gebhart/patrepeval huggingface dataset:
Protein Ontology: a controlled structured network of protein entities (2013)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to UniProtKB in that PRO's organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO's representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments.
A cryptographic approach for secure client - server chat application using public key infrastructure (PKI) (2016)

Nowadays, while the popularity of chat applications increases, this popularity brings some security problems with it. A variety of authentication mechanisms and encrypting methods are suggested and applied between server and client to minimize the increasing security problems in literature and marketing companies. In this study, various security measures have been considered for instant messaging applications, a java based client-server chat application developed by Professor Dan Boneh [1] and his assistants from Stanford University has been made secure and a secured chat application model which has three steps has been developed. At the first step, server has been identified itself to certificate authority and password authentication procedure has been performed to identify client itself to server. The second step is called as connection and client connects to chat room via ticket granting ticket (TGT) request in this step. Messages written by clients are sent to server cryptically through symmetric encryption method Advanced Encryption Standard (AES) in the third step which is called as encrypted messaging too. Source code of this application is accessible to everyone from the reference [9].
Towards a Job Title Classification System (2016)

Document classification for text, images and other applicable entities has long been a focus of research in academia and also finds application in many industrial settings. Amidst a plethora of approaches to solve such problems, machine-learning techniques have found success in a variety of scenarios. In this paper we discuss the design of a machine learning-based semi-supervised job title classification system for the online job recruitment domain currently in production at CareerBuilder.com and propose enhancements to it. The system leverages a varied collection of classification as well clustering algorithms. These algorithms are encompassed in an architecture that facilitates leveraging existing off-the-shelf machine learning tools and techniques while keeping into consideration the challenges of constructing a scalable classification system for a large taxonomy of categories. As a continuously evolving system that is still under development we first discuss the existing semi-supervised classification system which is composed of both clustering and classification components in a proximity-based classifier setup and results of which are already used across numerous products at CareerBuilder. We then elucidate our long-term goals for job title classification and propose enhancements to the existing system in the form of a two-stage coarse and fine level classifier augmentation to construct a cascade of hierarchical vertical classifiers. Preliminary results are presented using experimental evaluation on real world industrial data.
The Link between Clay Mineral Weathering and the Stabilization of Ni Surface Precipitates (1999)

The formation of transition-metal surface precipitates may occur during sorption to clay minerals under ambient soil conditions. This process may lead to significant long-term stabilization of the metal within the soil profile. However, the rates and mechanisms controlling surface precipitate formation are poorly understood. We monitored changes in the reversibility of Ni sorbed to a clay mineral, pyrophyllite, in model batch experiments maintained at pH 7.5 for up to 1 year. The macroscopic sorption and dissolution study was complemented by a time-resolved characterization of the sorbed phase via spectroscopic and thermal methods. We found that nickel became increasingly resistant, over time, to extraction with EDTA. Initially, the sorbed phase consisted of a Ni−Al layered double hydroxide (LDH). With time, the anionic species in the interlayer space of the LDH changed from nitrate to silica polymers transforming the LDH gradually into a precursor Ni−Al phyllosilicate. We believe that this phase transformation is responsible for a substantial part of the observed increase in dissolution resistance. Thus, clay mineral weathering and the time-dependent release of Al and Si ions controlled Ni precipitate nucleation and transformation. Our results suggest a potential pathway for long-term Ni stabilization in soil.
Application of tRNA Intergenic Spacer PCR for Identification of <i>Enterococcus</i> Species (2000)

tRNA intergenic spacer PCR (tDNA-PCR) was evaluated for its usefulness in the differentiation of enterococcal species of human and animal origin. This technique was carried out for 124 strains belonging to 17 enterococcal species and generated DNA fragments, which were separated by capillary electrophoresis. tDNA-PCR enabled us to discriminate for all species tested. Enterococcus faecium showed minor but reproducible differences with Enterococcus durans, while Enterococcus hirae was easily distinguishable. Enterococcus avium, Enterococcus malodoratus, and Enterococcus raffinosus generated highly similar though distinctive patterns.
A 24 GHz Highly Linear Up-Conversion Mixer in CMOS 0.13 <formula formulatype="inline"><tex Notation="TeX">$\mu{\rm m}$</tex></formula> Technology (2015)

