activity, which have an impact on the regulation of glucose homeostasis in adipocytes, muscle cells, and brain. In addition, LRP1 has the potential to inhibit or sustain inflammation in macrophages, depending on its cellular expression, as well as the presence of particular types of ligands in the extracellular microenvironment. In this review, we summarize existing perspectives and the latest innovations concerning the role of tissue-specific LRP1 in lipoprotein and glucose metabolism, and examine its ability to mediate inflammatory processes related to MetS and atherosclerosis.
Modeling Musical Taste Evolution with Recurrent Neural Networks

Finding the music of the moment can often be a challenging problem, even for well-versed music listeners. Musical tastes are constantly in flux, and the problem of developing computational models for musical taste dynamics presents a rich and nebulous problem space. A variety of factors all play some role in determining preferences (e.g., popularity, musicological, social, geographical, generational), and these factors vary across different listeners and contexts. In this paper, we leverage a massive dataset on internet radio station creation from a large music streaming company in order to develop computational models of listener taste evolution. We delve deep into the complexities of this domain, identifying some of the unique challenges that it presents, and develop a model utilizing recurrent neural networks. We apply our model to the problem of next station prediction and show that it not only outperforms several baselines, but excels at long tail music personalization, particularly by learning the long-term dependency structure of listener music preference evolution.
Bayesian analysis for multivariate skew-normal reproductive dispersion random effects models

Normality assumption of the random errors and the random effects is a routinely used technique in data analysis. However, this assumption might be unreasonable in many practical cases. In this paper the limitation is relaxed by assuming that the random error follows a reproductive dispersion model and the random effect is distributed as a skew-normal distribution, which is termed as a multivariate skew-normal reproductive dispersion random effects model. We propose a Bayesian procedure to simultaneously estimate the random effects and the unknown parameters on the basis of the Gibbs sampler and Metropolis-Hastings algorithm. In the end, the Framingham cholesterol data example is employed to demonstrate the preceding proposed Bayesian methodologies.
Pediatric Complicated Pneumonia Caused by Streptococcus pneumoniae Serotype 3 in 13-Valent Pneumococcal Conjugate Vaccinees, Portugal, 2010–2015

Despite use of 7-valent pneumococcal conjugate vaccine, incidence of pleural effusion and empyema (pediatric complicated pneumococcal pneumonia [PCPP]) is reportedly increasing globally. We cultured and performed PCR on 152 pleural fluid samples recovered from pediatric patients in Portugal during 2010–2015 to identify and serotype Streptococcus pneumoniae. We identified only 17 cases by culture, but molecular methods identified S. pneumoniae in 68% (92/135) of culture-negative samples. The most frequent serotypes were 3, 1, and 19A, together accounting for 62% (68/109) of cases. Nineteen cases attributable to 13-valent pneumococcal conjugate vaccine (PCV13) serotypes (mostly serotype 3) were detected among 22 children age-appropriately vaccinated with PCV13. The dominance of the additional serotypes included in PCV13 among PCPP cases in Portugal continues, even with PCV13 available on the private market (without reimbursement) since 2010 and with average annual coverage of 61% among age-eligible children. Our data suggest reduced effectiveness of PCV13 against serotype 3 PCPP.