gebhart/patrepeval huggingface dataset:
A new signaling pathway of dioxin receptor ligands through targeted protein degradation (2008)

Fat-soluble ligands for ligand binding-dependent sequence-specific transcription factors, such as sex steroid hormones and environmental toxins, transduce signals via a target gene-selective transcriptional regulatory system. However, the mechanisms of cellular perception of fat-soluble ligand signals through other targetselective systems are unclear. The ubiquitin-proteasome system regulates target protein-selective degradation, in which the E3 ubiquitin ligases determine target selectivity. Here, we characterise a fat-soluble liganddependent ubiquitin ligase complex, where dioxin receptor (AhR) acts as a ligand-dependent component of the cullin 4B ubiquitin ligase complex, CUL4B AhR . The ligand-activated AhR is integrated as a substratespecific adapter component within the CUL4B AhR complex to promote degradation of sex steroid receptors, reflecting adverse sex hormone-related actions of AhR ligands. Our findings uncover a novel role for AhR as an atypical component of ubiquitin ligase, and demonstrate a signaling pathway in which fat-soluble ligands regulate target protein-selective degradation through a ubiquitin ligase complex.
An Entropy-based Clustering in Mobile Ad hoc Networks (2006)

The distributiveness of mobile ad hoc networks makes resource allocation strategies very challenging since there is no central node to coordinate and monitor the activities of all the nodes in the network. Since a single node cannot be delegated to act as a centralized authority due to limitations in the transmission range, several delegated nodes may coordinate the activities in certain zones. This methodology is generally referred to as clustering and the nodes are called clusterheads. The clusterheads employ centralized algorithms in its cluster; however, the clusterheads themselves are distributive in nature. In this paper, we propose a clustering method i.e., identify the clusterheads among all the nodes. Though there are several clustering algorithms that have been proposed; however, to the best of our knowledge, there is none that characterizes the different node parameters in terms of entropy. Entropy is a measure of information. We use the local information available to every node to determine the mutual information. We considered two parameters in the selection procedure, namely, energy and mobility. Extensive simulations have been conducted and the performance of the proposed clustering scheme has been shown in terms of the average number of clusterheads or clusters, the average number of cluster changes, and the average connectivity. The results demonstrate that the mutual information captured through entropy is very effective in determining the most suitable clusterheads
Real-Time 4D Full-Range Complex Fourier-domain OCT with Non-Uniform Fast Fourier Transform Based on Dual Graphics Processing Units Architecture (2011)

We implemented real-time 4D full-range complex FD-OCT with non-uniform fast Fourier transform processed in dual graphics processing units architecture. With a 128,000 A-scan/second line scan spectrometer, we obtained 5.0 volume/second C-scan speed.
Common polymorphisms and alternative splicing in the ILT3 gene are not associated with atopy (2000)

Abstract Recently, a linkage of the chromosomal region 19q13.4 with bronchial asthma has been demonstrated. This region harbours the so‐called leucocyte receptor cluster with the gene for immunoglobulin‐like‐transcript 3 (ILT3) as a member. ILT3 represents an inhibitory receptor bearing three immunoreceptor tyrosine inhibitory motifs (ITIM). The protein mediates downregulation of cell activation through recruitment of different SH2‐containing protein tyrosine phosphatases. With regard to the negative immunoregulatory function particularly on B‐cells, ILT3 represents a candidate gene for atopy and asthma. The aim of this study was to screen for common polymorphisms in the gene coding for ILT3 and to test for association with the atopic phenotype. Using single‐stranded conformal polymorphism‐analysis and direct genomic sequencing seven polymorphisms, three mutations, a common deletion of 7 bp in the third intron and evidence for further alternative splicing of the ILT3 gene were found. Although no association was found with atopy phenotypes, it might prove useful to test for association with bronchial asthma.
Time Symmetry in the Quantum Process of Measurement (1964)

