Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a conserved DNA sulfur recognition domain by characterizing the phosphorothioate‐specific endonuclease SprMcrA from Streptomyces pristinaespiralis

Streptomyces species have been valuable models for understanding the phenomenon of DNA phosphorothioation in which sulfur replaces a non‐bridging oxygen in the phosphate backbone of DNA. We previously reported that the restriction endonuclease ScoMcrA from Streptomyces coelicolor cleaves phosphorothioate DNA and Dcm‐methylated DNA at sites 16–28 nucleotides away from the modification sites. However, cleavage of modified DNA by ScoMcrA is always incomplete and accompanied by severe promiscuous activity on unmodified DNA. These features complicate the studies of recognition and cleavage of phosphorothioate DNA. For these reasons, we here characterized SprMcrA from Streptomyces pristinaespiralis, a much smaller homolog of ScoMcrA with a rare HRH motif, a variant of the HNH motif that forms the catalytic center of these endonucleases. The sulfur‐binding domain of SprMcrA and its phosphorothioation recognition site were determined. Compared to ScoMcrA, SprMcrA has higher specificity in discerning phosphorothioate DNA from unmodified DNA, and this enzyme generally cuts both strands at a distance of 11–14 nucleotides from the 5′ side of the recognition site. The HRH/HNH motif has its own sequence specificity in DNA hydrolysis, leading to failure of cleavage at some phosphorothioated sites. An R248N mutation of the central residue in HRH resulted in 30‐fold enhancement in cleavage activity of phosphorothioate DNA and altered the cleavage efficiency at some sites, whereas mutation of both His residues abolished restriction activity. This is the first report of a recognition domain for phosphorothioate DNA and phosphorothioate‐dependent and sequence‐specific restriction activity.
Unsupervised Statistical Machine Translation

While modern machine translation has relied on large parallel corpora, a recent line of work has managed to train Neural Machine Translation (NMT) systems from monolingual corpora only (Artetxe et al., 2018c; Lample et al., 2018). Despite the potential of this approach for low-resource settings, existing systems are far behind their supervised counterparts, limiting their practical interest. In this paper, we propose an alternative approach based on phrase-based Statistical Machine Translation (SMT) that significantly closes the gap with supervised systems. Our method profits from the modular architecture of SMT: we first induce a phrase table from monolingual corpora through cross-lingual embedding mappings, combine it with an n-gram language model, and fine-tune hyperparameters through an unsupervised MERT variant. In addition, iterative backtranslation improves results further, yielding, for instance, 14.08 and 26.22 BLEU points in WMT 2014 English-German and English-French, respectively, an improvement of more than 7-10 BLEU points over previous unsupervised systems, and closing the gap with supervised SMT (Moses trained on Europarl) down to 2-5 BLEU points. Our implementation is available at https://github.com/artetxem/monoses.
Connecting people with city cultural heritage through proximity-based digital storytelling

This paper describes a research investigation on a project led by two libraries, Hamilton Public Library and McMaster University Library, in Hamilton, Canada, concerning the use of proximity-based technologies to share digital stories about a city’s culture. Proximity-based technology systems, such as iBeacons, allow users to receive information automatically when they are close to a physical spot. The project involved the setup of iBeacons that disseminated digital stories pertaining to Gore Park – a prominent historical park in the heart of downtown Hamilton. To test the viability of using iBeacon technologies to raise interest in a city and promote appreciation for a city’s cultural heritage, a pilot study was conducted. The study included one-on-one interviews and a short survey with 50 participants from the general public immediately after these participants used an iBeacon app to experience digital stories about Gore Park. Findings suggest iBeacons are viable tools to share city cultural heritage stories that yield improved perceptions of a city and greater appreciation for a city’s culture and history. Participants were appreciative of the digital stories and the iBeacon app. All participants mentioned that they learned something new about the city and that the app was very informative. Findings indicate that individual differences are important and can affect not only the acceptance and use of an iBeacon digital storytelling app, but also the extent to which the app can promote interest in a city and appreciation for a city’s cultural heritage.
Failures of LEDs in Real-World Applications: A Review

