Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential activity of interferon-α8 promoter is regulated by Oct-1 and a SNP that dictates prognosis of glioma

We have previously reported that the single nucleotide polymorphism (SNP) rs12553612 in IFNA8 is associated with better overall survival of glioma patients with the AA-genotype compared with patients with the AC-genotype. As rs12553612 is located in the IFNA8 promoter, we hypothesized that the A-allele allows for an enhanced IFNA8 promoter activity compared with the C-allele. Reporter assays in the human monocyte derived THP-1 cell line demonstrated a superior promoter activity of the A-allele compared with the C-allele. Electrophoretic mobility shift assays (EMSA) further demonstrated that the A-genotype specifically binds to more nuclear proteins than the C-genotype, including the transcription factor Oct-1. Further, co-transfection of plasmids encoding Oct-1 and the reporter constructs revealed that Oct-1 enhanced the promoter activity with the A- but not the C-allele. Taken together, our data demonstrate that the A-allele in the rs12553612 SNP, which is associated with better glioma patient survival, allows for IFNA8 transcription by allowing for Oct-1 binding, which is absent in patients with C allele, and suggests a molecular mechanism of IFNA8 mediated immune-surveillance of glioma progression.
Abacavir-lamivudine-zidovudine vs indinavir-lamivudine-zidovudine in antiretroviral-naive HIV-infected adults: A randomized equivalence trial.

CONTEXT Abacavir, a nucleoside analogue, has demonstrated suppression of human immunodeficiency virus (HIV) replication alone and in combination therapy. However, the role of abacavir in a triple nucleoside combination regimen has not been evaluated against a standard protease inhibitor-containing regimen for initial antiretroviral treatment. OBJECTIVE To evaluate antiretroviral equivalence and safety of an abacavir-lamivudine-zidovudine regimen compared with an indinavir-lamivudine-zidovudine regimen. DESIGN AND SETTING A multicenter, phase 3, randomized, double-blind trial with an enrollment period from August 1997 to June 1998, with follow-up through 48 weeks at 73 clinical research units in the United States, Canada, Australia, and Europe. PATIENTS Five hundred sixty-two antiretroviral-naive, HIV-infected adults with a plasma HIV RNA level of at least 10 000 copies/mL and a CD4 cell count of at least 100 x 10(6)/L. INTERVENTIONS Patients were stratified by baseline HIV RNA level and randomly assigned to receive a combination tablet containing 150 mg of lamivudine and 300 mg of zidovudine twice daily plus either 300 mg of abacavir twice daily and indinavir placebo or 800 mg of indinavir every 8 hours daily plus abacavir placebo. After 16 weeks, patients with confirmed HIV RNA levels greater than 400 copies/mL were eligible to continue receiving randomized treatment or receive open-label therapy. MAIN OUTCOME MEASURE Virologic suppression, defined as HIV RNA concentration of 400 copies/mL or less at week 48. RESULTS The proportion of patients who met the end point of having an HIV RNA level of 400 copies/mL or less at week 48 was equivalent in the abacavir group (51% [133/262]) and in the indinavir group (51% [136/265]) with a treatment difference of -0.6% (95% confidence interval [CI], -9% to 8%). In patients with baseline HIV RNA levels greater than 100 000 copies/mL, the proportion of patients achieving less than 50 copies/mL was greater in the indinavir group than in the abacavir group with 45% (45/100) vs 31% (30/96) and a treatment diference of -14% (95% CI, -27% to 0%). The 2 treatments were comparable with respect to their effects on CD4 cell count. There was no difference between groups in the frequency of treatment-limiting adverse events or laboratory abnormalities. One death in the abacavir group was attributed to hypersensitivity reaction, which occurred following rechallenge with abacavir, approximately 3 weeks after initiating study treatment. CONCLUSIONS In this study of antiretroviral-naive HIV-infected adults, the triple nucleoside regimen of abacavir-lamivudine-zidovudine was equivalent to the regimen of indinavir-lamivudine-zidovudine in achieving a plasma HIV RNA level of less than 400 copies/mL at 48 weeks.
Soft Elastomeric Capacitor Network for Strain Sensing Over Large Surfaces

Field applications of existing sensing solutions to structural health monitoring (SHM) of civil structures are limited. This is due to economical and/or technical challenges in deploying existing sensing solutions to monitor geometrically large systems. To realize the full potential of SHM solutions, it is imperative to develop scalable cost-effective sensing strategies. We present a novel sensor network specifically designed for strain sensing over large surfaces. The network consists of soft elastomeric capacitors (SECs) deployed in an array form. Each SEC acts as a surface strain gage transducing local strain into changes in capacitance. Results show that the sensor network can track strain history above levels of 25 με using an inexpensive off-the-shelf data acquisition system. Tests at large strains show that the sensor's sensitivity is almost linear over strain levels of 0-20%. We demonstrate that it is possible to reconstruct deflection shapes for a simply supported beam subjected to quasi-static loads, with accuracy comparable to resistive strain gages.
Mining interesting sets and rules in relational databases

