gebhart/patrepeval huggingface dataset:
Clinically relevant drug–drug interactions in oncology (1998)

Although anticancer agents are one of the most toxic classes of medication prescribed today, there is relatively little information available about clinically relevant drug-drug interactions. Pharmacokinetic drug interactions have been described, including alterations in absorption, catabolism, and excretion. For example, an increased bioavailability of 6-mercaptopurine has been observed when combined with either allopurinol or methotrexate, leading to increased toxicity in some patients. Induction of etoposide or teniposide clearance by anticonvulsants has also been described, resulting in a lower systemic exposure and risk for lower anticancer activity. Alterations in elimination of methotrexate has been observed with probenecid, presumably through competition for renal secretion. There are also several examples of pharmacodynamic interactions. The combination of 5-fluorouracil plus folinic acid results in more efficient inhibition of thymidylate synthase, a finding which is now utilized routinely in the treatment of colorectal cancer. Improvements in the in vitro and early clinical testing now allow a relatively high degree of prediction of potential clinical drug interactions, prior to observations of untoward drug effects. In conclusion, drug interactions among commonly used anticancer agents have been identified. Their clinical significance can have more impact than many other classes of medications due to the narrow therapeutic index of antineoplastic agents and the potential for lethal side-effects. It is only through prospective, preclinical and early clinical evaluation that the presence of clinically significant drug interactions can be identified and the information used to provide better therapy for this significant health problem.
Use of Workflow Technology Tools to Analyze Medical Data (2006)

Workflow editors and engines can be used to model medical processes and execute them on real coded medical data from large data repositories. Such framework re-uses existing workflow technology and applies it to the healthcare domain. It satisfies many requirements for collaboration of champion clinicians with data analysts and developers of future potential decision support modules. Results enable to have insights into differences in workflows, data collection patterns and patient structure among different hospitals or providers. The methodology can provide support to descriptive clinical research studies, quality improvement teams and decision support development teams.
A minutiae matching algorithm in fingerprint verification (2002)

Fingerprint matching is one of the most important problems in AFIS. In general, we use minutiae such as ridge endings and ridge bifurcation to represent a fingerprint and do fingerprint matching through minutiae matching. We propose a minutiae matching algorithm which modified Jain et al.'s algorithm (1997). Our algorithm can better distinguish two images from different fingers and is more robust to nonlinear deformation. Experiments done on a set of fingerprint images captured with an inkless scanner shows that our algorithm is fast and has high accuracy.
Field Evaluation of CDC and Mosquito Magnet® X Traps Baited With Dry Ice, Co<sub>2</sub>Sachet, and Octenol Against Mosquitoes (2008)

The Centers for Disease Control and Prevention (CDC) light traps and Mosquito Magnet X (MMX) traps baited with dry ice, octenol, and a new formulation (granular) of carbon dioxide (CO2) were evaluated against adult mosquitoes in the field. The results showed that the MMX traps (68.6%) baited with dry ice collected more mosquitoes compared to the CDC light traps (32.4%) only. The CDC traps baited with dry ice (64%) collected significantly more mosquitoes than traps baited with CO2 sachets (11%) or octenol (23%). The MMX traps baited with dry ice (85.5%) collected significantly more mosquitoes than traps baited with CO2 sachets (6.5%) or octenol (9%). The CDC traps baited with the formulations of normal and slow release CO2 sachets collected more mosquitoes than the formulation of fast release sachets. The CDC traps baited with fresh sachets and 24-h-exposed sachets collected significantly more mosquitoes than the traps baited with 48-h- and 72-h-exposed sachets.
High-Gain and High-Bandwidth AlGaN/GaN High Electron Mobility Transistor Comparator with High-Temperature Operation (2011)

This paper presents the dc and dynamic characterizations of a GaN-based voltage comparator, fabricated with monolithic integration of enhancement-mode (E-mode) and depletion-mode (D-mode) AlGaN/GaN high electron mobility transistors (HEMTs). The comparator features high gain (>31 dB) and wide bandwidth (>4 MHz), and small propagation delay time (<20 ns) over a wide temperature range up to 250 °C. Its dc gain is still 27.1 dB at 400 °C. These results demonstrate the potential of the AlGaN/GaN HEMT technology for mixed-signal integrated circuits used in GaN power electronics that promises high-voltage, high-current, and high-temperature operation.
Identification of functionally variant MDR1 alleles among European Americans and African Americans (2001)