This letter reports a 24 GHz linear up-conversion mixer for high-power IF signal. In the proposed mixer, the double-balanced Gilbert-cell topology is employed with a low-distortion transconductance stage which combines voltage feedback and adaptive biasing schemes. The proposed adaptive biasing circuit improves the linearity of the transconductance stage by providing an additional bias current when IF input signals exceed the current-limited linear input range. Implemented in a 0.13 μm CMOS technology, the mixer showed a conversion gain of -1.9 dB and output 1 dB compression point of 0.3 dBm for the IF, LO, and RF frequency ranges of 10.0-314.7 MHz, 18.9-29.0 GHz, and 23.4-29.2 GHz, respectively, while dissipating 22.8 and 16.5 mW for the mixer and the LO buffer, respectively, from a 1.5 V supply.
Multiplexed tandem PCR: gene profiling from small amounts of RNA using SYBR Green detection (2005)

Multiplexed tandem PCR (MT-PCR) is a process for highly multiplexed gene expression profiling. In the first step, multiple primer pairs are added to the RNA to be analysed together with reverse transcriptase and Taq DNA polymerase. Following reverse transcription, the multiplexed amplicons are simultaneously amplified for a small number of cycles so as to avoid competition between amplicons. The reaction product is then diluted and analysed in multiple individual PCRs using primers nested inside the primers used for the multiplexed amplification. As the second PCR uses a template enriched in the amplicons of interest, the conditions can be optimized to significantly reduce 'primer dimer' formation allowing SYBR Green chemistry to be used for quantification. MT-PCR can be configured for as little as 10 pg RNA (equivalent to a single mammalian cell) and works well with RNA extracted from archival formalin-fixed paraffin-embedded sections. We illustrate MT-PCR with gene expression profiles of breast cancer cell lines.
Emergence of <i>Pseudomonas aeruginosa</i> Strains Producing High Levels of Persister Cells in Patients with Cystic Fibrosis (2010)

The majority of cystic fibrosis (CF) patients succumb to a chronic infection of the airway with Pseudomonas aeruginosa. Paradoxically, pathogenic strains are often susceptible to antibiotics, but the infection cannot be eradicated with antimicrobial therapy. We find that in a majority of patients with airway infections, late isolates of P. aeruginosa produce increased levels of drug-tolerant persister cells. The genomes of a clonal pair of early/late isolates from a single patient have been previously sequenced, and the late isolate (obtained at age 96 months) showed a 100-fold increase in persister levels. The 96-month isolate carries a large number of mutations, including a mutation in mutS that confers a hypermutator phenotype. There is also a mutation in the mexZ repressor controlling the expression of the MexXY-OprM multidrug pump, which results in a moderate increase in the ofloxacin, carbenicillin, and tobramycin MICs. Knocking out the mexXY locus restored the resistance to that of the parent strain but did not affect the high levels of persisters formed by the 96-month isolate. This suggests that the late isolate is a high-persister (hip) mutant. Increased persister formation was observed in exponential phase, stationary phase, and biofilm populations of the 96-month isolate. Analysis of late isolates from 14 additional patients indicated that 10 of them are hip mutants. Most of these hip mutants did not have higher drug resistance. Increased persister formation appears to be their sole mechanism for surviving chemotherapy. Taken together, these findings suggest a link between persisters and recalcitrance of CF infection and identify an overlooked culprit-high-persister mutants producing elevated levels of drug-tolerant cells. Persisters may play a similarly critical role in the recalcitrance of other chronic infections.
The effects of copper and titanium on silicon solar cells (1978)

