gebhart/patrepeval huggingface dataset:
Cloning and Characterization of a Hemolysin Gene from <i>Actinobacillus (Haemophilus) pleuropneumoniae</i> (1989)

Neutralizing antisera to the leukotoxin secreted by Pasteurella haemolytica neutralized the hemolysin of Actinobacillus pleuropneumoniae and recognized a 110-kD antigen in cell-free culture supernatants from this organism. A series of nine overlapping recombinant phage clones carrying the gene for this 110-kD antigen were identified using affinity-purified anti-hemolysin antibody and a DNA probe containing sequences from the P. haemolytica lktCA genes. Eight of the nine clones expressed a 110-kD protein recognized by both anti-leukotoxin and anti-hemolysin antisera. The remaining clone expressed a truncated 80-kD antigen which was also recognized by both antisera. Sequence analysis of a region of the cloned DNA revealed two open reading frames encoding proteins with predicted masses of 18.5 and 102.5 kD. These genes, which we designate appC and appA, respectively, are similar in sequence to the hlyCA genes of Escherichia coli and the lktCA genes of P. haemolytica. Hemolytic activity could be detected in lysates of E. coli harboring plasmids containing the appCa genes.
Local Synthesis and Tooth Contact Analysis of Face-Milled, Uniform Tooth Height Spiral Bevel Gears (1996)

Face-milled spiral bevel gears with uniform tooth height are considered. An approach is proposed for the design of low-noise and localized bearing contact of such gears. The approach is based on the mismatch of contacting surfaces and permits two types of bearing contact either directed longitudinally or across the surface to be obtained. Conditions to avoid undercutting were determined. A Tooth Contact Analysis (TCA) was developed. This analysis was used to determine the influence of misalignment on meshing and contact of the spiral bevel gears. A numerical example that illustrates the theory developed is provided.
2D simulations of an inverse-geometry volumetric CT system with multiple detector arrays (2005)

The performance of an inverse geometry volumetric CT (IGCT) system with multiple detector arrays is being investigated. The system is capable of a complete acquisition of a volume free from cone-beam artifacts with only a single rotation of the gantry. The IGCT system is composed of a large source array opposite three small detector arrays with a field-of-view (FOV) large enough for clinical imaging (45cm). Simulations were conducted to estimate the MTF at different points in the FOV. The simulations involved generating 2D projection data of a 100um circular object followed by a reconstruction algorithm that uses gridding and filtered backprojection. The simulations also modeled finite source spot and detector element sizes. The estimated MTF’s were compared with theoretical MTF’s at 0 cm, 10 cm, and 20 cm away from the isocenter. The simulated MTF’s closely matched the theoretical MTF’s. The MTF in the radial direction was over 10% at 16 lp/cm across the entire FOV while the azimuthal MTF 10% point degraded to 10.4 lp/cm at the edge of the FOV. This degradation in azimuth, which can be corrected for, is due to gridding in the angular direction which is magnified at large distances away from the isocenter. The simulations show promising results for the in-plane resolution of the multiple detector array IGCT system. Noise properties and other factors impacting performance are currently being investigated.
[Growth inhibition of Borrelia burgdorferi sensu lato by antibodies. A contribution to understanding the pathogenesis and improving diagnosis of Lyme borreliosis]. (1995)

Phenomenon of growth inhibition of Borrelia burgdorferi sensu lato (BBSL), the agent of Lyme disease, by antiborrelial antibodies was observed and investigated. Some of the antiborrelial antibodies were bactericidal in the absence of complement and phagocytes. Based on growth inhibition phenomenon we developed and evaluated the function-oriented in vitro growth inhibition assay (GIA). GIA proved to be more strain-specific and a better predictor of protection against infectious challenge than matrix-based assays, such as ELISA and Western blot. Growth inhibition phenomenon was also applied as a tool for selection of antibody-resistant BBSL mutants. All BBSL isolates characterized to date have one or a combination of several major outer surface proteins (Osps). Mutants of BBSL with altered or absent Osps were selected with polyclonal or monoclonal antibodies (mAbs) at a frequency of 10(-2) to 10(-6). Based on PAGE and Western blot analysis all examined mutants were catalogued into 4 classes. Some of these mutants were later employed in studies of functional importance of Osps in immunopathogenesis of BBSL. Several studies revealed some possible functions of Osp proteins in borrelias. In one study, Osp-lacking mutant was distinguished from its Osp-bearing parent by autoaggregation and slower growth rate, diminished capacity to adhere to human umbilical vein endothelial cells, decreased plating efficiency on solid medium as well as serum and complement sensitivity. Mutant also was unable to evoke a detectable immune response after intradermal live cell immunization even though mutant cells survived in mouse skin for the same duration as wild type cells.(ABSTRACT TRUNCATED AT 250 WORDS)
Above-soil and in-soil degradation of oxo- and bio-degradable mulches: a qualitative approach (2016)