In this paper we propose a new and elegant approach toward the generalization of frequent itemset mining to the multi-relational case. We define relational itemsets that contain items from several relations, and a support measure that can easily be interpreted based on the key dependencies as defined in the relational scheme. We present an efficient depth-first algorithm, which mines relational itemsets directly from arbitrary relational databases. Several experiments show the practicality and usefulness of the proposed approach.
Fin ray sensation participates in the generation of normal fin movement in the hovering behavior of the bluegill sunfish (Lepomis macrochirus)

ABSTRACT For many fish species, the pectoral fins serve as important propulsors and stabilizers and are precisely controlled. Although it has been shown that mechanosensory feedback from the fin ray afferent nerves provides information on ray bending and position, the effects of this feedback on fin movement are not known. In other taxa, including insects and mammals, sensory feedback from the limbs has been shown to be important for control of limb-based behaviors and we hypothesized that this is also the case for the fishes. In this study, we examined the impact of the loss of sensory feedback from the pectoral fins on movement kinematics during hover behavior. Research was performed with bluegill sunfish (Lepomis macrochirus), a model for understanding the biomechanics of swimming and for bio-inspired design of engineered fins. The bluegill beats its pectoral fins rhythmically, and in coordination with pelvic and median fin movement, to maintain a stationary position while hovering. Bilateral deafferentation of the fin rays results in a splay-finned posture where fins beat regularly but at a higher frequency and without adducting fully against the side of the body. For unilateral transections, more irregular changes in fin movements were recorded. These data indicate that sensory feedback from the fin rays and membrane is important for generating normal hover movements but is not necessary for generating rhythmic fin movement. Summary: Sensory feedback from the fin rays and membrane of bluegill sunfish is important for generating normal hover movements but is not necessary for generating rhythmic fin movement.
Shear wave arrival time estimates correlate with local speckle pattern

We present simulation and phantom studies demonstrating a strong correlation between errors in shear wave arrival time estimates and the lateral position of the local speckle pattern in targets with fully developed speckle. We hypothesize that the observed arrival time variations are largely due to the underlying speckle pattern, and call the effect speckle bias. Arrival time estimation is a key step in quantitative shear wave elastography, performed by tracking tissue motion via cross-correlation of RF ultrasound echoes or similar methods. Variations in scatterer strength and interference of echoes from scatterers within the tracking beam result in an echo that does not necessarily describe the average motion within the beam, but one favoring areas of constructive interference and strong scattering. A swept-receive image, formed by fixing the transmit beam and sweeping the receive aperture over the region of interest, is used to estimate the local speckle pattern. Metrics for the lateral position of the speckle are found to correlate strongly (r > 0.7) with the estimated shear wave arrival times both in simulations and in phantoms. Lateral weighting of the swept-receive pattern improved the correlation between arrival time estimates and speckle position. The simulations indicate that high RF echo correlation does not equate to an accurate shear wave arrival time estimate-a high correlation coefficient indicates that motion is being tracked with high precision, but the location tracked is uncertain within the tracking beam width. The presence of a strong on-axis speckle is seen to imply high RF correlation and low bias. The converse does not appear to be true-highly correlated RF echoes can still produce biased arrival time estimates. The shear wave arrival time bias is relatively stable with variations in shear wave amplitude and sign (-20 μm to 20 μm simulated) compared with the variation with different speckle realizations obtained along a given tracking vector. We show that the arrival time bias is weakly dependent on shear wave amplitude compared with the variation with axial position/ local speckle pattern. Apertures of f/3 to f/8 on transmit and f/2 and f/4 on receive were simulated. Arrival time error and correlation with speckle pattern are most strongly determined by the receive aperture.
Primary esophageal Burkitt’s lymphoma: a rare case report and review of literature

