gebhart/patrepeval huggingface dataset:
Beyond mass spectrometry, the next step in proteomics (2020)

Proteins can be the root cause of a disease, and they can be used to cure it. The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. With the advent of scalable, single-molecule DNA sequencing, genomics and transcriptomics have since propelled medicine through improved sensitivity and lower costs, but proteomics has lagged behind. Currently, proteomics relies mainly on mass spectrometry (MS), but instead of truly sequencing, it classifies a protein and typically requires about a billion copies of a protein to do it. Here, we offer a survey that illuminates a few alternatives with the brightest prospects for identifying whole proteins and displacing MS for sequencing them. These alternatives all boast sensitivity superior to MS and promise to be scalable and seem to be adaptable to bioinformatics tools for calling the sequence of amino acids that constitute a protein.
Secure Password Transmission for Web Applications over Internet using Cryptography and Image Steganography (2015)

The significance of digital information security has been enhanced due to the boost of internet communication. Providing security for server client communication over the internet is a critical issue due to open world digital eavesdroppers. Generally, password authentication is required for establishing a connection between server and client environment. The client password is verified by the server ends to establish a valid connection. Successful password verification initiates the client and server to perform further secured request and response mechanisms. The problem of password authentication over insecure networks presents in many application areas, such as web login, remote logins of computer networks. Hence the significance of confidential password transmission over insecure internet becomes the necessity of secure authentication. In this paper, we proposed a secure password transmission over the internet for authentication of server/client environment using encryption and image steganography. Client password is first encrypted and embedded in an image using steganographic algorithm at client side and transmitted over unsecured network to the web server. On the other side server extract safely password from image steganography decoding algorithm, decrypt and verified it's with SQL database server. In case if the intruder steals the image over network he/she will be unable to decode the password from the image. The prototype of the proposed method is implemented using JavaScript, Html, and ASP.net for verification purpose.
A Method for Signal Coordination in Large-Scale Urban Road Networks (2015)

Signal coordination methods have been widely investigated to improve the performance of traffic control system in urban road networks. Due to the large-scale of road networks and numerous time-varying parameters, a basic challenge faced by these methods is the high computational complexity. In this research, a method to optimize and coordinate the traffic signal in urban road networks is developed, which deals with this challenge by decomposing the network into several arterial roads and scattered intersections. As a result, an area coordination problem has been solved by coordinating several principal arterial roads and isolated intersections. Firstly, we propose a bandwidth oriented two-way arterial coordination approach. In contrast to previous methods, one important feature of the proposed approach is that not only the phases which provide right of way to the coordinated directions but the phases which provide right of way to the uncoordinated directions are considered. Secondly, to reduce the computational complexity a network decomposition approach is designed, in which a priority level index is defined to quantify the priority level of each road. Then, a coordination algorithm for the whole road network is developed. Finally, effectiveness and efficiency of the proposed method are validated by simulations on VISSIM.
Object-oriented techniques in robot manipulator control software development (2001)

Software development for the control of robotic manipulators is a complex task because it requires expertise in many areas (e.g., robotics, real-time programming, hardware integration, concurrency, etc.). Because of this fact, it is difficult to develop a common software platform supporting the diversity of robotic research areas and robotic hardware. Even though a large number of robotic languages, libraries, and tools have been created, they are seldom reused. That is, many research teams develop their own software platform from scratch because existing platforms are too inflexible with regard to modifications and too complex to understand. The authors of this paper believe that code reuse is fostered by providing a lightweight platform rather than requiring the user to modify a complex system. Along this line of reasoning, this paper describes the QMotor Robotic Toolkit (QMotor RTK). The RTK is a set of C++ libraries and programs that follow object-oriented concepts to ensure code reuse, modularity, scalability, and an intuitive code structure. The RTK is a homogeneous system that consists only of PC software. The RTK includes joint level control programs for the Puma 560 manipulator, the Barren Whole Arm Manipulator (WAM), and the Integrated Motion Inc. (IMI) two-link manipulator as well as a joint level trajectory generator and a graphical user interface (GUI).
A parallel processor for evaluation studies (1976)

