gebhart/patrepeval huggingface dataset:
Characterization of Reactions between Water-Soluble Trialkylphosphines and Thiol Alkylating Reagents: Implications for Protein-Conjugation Reactions (2016)

Water-soluble trialkylphosphines such as tris(carboxyethyl)phosphine (TCEP) and trishydroxypropyl phosphine (THPP) are effective agents for reducing disulfide bonds in proteins and are increasingly becoming the reagents of choice for bioconjugation strategies that modify cysteine (thiol containing) amino acids. These reducing agents are often considered as being chemically compatible with Michael acceptors such as maleimides and, as such, are often not removed prior to performing protein conjugation reactions. Here, we demonstrate the rapid and irreversible reaction of both TCEP and THPP with derivatives of the commonly employed thiol alkylating groups, maleimide and vinyl sulfone. Mechanistic investigations revealed distinct differences between the reactions of TCEP and THPP with maleimide, leading to the production of either nonproductive ylenes or succidimidyl derivatives, respectively. Importantly, we also demonstrate the incorporation of nonproductive ylenes formed between maleimide and TCEP into the Pneumococcal capsular polysaccharide Pn6b following strategies employed toward the production of conjugate vaccines.
Bacterial glyphosate resistance conferred by overexpression of an <i>E. coli</i> membrane efflux transporter (2011)

Glyphosate herbicide-resistant crop plants, introduced commercially in 1994, now represent approximately 85% of the land area devoted to transgenic crops. Herbicide resistance in commercial glyphosate-resistant crops is due to expression of a variant form of a bacterial 5-enolpyruvylshikimate-3-phosphate synthase with a significantly decreased binding affinity for glyphosate at the target site of the enzyme. As a result of widespread and recurrent glyphosate use, often as the only herbicide used for weed management, increasing numbers of weedy species have evolved resistance to glyphosate. Weed resistance is most often due to changes in herbicide translocation patterns, presumed to be through the activity of an as yet unidentified membrane transporter in plants. To provide insight into glyphosate resistance mechanisms and identify a potential glyphosate transporter, we screened Escherichia coli genomic DNA for alternate sources of glyphosate resistance genes. Our search identified a single non-target gene that, when overexpressed in E. coli and Pseudomonas, confers high-level glyphosate resistance. The gene, yhhS, encodes a predicted membrane transporter of the major facilitator superfamily involved in drug efflux. We report here that an alternative mode of glyphosate resistance in E. coli is due to reduced accumulation of glyphosate in cells that overexpress this membrane transporter and discuss the implications for potential alternative resistance mechanisms in other organisms such as plants.
Combined Temperature and Pressure Data Interpretation: Applications to Characterization of Near-Wellbore Reservoir Structures (2011)

Abstract The models that describe distributed temperature behavior in a reservoir appear as advection-diffusion equations with forcing terms that include compressibility effects due to Joule-Thomson and adiabatic expansion. The model lends itself to solution techniques like Operator Splitting which decomposes a multiphysics, multiscale problem into components representing different simple physics and scales, where each component can be solved independently at each time step using any appropriate technique for the physical process. Unlike diffusion, advection does not destroy information and it is nonsmoothing and preserves sharp boundaries. By Method of Characteristics (MOC), a process can be estimated as it is advected downstream, from an initial data line, along characteristic paths at some characteristic velocity. This idea has useful implications on what information is carried by the advection processes that occur in a reservoir, such as heat advection. In this paper, the results of solving the temperature model by Operator Splitting are presented. This approach utilizes the fact that temperature signatures, generated by spatial pressure changes in the reservoir due to Joule-Thomson and adiabatic expansion effects, are transported downstream in time from the initial line of generation to the wells. Along the corresponding characteristic curves, this transport is described by the characteristic velocity, and time to reach the well. Importantly these curves are independent of the pressure model but are dependent on the convective thermal velocity. The result is that reservoir structures that generate significant spatial pressure changes produce temperature signatures that are transported along the characteristic solution lines from the point of generation to the wells. Back calculations using the arrival times and and corresponding velocities give the location of the reservoir structures. This technique was applied to the calculation of damaged radius, stimulated radius and inner boundaries of a multiring reservoir system, using temperature measurements and showed that near wellbore properties that are masked by wellbore storage in pressure transient analysis can be revealed by the slower moving temperature field. A proposal for new well test design to utilize this approach is also presented.
Overview of wireless power transfer for electric vehicle charging (2013)