MDR1 (P-glycoprotein) is an important factor in the disposition of many drugs, and the involved processes often exhibit considerable interindividual variability that may be genetically determined. Single-strand conformational polymorphism analysis and direct sequencing of exonic MDR1 deoxyribonucleic acid from 37 healthy European American and 23 healthy African American subjects identified 10 single nucleotide polymorphisms (SNPs), including 6 nonsynonymous variants, occurring in various allelic combinations. Population frequencies of the 15 identified alleles varied according to racial background. Two synonymous SNPs (C1236T in exon 12 and C3435T in exon 26) and a nonsynonymous SNP (G2677T, Ala893Ser) in exon 21 were found to be linked (MDR1*2 ) and occurred in 62% of European Americans and 13% of African Americans. In vitro expression of MDR1 encoding Ala893 (MDR1*1 ) or a site-directed Ser893 mutation (MDR1*2 ) indicated enhanced efflux of digoxin by cells expressing the MDR1-Ser893 variant. In vivo functional relevance of this SNP was assessed with the known P-glycoprotein drug substrate fexofenadine as a probe of the transporter's activity. In humans, MDR1*1 and MDR1*2 variants were associated with differences in fexofenadine levels, consistent with the in vitro data, with the area under the plasma level-time curve being almost 40% greater in the *1/*1 genotype compared with the *2/*2 and the *1/*2 heterozygotes having an intermediate value, suggesting enhanced in vivo P-glycoprotein activity among subjects with the MDR1*2 allele. Thus allelic variation in MDR1 is more common than previously recognized and involves multiple SNPs whose allelic frequencies vary between populations, and some of these SNPs are associated with altered P-glycoprotein function.
Noncontact and Wide-Field Characterization of the Absorption and Scattering Properties of Apple Fruit Using Spatial-Frequency Domain Imaging (2016)

Spatial-frequency domain imaging (SFDI), as a noncontact, low-cost and wide-field optical imaging technique, offers great potential for agro-product safety and quality assessment through optical absorption (μ<sub>a</sub>) and scattering (μ) property measurements. In this study, a laboratory-based SFDI system was constructed and developed for optical property measurement of fruits and vegetables. The system utilized a digital light projector to generate structured, periodic light patterns and illuminate test samples. The diffuse reflected light was captured by a charge coupled device (CCD) camera with the resolution of 1280 × 960 pixels. Three wavelengths (460, 527, and 630 nm) were selected for image acquisition using bandpass filters in the system. The μ<sub>a</sub> and μ were calculated in a region of interest (ROI, 200 × 300 pixels) via nonlinear least-square fitting. Performance of the system was demonstrated through optical property measurement of 'Redstar' apples. Results showed that the system was able to acquire spatial-frequency domain images for demodulation and calculation of the μ<sub>a</sub> and μ. The calculated μ<sub>a</sub> of apple tissue experiencing internal browning (IB) were much higher than healthy apple tissue, indicating that the SFDI technique had potential for IB tissue characterization.
Scaffold-forming and Adhesive Contributions of Synthetic Laminin-binding Proteins to Basement Membrane Assembly (2009)

Laminins that possess three short arms contribute to basement membrane assembly by anchoring to cell surfaces, polymerizing, and binding to nidogen and collagen IV. Although laminins containing the alpha4 and alpha5 subunits are expressed in alpha2-deficient congenital muscular dystrophy, they may be ineffective substitutes because they bind weakly to cell surfaces and/or because they lack the third arm needed for polymerization. We asked whether linker proteins engineered to bind to deficient laminins that provide such missing activities would promote basement membrane assembly in a Schwann cell model. A chimeric fusion protein (alphaLNNd) that adds a short arm terminus to laminin through the nidogen binding locus was generated and compared with the dystrophy-ameliorating protein miniagrin (mAgrin) that binds to the laminin coiled-coil dystroglycan and sulfatides. alphaLNNd was found to mediate laminin binding to collagen IV, to bind to galactosyl sulfatide, and to selectively convert alpha-short arm deletion-mutant laminins LmDeltaalphaLN and LmDeltaalphaLN-L4b into polymerizing laminins. This protein enabled polymerization-deficient laminin but not an adhesion-deficient laminin lacking LG domains (LmDeltaLG) to assemble an extracellular matrix on Schwann cell surfaces. mAgrin, on the other hand, enabled LmDeltaLG to form an extracellular matrix on cell surfaces without increasing accumulation of non-polymerizing laminins. These gain-of-function studies reveal distinct polymerization and anchorage contributions to basement membrane assembly in which the three different LN domains mediate the former, and the LG domains provide primary anchorage with secondary contributions from the alphaLN domain. These findings may be relevant for an understanding of the pathogenesis and treatment of laminin deficiency states.
UTAP: User-friendly Transcriptome Analysis Pipeline (2019)