The Multi Associative Processor system is a multiple control unit parallel processor capable of executing a maximum of 8 single-instruction-stream, multiple-data-stream programs simultaneously. The architecture supports parallelism at two levels: the lower level is the tightly coupled parallelism typical of array processors, and the higher level is the more loosely coupled parallelism between independent processes. The architecture of the machine is described and an example program for the machine is given to illustrate many of the concepts of the architecture. Measurement and evaluation studies on the machine are also briefly discussed.
Application of Arbuscular Mycorrhizae Glomus iranicum var. tenuihypharum var. nova in Intensive Agriculture: A Study Case (2017)

Intensive agriculture contributes to a decrease in microbial biomass and crop yields, while accelerating soil degradation. Arbuscular mycorrhizae associations have direct benefits for plant nutrition, and may be considered a useful tool in modern agriculture. Notwithstanding the widespread knowledge of these benefits, their use in intensive farming systems has until now been ineffectual, because most mycorrhizal species have low tolerance toward high concentrations of nutrients and are poorly adapted to the soil and/or mycorrhizal functioning. The aim of this work was to test the efficacy of an arbuscular mycorrhizal (AM) fungus, Glomus iranicum var. tenuihypharum on lettuce and table grape crops in different intensive farming systems. The variables studied were root colonization percentage, external mycelium concentration, gas exchange, photosynthetic activity, root starch concentration and plant nutrition. The main finding was that the fungus is tolerant of a wide range of soil pH values, high salinity levels and abundant external mycelium. In lettuce, it produced significant increases in plant physiological activity and productivity (10%-15%); and in table grapes, increases of 12%-45% in yield were achieved for more than three years in Crimson variety, and significant increases in fruit cluster weight, color uniformity and Brix (Bx). The AM species is protected by two patents and is a component of MycoUp, MycoUp Activ, Resid HC and Resid MG, whose commercial application has spread to more than 30 countries, with increments in crop yields of 8%-45% in lines as varied as leaf vegetables, berries, fruit, olives, grapes, greenhouse crops and cereals.
B cell signatures and tertiary lymphoid structures contribute to outcome in head and neck squamous cell carcinoma (2021)

Current immunotherapy paradigms aim to reinvigorate CD8<sup>+</sup> T cells, but the contribution of humoral immunity to antitumor immunity remains understudied. Here, we demonstrate that in head and neck squamous cell carcinoma (HNSCC) caused by human papillomavirus infection (HPV<sup>+</sup>), patients have transcriptional signatures of germinal center (GC) tumor infiltrating B cells (TIL-Bs) and spatial organization of immune cells consistent with tertiary lymphoid structures (TLS) with GCs, both of which correlate with favorable outcome. GC TIL-Bs in HPV<sup>+</sup> HNSCC are characterized by distinct waves of gene expression consistent with dark zone, light zone and a transitional state of GC B cells. Semaphorin 4a expression is enhanced on GC TIL-Bs present in TLS of HPV<sup>+</sup> HNSCC and during the differentiation of TIL-Bs. Our study suggests that therapeutics to enhance TIL-B responses in HNSCC should be prioritized in future studies to determine if they can complement current T cell mediated immunotherapies.
Topical Imiquimod Plus Nab-paclitaxel for Breast Cancer Cutaneous Metastases (2017)

clinicaltrials.gov Identifier: NCT00821964.
Analysis of ground fault currents in isolated and non-isolated charging modules in electric vehicles (2015)

The paper compares generic on board charger module (OBCM) topologies with respect to ground fault current detection and interruption. Ground fault current in isolated charging modules is very small due to the galvanic isolation between the input and output sides. In non-isolated charging modules, the paper shows the contributing components of the system to the generation of ground fault current. The ground fault current interrupt circuit is explained and compared in both topologies. Performance and parametric measures are used to compare the two topologies in MATLAB/Simulink.
A comparison of hashing schemes for address lookup in computer networks (1992)