Esophageal lymphoma is a rare condition, accounting for less than 1% of all gastrointestinal lymphomas. Primary extra nodal esophageal lymphoma constitutes less than 0.2% cases of the total esophageal lymphomas. The definition of primary GI lymphoma has differed among authors. The etiology of the disease is unknown, with the role of Epstein-Barr virus being controversial. The common symptoms of patients with esophageal lymphoma include dysphasia, odynophagia, weight loss, chest pain or present as a result of complications. Burkitt’s lymphoma is one of the fastest growing human malignancies, with a 100% replication rate. Endemic, sporadic (non-endemic) and immunodeficient variants have been recognized. The diagnosis of Burkitt’s lymphoma relies on morphologic findings, immunophenotyping results, and cytogenetic features. Burkitt’s lymphoma is usually treated with LMB-96 protocol depending on the risk stratification. We present a case of primary esophageal Burkitt’s lymphoma, which has been successfully treated with LMB-96 protocol. An extensive review of literature did not reveal a single case of esophageal Burkitt’s lymphoma. To the best of our knowledge this is the first case report in the world literature with diagnosis of primary esophageal Burkitt’s lymphoma.
Assisted Peer-to-Peer Search with Partial Indexing

In the past few years, peer-to-peer (P2P) networks have become a promising paradigm for building a wide variety of distributed systems and applications. The most popular P2P application till today is file sharing, e.g., Gnutella, Kazza, etc. These systems are usually referred to as unstructured, and search in unstructured P2P networks usually involves flooding or random walking. On the other hand, in structured P2P networks (DHTs), search is usually performed by looking up a distributed inverted index. The efficiency of the search mechanism is the key to the scalability of a P2P content sharing system. So far, neither unstructured nor structured P2P networks alone can solve the search problem in a satisfactory way. In this paper, we propose to combine the strengths of both unstructured and structured P2P networks to achieve more efficient search. Specifically, we propose to enhance search in unstructured P2P overlay networks by building a partial index of shared data using a structured P2P network. The index maintains two types of information: the top interests of peers and globally unpopular data, both characterized by data properties. The proposed search protocol, assisted search with partial indexing, makes use of the index to improve search in three ways: first, the index assists peers to find other peers with similar interests and the unstructured search overlay is formed to reflect peer interests. Second, the index also provides search hints for those data difficult to locate by exploring peer interest locality, and these hints can be used for second-chance search. Third, the index helps to locate unpopular data items. Experiments based on a P2P file sharing trace show that the assisted search with a lightweight partial indexing service can significantly improve the success rate in locating data than Gnutella and a hit-rate-based protocol in unstructured P2P systems, while incurring low search latency and overheads.
Managing Polyploidy in Ex Situ Conservation Genetics: The Case of the Critically Endangered Adriatic Sturgeon (Acipenser naccarii)

While the current expansion of conservation genetics enables to address more efficiently the management of threatened species, alternative methods for genetic relatedness data analysis in polyploid species are necessary. Within this framework, we present a standardized and simple protocol specifically designed for polyploid species that can facilitate management of genetic diversity, as exemplified by the ex situ conservation program for the tetraploid Adriatic sturgeon Acipenser naccarii. A critically endangered endemic species of the Adriatic Sea tributaries, its persistence is strictly linked to the ex situ conservation of a single captive broodstock currently decimated to about 25 individuals, which represents the last remaining population of Adriatic sturgeon of certain wild origin. The genetic variability of three F1 broodstocks available as future breeders was estimated based on mitochondrial and microsatellite information and compared with the variability of the parental generation. Genetic data showed that the F1 stocks have only retained part of the genetic variation present in the original stock due to the few parent pairs used as founders. This prompts for the urgent improvement of the current F1 stocks by incorporating new founders that better represent the genetic diversity available. Following parental allocation based on band sharing values, we set up a user-friendly tool for selection of candidate breeders according to relatedness between all possible parent-pairs that secures the use of non-related individuals. The approach developed here could also be applied to other endangered tetraploid sturgeon species overexploited for caviar production, particularly in regions lacking proper infrastructure and/or expertise.
Field monitoring and comparison of thermal- and load-induced strains in asphalt pavement

The influence of pavement temperature variations on field thermal-induced strains has not been well studied. Measuring the thermal- and load-induced strains in field conditions will assist in developing realistic pavement performance fatigue models. A field investigation programme was developed at the University of Waterloo to quantify thermal-induced strains in typical Eastern Canadian climate conditions. The main objective of this field study was to measure and compare the amplitude of load- and thermal-induced strains over a 1-year monitoring period. Results indicated that the average monthly thermal-induced strains were higher than the load-induced strains by a 49 kN wheel load moving at 25 km/h. Although the frequency of thermal-induced strains is lower than the traffic loads, damage from thermal-induced strains could be more than load-induced strains due to higher amplitudes.
End-to-End Relation Extraction using LSTMs on Sequences and Tree Structures