We examine the assertion that the "reduction of the wave packet," implicit in the quantum theory of measurement introduces into the foundations of quantum physics a time-asymmetric element, which in turn leads to irreversibility. We argue that this time assymmetry is actually related to the manner in which statistical ensembles are constructed. If we construct an ensemble time symmetrically by using both initial and final states of the system to delimit the sample, then the resulting probability distribution turns out to be time symmetric as well. The conventional expressions for prediction as well as those for "retrodiction" may be recovered from the time-symmetric expressions formally by separating the final (or the initial) selection procedure from the measurements under consideration by sequences of "coherence destroying" manipulations. We can proceed from this situation, which resembles prediction, to true prediction (which does not involve any postselection) by adding to the time-symmetric theory a postulate which asserts that ensembles with unambiguous probability distributions may be constructed on the basis of preselection only. If, as we believe, the validity of this postulate and the falsity of its time reverse result from the macroscopic irreversibility of our universe as a whole, then the basic laws of quantum physics, including those referring to measurements, are as completely time symmetric as the laws of classical physics. As a by-product of our analysis, we also find that during the time interval between two noncommuting observations, we may assign to a system the quantum state corresponding to the observation that follows with as much justification as we assign, ordinarily, the state corresponding to the preceding measurement.
Photon-Counting OTDR for Local Birefringence and Fault Analysis in the Metro Environment (2004)

Optical time domain reflectometery (OTDR) is one of the most used measurement techniques in the characterization of optical fiber links. In this paper, we present a thorough investigation of an OTDR using a Peltier cooled photon-counting detector at 1.55 um. Due to its superior spatial resolution and the absence of classical dead-zones, it is well suited for detailed, high resolution analysis of problem zones. We give a detailed analysis of its performance, and also demonstrate that a polarization-sensitive photon-counting OTDR can be used to extract local birefringences too large to be measured with standard P-OTDRs.
Digitally Implemented Average Current-Mode Control in Discontinuous Conduction Mode PFC Rectifier (2011)

This paper proposes a digital average current-mode control method in discontinuous conduction mode (DCM) power factor correction rectifier. The proposed control technique does not estimate, but directly senses the average value of the inductor current in each switching cycle. It is implemented by means of a conventional current sensing circuit and a microcontroller. The calculation burden of the microcontroller is the same with that of conventional two-loop-controlled converter because the additional calculation process is not required. The control method achieves lower total harmonic distortion and higher power factor than the conventional technique. Experimental results with a 200-W prototype verify the feasibility and performance of the proposed control method.
RS‐127445: a selective, high affinity, orally bioavailable 5‐HT<sub>2B</sub> receptor antagonist (1999)

Efforts to define precisely the role of 5-HT2B receptors in normal and disease processes have been hindered by the absence of selective antagonists. To address this deficiency, we developed a series of naphthylpyrimidines as potentially useful 5-HT2B receptor antagonists. RS-127445 (2-amino-4-(4-fluoronaphth-1-yl)-6-isopropylpyrimidine) was found to have nanomolar affinity for the 5-HT2B receptor (pKi = 9.5+/-0.1) and 1,000 fold selectivity for this receptor as compared to numerous other receptor and ion channel binding sites. In cells expressing human recombinant 5-HT2B receptors, RS-127445 potently antagonized 5-HT-evoked formation of inositol phosphates (pK(B) = 9.5+/-0.1) and 5-HT-evoked increases in intracellular calcium (pIC50 = 10.4+/-0.1). RS-127445 also blocked 5-HT-evoked contraction of rat isolated stomach fundus (pA2 = 9.5+/-1.1) and (+/-)alpha-methyl-5-HT-mediated relaxation of the rat jugular vein (pA2 = 9.9+/-0.3). RS-127445 had no detectable intrinsic activity in these assays. In rats, the fraction of RS-127445 that was bioavailable via the oral or intraperitoneal routes was 14 and 60% respectively. Intraperitoneal administration of RS-127445 (5 mg kg(-1)) produced plasma concentrations predicted to fully saturate accessible 5-HT2B receptors for at least 4 h. In conclusion, RS-127445 is a selective, high affinity 5-HT2B receptor antagonist suitable for use is vivo. The therapeutic potential of this molecule is being further evaluated.
Mice with Very Low Expression of the Vesicular Monoamine Transporter 2 Gene Survive into Adulthood: Potential Mouse Model for Parkinsonism (2001)