Using a trace of address references, the author compares the efficiency of several different hashing functions such as cyclic redundancy checking polynomials, Fletcher checksum, folding of address octets using the exclusive-OR operation, and bit extraction from the address. Guidelines are provided for determining the size of hash masks required to achieve a specified level of performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Minicell‐based fungal RNAi delivery for sustainable crop protection (2021)

Spray-induced gene silencing (SIGS) using topical dsRNA applications has risen as a promising, target-specific, and environmentally friendly disease management strategy against phytopathogenic fungi. However, dsRNA stability, efficacy, and scalability are still the main constraints facing SIGS broader application. Here we show that Escherichia coli-derived anucleated minicells can be utilized as a cost-effective, scalable platform for dsRNA production and encapsulation. We demonstrated that minicell-encapsulated dsRNA (ME-dsRNA) was shielded from RNase degradation and stabilized on strawberry surfaces, allowing dsRNA persistence in field-like conditions. ME-dsRNAs targeting chitin synthase class III (Chs3a, Chs3b) and DICER-like proteins (DCL1 and DCL2) genes of Botryotinia fuckeliana selectively knocked-down the target genes and led to significant fungal growth inhibition in vitro. We also observed a compensatory relationship between DCL1 and DCL2 gene transcripts, where the silencing of one gene upregulated the expression of the other. Contrary to naked-dsRNAs, ME-dsRNAs halted disease progression in strawberries for 12 days under greenhouse conditions. These results elucidate the potential of ME-dsRNAs to enable the commercial application of RNAi-based, species-specific biocontrols comparable in efficacy to conventional synthetics. ME-dsRNAs offer a platform that can readily be translated to large-scale production and deployed in open-field applications to control grey mould in strawberries.
Language Identification in Short Utterances Using Long Short-Term Memory (LSTM) Recurrent Neural Networks (2016)

Long Short Term Memory (LSTM) Recurrent Neural Networks (RNNs) have recently outperformed other state-of-the-art approaches, such as i-vector and Deep Neural Networks (DNNs), in automatic Language Identification (LID), particularly when dealing with very short utterances (∼3s). In this contribution we present an open-source, end-to-end, LSTM RNN system running on limited computational resources (a single GPU) that outperforms a reference i-vector system on a subset of the NIST Language Recognition Evaluation (8 target languages, 3s task) by up to a 26%. This result is in line with previously published research using proprietary LSTM implementations and huge computational resources, which made these former results hardly reproducible. Further, we extend those previous experiments modeling unseen languages (out of set, OOS, modeling), which is crucial in real applications. Results show that a LSTM RNN with OOS modeling is able to detect these languages and generalizes robustly to unseen OOS languages. Finally, we also analyze the effect of even more limited test data (from 2.25s to 0.1s) proving that with as little as 0.5s an accuracy of over 50% can be achieved.
Job Stress, Heart Rate Variability and Metabolic Syndrome (2004)

3 ) Objective: A growing body of literature has documented that job stress is associated with the development of cardiovascular disease. Nevertheless, the pathophysiological mechanism of this association remains unclear. Therefore, we tried to elucidate the relationship between job stress, heart rate variability and metabolic syndrome. Method: The study design was cross-sectional, and 169 industrial workers were recruited. A structured-questionnaire was used to assess the general characteristics and job characteristics (work demand, decision latitude). Heart rate variability (HRV) was recorded using SA-2000 (medi-core). HRV was assessed by time-domain and by frequency-domain analyses. Time domain analysis was performed for SDNN (Standard Deviation of NN interval), and spectral analysis for low-frequency (LF), high-frequency (HF) and total frequency power. Metabolic syndrome was defined on the basis of clustering of risk factors, when three or more of the fol - lowing cardiovascular risk factors were included in the fifth quintile: glucose, systolic blood pressure, HDL-cholesterol (bottom quintile), triglyceride and waist-hip ratio. Results: The results showed that job characteristics were not associated with cardiovascular risk factors. The high strain group had a less favorable cardiovascular risk profile with higher levels of blood pressure, glucose, homocysteine, and clotting factor than the lower strain group (low strain+passive+active group), but the difference was not statistically significant. The SDNN of HRV was significantly lower in the high strain group than in the low strain group. The prevalence of metabolic syndrome in the low strain, passive, active and high strain groups was 9.7%, 13.9%, 14.9% and 23.8%, respectively. In the high strain group, the metabolic syn - drome was significantly related to a decreased SDNN. However, we could not find a significant association in LF/HF ratio. Conclusion: This result suggests that decreased HRV does not play a role in the development of disease; however, it can induce cardiovascular abnormalities or dysfunctions related to the onset of heart disease among high risk groups.
A quantitative conduction model for a low-resistance nonalloyed ohmic contact structure utilizing low-temperature-grown GaAs (2000)

