gebhart/patrepeval huggingface dataset:
ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization (2015)

Reactome is a manually curated pathway annotation database for unveiling high-order biological pathways from high-throughput data. ReactomePA is an R/Bioconductor package providing enrichment analyses, including hypergeometric test and gene set enrichment analyses. A functional analysis can be applied to the genomic coordination obtained from a sequencing experiment to analyze the functional significance of genomic loci including cis-regulatory elements and non-coding regions. Comparison among different experiments is also supported. Moreover, ReactomePA provides several visualization functions to produce highly customizable, publication-quality figures. The source code and documents of ReactomePA are freely available through Bioconductor (http://www.bioconductor.org/packages/ReactomePA).
Designing and Observing Human-Robot Interactions for the Study of Social Development and its Disorders (2005)

This paper describes the design principle of our robot, Keepon, and reports the longitudinal observation of the interactions between the robot and children with developmental disorders. The robot, Keepon, is a small (12cm tall), simple (like a yellow snowman), soft (made of silicone rubber), creature-like robot, which was designed for studies on human social development and possible remedies for developmental disorders. We observed how children with developmental disorders interacted with the robot in an unconstrained playroom for more than a year (over 500 child-sessions). From these observations, we found that the children changed their ontological understanding of the robot, and consequently their way of interaction, as the interaction unfolded. We conclude that the robot's rather predictable responses gave the children a relaxed mood for spontaneous play, from which social communication with the robot and with another person would naturally emerge.
Study on moire between screen and panel structure in a LCD rear projection for HDTV (2002)

On an LCD (liquid crystal display) rear projector, dot matrix and screen structures make complex moire patterns. These disturbances have been alleviated by making the pitch of the screen pattern finer and by the introduction of a diffusion film between the Fresnel lens and the lenticular lens. an experiment for evaluation of the LCD projection system with rear screen was conducted. The results and the problems that remain to be solved are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Antibodies against Immunodominant Antigens of <i>Mycobacterium tuberculosis</i> in Subjects with Suspected Tuberculosis in the United States Compared by HIV Status (2010)

The immunodominance of Mycobacterium tuberculosis proteins malate synthase (MS) and MPT51 has been demonstrated in case-control studies with patients from countries in which tuberculosis (TB) is endemic. The value of these antigens for the serodiagnosis of TB now is evaluated in a cross-sectional study of pulmonary TB suspects in the United States diagnosed to have TB, HIV-associated TB, or other respiratory diseases (ORD). Serum antibody reactivity to recombinant purified MS and MPT51 was determined by enzyme-linked immunosorbent assays (ELISAs) of samples from TB suspects and well-characterized control groups. TB suspects were diagnosed with TB (n = 87; 49% sputum microscopy negative, 20% HIV(+)) or ORD (n = 63; 58% HIV(+)). Antibody reactivity to MS and MPT51 was significantly higher in U.S. HIV(+)/TB samples than in HIV(-)/TB samples (P < 0.001), and it was significantly higher in both TB groups than in control groups with latent TB infection (P < 0.001). Antibody reactivity to both antigens was higher in U.S. HIV(+)/TB samples than in HIV(+)/ORD samples (P = 0.052 for MS, P = 0.001 for MPT51) but not significantly different between HIV(-)/TB and HIV(-)/ORD. Among U.S. HIV(+) TB suspects, a positive anti-MPT51 antibody response was strongly and significantly associated with TB (odds ratio, 11.0; 95% confidence interval, 2.3 to 51.2; P = 0.002). These findings have implications for the adjunctive use of TB serodiagnosis with these antigens in HIV(+) subjects.
A novel method for parsing complex sentences in syntactically free languages (2002)

Free word-order languages cause problems when being analysed due to their great composing power and flexibility. The paper deals with the problems stemming from the analysis of complex sentences as well as with the adoption of suitable grammars to parse them in free word-order languages. Based on a careful study of large Greek corpora, we propose a method for parsing complex sentences in such languages that combines heuristic information and pattern matching techniques in early processing levels. Although this method has been implemented and tested in the Greek language, its theoretical background and results are language independent and can be proved useful for many practical applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Deciphering the Hidden Informational Content of Protein Sequences (2010)

