gebhart/patrepeval huggingface dataset:
Ser <sup>1292</sup> Autophosphorylation Is an Indicator of LRRK2 Kinase Activity and Contributes to the Cellular Effects of PD Mutations (2012)

Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene are the most common cause of familial Parkinson's disease (PD). Although biochemical studies have shown that certain PD mutations confer elevated kinase activity in vitro on LRRK2, there are no methods available to directly monitor LRRK2 kinase activity in vivo. We demonstrate that LRRK2 autophosphorylation on Ser(1292) occurs in vivo and is enhanced by several familial PD mutations including N1437H, R1441G/C, G2019S, and I2020T. Combining two PD mutations together further increases Ser(1292) autophosphorylation. Mutation of Ser(1292) to alanine (S1292A) ameliorates the effects of LRRK2 PD mutations on neurite outgrowth in cultured rat embryonic primary neurons. Using cell-based and pharmacodynamic assays with phosphorylated Ser(1292) as the readout, we developed a brain-penetrating LRRK2 kinase inhibitor that blocks Ser(1292) autophosphorylation in vivo and attenuates the cellular consequences of LRRK2 PD mutations in vitro. These data suggest that Ser(1292) autophosphorylation may be a useful indicator of LRRK2 kinase activity in vivo and may contribute to the cellular effects of certain PD mutations.
Expression of a <i>Drosophila</i> mRNA is under circadian clock control during pupation (1989)

Rhythmic eclosion of Drosophila adults requires per gene function. We have found that a previously identified 0.9 kb RNA transcribed from DNA adjacent to per becomes abundantly expressed during pupation, just prior to eclosion. The daily synchronized emergence of young adults, coupled with a subsequent rapid decay of the transcript, is responsible for what previously appeared to be cycling of the 0.9 kb RNA in adults. In situ hybridization analyses localize the 0.9 kb transcript to the epidermis of newly eclosed adults. Conceptual translation of genomic DNA and cDNA sequences predicts that the 0.9 kb transcript produces a 261 amino acid protein containing a putative signal sequence for membrane transport at its amino terminus. Pupae that reach the same stage of development at slightly different times of day show a subsequent synchronized rise in 0.9 kb RNA levels, indicating that the expression of this transcript is under circadian clock control.
Anomaly Detection Based on Sensor Data in Petroleum Industry Applications (2015)

Anomaly detection is the problem of finding patterns in data that do not conform to an a priori expected behavior. This is related to the problem in which some samples are distant, in terms of a given metric, from the rest of the dataset, where these anomalous samples are indicated as outliers. Anomaly detection has recently attracted the attention of the research community, because of its relevance in real-world applications, like intrusion detection, fraud detection, fault detection and system health monitoring, among many others. Anomalies themselves can have a positive or negative nature, depending on their context and interpretation. However, in either case, it is important for decision makers to be able to detect them in order to take appropriate actions. The petroleum industry is one of the application contexts where these problems are present. The correct detection of such types of unusual information empowers the decision maker with the capacity to act on the system in order to correctly avoid, correct or react to the situations associated with them. In that application context, heavy extraction machines for pumping and generation operations, like turbomachines, are intensively monitored by hundreds of sensors each that send measurements with a high frequency for damage prevention. In this paper, we propose a combination of yet another segmentation algorithm (YASA), a novel fast and high quality segmentation algorithm, with a one-class support vector machine approach for efficient anomaly detection in turbomachines. The proposal is meant for dealing with the aforementioned task and to cope with the lack of labeled training data. As a result, we perform a series of empirical studies comparing our approach to other methods applied to benchmark problems and a real-life application related to oil platform turbomachinery anomaly detection.
Modular concepts for a new generation of light weight robots (2002)

The paper outlines DLR's mechatronic developments in the robotics area over the last five years. They aim at designing a new multisensory, modularly configurable light weight robot generation in a unified and integral way. A first step in this direction has been the development of a complex multisensory gripper based on a fully modular hard- and software-concept. It turned out to be a key element in ROTEX, the first real robot in space which flew with shuttle COLUMBIA in early 1993. Sensors and actuators in DLR's new ultra-light-weight robot show up miniaturized integration of mechanics, electronics and of course microprocessor control. Joint torque based on inductive sensing may be combined with different type of gearings: translational ones (using a new spindle drive concept), originally developed for grippers but easily usable, e.g. in tendon driven elbow-like joints, as well as compact, highly reducing rotational ones. In combination with optimized carbon fibre grid structures and optical information transfer between the joints a new, extremely light-weight type of robot arises. All power and signal electronics is integrated into the arm which shows up a 1:1 ratio between load and own weight.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Evaluation of the porcine intestinal collagen layer as a biomaterial (2000)