We present a quantitative conduction model for nonalloyed ohmic contacts to n-type GaAs (n:GaAs) which employ a surface layer of low-temperature-grown GaAs (LTG:GaAs). The energy band edge profile for the contact structure is calculated by solving Poisson’s equation and invoking Fermi statistics using deep donor band and acceptor state parameters for the LTG:GaAs which are consistent with measured bulk and surface electrical properties of this material. The specific contact resistance is then calculated using an analytic expression for tunneling conduction through an equivalent uniformly doped Schottky barrier. The model has been used to fit measured specific contact resistances versus LTG:GaAs layer thickness and versus measurement temperature. These comparisons provide insights into the contact mechanism (electron tunneling between metal states and conduction band states in n:GaAs) and indicate that low barrier heights (0.3–0.5 V) and high activated donor densities (∼1×1020 cm−3) have been achieved in these ex situ contacts.
Phage Display Derived Monoclonal Antibodies: From Bench to Bedside (2020)

Monoclonal antibodies (mAbs) have become one of the most important classes of biopharmaceutical products, and they continue to dominate the universe of biopharmaceutical markets in terms of approval and sales. They are the most profitable single product class, where they represent six of the top ten selling drugs. At the beginning of the 1990s, an <i>in vitro</i> antibody selection technology known as antibody phage display was developed by John McCafferty and Sir. Gregory Winter that enabled the discovery of human antibodies for diverse applications, particularly antibody-based drugs. They created combinatorial antibody libraries on filamentous phage to be utilized for generating antigen specific antibodies in a matter of weeks. Since then, more than 70 phage-derived antibodies entered clinical studies and 14 of them have been approved. These antibodies are indicated for cancer, and non-cancer medical conditions, such as inflammatory, optical, infectious, or immunological diseases. This review will illustrate the utility of phage display as a powerful platform for therapeutic antibodies discovery and describe in detail all the approved mAbs derived from phage display.
Figurative Privacy Control of SIP-Based Narrowcasting (2008)

In traditional conferencing systems, participants have little or no privacy, as their voices are by default shared with all others in a session. Such systems cannot offer participants the options of muting and deafening other members. The concept of narrowcasting can be applied to make these kinds of filters available in multimedia conferencing systems. Our system treats media sinks (in the simplest case, listeners) as full citizens, peers of the media sources (con- versants' voices), and we defined therefore duals of mute & select : deafen & attend, which respectively block a sink or focus on it to the exclusion of others. In this article, we describe our prototyped system, which uses existing standard Session Initiation Protocol (SIP) methods to control fine-grained narrowcasting sessions. The design considers the policy configured by the participants and provides a policy evaluation algorithm for media mixing and delivery. We have integrated a "virtual reality"-style interface with this SIP backend to display and control articulated narrowcasting with figurative avatars.
Climbing droplets driven by mechanowetting on transverse waves (2019)