Protein sequences encode both structure and foldability. Whereas the interrelationship of sequence and structure has been extensively investigated, the origins of folding efficiency are enigmatic. We demonstrate that the folding of proinsulin requires a flexible N-terminal hydrophobic residue that is dispensable for the structure, activity, and stability of the mature hormone. This residue (Phe(B1) in placental mammals) is variably positioned within crystal structures and exhibits (1)H NMR motional narrowing in solution. Despite such flexibility, its deletion impaired insulin chain combination and led in cell culture to formation of non-native disulfide isomers with impaired secretion of the variant proinsulin. Cellular folding and secretion were maintained by hydrophobic substitutions at B1 but markedly perturbed by polar or charged side chains. We propose that, during folding, a hydrophobic side chain at B1 anchors transient long-range interactions by a flexible N-terminal arm (residues B1-B8) to mediate kinetic or thermodynamic partitioning among disulfide intermediates. Evidence for the overall contribution of the arm to folding was obtained by alanine scanning mutagenesis. Together, our findings demonstrate that efficient folding of proinsulin requires N-terminal sequences that are dispensable in the native state. Such arm-dependent folding can be abrogated by mutations associated with β-cell dysfunction and neonatal diabetes mellitus.
Kinetic Analysis of Oxygen Reduction on Pt(111) in Acid Solutions:  Intrinsic Kinetic Parameters and Anion Adsorption Effects (2004)

Oxygen reduction reaction (ORR) kinetics in acid solutions was studied by analysis of the polarization curves obtained by rotating disk electrode method for Pt(111) in HClO4 and H2SO4 solutions. The model for ORR kinetic currents assumes that the intrinsic exchange current and Tafel slope are independent of anion adsorption. The site blocking and electronic effects of adsorbed OH (in HClO4) and bisulfate (in H2SO4) were evaluated with the adsorption isotherms incorporated in the model. The best fits yielded the intrinsic Tafel slope in the range from −118 to −130 mV/dec, supporting single electron transfer in the rate-determining step with the corresponding transfer coefficients equal to 0.50 and 0.45, respectively. In addition to site blocking, a negative electronic effect on ORR kinetics was found for both OH and bisulfate with the effect of the latter being much stronger. The deviation of the apparent Tafel slope in HClO4 from its intrinsic value can be fully accounted for by the site blocking and electronic effects of adsorbed OH ions, which vary with coverage over the mixed kinetic-diffusion controlled region. For Pt nanoparticle catalysts, the apparent Tafel slope is similar to that for Pt(111) in HClO4 and the positive potential shift is mainly due to the increase in apparent exchange current as effective surface area increases.
Basement membrane components in healing rabbit corneal epithelial wounds: immunofluorescence and ultrastructural studies. (1984)

The nature of the substrate that supports epithelial migration in vivo is of interest, particularly with respect to mechanisms of wound healing. Immunofluorescence and electron microscopy were used to search for common substrate components in prototype rabbit corneal wounds: epithelial scrape wounds, in which the corneal or conjunctival epithelium migrated over the denuded lamina densa of the corneal basement membrane (CBM), and superficial keratectomy, in which the corneal epithelium migrated over a bare stroma without CBM. The corneal epithelium moved rapidly over the CBM or stroma to cover the defect within 2-3 d, whereas the conjunctival epithelium required 1-2 wk. In all wounds, fibronectin and fibrin/fibrinogen were deposited onto the bare surface within 8 h after wounding and persisted under the migrating epithelium until migration was complete. Bullous pemphigoid antigen (BPA), a normal component of the CBM, was removed with the epithelium upon scrape wounding and reappeared in the CBM after migration was completed. In contrast, the conjunctival epithelium had a continuous subepithelial band of BPA out to the migrating tip. Laminin, also a normal component of the CBM, was not removed in the scrape wounds, indicating that the region of least resistance to shear stress was between the BPA and laminin layers. Laminin was removed by superficial keratectomy and was not detectable under the leading edge of the migrating cells. Laminin and BPA were restored in the CBM by 2-4 wk. Type IV collagen could not be detected in normal CBM, but was conspicuously present in conjunctival basement membrane and in blood vessels. Focal bands of type IV collagen did appear in the newly synthesized CBM 2-4 wk after keratectomy. These results argue that BPA, laminin, and type IV collagen are not essential for the migration of corneal epithelium during wound healing and support the hypothesis that fibronectin and fibrin/fibrinogen are the common, perhaps the essential, components of the provisional matrix that serves as a substrate until the permanent attachment components are regenerated.
Sensorless control of permanent magnet synchronous motor using extended Kalman filter (2004)