This paper presents an overview of current wireless power transfer (WPT) technologies for the application of electric vehicles (EV) wireless charging. The basic principles of each technology are introduced. Followed by classification, the advantages and limitations of each technology for EV charging are discussed. Promising technologies such as coupled magnetic resonance and magnetic gear technologies are systematically reviewed. The latest development, key technical issues, challenges and state-of-art researches are introduced. The research trends are also been given.
Discovery of Isoquinolinone Indole Acetic Acids as Antagonists of Chemoattractant Receptor Homologous Molecule Expressed on Th2 Cells (CRTH2) for the Treatment of Allergic Inflammatory Diseases (2014)

Previously we reported the discovery of CRA-898 (1), a diazine indole acetic acid containing CRTH2 antagonist. This compound had good in vitro and in vivo potency, low rates of metabolism, moderate permeability, and good oral bioavailability in rodents. However, it showed low oral exposure in nonrodent safety species (dogs and monkeys). In the current paper, we wish to report our efforts to understand and improve the poor PK in nonrodents and development of a new isoquinolinone subseries that led to identification of a new development candidate, CRA-680 (44). This compound was efficacious in both a house dust mouse model of allergic lung inflammation (40 mg/kg qd) as well as a guinea pig allergen challenge model of lung inflammation (20 mg/kg bid).
Bipolar disorder: Evidence for a major locus (1995)

Complex segregation analyses were conducted on families of bipolar I and bipolar II probands to delineate the mode of inheritance. The probands were ascertained from consecutive referrals to the Mood Disorder Service, University Hospital, University of British Columbia and diagnosed by DSM-III-R and Research Diagnostic Criteria. Data were available on over 1,500 first-degree relatives of the 186 Caucasian probands. The purpose of the analyses was to determine if, after correcting for age and birth cohort, there was evidence for a single major locus. Five models were fit to the data using the statistical package SAGE: i) dominant, ii) recessive, iii) arbitrary mendelian inheritance, iv) environmental, and v) no major effects. A single dominant, mendelian major locus was the best fitting of these models for the sample of bipolar I and II probands when only bipolar relatives were defined as affected (polygenic inheritance could not be tested). Adding recurrent major depression to the diagnosis "affected" for relatives reduced the evidence for a major locus effect. Our findings support the undertaking of linkage studies and are consistent with the analyses of the National Institutes of Mental Health (NIMH) Collaborative Study data by Rice et al. (Arch Gen Psychiatry 44: 441-447, 1987) and Blangero and Elston (Genet Epidemiol 6:221-227, 1989).
Inflammatory Cytokine Concentrations Are Elevated in Seminal Plasma of Men With Spinal Cord Injuries (2004)

The semen of most men with spinal cord injury (SCI) contains sperm with abnormally low motility. Studies suggest that the seminal plasma is the source of this condition. The seminal plasma of men with SCI contains an abnormally high number of white blood cells (WBC), specifically, activated T cells. It is known that activated T cells secrete cytokines and elevated concentrations of cytokines can be harmful to sperm. It is not known if the seminal plasma of men with SCI contains elevated concentrations of cytokines. The purpose of this study was to determine if the seminal plasma of men with SCI contained elevated concentrations of cytokines. Using the method of enzyme-linked immunosorbant assay (ELISA), ten cytokines were measured in the seminal plasma of men with SCI as well as healthy non-SCI control subjects. The cytokines of interest were grouped according to Th1 effector functions: interleukin 1 beta, interleukin 2, interleukin 12, tumor necrosis factor alpha, tumor necrosis factor beta, interferon gamma (IL1 beta, IL2, IL12, TNF alpha, TNF beta, INF gamma, respectively) and Th2 effector functions: interleukin 4, interleukin 6, interleukin 10, transforming growth factor beta 1 (IL4, IL6, IL10, TGF beta 1, respectively). The results showed a predominance of Th1 versus Th2 cytokine production in the seminal plasma of men with SCI compared with that of control subjects. This finding suggests an immunologic basis for infertility as a possible avenue of investigation in these men.
Optimum Efficiency Control of Traveling-Wave Ultrasonic Motor System (2011)