Degradable materials have been suggested to overcome accumulation in the field of persistent plastic residues associated with the increasing use of polyethylene mulches. New degradable materials have been proven successful for increasing crop productivity; however, their degradation in the field has been hardly addressed. A qualitative scale was used in the present study to assess the above-soil and in-soil degradation of degradable mulches during the cropping season. Degradation was determined in three biodegradable plastic mulches (Biofilm, BF; Mater-Bi, MB; Bioflex, BFx), two paper sheet mulches (Saikraft, PSA; MimGreen, PMG) and one oxo-degradable plastic mulch (Enviroplast, EvP). Polyethylene (PE) mulch was used as control. Mulches were tested in five Spanish locations (Castilla-La Mancha, La Rioja, Navarra, Aragón and Catalunya), with three crop seasons of processing tomato. Biodegradable plastic mulches BF and MB degraded more and faster above-soil than paper mulches; among biodegradable mulches BF degraded more than MB, and MB more than BFx. The above-soil degradation of the oxo-degradable mulch EvP was highly dependent on location and crop season, and it degraded more than PE. Main environmental factors triggering above-soil degradation were radiation, rainfall and crop cover. In-soil, paper mulches and BF degraded more and faster than MB, whereas BFx and EvP barely degraded. Environmental factors triggering in-soil degradation during the crop season were rainfall and irrigation water. The effect of soil parameters (organic matter, nutrient availability) on degradation during the cropping season was not evidenced. The qualitative scale used proved convenient for determining mulch field degradation. A visual scale for supporting the qualitative evaluation is provided. In order to standardise parameters and criteria for future studies on field mulching degradation evaluation, a unified degradation qualitative scale is suggested.
Extraction and reconstitution of membrane proteins into lipid nanodiscs encased by zwitterionic styrene-maleic amide copolymers (2020)

Membrane proteins can be reconstituted in polymer-encased nanodiscs for studies under near-physiological conditions and in the absence of detergents, but traditional styrene-maleic acid copolymers used for this purpose suffer severely from buffer incompatibilities. We have recently introduced zwitterionic styrene-maleic amide copolymers (zSMAs) to overcome this limitation. Here, we compared the extraction and reconstitution of membrane proteins into lipid nanodiscs by a series of zSMAs with different styrene:maleic amide molar ratios, chain sizes, and molecular weight distributions. These copolymers solubilize, stabilize, and support membrane proteins in nanodiscs with different efficiencies depending on both the structure of the copolymers and the membrane proteins.
Bent-core liquid crystal (LC) decorated gold nanoclusters: synthesis, self-assembly, and effects in mixtures with bent-core LC hosts (2008)

We present the first synthesis of a series of thiol-, thioacetate-, and xanthate-terminated bent-core derivatives, as well as the preparation of gold nanoclusters using the thiol-terminated bent-core compounds. The mesomorphic properties of the bent-core compounds have been investigated by polarizing optical microscopy (POM), differential scanning calorimetry (DSC), small angle X-ray scattering (SAXS), and electro-optic tests. From this series, the mono-xanthate derivatives form rectangular or hexagonal columnar phases, and the mono-thiol derivative with shorter alkyl chains forms a metastable, likely smectic, phase. All other bent-core compounds and intermediates exclusively form disordered or multi-layer lamellar crystalline solid modifications. High-resolution transmission electron microscopy (HR-TEM) images of the bent-core functionalized gold nanoclusters prepared from the thiol-terminated derivatives, taken after slow evaporation of the solvent, provide evidence for the formation of self-assembled nanocluster arrays. Upon dispersion of these gold nanoclusters in two structurally related bent-core LC hosts (one forming a SmCPA, and the second with a terminal double bond displaying a Colr phase), a shift in the surface plasmon resonance was observed indicating a LC host-dependent aggregation of the nanoparticles. Finally, we report initial results on the effects of different concentrations of these nanoclusters on the thermal properties as well as the applied voltage/current response of the parent SmCPA host.
Detection of a transforming fragment of herpes simplex virus type 2 in clinical specimens by PCR. The Canadian Women's HIV Study Group (1996)

A PCR assay for the sensitive detection of a transforming fragment of herpes simplex virus type 2 (HSV-2) was developed. Oligonucleotide primers were selected in Xho-2, a transforming region of the BglII N fragment of HSV-2. The assay reached a sensitivity endpoint of 10 copies of the Xho-2 subfragment and did not show cross-reactivity with other herpesviruses, including HSV-1. All 42 HSV-2 isolates scored positive in the assay. The Xho-2 PCR assay was evaluated with 216 clinical specimens and the results were compared with those of cell culture. The best protocol for processing specimens contained in viral transport medium included a centrifugation step followed by cell lysis. Of the 107 specimens positive for HSV-2 by culture, 105 were PCR positive (sensitivity, 98.1%). For one of the two falsely negative samples, beta-globin as well as sequences from the HSV-2 DNA polymerase gene could not be amplified. The other sample scored positive in both of these reactions but was indeterminate in duplicate tests by Xho-2 PCR. Two of 109 HSV-2 culture-negative specimens tested positive in the PCR assay (specificity, 98.2%). The latter two samples tested positive in a PCR test for the HSV-2 DNA polymerase gene. This novel tool was shown to be sensitive and specific for HSV-2 sequences and should allow for the investigation of the role of HSV-2 in genital cancers.
A New Practical Method for the Osmium-Catalyzed Dihydroxylation of Olefins using Bleach as the Terminal Oxidant (2003)