We present a novel end-to-end neural model to extract entities and relations between them. Our recurrent neural network based model captures both word sequence and dependency tree substructure information by stacking bidirectional tree-structured LSTM-RNNs on bidirectional sequential LSTM-RNNs. This allows our model to jointly represent both entities and relations with shared parameters in a single model. We further encourage detection of entities during training and use of entity information in relation extraction via entity pretraining and scheduled sampling. Our model improves over the state-of-the-art feature-based model on end-to-end relation extraction, achieving 12.1% and 5.7% relative error reductions in F1-score on ACE2005 and ACE2004, respectively. We also show that our LSTM-RNN based model compares favorably to the state-of-the-art CNN based model (in F1-score) on nominal relation classification (SemEval-2010 Task 8). Finally, we present an extensive ablation analysis of several model components.
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference

Motivation: Accurate orthology inference is a fundamental step in many phylogenetics and comparative analysis. Many methods have been proposed, including OMA (Orthologous MAtrix). Yet substantial challenges remain, in particular in coping with fragmented genes or genes evolving at different rates after duplication, and in scaling to large datasets. With more and more genomes available, it is necessary to improve the scalability and robustness of orthology inference methods. Results: We present improvements in the OMA algorithm: (i) refining the pairwise orthology inference step to account for same‐species paralogs evolving at different rates, and (ii) minimizing errors in the pairwise orthology verification step by testing the consistency of pairwise distance estimates, which can be problematic in the presence of fragmentary sequences. In addition we introduce a more scalable procedure for hierarchical orthologous group (HOG) clustering, which are several orders of magnitude faster on large datasets. Using the Quest for Orthologs consortium orthology benchmark service, we show that these changes translate into substantial improvement on multiple empirical datasets. Availability and Implementation: This new OMA 2.0 algorithm is used in the OMA database (http://omabrowser.org) from the March 2017 release onwards, and can be run on custom genomes using OMA standalone version 2.0 and above (http://omabrowser.org/standalone). Contact: christophe.dessimoz@unil.ch or adrian.altenhoff@inf.ethz. ch
A Sound and Complete Algorithm for Learning Causal Models from Relational Data

The PC algorithm learns maximally oriented causal Bayesian networks. However, there is no equivalent complete algorithm for learning the structure of relational models, a more expressive generalization of Bayesian networks. Recent developments in the theory and representation of relational models support lifted reasoning about conditional independence. This enables a powerful constraint for orienting bivariate dependencies and forms the basis of a new algorithm for learning structure. We present the relational causal discovery (RCD) algorithm that learns causal relational models. We prove that RCD is sound and complete, and we present empirical results that demonstrate effectiveness.
Three distinct mechanisms predominate in non-contact anterior cruciate ligament injuries in male professional football players: a systematic video analysis of 39 cases

Background Current knowledge on anterior cruciate ligament (ACL) injury mechanisms in male football players is limited. Aim To describe ACL injury mechanisms in male professional football players using systematic video analysis. Methods We assessed videos from 39 complete ACL tears recorded via prospective professional football injury surveillance between 2001 and 2011. Five analysts independently reviewed all videos to estimate the time of initial foot contact with the ground and the time of ACL tear. We then analysed all videos according to a structured format describing the injury circumstances and lower limb joint biomechanics. Results Twenty-five injuries were non-contact, eight indirect contact and six direct contact injuries. We identified three main categories of non-contact and indirect contact injury situations: (1) pressing (n=11), (2) re-gaining balance after kicking (n=5) and (3) landing after heading (n=5). The fourth main injury situation was direct contact with the injured leg or knee (n=6). Knee valgus was frequently seen in the main categories of non-contact and indirect contact playing situations (n=11), but a dynamic valgus collapse was infrequent (n=3). This was in contrast to the tackling-induced direct contact situations where a knee valgus collapse occurred in all cases (n=3). Conclusions Eighty-five per cent of the ACL injuries in male professional football players resulted from non-contact or indirect contact mechanisms. The most common playing situation leading to injury was pressing followed by kicking and heading. Knee valgus was frequently seen regardless of the playing situation, but a dynamic valgus collapse was rare.
An Electrophysiological Analysis of the Time Course of Conceptual and Syntactic Encoding during Tacit Picture Naming

A central question in psycholinguistic research is when various types of information involved in speaking (conceptual/ semantic, syntactic, and phonological information) become available during the speech planning process. Competing theories attempt to distinguish between parallel and serial models. Here, we investigated the relative time courses of conceptual and syntactic encoding in a tacit picture-naming task via event-related brain potential (ERP) recordings. Participants viewed pictures and made dual-choice go/no-go decisions based on conceptual features (whether the depicted item was heavier or lighter than 500 g) and syntactic features (whether the picture's German name had feminine or masculine syntactic gender). In support of serial models of speech production, both the lateralized readiness potential, or LRP (related to response preparation), and the N200 (related to response inhibition) measures indicated that conceptual processing began approximately 80 msec earlier than syntactic processing.