The operational efficiency of ultrasonic motor motion control systems is much lower than that of traditional electromagnetic motors, which badly restricts the application of ultrasonic motor in portable devices. Lower efficiency, robustness, and wear condition are the main problems of ultrasonic motor systems. This paper studies on the optimum efficiency control strategy of an ultrasonic motor system and selects the commercially used ultrasonic motor Shinsei USR60 as the experimental motor. To provide a basis for the optimum efficiency control, the control characteristic of system efficiency is studied first under speed closed-loop control condition. Then, a novel feedforward speed controller compounded with a pole-assignment controller is designed to compensate the disturbance caused by the efficiency optimization process. After that, the optimum efficiency control strategy with varying step length based on fuzzy reasoning is proposed. Experiments show that the proposed optimum control methods can greatly increase the operational efficiency of the ultrasonic motor system.
Evaluating Patients with Cirrhosis for Hepatocellular Carcinoma: Value of Clinical Symptomatology, Imaging and Alpha-Fetoprotein (2007)

The study highlights the importance of symptomatology of weight loss, abdominal pain or anorexia as markers for HCC in patients with cirrhosis. AFP was not found to be a useful screening test. TPCT should be undertaken in all cirrhotics presenting to the hospital for the first time.
Molecular Genetics of Dopa-Responsive Dystonia (1999)

The causative genes of two types of hereditary dopa-responsive dystonia (DRD) due to dopamine (DA) deficiency in the nigrostriatum DA neurons have been elucidated. Autosomal dominant DRD (AD-DRD) was originally described by Segawa as hereditary progressive dystonia with marked diurnal fluctuation (HPD). We cloned the human GTP cyclohydrolase I (GCH1) gene, and mapped the gene to chromosome 14q22.1-q22.2 within the HPD/DRD locus, which had been identified by linkage analysis. GCH1 isthe rate-limiting enzyme for the biosynthesis of tetrahydrobiopterin (BH4), the cofactor for tyrosine hydroxylase (TH), which is the first and rate-limiting enzyme of DA synthesis. We proved that the GCH1 gene is the causative gene for HPD/DRD based on the identification of mutations of the gene in the patients and decreases in the enzyme activity expressed in mononuclear blood cells to 2-20% of the normal value. About 60 different mutations (missense, nonsense, and frameshift mutations) in the coding region or in the exon-intron junctions of the GCH1 gene have been reported in patients with AD-DRD all over the world. Recent findings indicate that the decreased GCH1 activity in AD-DRD may be caused by the negative interaction of the mutated subunit with the wild-type one, i.e., a dominant negative effect, and/or by decreases in the levels of GCH1 mRNA and protein caused by inactivation of one allele of the GCH1 gene. Autosomal recessive DRD (AR-DRD) with Segawa's syndrome was discovered in Germany. The AR-DRD locus was mapped to chromosome 11p15.5 in the chromosomal site of the TH gene. In the AR-DRD with Segawa's syndrome, a point mutation in TH (Gln381Lys) resulted in a pronounced decrease in TH activity to about 15% of that of the wild type. Several missense mutations in the TH gene have been found in AR-DRD in Europe. The phenotype of AR-DRD with the Leu205Pro mutation in the TH gene, which produces a severe decrease in TH activity to 1.5% of that of the wild type, was severe, not dystonia/Segawa's syndrome, but early-onset parkinsonism. However, a marked improvement of all clinical symptoms with a low dose of L-dopa was reported in AR-DRD/parkinsonism patients. These findings on DRD indicate that the nigrostriatal DA neurons may be most susceptible to the decreases in GCH1 activity, BH4 level, TH activity, and DA level, and that DRD is the DA deficiency without neuronal death in contrast to juvenile parkinsonism or Parkinson's disease with DA cell death.
Pulmonary Endarterectomy. Patient Selection, Technical Challenges, and Outcomes (2016)

In chronic thromboembolic pulmonary hypertension, thromboemboli do not undergo resolution but instead become highly organized and fibrotic, resulting in obstruction of segments of the pulmonary vascular tree. Progressive pulmonary hypertension ensues, with substantial associated morbidity and mortality. Despite advances in medical therapy for some types of pulmonary hypertension, surgical pulmonary endarterectomy, also referred to as pulmonary thromboendarterectomy, remains the only potentially curative option for patients with chronic thromboembolic pulmonary hypertension. This article reviews patient selection, surgical technique, and outcomes for pulmonary endarterectomy in this patient population.
<i>O</i>-Sialylation with<i>N</i>-Acetyl-5-<i>N</i>,4-<i>O</i>-Carbonyl-Protected Thiosialoside Donors in Dichloromethane:  Facile and Selective Cleavage of the Oxazolidinone Ring (2007)