With this paper, we review several different failure mechanisms of commercial light emitting diodes operating in real-life applications. We consider both high power and mid power devices, which represent the biggest share of the market. Real-life applications are particularly interesting since they reveal potential reliability issues and weaknesses of the optoelectronic devices, which are not detected/studied during conventional laboratory testing, due to their extrinsic origin. The analyzed failures mechanisms are mainly due to: 1) electrical overstress (surge and hot plugging); 2) assembly issues; 3) mishandling; and 4) chemical contamination. The results presented within this paper provide relevant data for the improvement of the reliability and robustness of current solid-state lighting systems.
Chlorhexidine–Alcohol Compared with Povidone–Iodine Preoperative Skin Antisepsis for Cesarean Delivery: A Systematic Review and Meta-Analysis

Abstract Objective To compare chlorhexidine–alcohol with povidone–iodine solutions for skin antisepsis prior to cesarean delivery for the prevention of surgical site infection. Study Design Electronic databases MEDLINE, Embase, Scopus, and Clinicaltrials.gov were searched from inception to August 2017. Eligible studies included randomized controlled trials comparing chlorhexidine–alcohol with povidone–iodine skin preparation solutions for women undergoing cesarean delivery. The primary outcome was surgical site infection including superficial or deep wound infection. Meta-analysis was performed, and risk ratios (RRs) with 95% confidence interval (CI) were calculated using the Mantel–Haenszel random effects model. Statistical heterogeneity was assessed using Higgin's I 2. Results Of 61 abstracts identified in the primary search, four studies (3,059 women) met the eligibility criteria. The risk of surgical site infection was significantly reduced with chlorhexidine–alcohol (RR: 0.72; 95% CI: 0.52–0.98). No heterogeneity across studies was observed with I 2 = 0%. Subgroup analysis of superficial infection only or deep infection only showed no statistically significant difference (RR: 0.76, 95% CI: 0.54–1.08; and RR: 0.50, 95% CI: 0.23–1.10, respectively). Conclusion Preoperative skin cleansing prior to cesarean delivery with chlorhexidine–alcohol reduces surgical site infection as compared with povidone–iodine solutions.
Detection of atrial fibrillation from ECG recordings using decision tree ensemble with multi-level features

Objective: Detecting atrial fibrillation (AF) from electrocardiogram (ECG) recordings remains a challenging task. In this paper, a new AF detection method was proposed to classify the ECG recordings into one of four classes: Normal rhythm, AF, Other rhythm, and Noisy recordings. Approach: The proposed method comprised preprocessing, feature extraction, and classification. In preprocessing, R-peaks were detected, and RR intervals and delta RR intervals were extracted. In feature extraction, 30 multi-level features were extracted, including AF features (n = 4), morphology features (n = 20), RR interval features (n = 2), and features of similarity index between beats (n = 4). In classification, these features were used to train an AdaBoosted decision tree ensemble for classifying ECG recordings into the four classes. The decision tree ensemble was trained with 100-fold cross-validation on the training dataset (n = 8528) provided by the 2017 PhysioNet/Computing in Cardiology (CinC) Challenge. Main results: The trained classifier was submitted to the Challenge for testing on the unavailable test dataset (n = 3658); the official F1 scores for ‘Normal’, ‘AF’, ‘Other’ were 0.91, 0.82, and 0.73, respectively, and the overall F1 score was 0.82 (ranking equal 5th with eight other algorithms in the 2017 PhysioNet/CinC Challenge). Significance: The proposed algorithm may be used as a new method for AF detection.
Cell Therapy : A Door Is Open to Find Innumerable Possibilities of Treatments for Cancer Patients