We have created a transgenic mouse with a hypomorphic allele of the vesicular monoamine transporter 2 (Vmat2) gene by gene targeting. These mice (KA1) have profound changes in monoamine metabolism and function and survive into adulthood. Specifically, these animals express very low levels of VMAT2, an endogenous protein which sequesters monoamines intracellularly into vesicles, a process that, in addition to being important in normal transmission, may also act to keep intracellular levels of the monoamine neurotransmitters below potentially toxic thresholds. Homozygous mice show large reductions in brain tissue monoamines, motor impairments, enhanced sensitivity to dopamine agonism, and changes in the chemical neuroanatomy of the striatum that are consistent with alterations in the balance of the striatonigral (direct) and striatopallidal (indirect) pathways. The VMAT2-deficient KA1 mice are also more vulnerable to the neurotoxic effects of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine in terms of nigral dopamine cell death. We suggest that the mice may be of value in examining, long term, the insidious damaging consequences of abnormal intracellular handling of monoamines. On the basis of our current findings, the mice are likely to prove of immediate interest to aspects of the symptomatology of parkinsonism. They may also, however, be of use in probing other aspects of monoaminergic function and dysfunction in the brain, the latter making important contributions to the pathogenesis of schizophrenia and addiction.
All Your IFCException Are Belong to Us (2013)

Existing designs for fine-grained, dynamic information-flow control assume that it is acceptable to terminate the entire system when an incorrect flow is detected-i.e, they give up availability for the sake of confidentiality and integrity. This is an unrealistic limitation for systems such as long-running servers. We identify public labels and delayed exceptions as crucial ingredients for making information-flow errors recoverable in a sound and usable language, and we propose two new error-handling mechanisms that make all errors recoverable. The first mechanism builds directly on these basic ingredients, using not-a-values (NaVs) and data flow to propagate errors. The second mechanism adapts the standard exception model to satisfy the extra constraints arising from information flow control, converting thrown exceptions to delayed ones at certain points. We prove that both mechanisms enjoy the fundamental soundness property of non-interference. Finally, we describe a prototype implementation of a full-scale language with NaVs and report on our experience building robust software components in this setting.
Perceiving, remembering, and communicating structure in events. (2001)

How do people perceive routine events, such as making a bed, as these events unfold in time? Research on knowledge structures suggests that people conceive of events as goal-directed partonomic hierarchies. Here, participants segmented videos of events into coarse and fine units on separate viewings; some described the activity of each unit as well. Both segmentation and descriptions support the hierarchical bias hypothesis in event perception: Observers spontaneously encoded the events in terms of partonomic hierarchies. Hierarchical organization was strengthened by simultaneous description and, to a weaker extent, by familiarity. Describing from memory rather than perception yielded fewer units but did not alter the qualitative nature of the descriptions. Although the descriptions were telegraphic and without communicative intent, their hierarchical structure was evident to naive readers. The data suggest that cognitive schemata mediate between perceptual and functional information about events and indicate that these knowledge structures may be organized around object/action units.
Picomolar Inhibition of Plasmepsin V, an Essential Malaria Protease, Achieved Exploiting the Prime Region (2015)