This paper presents the modeling, analysis, design and experimental validation of a robust sensorless control method for permanent magnet synchronous motor (PMSM) based on extended Kalman filter (EKF). A real-time PMSM and its EKF models in the MATLAB/Simulink simulation environment are developed. The position/speed sensorless control scheme along with the power electronic circuitry is modeled. The performance of the proposed control is assessed and verified for different types of dynamic and static torque loads. The robustness of the sensorless method is demonstrated by starting the motor with different rotor initial positions. The proposed EKF speed/position estimation method is also proved insensitive to the PMSM parameter variations. Proper operations of this EKF based sensorless control method for a high-speed permanent magnet synchronous machine are verified experimentally in the research laboratory at Honeywell.
Characterization of Electrogenerated Polypyrrole−Benzophenone Films Coated on Poly(pyrrole-methyl metacrylate) Optic-Conductive Fibers (2009)

A conductive surface was created for the development of a biosensing platform via chemical polymerization of pyrrole onto the surface of poly(methyl methacrylate) (PMMA) fibers, with a subsequent electrogeneration of a photoactive linker pyrrole-benzophenone (PyBz) monomer on the fiber surface. Irradiation of the benzophenone groups embedded in the polypyrrole (Ppy) films by UV (350 nm) formed active radicals, allowing covalent attachment of the desired biomaterials. Characterization and optimization of this platform were carried out, with the platform showing conductive, stable, thin, controllable, and light-transmissible film features. Various parameters such as time deposition, process temperature, and activator plus pyrrole monomer concentrations were examined in the study. The morphology and permeability of the optic-fiber PMMA fibers were investigated to examine mass transfer ability. Cyclic voltammetry and amperometry techniques were applied to characterize the electrical features of the surface and charge transfer. The platform potential was then demonstrated by the construction of both amperometric and optical biosensors.
G-749, a novel FLT3 kinase inhibitor, can overcome drug resistance for the treatment of acute myeloid leukemia (2014)

Aberrant activations of Fms-like tyrosine receptor kinase (FLT) 3 are implicated in the pathogenesis of 20% to 30% of patients with acute myeloid leukemia (AML). G-749 is a novel FLT3 inhibitor that showed potent and sustained inhibition of the FLT3 wild type and mutants including FLT3-ITD, FLT3-D835Y, FLT3-ITD/N676D, and FLT3-ITD/F691L in cellular assays. G-749 retained its inhibitory potency in various drug-resistance milieus such as patient plasma, FLT3 ligand surge, and stromal protection. Furthermore, it displayed potent antileukemic activity in bone marrow blasts from AML patients regardless of FLT3 mutation status, including those with little or only minor responses to AC220 or PKC412. Oral administration of G-749 yielded complete tumor regression and increased life span in animal models. Thus, G-749 appears to be a promising next-generation drug candidate for the treatment of relapsed and refractory AML patients with various FLT3-ITD/FLT3-TKD mutants and further shows the ability to overcome drug resistance.
Chemotherapeutic Compounds Targeting the DNA Double-Strand Break Repair Pathways: The Good, the Bad, and the Promising (2014)

The repair of DNA double-strand breaks (DSBs) is a critical cellular mechanism that exists to ensure genomic stability. DNA DSBs are the most deleterious type of insult to a cell's genetic material and can lead to genomic instability, apoptosis, or senescence. Incorrectly repaired DNA DSBs have the potential to produce chromosomal translocations and genomic instability, potentially leading to cancer. The prevalence of DNA DSBs in cancer due to unregulated growth and errors in repair opens up a potential therapeutic window in the treatment of cancers. The cellular response to DNA DSBs is comprised of two pathways to ensure DNA breaks are repaired: homologous recombination and non-homologous end joining. Identifying chemotherapeutic compounds targeting proteins involved in these DNA repair pathways has shown promise as a cancer therapy for patients, either as a monotherapy or in combination with genotoxic drugs. From the beginning, there have been a number of chemotherapeutic compounds that have yielded successful responses in the clinic, a number that have failed (CGK-733 and iniparib), and a number of promising targets for future studies identified. This review looks in detail at how the cell responds to these DNA DSBs and investigates the chemotherapeutic avenues that have been and are currently being explored to target this repair process.
An over 100 W AlGaN/GaN enhancement‐mode HEMT power amplifier with piezoelectric‐induced cap structure (2009)