Copper-doped N/P silicon solar cells fabricated from the Czochralski grown single-crystal wafers were found to have good electrical characteristics, but the titanium-doped N/P silicon solar cells has considerably lower conversion efficiency. However, in the copper/titanium-doped solar cells, copper seems to mitigate the unfavorable effects of titanium. To explain this behavior, microstructural tests were performed on silicon wafers and solar cells doped with copper, titanium and copper/titanium. Dark forward and reverse I-V measurements were performed on the solar cells to correlate the microstructural defects with the p-n junction properties. It was found that copper precipitates were formed in the copper-doped and copper/titanium-doped wafers and cells. There was a significant voltage drop in the dark reverse I-V measurements of the titanium solar cells. Also, there were some electronically active defects in the depletion region of some titanium-doped cells. Reasons that lead to the above results are given in detail.
Evaluation of MnO<sub><i>x</i></sub>, Mn<sub>2</sub>O<sub>3</sub>, and Mn<sub>3</sub>O<sub>4</sub> Electrodeposited Films for the Oxygen Evolution Reaction of Water (2014)

Different manganese oxide phases were prepared as thin films to elucidate their structure–function relationship with respect to oxygen evolution in the process of water splitting. For this purpose, amorphous MnOx films anodically deposited on F:SnO2/glass and annealed at different temperatures (to improve film adherence and crystallinity) were tested in neutral and alkaline electrolytes. Differential electrochemical mass spectroscopy showed that the anodic current correlated well with the onset of the expected oxygen evolution, where in 1 M KOH, the anodic current of crystalline α-Mn2O3 films was determined to onset at an overpotential (η) of 170 mVRHE (at J = 0.1 mA/cm2) with current densities of ca. 20 mA/cm2 at η = 570 mVRHE. Amorphous MnOx films heated at 573 K (MnOx-573 K) were found to improve their adherence to F:SnO2/glass substrate after heat treatment with a slight crystallization detected by Raman spectroscopy. The onset of water oxidation of MnOx-573 K films was identified at η = 230 mVRHE (at J = 0.1 mA/cm2) with current densities of ca. 20 mA/cm2 at η = 570 mVRHE (1 M KOH). The least active of the investigated manganese oxides was Mn3O4 with an onset at η = 290 mVRHE (at J = 0.1 mA/cm2) and current densities of ca. 10 mA/cm2 at η = 570 mVRHE (1 M KOH). In neutral solution (1 M KPi), a similar tendency was observed with the lowest overpotential found for α-Mn2O3 followed by MnOx-573 K and Mn3O4. X-ray photoelectron spectroscopy revealed that after electrochemical treatment, the surfaces of the manganese oxide electrodes exhibited oxidation of Mn II and Mn III toward Mn IV under oxygen evolving conditions. In the case of α-Mn2O3 and MnOx-573 K, the manganese oxidation was found to be reversible in KPi when switching the potential above and below the oxygen evolution reaction (OER) threshold potential. Furthermore, scanning electron microscopy (SEM) images displayed the presence of an amorphous phase on top of all manganese oxide films here tested after oxygen evolution. The results indicate that structural changes played an important role in the catalytic activity of the manganese oxides, in addition to oxidation states, a large variety of Mn–O bond lengths and a high concentration of oxygen point defects. Thus, compared to Mn3O4, crystalline α-Mn2O3 and MnOx-573 K are the most efficient catalyst for water oxidation in the manganese–oxygen system.
Novel α-MSH analog causes weight loss in obese rats and minipigs and improves insulin sensitivity (2013)