Malaria is an infectious disease caused by Plasmodium parasites. It results in an annual death-toll of ~ 600,000. Resistance to all medications currently in use exists, and novel antimalarial drugs are urgently needed. Plasmepsin V (PmV) is an essential Plasmodium protease and a highly promising antimalarial target, which still lacks molecular characterization and drug-like inhibitors. PmV, cleaving the PExEl motif, is the key enzyme for PExEl-secretion, an indispensable parasitic process for virulence and infection. Here, we describe the accessibility of PmV catalytic pockets to inhibitors and propose a novel strategy for PmV inhibition. We also provide molecular and structural data suitable for future drug development. Using high-throughput platforms, we identified a novel scaffold that interferes with PmV in-vitro at picomolar ranges (~ 1,000-fold more active than available compounds). Via systematic replacement of P and P' regions, we assayed the physico-chemical requirements for PmV inhibition, achieving an unprecedented IC50 of ~20 pM. The hydroxyethylamine moiety, the hydrogen acceptor group in P2', the lipophilic groups upstream to P3, the arginine and other possible substitutions in position P3 proved to be critically important elements in achieving potent inhibition. In-silico analyses provided essential QSAR information and model validation. Our inhibitors act 'on-target', confirmed by cellular interference of PmV function and biochemical interaction with inhibitors. Our inhibitors are poorly performing against parasite growth, possibly due to poor stability of their peptidic component and trans-membrane permeability. The lowest IC50 for parasite growth inhibition was ~ 15 μM. Analysis of inhibitor internalization revealed important pharmacokinetic features for PExEl-based molecules. Our work disclosed novel pursuable drug design strategies for highly efficient PmV inhibition highlighting novel molecular elements necessary for picomolar activity against PmV. All the presented data are discussed in respect to human aspartic proteases and previously reported inhibitors, highlighting differences and proposing new strategies for drug development.
An approach of a knowledge management system in an automated manufacturing environment (2008)

In this paper, our focus is towards incorporation of a knowledge management systems in remote human machine interface devices (e.g. Personal Digital Assistants) for extracting concrete and precise information and knowledge about manufacturing systems and processes in highly automated manufacturing environment. By introducing the information system based on precise knowledge management approach in the manufacturing environment helps the user in accessing the information material in an organized form so that on-process modification and optimization can be done faster, safer and simpler depending upon the maturity level of the user.
Survey of indoor optical camera communication (OCC) systems for the Internet of lights (2017)

In this paper, we propose the architecture and schemes of optical camera communication (OCC) system for the internet of lights (IoL) comprising an attentive indoor environment in which rolling-shutter cameras (including smartphone cameras) are used to receive data from light sources. Evidently, the challenges of system mainly come from the receiver side because the primary purpose of cameras is to capture image while the communication purpose is secondary. The challenges include the camera's rolling shutter mechanism, its low and time-variant frame rate (e.g. no greater than 30fps), and the narrow bandwidth response (i.e. several kHz baseband). Also, for the illumination purpose that is the primary functionality of lighting system, the requirements of flicker-free modulation enabling the dimming capacity in the indoor environment are within the discussion. Simulation, numerical analysis and experiment results are given to compare different OCC systems that serve the connected lighting platform.
Eigenvalue based Spectrum Sensing Algorithms for Cognitive Radio (2008)

Spectrum sensing is a fundamental component is a cognitive radio. In this paper, we propose new sensing methods based on the eigenvalues of the covariance matrix of signals received at the secondary users. In particular, two sensing algorithms are suggested, one is based on the ratio of the maximum eigenvalue to minimum eigenvalue; the other is based on the ratio of the average eigenvalue to minimum eigenvalue. Using some latest random matrix theories (RMT), we quantify the distributions of these ratios and derive the probabilities of false alarm and probabilities of detection for the proposed algorithms. We also find the thresholds of the methods for a given probability of false alarm. The proposed methods overcome the noise uncertainty problem, and can even perform better than the ideal energy detection when the signals to be detected are highly correlated. The methods can be used for various signal detection applications without requiring the knowledge of signal, channel and noise power. Simulations based on randomly generated signals, wireless microphone signals and captured ATSC DTV signals are presented to verify the effectiveness of the proposed methods.
Acceleration of Dijkstra's algorithm on multi-core processors (2018)