Our User-friendly Transcriptome Analysis Pipeline (UTAP) is an open source, web-based intuitive platform available to the biomedical research community, enabling researchers to efficiently and accurately analyse transcriptome sequence data.
AutoExtend: Combining Word Embeddings with Semantic Resources (2017)

We present AutoExtend, a system that combines word embeddings with semantic resources by learning embeddings for non-word objects like synsets and entities and learning word embeddings that incorporate the semantic information from the resource. The method is based on encoding and decoding the word embeddings and is flexible in that it can take any word embeddings as input and does not need an additional training corpus. The obtained embeddings live in the same vector space as the input word embeddings. A sparse tensor formalization guarantees efficiency and parallelizability. We use WordNet, GermaNet, and Freebase as semantic resources. AutoExtend achieves state-of-the-art performance on Word-in-Context Similarity and Word Sense Disambiguation tasks.
Characterization of Serratia odorifera, S. fonticola and S. ficaria by the Electrophoretic Patterns of their Esterases (1981)

Esterases of 15 strains of Serratia odorifera, 14 strains of S. fonticola and 13 strains of S. ficaria were resolved by horizontal electrophoresis in polyacrylamide-agarose gel. Esterase bands were defined by their range of activity towards several synthetic substrates and their sensitivity or resistance to di-isopropyl fluorophosphate. Serratia odorifera strains showed three to five major esterase bands and three minor bands. Serratia fonticola strains showed three or four major bands and one minor band. Serratia ficaria strains showed three to five major bands and one minor band. The comparative distribution of bands revealed that these three newly described species could be distinguished by the electrophoretic patterns of their esterases. Congruence was found between biotypes 1 and 2 of S. odorifera and electrophoretic patterns. These species-specific patterns were different from those of S. marcescens, S. liquefaciens, S. plymuthica and S. marinorubra previously characterized.
Purification, Characterization, and Kinetic Mechanism of Cyclin D1·CDK4, a Major Target for Cell Cycle Regulation (1998)

The cyclin D1.CDK4-pRb (retinoblastoma protein) pathway plays a central role in the cell cycle, and its deregulation is correlated with many types of cancers. As a major drug target, we purified dimeric cyclin D1.CDK4 complex to near-homogeneity by a four-step procedure from a recombinant baculovirus-infected insect culture. We optimized the kinase activity and stability and developed a reproducible assay. We examined several catalytic and kinetic properties of the complex and, via steady-state kinetics, derived a kinetic mechanism with a peptide (RbING) and subsequently investigated the mechanistic implications with a physiologically relevant protein (Rb21) as the phosphoacceptor. The complex bound ATP 130-fold tighter when Rb21 instead of RbING was used as the phosphoacceptor. By using staurosporine and ADP as inhibitors, the kinetic mechanism of the complex appeared to be a "single displacement or Bi-Bi" with Mg2+.ATP as the leading substrate and phosphorylated RbING as the last product released. In addition, we purified a cyclin D1-CDK4 fusion protein to homogeneity by a three-step protocol from another recombinant baculovirus culture and observed similar kinetic properties and mechanisms as those from the complex. We attempted to model staurosporine in the ATP-binding site of CDK4 according to our kinetic data. Our biochemical and modeling data provide validation of both the complex and fusion protein as highly active kinases and their usefulness in antiproliferative inhibitor discovery.
Electrodeposition at Highly Negative Potentials of an Iron‐Cobalt Oxide Catalyst for Use in Electrochemical Water Splitting (2019)