The submucosal layer of the small intestine has been investigated as a source of collagenous tissue with the potential to be used as a biomaterial because of its inherent strength and biocompatibility. In this study we utilized a novel method for processing the tissue to generate an acellular intestinal collagen layer (ICL). This nondetergent, nonenzymatic chemical cleaning protocol removes cells and cellular debris without damaging the native collagen structure. Multilayer laminates of ICL crosslinked with a water-soluble carbodiimide (EDC) were evaluated as a tissue repair material in a rabbit abdominal hernia model. The ICL laminates provided the requisite physical properties and did not lead to adhesion formation. No immune response to the porcine collagen was detectable, and this material did not show any calcification in either the rabbit model or in the juvenile rat model.
A Cloud-Based Internet of Things Platform for Ambient Assisted Living (2014)

A common feature of ambient intelligence is that many objects are inter-connected and act in unison, which is also a challenge in the Internet of Things. There has been a shift in research towards integrating both concepts, considering the Internet of Things as representing the future of computing and communications. However, the efficient combination and management of heterogeneous things or devices in the ambient intelligence domain is still a tedious task, and it presents crucial challenges. Therefore, to appropriately manage the inter-connection of diverse devices in these systems requires: (1) specifying and efficiently implementing the devices (e.g., as services); (2) handling and verifying their heterogeneity and composition; and (3) standardizing and managing their data, so as to tackle large numbers of systems together, avoiding standalone applications on local servers. To overcome these challenges, this paper proposes a platform to manage the integration and behavior-aware orchestration of heterogeneous devices as services, stored and accessed via the cloud, with the following contributions: (i) we describe a lightweight model to specify the behavior of devices, to determine the order of the sequence of exchanged messages during the composition of devices; (ii) we define a common architecture using a service-oriented standard environment, to integrate heterogeneous devices by means of their interfaces, via a gateway, and to orchestrate them according to their behavior; (iii) we design a framework based on cloud computing technology, connecting the gateway in charge of acquiring the data from the devices with a cloud platform, to remotely access and monitor the data at run-time and react to emergency situations; and (iv) we implement and generate a novel cloud-based IoT platform of behavior-aware devices as services for ambient intelligence systems, validating the whole approach in real scenarios related to a specific ambient assisted living application.
Fiber-Tractography in Human Brain Using Diffusion Tensor MRI (DT-MRI) (2000)

Introduction The elucidation of fiber tract trajectories in brain and in other fibrous tissues should provide valuable information to assess fiber connectivity and continuity, and provide insight into the natural history of normal and abnormal development and of related diseases, Since the tractograhy algorithm used here was first proposed (1) several novel methods have been advanced to follow fiber tract trajectories using measured DT-MRI data (2-5). The work here is relevant to these studies as we show several artifacts that have not been considered to date, and suggest means of remediating them.
Expedited Solid-Phase Synthesis of Fluorescently Labeled and Biotinylated Aminoalkane Diphenyl Phosphonate Affinity Probes for Chymotrypsin- and Elastase-Like Serine Proteases (2009)

In this study, we report on a novel, expedited solid-phase approach for the synthesis of biotinylated and fluorescently tagged irreversible affinity based probes for the chymotrypsin and elastase-like serine proteases. The novel solid-phase biotinylation or fluorescent labeling of the aminoalkane diphenyl phosphonate warhead using commercially available Biotin-PEG-NovaTag or EDANS NovaTag resin permits rapid, facile synthesis of these reagents. We demonstrate the kinetic evaluation and utilization of a number of these irreversible inactivators for chymotrypsin-like (chymotrypsin/human cathepsin G) and elastase-like serine proteases. Encouragingly, these compounds display comparable potency against their target proteases as their N-benzyloxycarbonyl (Cbz)-protected parent compounds, from which they were derived, and function as efficient active site-directed inactivators of their target proteases. We subsequently applied the biotinylated reagents for the sensitive detection of protease species via Western blot, showing that the inactivation of the protease was specifically mediated through the active site serine. Furthermore, we also demonstrate the successful detection of serine protease species with the fluorescently labeled derivatives "in-gel", thus avoiding the need for downstream Western blotting. Finally, we also show the utility of biotinylated and pegylated affinity probes for the isolation/enrichment of serine protease species, via capture with immobilized streptavidin, and their subsequent identification via de novo sequencing. Given their selectivity of action against the serine proteases, we believe that these reagents can be exploited for the direct, rapid, and selective identification of these enzymes from biological milieu containing multiple protease subclasses.
Shoot & copy (2007)