Received/Geliş tarihi: June 06, 2018 Accepted/Kabul tarihi: September 05, 2018 Address for Correspondence/Yazışma Adresi: Beatriz MARTÍN-ANTONIO, M.D., Institut d’Investigacions Biomèdiques August Pi i Sunyer Hospital, Clinic of Hematology, Barcelona, Spain Phone : +34 610 980 307 E-mail : bmartina@clinic.ub. es ORCID-ID: orcid.org/0000-0003-0674-4660 Seven years ago a chronic lymphocytic leukemia patient was for the first time successfully treated with chimeric antigen receptor (CAR)-modified T cells (CAR-T cells) to target CD19 overexpression in tumor cells. This was the beginning of the development of a new type of immunotherapy treatment in cancer patients. Since then, identification of novel antigens expressed in tumor cells and optimization of both CAR constructs and protocols of administration have opened up new avenues for the successful treatment of other hematological malignancies. However, research still continues to avoid some problems such as toxicities associated with the treatment and to find strategies to avoid tumor cell immune evasion mechanisms. On the other hand, for solid tumors, CAR-T therapy results are still in an early phase. In contrast to hematological malignancies, the complex tumor heterogeneity of solid tumors has led to the research of novel and challenging strategies to improve CAR-T cell activity. Here, we will review the main clinical results obtained with CAR-T cells in hematological malignancies, specifically focusing on CAR-T-19 and CAR-T against B-cell maturation antigen (CAR-T-BCMA). Moreover, we will mention the main problems that decrease CAR-T cell activity in solid tumors and the strategies to overcome them. Finally, we will present some of the first clinical results obtained for solid tumors.
Content of Selected Vitamins and Antioxidants in Colored and Nonpigmented Varieties of Quinoa, Barley, and Wheat Grains.

The diversity in human diets that can be reached by proper use of different crops and varieties, including some underutilized ones, is a potentially powerful strategy to ensure food security and prevent serious health problems caused by current diets that are often not fulfilling nutritional requirements. In the framework of this research, the content of tocopherols and tocotrienols, thiamine, riboflavin, pyridoxine, and superoxide dismutase in nine varieties of quinoa, both colored and nonpigmented, obtained from 4 different countries, was investigated and compared to the content of the same vitamins and antioxidants in barley and wheat, both colored and nonpigmented, cultivated in the same experimental field. The aim of this work was to create a crop diversity strategy and encourage the consumption of underutilized crops to ensure that the human diet fulfills nutritional requirements. The contents of vitamin B1, B2, B6, tocopherol, and tocotrienol isomers and superoxide dismutase were determined via HPLC; imaging techniques were used to evaluate the seed color. Quinoa grains had the greatest concentration of tocopherol isomers and activity, represented mainly by α-tocopherol and γ-tocopherol. Wheat and barley seeds had substantial concentrations of tocopherols and tocotrienols. The concentration of riboflavin was greater in barley and wheat than in quinoa, the concentrations of pyridoxine and thiamine were variety-dependent in all grains. Quinoa grains had greater concentration of superoxide dismutase compared to wheat and barley. The richness of each variety and crop should be recognized and used integrally to improve the diet quality. PRACTICAL APPLICATION Nutritional potential of crops was evaluated from the viewpoint of selected vitamins and antioxidants to create a well-balanced diet. Combined use of both traditional (wheat, barley) and underutilized crops (quinoa) is recommended. HPLC methods and image analysis were successfully used as viable tools for food quality determination.
Assessment of diastolic function and atrial remodeling by MRI – validation and correlation with echocardiography and filling pressure