Earth-abundant transition metal-based catalysts have been extensively investigated for their applicability in water electrolysers to enable overall water splitting to produce clean hydrogen and oxygen. In this study a Fe-Co based catalyst is electrodeposited in 30 seconds under vigorous hydrogen evolution conditions to produce a high surface area material that is active for both the oxygen evolution reaction (OER) and the hydrogen evolution reaction (HER). This catalyst can achieve high current densities of 600 mAcm<sup>-2</sup> at an applied potential of 1.6 V (vs RHE) in 1 M NaOH with a Tafel slope value of 48 mV dec<sup>-1</sup> for the OER. In addition, the HER can be facilitated at current densities as high as 400 mA cm<sup>-2</sup> due to the large surface area of the material. The materials were found to be predominantly amorphous but did contain crystalline regions of CoFe<sub>2</sub> O<sub>4</sub> which became more evident after the OER indicating interesting compositional and structural changes that occur to the catalyst after an electrocatalytic reaction. This rapid method of creating a bimetallic oxide electrode for both the HER and OER could possibly be adopted to other bimetallic oxide systems suitable for electrochemical water splitting.
Effect of the Type of Bean, Processing, and Geographical Location on the Biodiesel Produced from Waste Coffee Grounds (2014)

Waste coffee grounds offer a viable waste feedstock for biodiesel production. Approximately 8 million tonnes of coffee are produced globally each year and contain up to 15 wt % lipid, of which the glyceride portion is predominantly made up of palmitic, stearic, oleic, and linoleic acids. In this investigation, the variation in the oil content, saponifiable lipids, and lipid profile according to the regional location and processing or brewing techniques was assessed. A number of key fuel properties were also investigated. The oil content for fresh coffee grounds (FCGs) ranged from 11 to 15% across the range of coffees examined. Spent coffee grounds (SCGs) had slightly reduced levels of lipid, between 7 and 13 wt %, for the coffees under investigation. The lipids contained between 0 and 40% unsaponifiable material, which could not be processed to fatty acid methyl ester (FAME). For all samples, with the exception of Vietnamese coffee, the FAME profile of the resulting biodiesel was consistent; the oils contained between 35 and 40% palmitic acid, between 7 and 8% oleic acid, between 44 and 50% linolenic acid, and between 7 and 8% stearic acid, although the fuel properties were reasonably variable across the data set. The kinematic viscosity ranged between 4.0 and 5.5 mm2 s–1; the density ranged between 841 and 927 kg m–3; and the pour point ranged between −1 and 16 °C. This variation was also observed in previous reports, suggesting that these fuel properties are not solely determined by the FAME profile but other lipid-soluble biomolecules present in the coffee biodiesel.
Primeiro registro de Thamnophilus doliatus (Aves, Passeriformes, Thamnophilidae) para o estado de Santa Catarina, sul do Brasil (2019)

Thamnophilus doliatus (choca-barrada) tem ampla distribuição na região neotropical, do México até a Argentina. No Brasil essa espécie ocorre em todas as regiões; no Sul era conhecida apenas no estado do Paraná. O primeiro registro da espécie em Santa Catarina foi realizado por meio de documentação com fotos, gravação de sua vocalização e vídeo de um espécime macho. O indivíduo foi encontrado em um pequeno fragmento florestal às margens de um lago artificial formado pelo Rio Chapecó, no município de Ipuaçu, região oeste do estado. Possivelmente essa espécie está expandindo sua distribuição, como observado em outras localidades.
A New Type of Transmission Line-Based Metamaterial Resonator and Its Implementation in Original Applications (2013)