Abstract A novel piezoelectric‐induced cap structure in an AlGaN/GaN high electron mobility transistor (HEMT) was developed for enhancement‐mode (E‐mode) operation with high maximum drain current density ( I dmax ), high breakdown voltage ( BV gd ) and small current collapse. Our developed cap structure consists of a thin GaN/AlN/ GaN triple‐layer, which reduces the sheet resistance ( R sh ) due to conduction band bending. The threshold voltage ( V th ) is +0.25 V with a high I dmax of 520 mA/mm, a high BV gd of 336 V and small current collapse by using the developed cap structure and a gate recess technique. The single‐chip AlGaN/GaN E‐mode HEMT amplifier achieved a high output power of 126 W at 2.5 GHz with improved distortion characteristics. This is the first report of an AlGaN/GaN E‐mode HEMT with an output power of over 100 W. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Maternal and perinatal implications of the use of human recombinant erythropoietin (1996)

Among the cases presented, no maternal and perinatal complications attributable to rHuEPO were registered. It is important that institutions report their experiences with the use of rHuEPO, given its restrictive indications and the limited experience of each institution.
Elastic Modulus Prediction of Asphalt Concrete (1999)

The distresses of asphalt pavement, which include fatigue, rutting, and low temperature cracking, are related to the elastic modulus of asphalt concrete (AC). In addition, the elastic modulus of AC is a design variable for asphalt pavement structural design when elastic-layer system theory is employed. However, in the most commonly used AC design methods (the Marshall, Hveem, and Superpave methods), the elastic modulus is not used as a control variable. Therefore, these design methods do not ensure that the desired elastic modulus of AC will be obtained. In this paper, AC is treated as a two-phase composite with aggregates dispersed in the asphalt matrix. Based on this treatment, a two-layer built-in micromechanical model of AC is developed by embedding an asphalt-coated circular aggregate into an equivalent AC medium. Using this model, an equation predicting the elastic modulus of AC is derived. The elastic modulus of AC predicted by the present model is compared with the Hashin and Shtrikman theoretical bounds and the Heukelom and Klomp equation. Using these comparisons, the proposed model is shown to be reasonable and applicable for predicting the elastic modulus of AC. Thus, the existing mix design approaches can be improved by using the modulus prediction model presented in this paper.
Esterification of Cellulose with Long Fatty Acid Chain through Mechanochemical Method (2021)

Mechanochemical reaction, a green synthetic esterification route was utilized to prepare long-chain cellulose esters from microcrystalline cellulose. The influence of reaction conditions such as reaction temperature and time were elucidated. Only low dosage of oleic acid, 1-butyl-3-metylimidazolium acetate, and p-toluenesulfonyl chloride were required. The success of modification reaction was confirmed by Fourier transforms infrared spectroscopy as a new absorbance peak at 1731 cm−1 was observed, which indicated the formation of carbonyl group (C=O). Solid-state nuclear magnetic resonance was also performed to determine the structural property and degree of substitution (DS) of the cellulose oleate. Based on the results, increasing reaction temperature and reaction time promoted the esterification reaction and DS. DS values of cellulose oleates slightly decreased after 12 h reaction time. Besides, X-ray diffraction analysis showed the broadening of the diffraction peaks and thermal stability decreased after esterification. Hence, the findings suggested that grafting of oleic acid’s aliphatic chain onto the cellulose backbone lowered the crystallinity and thermal stability.
Chemical Expansion and Change in Lattice Constant of Y‐Doped <scp> <scp>BaZrO</scp> </scp> <sub>3</sub> by Hydration/Dehydration Reaction and Final Heat‐Treating Temperature (2013)