The Single Source Shortest Path (SSSP) problem has been solved using various algorithms. We focus on accelerating a well known SSSP algorithm, the Dijkstra's algorithm using a multi-core CPU. We achieve acceleration by using the iParallel kernel, a hybrid kernel that runs on the sequential as well as parallel kernels intelligently. Our experimental results help find an optimal threshold to exploit parallelism for different sizes of the search terrain. We have achieved an overall acceleration of -48% and -51% on a dual-core ARM A9 processor and a 16-core Epiphany co-processor respectively.
Microbial Transglutaminase and c‐myc‐Tag: A Strong Couple for the Functionalization of Antibody‐Like Protein Scaffolds from Discovery Platforms (2015)

Antibody-like proteins selected from discovery platforms are preferentially functionalized by site-specific modification as this approach preserves the binding abilities and allows a side-by-side comparison of multiple conjugates. Here we present an enzymatic bioconjugation platform that targets the c-myc-tag peptide sequence (EQKLISEEDL) as a handle for the site-specific modification of antibody-like proteins. Microbial transglutaminase (MTGase) was exploited to form a stable isopeptide bond between the glutamine on the c-myc-tag and various primary-amine-functionalized substrates. We attached eight different functionalities to a c-myc-tagged antibody fragment and used these bioconjugates for downstream applications such as protein multimerization, immobilization on surfaces, fluorescence microscopy, fluorescence-activated cell sorting, and in vivo nuclear imaging. The results demonstrate the versatility of our conjugation strategy for transforming a c-myc-tagged protein into any desired probe.
Poured feed blocks using distillery by‐products as supplements for ruminants (1991)

Abstract A technique was developed in this study for preparing solid poured feed blocks as supplements for ruminants. Blocks containing liquid condensed solubles and dried distillers grain with solubles as the base material and protein source were prepared with different cementing agents. A method for testing the hardness of blocks, an index of the physical durability, was also developed. The hardness of blocks was positively related to the concentration of magnesium oxide and to the length of storage time. Ferrous sulphate, on the other hand, had a synergistic effect with magnesium oxide which accelerated the setting of blocks after 24 h. A feeding trial revealed a negative relationship between daily intake by cattle and hardness of blocks. Blocks prepared with about 4% magnesium oxide and 3% ferrous sulphate provide a dry, weather‐resistant supplement with a degree of hardness that allows an optimum rate of intake.
Responses to Bacteria, Virus, and Malaria Distinguish the Etiology of Pediatric Clinical Pneumonia (2015)

Combinations of plasma proteins accurately identified children with a respiratory syndrome who were likely to have bacterial infections and who would benefit from antibiotic therapy. When used in conjunction with malaria diagnostic tests, they may improve diagnostic specificity and simplify treatment decisions for clinicians.
A Users Guide for the NASA ANOPP Propeller Analysis System (1997)

The purpose of this report is to document improvements to the Propeller Analysis System of the Aircraft Noise Prediction Program (PAS-ANOPP) and to serve as a users guide. An overview of the functional modules and modifications made to the Propeller ANOPP system are described. Propeller noise predictions are made by executing a sequence of functional modules through the use of ANOPP control statements. The most commonly used ANOPP control statements are discussed with detailed examples demonstrating the use of each control statement. Originally, the Propeller Analysis System included the angle-of-attack only in the performance module. Recently, modifications have been made to also include angle-of-attack in the noise prediction module. A brief description of PAS prediction capabilities is presented which illustrate the input requirements necessary to run the code by way of ten templates. The purpose of the templates are to provide PAS users with complete examples which can be modified to serve their particular purposes. The examples include the use of different approximations in the computation of the noise and the effects of synchrophasing. Since modifications have been made to the original PAS-ANOPP, comparisons of the modified ANOPP and wind tunnel data are also included. Two appendices are attached at the end of this report which provide useful reference material. One appendix summarizes the PAS functional modules while the second provides a detailed discussion of the TABLE control statement.