Large public displays have become pervasive in our everyday lives, but up to now, they are mostly information screens without any interaction possibilities. Users tend to forget what they saw relatively fast after leaving such a display. In this paper, we present a new interaction technique for transferring information from a public display onto a personal mobile phone with its built-in camera. Instead of having to rely on their memory, users simply take a picture of the information of interest. Instead of just storing the image, our system then retrieves the actual data represented on the screen, such as a stock quote, news text, or piece of music. The Shoot & Copy technique does not require visual codes that interfere with shown content or reduce screen real estate. Our prototype allows users to capture an arbitrary region of a standard desktop screen, containing icons, which represent pieces of data. The captured image is then analyzed and a reference to the corresponding data is sent back to the mobile phone. Once the user has time to view the information in more detail, our system allows retrieving the actual data from this reference. We present our prototype and the methods it uses for image processing, as well as an evaluation of our interaction technique illustrating its potential use and applications.
Mass Transfer Of Contaminants In Rotary Enthalpy Exchangers (1993)

The present work is a study of reentrainment of a tracer gas formaldehyde via six rotary air-to-air heat exchangers (all enthalpy exchangers) in the northern part of Sweden. Five exchangers installed in office buildings and one in a day-care centre were included in the study. Formaldehyde in indoor was used as a monitor pollutant and was determined in air samples collected in the ducts at four positions around the rotor of the exchanger, in the supply-air duct and in the exhaust-air duct. Air sampling of homogeneous duct air was performed simultaneously at the four positions using 2, 4-dinitrophenylhydrazine-impregnated glass fibre filters. The sample analysis of formaldehyde was made by high-performance liquid chromatography. The reentrainment of formaldehyde was calculated and found to be 1-9%. These results show that a rotary heat exchanger can be used in buildings where activities produce low levels of air pollutants, provided that the exchanger is properly installed and maintained.
Oxidation of Nano-Multilayered CrAlCuN Thin Films Between 800 and 1000 °C in Air (2014)

Thin CrAlCuN films with a composition of 21.5Cr-18.6Al-5.6Cu-54.3N (at.%) were deposited on steel substrates by the cathodic arc plasma deposition, and oxidized for up to 50 h in air. They consisted of alternating crystalline CrN/AlN nano-multilayers where Cu was incorporated. At 800 degrees C, a thin Cr2O3 layer formed. At 900 and 1000 degrees C, an outer Cr2O3 layer and an inner (α-Al2O3, Cr2O3)-mixed layer formed. Copper diffused outward to a small extent during oxidation. The film had good oxidation resistance, owing to the formation of the protective Cr2O3 and α-Al2O3.
Identification of epitope-based peptide vaccine candidates against enterotoxigenic <i>Escherichia coli</i> : a comparative genomics and immunoinformatics approach (2016)

Enterotoxigenic Escherichia coli (ETEC) associated diarrhea remains a global killer with an estimated annual incidence rate of 840 million infections and 3 800 000 deaths worldwide. There are no vaccines available for ETEC and the traditional vaccine development approach is arduous and time consuming. Thus, alternative in silico approaches for epitope prediction have engrossed the interest of researchers to reduce resources and time of vaccine development. Computational approaches are playing a crucial role in fighting against rapidly growing infectious organisms. In this study we employed an integrated comparative genomics and immunoinformatics approach for proteome scale identification of peptide vaccine candidates. The proteins shared between both ETEC E24377A and H10407 strains, but lacking in commensal E. coli SE11, were subjected to immunoinformatics analysis. For a protein pool shared between different pathogenic ETEC strains, we investigated varied physicochemical and immunogenic properties to prioritize potential vaccine candidates. Epitopes were further tested using docking studies to bind in the MHC-I binding cleft. Predicted epitopes provided more than a 95% population coverage in diarrhea endemic regions presented by major MHC-I supertypes, and bind efficiently to a MHC molecule. We conclude by accentuating that the epitopes predicted in this study are believed to accelerate the development of successful vaccines to control or prevent ETEC infections, albeit the results require experimental validation using model organisms. This study underscores that in silico approaches, together with omics data, hold great potential to be utilized for rapid and reliable genome-wide screening for identification of vaccine candidates against devastating infectious diseases.
Compiler-Assisted Loop Hardening Against Fault Attacks (2017)

Secure elements widely used in smartphones, digital consumer electronics, and payment systems are subject to fault attacks. To thwart such attacks, software protections are manually inserted requiring experts and time. The explosion of the Internet of Things (IoT) in home, business, and public spaces motivates the hardening of a wider class of applications and the need to offer security solutions to non-experts. This article addresses the automated protection of loops at compilation time, covering the widest range of control- and data-flow patterns, in both shape and complexity. The security property we consider is that a sensitive loop must always perform the expected number of iterations; otherwise, an attack must be reported. We propose a generic compile-time loop hardening scheme based on the duplication of termination conditions and of the computations involved in the evaluation of such conditions. We also investigate how to preserve the security property along the compilation flow while enabling aggressive optimizations. We implemented this algorithm in LLVM 4.0 at the Intermediate Representation (IR) level in the backend. On average, the compiler automatically hardens 95% of the sensitive loops of typical security benchmarks, and 98% of these loops are shown to be robust to simulated faults. Performance and code size overhead remain quite affordable, at 12.5% and 14%, respectively.
Automated hearing screening for children: A pilot study in China (2013)