Atrial fibrosis can be estimated noninvasively by magnetic resonance imaging (MRI) using late gadolinium enhancement (LGE), but diastolic dysfunction is clinically assessed by transthoracic echocardiography (TTE), and rarely by MRI. This study aimed to evaluate well‐established diastolic parameters using MRI, and validate them with TTE and left ventricular (LV) filling pressures, and to study the relationship between left atrial (LA) remodeling and parameters of diastolic function. The study retrospectively included 105 patients (53 ± 16 years, 39 females) who underwent 3D LGE MRI between 2012 and 2016. Medical charts were reviewed for the echocardiographic diastolic parameters E, A, and e′ by TTE, and pressure catheterizations. E and A were measured from in‐plane phase‐contrast cardiac MRI images, and e′ by feature‐tracking, and validated with TTE. Interobserver and intraobserver variability was examined. Furthermore, LA volumes, function, and atrial LGE was correlated with diastolic parameters. Evaluation of e′ in MRI had strong agreement with TTE (r = 0.75, P < 0.0001), and low interobserver and intraobserver variability. E and A by TTE showed strong agreement to MRI (r = 0.77, P = 0.001; r = 0.73, P = 0.003, for E and A, respectively). Agreement between E/e′ by TTE and MRI was strong (r = 0.85, P = 0.0004), and E/e′ by TTE correlated moderately to invasive pressures (r = 0.59, P = 0.03). There was a strong relationship between LA LGE and pulmonary capillary wedge pressure (r = 0.81, P = 0.01). In conclusion, diastolic parameters can be measured with good reproducibility by cardiovascular MRI. LA LGE exhibited a strong relationship with pulmonary capillary wedge pressure, an indicator of diastolic function.
Design and Integration of an Inexpensive Wearable Mechanotactile Feedback System for Myoelectric Prostheses

The aim of this paper was to demonstrate the functionality of an inexpensive mechanotactile sensory feedback system for transhumeral myoelectric prostheses. We summarize the development of a tactile-integrated prosthesis, including 1) evaluation of sensors that were retrofit onto existing commercial terminal devices; 2) design of two custom mechanotactile tactors that were integrated into a socket without compromising suction suspension; 3) design of a modular controller which translated sensor input to tactor output, was wirelessly adjusted, and fit within a prosthetic forearm; and 4) evaluation of the system with a single transhumeral participant. Prosthesis functionality was demonstrated over three test sessions; the participant was able to identify tactor stimulation location and demonstrated a reduction in grasp force with the mechanotactile stimulation. This system offers an inexpensive and modular solution for integration of a mechanotactile sensory feedback system into a prosthetic socket without compromising the suction seal. These principles can be applied in future studies to investigate the direct impact of sensory feedback on tangible outcomes for prosthetic users, thereby reducing barriers to clinical translation.
Epidemiology of Upper Extremity Soccer Injuries Among High School– and College-Aged Players in the United States: An Analysis of the 1999-2016 NEISS Database

Background: Although lower extremity injuries are more common than upper extremity injuries in high school– and college-aged soccer players, upper extremity injuries may be equally severe. The epidemiology of upper extremity injuries is poorly characterized in this population. Hypothesis: Upper extremity injuries are an important contributor to soccer-related morbidity among high school– and college-aged players. Study Design: Descriptive epidemiology study. Level of Evidence: Level 3. Methods: The National Electronic Injury Surveillance System (NEISS) is a nationally representative sample of 100 hospital emergency departments (EDs). Each record contains demographic and injury information. Records from 1999 to 2016 were analyzed, including patients between the ages of 14 and 23 years with a soccer-related injury sustained at school or during an athletic event. Results: A total of 1,299,008 high school– or college-aged patients presented to the ED for a soccer-related injury from 1999 to 2016, of which 20.4% were in the upper extremity. Patients were predominantly male (58.0%) and high school–aged (81.4%). Males constituted a greater proportion of upper extremity injuries when compared with other injury locations (63.5% male for upper extremity). Upper extremity injuries were more likely to be fractures (43.7% vs 13.9%) and dislocations (7.1% vs 3.4%) and less likely to be strains/sprains (27.8% vs 56.6%). Males suffered more shoulder dislocations (81.8% males among patients with shoulder dislocation vs 57.8% among those with other injuries), finger dislocations (72.0% vs 58.0%), upper arm fractures (74.9% vs 57.6%), and forearm fractures (68.3% vs 57.3%). Conclusion: Upper extremity injuries are frequent in high school– and college-aged soccer players presenting to the ED. Efforts to reduce soccer-related injuries should include strategies targeting the upper extremity, perhaps reducing the incidence of high-energy falls. Clinical Relevance: Efforts to reduce soccer-related injuries should include strategies targeting upper extremity injuries, particularly among males and college-aged players.
Runtime Support for Multiple Offload-Based Programming Models on Clustered Manycore Accelerators