Many applications in modern technology, such as self-cleaning surfaces and digital microfluidics, require control over individual fluid droplets on flat surfaces. Existing techniques may suffer from side effects resulting from high electric fields and high temperatures. Here, we introduce a markedly different method, termed "mechanowetting," that is based on the surface tension-controlled droplet motion on deforming surfaces. The method is demonstrated by transporting droplets using transverse surface waves on horizontal and (vertically) inclined surfaces at transport velocities equal to the wave speed. We fully capture the fundamental mechanism of the mechanowetting force numerically and theoretically and establish its dependence on the fluid properties, surface energy, and wave parameters. Mechanowetting has the potential to lead to a range of new applications that feature droplet control through dynamic surface deformations.
Negative refractive index metamaterials (2006)

Engineered materials composed of designed inclusions can exhibit exotic and unique electromagnetic properties not inherent in the individual constituent components. These artificially structured composites, known as metamaterials, have the potential to fill critical voids in the electromagnetic spectrum where material response is limited and enable the construction of novel devices. Recently, metamaterials that display negative refractive index – a property not found in any known naturally occurring material – have drawn significant scientific interest, underscoring the remarkable potential of metamaterials to facilitate new developments in electromagnetism.
Functional expression and characterization of a plant K<sup>+</sup> channel gene in a plant cell model (1998)

To express and characterize the function of a plant ion channel gene in plant cells, it is necessary to establish a model system that lacks the endogenous channel activity and can be genetically transformed. Patch-clamp techniques were used to survey voltage-dependent K+ channel activities in different cell types of tobacco plants. Interestingly, mesophyll cells lacked the inward K+ current found in guard cells. A transgene containing the inward K+ channel gene KAT1 from Arabidopsis was constructed and expressed in the mesophyll cells of transgenic tobacco plants. Expression of the KAT1 gene produced a large voltage-dependent inward current across the plasma membrane of mesophyll protoplasts. The KAT1 current was carried by K+ and activated at voltage more negative than -100 mV. This K+ current had a single-channel conductance of 6-10 pS and was highly sensitive to TEA, Cs+ and Ba2+. This study represents the first example in which a plant ion channel gene is functionally expressed and studied in plant cells. Tobacco mesophyll cells will provide a useful model for functional characterization of inward K+ channel genes from higher plants.
Synthesis and biological evaluations of some 2-thioxo-1,2,3,4-tetrahydropyrimidine derivatives. (1991)

Several 1,2,3,4-tetrahydro-6-methyl-4-(substituted phenyl)-2-thioxo-5-pyrimidinecarboxylic acid methyl esters were synthesized by condensing thiourea with methyl acetoacetate and substituted benzaldehydes according to Biginelli reaction. The structures of the compounds were confirmed by spectral and elemental analysis and their calcium antagonistic activities were investigated. Furthermore, the compounds synthesized in previous and present studies were evaluated for their antiaggregating activities.
Antioxidant activity of five vegetables traditionally consumed by south-Asian migrants in Bradford, Yorkshire, UK (2005)

Five vegetables traditionally consumed among South-Asian migrants in Bradford (Yorkshire, UK) were tested for their free radical scavenging activity (FRSA) in the DPPH (1,1-diphenyl-2-picrylhydrazil radical) screening assay (using extracts prepared both by cold maceration and also by boiling the plant in the solvent under reflux) and for their in vitro non-enzymatic inhibition of bovine brain lipid peroxidation. In both antioxidant assays a strong activity was shown by extracts derived from okra (Abelmoschus esculentus, Malvaceae) fruits and charungli (Caralluma edulis, Asclepiadaceae) aerial parts. Extracts from bitter melon (Momordica charantia, Cucurbitaceae) and angular loofah (Luffa acutangula) showed a significant difference in the FRSA between the extract obtained by using cold maceration and that prepared by boiling the plant in the solvent under reflux, suggesting the chemical composition of the plant changed during the heating process, leading to an increase in the amount of antioxidant components. These findings confirm the great interest of the nutraceutical sciences in extracts of Caralluma edulis, whose phytochemistry and phytopharmacology should be investigated further in order to detect possible phytotherapeutic uses in the prevention of ageing related diseases (ARDs) and Alzheimer disease (AD).