In this paper, a new type of transmission line-based metamaterial resonator is proposed. The structure is based on a modified uniplanar series resonator bent to form a close square loop inclusion which contains a distributed capacitance and inductance. Many advantages of the proposed structure over conventional split ring resonators are discussed. Based on simple transmission line theory, the resonance frequency at which a deep rejection frequency band occurs with sharp cutoff rates beside the stopband, due to the presence of negative effective permeability in the dielectric slab of the host transmission line in the vicinity of resonance, is calculated and verified with simulated and measured results. Two prototype microwave devices are designed to illustrate the potentiality of the proposed inclusion. The first design represents a dual-band bandstop filter with designed center band frequencies at 1.6 and 2.2 GHz. The lumped element model of this filter contains four series-connected parallel LC resonators which are implemented using our high Q-factor artificial magnetic materials (AMMs) patterned on the backside of a coplanar waveguide (CPW) transmission line. The second device is a miniaturized hybrid branch line coupler operating at 2.4 GHz, based on a special loading technique that increases the electric length of transmission lines by patterning the ground plane under the conductor trace in microstrip lines with the complementary, dual-behavior, configuration of AMMs. A size reduction factor up to 16.95% is achieved compared to conventional couplers. For both design examples the measured and simulated responses are in very good agreement which validates our work.
Field-emitter-array development for microwave applications (1996)

Microfabricated field-emitter arrays are being investigated as a means for gating or prebunching electrons in a microwave amplifier tube. The goals of the program are to demonstrate 10-dB gain at 50 W and 10 GHz in a gated klystrode■ amplifier tube with 50% efficiency. The cathode specifications call for 160-mA peak emission at 10-GHz rates from an annular emitter array having a 600-μm outer diameter and an inner diameter to be determined by cathode capacitance, emitter-tip loading, and transconductance (Gm) considerations. We have shown that an average array capacitance of 6 nF/cm2 and emitter-tip loadings of 10 μA/tip can be routinely achieved with Gm≊1 μS/tip. Calculations based on these results show that an array having 0.4-μm-diam gate apertures on 1-μm centers, a 600-μm outer diameter, and a 560-μm inner diameter would be a reasonable first design to meet the tube specifications. Such an array would have a predicted capacitance of 2.18 pF, a peak Gm of 29.4 mS, and would produce a peak emission of 160 mA with a tip loading of 4.4 μA/tip. The power dissipated in driving the gate at 10-GHz rates would be between 0.1 and 1.0 W.
Functional Viability Profiles of Breast Cancer (2011)

Despite the wealth of molecular profiling data that describe breast tumors and breast tumor cell models, our understanding of the fundamental genetic dependencies in this disease is relatively poor. Using high-throughput RNA interference screening of a series of pharmacologically tractable genes, we have generated comprehensive functional viability profiles for a wide panel of commonly used breast tumor cell models. Analysis of these profiles identifies a series of novel genetic dependencies, including that of PTEN-null breast tumor cells upon mitotic checkpoint kinases, and provides a framework upon which additional dependencies and candidate therapeutic targets may be identified.
The Generation of Extracellular DNA in SLE: the Role of Death and Sex (2006)

DNA is a large macromolecule that plays a central role in the pathogenesis of systemic lupus erythematosus (SLE), serving as a target antigen of autoantibodies as well as a major component of immune complexes. These complexes can both promote immune disturbances as well as deposit in the kidney to incite inflammation. While the origin of anti-DNA autoantibodies in SLE has received intense investigation, the mechanisms by which DNA exits cells to form immune complexes in the circulation is not well understood. To determine the origin of DNA circulating in the blood in SLE, our laboratory has been using a murine model system to track the in vivo fate of DNA from Jurkat T cells that have been made apoptotic or necrotic in vitro and then administered to mice. Results of these studies indicate that DNA from apoptotic and necrotic cells appears in the blood in a time- and dose-dependent manner. Irrespective of origin, this DNA has properties of nucleosomes as shown by its molecular weight. The process of release requires the presence of macrophages and can be modified by glucocorticoids as well as inflammation. In addition, sex may play a role in the generation of extracellular DNA from dead cells as male and female mice differ in their responses in this model. Together, these studies clarify the origin of extracellular DNA circulating in the blood in SLE and suggest steps in this process that can be interdicted by novel therapy.
Text Coherence Analysis Based on Deep Neural Network (2017)

In this paper, we propose a novel deep coherence model (DCM) using a convolutional neural network architecture to capture the text coherence. The text coherence problem is investigated with a new perspective of learning sentence distributional representation and text coherence modeling simultaneously. In particular, the model captures the interactions between sentences by computing the similarities of their distributional representations. Further, it can be easily trained in an end-to-end fashion. The proposed model is evaluated on a standard Sentence Ordering task. The experimental results demonstrate its effectiveness and promise in coherence assessment showing a significant improvement over the state-of-the-art by a wide margin.