Obesity is a major burden to people and to health care systems around the world. The aim of the study was to characterize the effect of a novel selective α-MSH analog on obesity and insulin sensitivity. The subchronic effects of the selective MC4-R peptide agonist MC4-NN1-0182 were investigated in diet-induced obese (DIO) rats and DIO minipigs by assessing the effects on food intake, energy consumption, and body weight. The acute effect of MC4-NN1-0182 on insulin sensitivity was assessed by a euglycemic-hyperinsulinemic clamp study in normal rats. Three weeks of treatment of DIO rats with MC4-NN1-0182 caused a decrease in food intake and a significant decrease in body weight 7±1%, P<0.05 compared with 3±1% increase with the vehicle control. In DIO minipigs, 8 weeks of treatment with MC4-NN1-0182 resulted in a body weight loss of 13.3±2.5 kg (13±3%), whereas the vehicle control group had gained 3.7±1.4 kg (4±1%). Finally, clamp studies in normal rats showed that acute treatment with MC4-NN1-0182 caused a significant increase in glucose disposal (Rd) compared with vehicle control (Rd, mg/kg per min, 17.0±0.7 vs 13.9±0.6, P<0.01). We demonstrate that treatment of DIO rats or minipigs with a selective MC4-R peptide agonist causes weight loss. Moreover, we have demonstrated weight-independent effects on insulin sensitivity. Our observations identify MC4 agonism as a viable target for the treatment of obesity and insulin resistance.
Zanthoxyli Fructus induces growth arrest and apoptosis of LNCaP human prostate cancer cells in vitro and in vivo in association with blockade of the AKT and AR signal pathways (2006)

Zanthoxyli Fructus belongs to the family of oranges and is used as a seasoning in Asian countries including Japan. This study found that a water extract of Zanthoxyli Fructus possessed anti-tumor activity against a wide variety of cancer cells including those from prostate (LNCaP, DU145, PC-3), breast (MCF-7, T47D, MDA-MB231), lung (NCI-H460, -H520), as well as leukemia (HL-60, NB4, Jurkat) in vitro, as measured by the trypan blue exclusion test. Importantly, Zanthoxyli Fructus slowed the proliferation of LNCaP, DU145, and MDA-MB231 cells present as xenografts in BALB/c nude mice without adverse effects. Further studies explored the molecular mechanism by which Zanthoxyli Fructus inhibited the proliferation of androgen-dependent human prostate cancer LNCaP cells because Zanthoxyli Fructus possessed the strongest anti-tumor activity against these cells. Zanthoxyli Fructus blocked androgen receptor (AR) signaling in conjunction with down-regulation of nuclear levels of AR and induced apoptosis of these cells, as measured by the reporter assay, Western blot analysis, and TUNEL assay, respectively. As expected, Zanthoxyli Fructus also decreased the level of the AR-target molecule, prostate-specific antigen in these cells. Furthermore, Zanthoxyli Fructus inhibited AKT kinase and down-regulated levels of cyclin D1 protein, as measured by the AKT kinase assay with GSK-3alpha/beta as a substrate and Western blot analysis, respectively. Taken together, Zanthoxyli Fructus might be useful as an adjunctive therapeutic agent for the treatment of individuals with a variety of cancer types.
Motion-free hybrid design laser beam propagation analyzer using a digital micromirror device and a variable focus liquid lens (2010)

To the best of our knowledge, we propose the first motion-free laser beam propagation analyzer with a hybrid design using a digital micromirror device (DMD) and a liquid electronically controlled variable focus lens (ECVFL). Unlike prior analyzers that require profiling the beam at multiple locations along the light propagation axis, the proposed analyzer profiles the beam at the same plane for multiple values of the ECVFL focal length, thus eliminating beam profiler assembly motion. In addition to measuring standard Gaussian beam parameters, the analyzer can also be used to measure the M(2) beam propagation parameter of a multimode beam. Proof-of-concept beam parameter measurements with the proposed analyzer are successfully conducted for a 633 nm laser beam. Given the all-digital nature of the DMD-based profiling and all-analog motion-free nature of the ECVFL beam focus control, the proposed analyzer versus prior art promises better repeatability, speed, and reliability.
Diagnosis of alkaptonuria by NMR urinalysis : Rapid qualitative and quantitative analysis of homogentisic acid. (1986)

Urinalysis of alkaptonuria using NMR spectroscopy revealed the abnormal amount of homogentisic acid. Qualitative and quantitative determination was performed simultaneously with untreated urine sample and within 15 min.
The effect of Tritrichomonas foetus infection on calving rates in beef cattle (1983)