An N-acetyl-5-N,4-O-carbonyl-protected thiosialoside donor, the structure of which has been defined through X-ray crystallography, was prepared and tested in couplings to a wide range of acceptors. This donor gives excellent yields and alpha-selectivities in linking with various primary alkyl and carbohydrate acceptors under the N-iodosuccinimide and trifluoromethanesulfonic acid in situ activation method at -40 degrees C in dichloromethane. The favorable affect of the oxazolidinone substructure for alpha-sialylation is illustrated by a comparison study with a N,N-diacetylsialyl donor, which exhibited inferior yields and alpha-selectivities. The sialylation selectivity is independent of the anomeric configuration of the donor, but is highly related to the reaction temperature under the NIS/TfOH activation method. In contrast to the NIS/TfOH method, the Ph2SO/Tf2O promotion gives beta-selective couplings in dichloromethane. The oxazolidinone of the N-acetyl-5-N,4-O-carbonyl protected sialosides, both alpha- and beta-anomers, could be cleaved cleanly by treatment with sodium methoxide under mild conditions without removal of the acetamide.
Dispersion and Property Enhancements in Polyolefin/Soy Flour Biocomposites Prepared via Melt Extrusion Followed by Solid‐State Shear Pulverization (2015)

Biocomposites of low‐density polyethylene (LDPE) and polypropylene (PP) with 5–40 wt% soy flour (SF) are produced by two‐step single‐screw extrusion (SSE) followed by solid‐state shear pulverization (SSSP). The SSE‐SSSP approach overcomes limitations with melt mixing, e.g poor SF dispersion and degradation, and limitations with single‐step SSSP. Microscopy shows that SF is well dispersed in SSE‐SSSP composites but agglomerated and degraded in melt‐mixed composites. The SSE‐SSSP composites exhibit major improvements in Young's modulus relative to neat polymer, including 74 and 43% increases in 80/20 wt% LDPE/SF and 95/5 wt% PP/SF composites, respectively. Relative to neat polymer, SSE‐SSSP composites exhibit the largest improvements in Young's modulus and best tensile strengths reported for polyolefin/SF composites. Crystallization and viscosity are only slightly affected by SF in the composites. At 20% and higher mass loss, char can result in greater thermo‐oxidative stability of 80/20 wt% polyolefin/SF composites relative to neat polymer.
Ethernet in the First Mile: Access for Everyone (2006)

IEEE Std 802.3ah-2004 is an outstanding resource for those building products compatible with the Ethernet in the First Mile standard. This book brings the standard to life by explaining the basic principles behind the standard, presenting the tradeoffs that led to the standardization of the specific technologies, and providing a guide to help you navigate through the formal prose. Presented in a concise and easy to read format, "Ethernet in the First Mile: Access for Everyone," is a must have for end users, deployers, service providers, venture capitalists, IT professionals, and students. In order to give readers quick access to the information they need, each chapter begins with an overview, defines what the reader should expect to learn in that section, and ends with a summary of concepts, which gives readers quick access to the information they seek. Authors Wael Diab and Howard Frazier provide the story of Ethernet in the First Mile: why it happened, how it happened, what exactly happened, and what it will do for you. As the leaders of the standards project, these authors saw it all, from beginning to end. Facts are separated from fiction, giving you the straight scoop, and the inside story. This work is meant to serve as a companion to the IEEE standard; a Rosetta stone to help you decipher the hieroglyphics. Tutorial material not allowed in formal standards documents is provided, giving insights and illuminating the murky corners of the standard. The end result is a must-have resource for anyone interested in Ethernet in the First Mile technology
A Variable Stiffness Magnetic Catheter Made of a Conductive Phase‐Change Polymer for Minimally Invasive Surgery (2022)