The results suggest that with further improvement in terms of its sensitivity and specificity, it may be feasible to use the automated hearing screening test system to conduct routine school hearing screenings.
A study on antennas for railway millimeter-wave radio communication system (2002)

This paper first presents an outline of a new train radio communication system between trains and ground facilities, forming a multimedia railway information and communication system for train operation and passengers, that we have proposed for aiming high-speed and large-capacity communication such as multi-channel quasi-videos. This paper then studies antennas used for mobile radio station and radio base station. Also, this paper describes performance estimation of this proposed antennas, obtained by computer simulation. Results of estimation show that this proposed antenna system has a high degree of feasibility.
Development of a Novel Bioelectrochemical Membrane Reactor for Wastewater Treatment (2011)

A novel bioelectrochemical membrane reactor (BEMR), which takes advantage of a membrane bioreactor (MBR) and microbial fuel cells (MFC), is developed for wastewater treatment and energy recovery. In this system, stainless steel mesh with biofilm formed on it serves as both the cathode and the filtration material. Oxygen reduction reactions are effectively catalyzed by the microorganisms attached on the mesh. The effluent turbidity from the BEMR system was low during most of the operation period, and the chemical oxygen demand and NH(4)(+)-N removal efficiencies averaged 92.4% and 95.6%, respectively. With an increase in hydraulic retention time and a decrease in loading rate, the system performance was enhanced. In this BEMR process, a maximum power density of 4.35 W/m(3) and a current density of 18.32 A/m(3) were obtained at a hydraulic retention time of 150 min and external resister of 100 Ω. The Coulombic efficiency was 8.2%. Though the power density and current density of the BEMR system were not very high, compared with other high-output MFC systems, electricity recovery could be further enhanced through optimizing the operation conditions and BEMR configurations. Results clearly indicate that this innovative system holds great promise for efficient treatment of wastewater and energy recovery.
Universal Sentence Representation Learning with Conditional Masked Language Model (2021)

This paper presents a novel training method, Conditional Masked Language Modeling (CMLM), to effectively learn sentence representations on large scale unlabeled corpora. CMLM integrates sentence representation learning into MLM training by conditioning on the encoded vectors of adjacent sentences. Our English CMLM model achieves state-ofthe-art performance on SentEval (Conneau and Kiela, 2018), even outperforming models learned using supervised signals. As a fully unsupervised learning method, CMLM can be conveniently extended to a broad range of languages and domains. We find that a multilingual CMLM model co-trained with bitext retrieval (BR) and natural language inference (NLI) tasks outperforms the previous state-of-the-art multilingual models by a large margin, e.g. 10% improvement upon baseline models on cross-lingual semantic search. We explore the same language bias of the learned representations, and propose a simple, post-training and model agnostic approach to remove the language identifying information from the representation while still retaining sentence semantics.
Surface EMG Biofeedback (2016)

This chapter focuses on the most common form of feedback in physical rehabilitation: surface electromyograph (sEMG) biofeedback. It provides an overview of technical considerations and guidelines for the use of sEMG biofeedback and reviews some of its most common clinical applications. The principle of sEMG biofeedback is to provide the subject with enhanced information about muscle activity. The most common goals are muscle relaxation, reduction of excessive and/or inappropriate muscle activation, or the learning or re learning of muscle control. The chapter considers some of the technical considerations when applying and interpreting sEMG biofeedback. It summarizes the use of sEMG biofeedback for various clinical conditions. Recent technological advances and discoveries in the field of motor control and learning prompted new solutions for sEMG biofeedback applications, possibly leading to more effective training.
A High Frame Rate Hybrid X-Ray Image Sensor (2014)

This paper describes a solid-state image sensor for high-speed X-ray imaging. The sensor is made up of a light sensitive detector layer bump-bonded to a readout integrated circuit (ROIC). The detector layer is high resistivity n-type silicon and is fully depleted in operation. The p-implanted islands are used to define pixel regions with 100-μm × 100-μm area. The detector layer contains 852 × 209 pixels indium bump-bonded to four identical CMOS ROICs. Each ROIC contains 213 × 209 pixels and is fabricated using a 0.25-μm CMOS process. The ROIC utilizes a capacitive transimpedance amplifier-type front-end coupled to a switched capacitor analog memory. This architecture allows storage of eight frames for high-speed burst imaging of up to a million frames per second, followed by a slower multiplexed readout. Details of the sensor design and operation are presented together with characterization results.