Knowledge of thermal behavior of electrolyte is important for fuel cell fabrication. In this study, using high‐temperature X ‐ray diffraction analysis ( HT ‐ XRD ) and thermo‐mechanical analysis ( TMA ), a systematic investigation of lattice constants was performed on Y‐doped BaZrO 3 , which is a promising candidate for electrolyte in protonic ceramic fuel cells. The results revealed that a chemical expansion was observed between 300°C and 450°C during the heating process in HT ‐ XRD , and was attributed to the dehydration of BZY . Furthermore, it was found that the lattice constants of the samples doped with Y, Sm, Eu, and Dy were larger for the ones finally heat‐treated at 1600°C for sintering than those heat‐treated at 1300°C for synthesizing. The similar behavior was not observed in Sc‐doped samples.
A Survey of Routing Algorithms in Vehicular Networks (2019)

Vehicular Ad hoc Network (VANET) is an advanced style and subcategory of a Mobile Ad hoc Network (MANET), the main objective of VANET's is to create an Intelligent Transport System (ITS). The routing in VANET has attracted many attentions during the last few years. Highly mobility of vehicles, irregular communication between the vehicles and the necessities of real time applications are some of the major challenges of multi-hop message delivery in VANETs. Because of the frequent changing topology of VANET it becomes difficult to route the packets effectively. In this research, we are focusing on the routing concept for the VANET i.e. principles for routing, decomposition of the routing function and requirement for Forwarding protocols unicast (Geographic based, Trajectory based and Link Stability based) and Probabilistic (Distance based) routing protocols in VANETs, To analyse the performance of the most suitable routing protocols and to determine the best efficient protocol for VANET environment.
Human Hydroxyindole- <i>O</i> -Methyltransferase: Presence of LINE-1 Fragment in a cDNA Clone and Pineal mRNA (1993)

Hydroxyindole-O-methyltransferase (HIOMT) catalyzes the last step in the synthesis of the pineal hormone melatonin. In this study, an HIOMT clone was isolated from a human pineal cDNA library using synthetic oligonucleotide probes based on the bovine HIOMT sequence. The human sequence is unusual because it contains a 3' fragment (84 bp) of the LINE-1 sequence, a highly repetitive sequence in the human genome and the genome of some primates and rodents. Exclusive of this LINE-1 fragment, the human HIOMT clone is 75% and 63% homologous to bovine and avian HIOMT sequences, respectively. The deduced amino acid sequence of the human cDNA clone encodes a 41.6-kD protein. In addition, the sequence is 70% and 57% identical and 81% and 73% similar to bovine and avian HIOMT, respectively. In agreement with the results of earlier studies, it was found that vertebrate HIOMT amino acid sequences are not homologous to any other vertebrate proteins, including several methyltransferases. However, HIOMT exhibits homology with a plant O-methyltransferase and an internal 120-amino-acid region is approximately 35% identical to a region of four bacterial O-methyltransferases. The results of PCR and Southern blot analysis indicate that three species of HIOMT mRNA are typically present in the human pineal gland, only one of which contains the LINE-1 fragment. An antiserum was raised against a mixture of three synthetic peptides, corresponding to three regions of the deduced amino acid sequence of human HIOMT. This antiserum detected a single immunoreactive protein in Western blot analysis of human pineal glands. The size of the protein (approximately 42 kD) is identical to that predicted from the HIOMT clone, including the LINE-1 fragment. The human HIOMT sequence should be useful in further studies of this enzyme and will also be of special importance in evaluating the functional significance of the inclusion of a fragment of the LINE-1 in an mRNA.
A method for constructing real-time FEM-based simulator of stomach behavior with large-scale deformation by neural networks (2012)

This paper presents a method for simulating the behavior of stomach with large-scale deformation. This simulator is generated by the real-time FEM-based analysis by using a neural network.<sup>4</sup> There are various deformation patterns of hollow organs by changing both its shape and volume. In this case, one network can not learn the stomach deformation with a huge number of its deformation pattern. To overcome the problem, we propose a method of constructing the simulator composed of multiple neural networks by 1)partitioning a training dataset into several subsets, and 2)selecting the data included in each subset. From our experimental results, we can conclude that our method can speed up the training process of a neural network while keeping acceptable accuracy.