Abstract Variable stiffness (VS) is an important feature that significantly enhances the dexterity of magnetic catheters used in minimally invasive surgeries. Existing magnetic catheters with VS consist of sensors, heaters, and tubular structures filled with low melting point alloys, which have a large stiffness change ratio but are toxic to humans. In this paper, a VS magnetic catheter is described for minimally invasive surgery; the catheter is based on a novel variable stiffness thread (VST), which is made of a conductive shape memory polymer (CSMP). The CSMP is nontoxic and simultaneously serves as a heater, a temperature sensor, and a VS substrate. The VST is made through a new scalable fabrication process, which consists of a dipping technique that enables the fabrication of threads with the desired electrical resistance and thickness (with a step size of 70 µm). Selective bending of a multisegmented VST catheter with a diameter of 2.0 mm under an external magnetic field of 20 mT is demonstrated. Compared to existing proof‐of‐concept VS catheters for cardiac ablation, each integrated VST segment has the lowest wall thickness of 0.75 mm and an outer diameter of 2.0 mm. The segment bends up to 51° and exhibits a stiffness change factor of 21.
Cytological expression of early response to infection by <i>Heterodera glycines</i> Ichinohe in resistant PI 437654 soybean (1996)

The soybean PI 437654 is resistant to all known races of the soybean cyst nematode (SCN) in the U.S.A. and became a new source of resistance genes in cultivar development. Race 3, a wide-ranging nematode pathotype, was used to examine root cells of PI 437654 and susceptible 'Essex', 2, 3, and 5 days after inoculation (DAI). In initial response to SCN, both genotypes formed syncytia by cell wall dissolutions. Hypertrophy of syncytium component cells and hyperplasia of cells near syncytia were observed. At 2 DAI, incompatible response of PI 437654 to SCN was exhibited: limited cell hypertrophy, inhibition of syncytium growth, initiation of necrosis, and wall appositions. At 3 DAI, cellular events appeared to be a sum of the operative mechanisms for SCN resistance: irregular wall thickening, pronounced wall appositions, necrosis, and nuclear breakdown followed by cytoplasmic collapse. The cells surrounding the syncytia showed necrosis, wall apposition, and accumulation of electron-dense bodies. By 5 DAI, syncytia and neighboring cells were totally devoid of ground plasma and the degeneration process was completed. The normal route for early syncytium development in 'Essex' (increased number of organelles, intense vacuolization, accumulation of dense deposits in vacuoles, and wall ingrowths) suggests the involvement of portions of the developmental pathway of differentiating tissues in organogenesis. Early onset of SCN resistance 2 DAI in PI 437654 suggests rapid activation of genes in a cascade reaction leading to cell death. Key words : soybean, nematode, syncytium, cell death.
Isolation of a rat liver delta-aminolevulinate dehydrase (ALAD) cDNA clone: evidence for unequal ALAD gene dosage among inbred mouse strains. (1986)

We have isolated several cDNA clones encoding delta-aminolevulinate dehydrase [ALAD; porphobilinogen synthase; 5-aminolevulinate hydro-lyase (adding 5-aminolevulinate and cyclizing), EC 4.2.1.24], the second enzyme in the heme biosynthetic pathway. We used a rabbit polyclonal antibody developed against the purified 35-kDa subunit of rat liver ALAD to screen a lambda gt11 cDNA expression library constructed from rat liver mRNA. A prototype clone (ALAD-1) contained a 680-base-pair insert and expressed a 140-kDa beta-galactosidase gene cDNA insert fusion protein immunoreactive with both polyclonal and monoclonal anti-ALAD. Identity of ALAD-1 was verified by hydridization to ALAD mRNA that had been enriched via immunopurification of rat liver polysomes with anti-ALAD. Intensity of such hybridization to a 1500-nucleotide-long mRNA was approximately equal to 200-fold greater than that realized with whole liver mRNA, a result consistent with the degree of immunoenrichment of ALAD mRNA found independently by analysis of cell-free translation products. A second ALAD cDNA clone (ALAD-3) was isolated when the rat liver cDNA expression library was rescreened with ALAD-1. The identity of both ALAD cDNA clones was established by correspondence between their nucleotide sequence and the reported amino-terminal protein sequence of bovine ALAD. Hybridization of ALAD cDNA to mouse genomic DNA indicates that the previously unexplained incremental differences in ALAD enzymatic activity among inbred mouse strains has arisen through alterations in ALAD gene dose.