Heterogeneous systems coupling a main host processor with one or more manycore accelerators are being adopted virtually at every scale to achieve ever-increasing GOps/Watt targets. The increased hardware complexity of such systems is paired at the application level by a growing number of applications concurrently running on the system. Techniques that enable efficient accelerator resources sharing, supporting multiple programming models will thus be increasingly important for future heterogeneous SoCs. In this paper we present a runtime system for a cluster-based manycore accelerator, optimized for the concurrent execution of offloaded computation kernels from different programming models. The runtime supports spatial partitioning, where clusters can be grouped into several virtual accelerator instances. Our runtime design is modular and relies on a generic component for resource (cluster) scheduling, plus specialized components which deploy generic offload requests into the target programming model semantics. We evaluate the proposed runtime system on two real heterogeneous systems, focusing on two concrete use cases: i) single-user, multi-application high-end embedded systems and ii) multi-user, multi-workload low-power microservers. In the first case, our approach achieves 93 percent efficiency in terms of available accelerator resource exploitation. In the second case, our support allows 47 percent performance improvement compared to single-programming model systems.
A Unified Feature Disentangler for Multi-Domain Image Translation and Manipulation

We present a novel and unified deep learning framework which is capable of learning domain-invariant representation from data across multiple domains. Realized by adversarial training with additional ability to exploit domain-specific information, the proposed network is able to perform continuous cross-domain image translation and manipulation, and produces desirable output images accordingly. In addition, the resulting feature representation exhibits superior performance of unsupervised domain adaptation, which also verifies the effectiveness of the proposed model in learning disentangled features for describing cross-domain data.
An End-to-End System for Large Scale P2P MPC-as-a-Service and Low-Bandwidth MPC for Weak Participants

Protocols for secure multiparty computation enable a set of parties to compute a joint function of their inputs, while preserving privacy, correctness and more. In theory, secure computation has broad applicability and can be used to solve many of the modern concerns around utilization of data and privacy. Huge steps have been made towards this vision in the past few years, and we now have protocols that can carry out large computations extremely efficiently, especially in the setting of an honest majority. However, in practice, there are still major barriers to widely deploying secure computation, especially in a decentralized manner. In this paper, we present the first end-to-end automated system for deploying large-scale MPC protocols between end users, called MPSaaS (for MPC system-as-a-service ). Our system enables parties to pre-enroll in an upcoming MPC computation, and then participate by either running software on a VM instance (e.g., in Amazon), or by running the protocol on a mobile app, in Javascript in their browser, or even on an IoT device. Our system includes an automation system for deploying MPC protocols, an administration component for setting up an MPC computation and inviting participants, and an end-user component for running the MPC protocol in realistic end-user environments. We demonstrate our system for a specific application of running secure polls and surveys, where the secure computation is run end-to-end with each party actually running the protocol (i.e., without relying on a set of servers to run the protocol for them). This is the first such system constructed, and is a big step forward to the goal of commoditizing MPC. One of the cryptographic difficulties that arise in this type of setting is due to the fact that end users may have low bandwidth connections, making it a challenge to run an MPC protocol with high bandwidth. We therefore present a protocol based on Beerliova-Trubiniova and Hirt (TCC 2008) with many optimizations, that has very low concrete communication, and the lowest published for small fields. Our protocol is secure as long as less than a third of the parties are malicious, and is well suited for computing both arithmetic and Boolean circuits. We call our protocol HyperMPC and show that it has impressive performance. In particular, 150 parties can compute statistics---mean, standard deviation and regression---on 4,000,000 inputs (with a circuit of size 16,000,000 gates of which 6,000,000 are multiplication) in just 45 seconds, and 150 parties can compute a circuit over GF[28] (which can be used for a Boolean computation) with 1,000,000 multiplication gates and depth-20 in just 2 seconds. Although our end-to-end system can be used to run any MPC protocol (and we have incorporated numerous protocols already), we demonstrate it for our new protocol that is optimized for end-users without~high~bandwidth.