The effect of Tritrichomonas foetus var. brisbane infection on calf production by Hereford cows was determined. The mean number of calves produced by cows that were kept continuously with bulls infected with T. foetus for 3 years was 17.6% less than the mean number produced by cows kept with a non-infected bull. Losses in production due to trichomoniasis occurred each year, but were greatest in the first 2 years in cows experiencing infection for the first time.
A visual information management system for the interactive retrieval of faces (1993)

The complex nature of two-dimensional image data has presented problems for traditional information systems designed strictly for alphanumeric data. Systems aimed at effectively managing image data have generally approached the problem from two different views: They either possess a strong database component with little image understanding, or they serve as an image repository for computer vision applications, with little emphasis on the image retrieval process. A general architecture for visual information-management systems (VIMS), which combine the strengths of both approaches, is presented. The system utilizes computer vision routines for both insertion and retrieval and allows easy query-by-example specifications. The vision routines are used to segment and evaluate objects based on domain-knowledge describing the objects and their attributes. The vision system can then assign feature values to be used for similarity-measures and image retrieval. A VIMS developed for face-image retrieval is presented to demonstrate these ideas.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A miniature fibre optic force microscope scan head (1993)

The authors have built a fibre optic force microscope scan head which scans the cantilever relative to a fixed sample. The design enables the fibre-to-cantilever distance to be altered by moving the fibre relative to the fixed cantilever. This design feature is particularly important when using the variable deflection mode and for acquiring force versus distance curves. The interferometer system reaches a resolution of 0.01 nm (peak-to-peak).
Cardiac mast cell-derived renin promotes local angiotensin formation, norepinephrine release, and arrhythmias in ischemia/reperfusion (2006)

Having identified renin in cardiac mast cells, we assessed whether its release leads to cardiac dysfunction. In Langendorff-perfused guinea pig hearts, mast cell degranulation with compound 48/80 released Ang I-forming activity. This activity was blocked by the selective renin inhibitor BILA2157, indicating that renin was responsible for Ang I formation. Local generation of cardiac Ang II from mast cell-derived renin also elicited norepinephrine release from isolated sympathetic nerve terminals. This action was mediated by Ang II-type 1 (AT1) receptors. In 2 models of ischemia/reperfusion using Langendorff-perfused guinea pig and mouse hearts, a significant coronary spillover of renin and norepinephrine was observed. In both models, this was accompanied by ventricular fibrillation. Mast cell stabilization with cromolyn or lodoxamide markedly reduced active renin overflow and attenuated both norepinephrine release and arrhythmias. Similar cardioprotection was observed in guinea pig hearts treated with BILA2157 or the AT1 receptor antagonist EXP3174. Renin overflow and arrhythmias in ischemia/reperfusion were much less prominent in hearts of mast cell-deficient mice than in control hearts. Thus, mast cell-derived renin is pivotal for activating a cardiac renin-angiotensin system leading to excessive norepinephrine release in ischemia/reperfusion. Mast cell-derived renin may be a useful therapeutic target for hyperadrenergic dysfunctions, such as arrhythmias, sudden cardiac death, myocardial ischemia, and congestive heart failure.
Purgative activity and Principals of the Fruits of Rosa multiflora and R. wichuraiana. (1992)

Pseudocarps or seeds of Rosa multiflora, crude drug "Eijitsu" have been used as purgative in Japanese traditional medicine. R. wichuraiana was generally thought to be able to substitute for the plant. The n-butanol fractions of both plant seeds were tested on purgative activities with mice, and the values of the 50% effective dose (ED50) were 5.6 g/kg as the seed weight for R. multiflora and 57 g/kg as the seed weight for R. wichuraiana. From pseudocarps of R. multiflora, a new purgative compound, multinoside A acetate, was isolated, and its ED50 value was tested to be 150 mg/kg (77-291 mg/kg, 95% confidence limit). The other isolated compounds were three known quercetin glycosides, quercetin 3-O-xyloside, isoquercitrin and hyperin. From pseudocarps of R. wichuraiana, three quercetin glycosides, isoquercitrin, hyperin and quercetin 3-O-beta-D-glucuronide were isolated similarly, but no purgative components of R. multiflora were detected.