A general procedure for the osmium-catalyzed dihydroxylation of various olefins using bleach as oxidant is reported for the first time. Aromatic and aliphatic olefins yield the corresponding cis-1,2-diols in the presence of dihydroquinine or dihydroquinidine derivatives (Sharpless ligands) with good to excellent chemo- and enantioselectivities under optimized pH conditions. In the presence of a small excess of bleach as reoxidant fast dihydroxylation takes place even at 0 °C. Under optimum reaction conditions it is possible to dihydroxylate terminal aliphatic and aromatic olefins as well as internal olefins. The low price of the oxidant and the simple handling of bleach make this dihydroxylation variant attractive for further applications.
Research progress of intrinsic polymer dielectrics with high permittivity (2023)

Abstract The high permittivity of polymer dielectrics facilitates their use in the electronics industry. Compared to inorganic ceramics and composites, intrinsic high permittivity polymer dielectrics have the advantages of easy solution processing and better homogeneity. The permittivity of common polymers is generally low, hence it would be worthwhile to explore avenues for augmenting the permittivity of polymer dielectrics via judicious and efficient structural design. The effective strategies used to increase the permittivity of intrinsic polymers encompass elevating local polarisabilities by fortifying electron delocalisation capabilities, exploiting ion pairs to generate atomic clusters with larger dipole moments, amplifying dipole density, augmenting dipole mobility, and so forth. Due to the rigidity and flexibility of the polymer backbone's decisive influence on the dielectric's all‐around performance, its selection also requires a total consideration of the requirements of practical applications. This work provides an overview and a brief evaluation of the dominant design strategies and mentions possible future design paradigms for polymer dielectrics.
Kynurenine metabolites of tryptophan (1990)

Over the past 2 decades, a number of studies have demonstrated that amino acids act as precursors for the biosynthesis of a variety of neuroactive compounds, including catecholamines and indoleamines. For example, the aromatic amino acid L-tryptophan is a precursor for serotonin biosynthesis. Based on this observed precursor relationship, dietary tryptophan supplementation is used to treat a number of neurologic disorders attributed to alterations in serotoninergic neurotransmission. Recent studies have revealed that, in addition to serotonin, a number of neuroactive compounds, the kynurenines, are metabolities of tryptophan. Of these, perhaps the most important is quinolinic acid, a neurotoxin that acts at the N-methyl-D-aspartate (NMDA) receptor and whose precursor responsiveness to tryptophan far exceeds that of serotonin. In the central nervous system, kynurenines, and in particular quinolinic acid, may modulate excitatory amino acid transmission, and may act as neurotoxic agents implicated in the pathogenesis of several neurologic diseases.
Localization of DNA damage and its role in altered antigen-presenting cell function in ultraviolet-irradiated mice. (1996)

Prior ultraviolet (UV) irradiation of the site of application of hapten on murine skin reduces contact sensitization, impairs the ability of dendritic cells in the draining lymph nodes (DLN) to present antigen, and leads to development of hapten-specific suppressor T lymphocytes. We tested the hypothesis that UV-induced DNA damage plays a role in the impaired antigen-presenting activity of DLN cells. First, we assessed the location and persistence of cells containing DNA damage. A monoclonal antibody specific for cyclobutyl pyrimidine dimers (CPD) was used to identify UV-damaged cells in the skin and DLN of C3H mice exposed to UV radiation. Cells containing CPD were present in the epidermis, dermis, and DLN and persisted, particularly in the dermis, for at least 4 d after UV irradiation. When fluorescein isothiocyanate (FITC) was applied to UV-exposed skin, the DLN contained cells that were Ia+, FITC+, and CPD+; such cells from mice sensitized 3 d after UV irradiation exhibited reduced antigen-presenting function in vivo. We then assessed the role of DNA damage in UV-induced modulation of antigen-presenting cell (APC) function by using a novel method of increasing DNA repair in mouse skin in vivo. Liposomes containing T4 endonuclease V (T4N5) were applied to the site of UV exposure immediately after irradiation. This treatment prevented the impairment in APC function and reduced the number of CPD+ cells in the DLN of UV-irradiated mice. Treatment of unirradiated skin with T4N5 in liposomes or treatment of UV-irradiated skin with liposomes containing heat-inactivated T4N5 did not restore immune function. These studies demonstrate that cutaneous immune cells sustain DNA damage in vivo that persists for several days, and that FITC sensitization causes the migration of these to the DLN, which exhibits impaired APC function. Further, they support the hypothesis that DNA damage is an essential initiator of one or more of the steps involved in impaired APC function after UV irradiation.
Analysis, Modeling, and Simulation of the Accuracy of Continuous Glucose Sensors (2008)

CGM accuracy was modeled via diffusion and additive ARMA noise, which allowed for designing a computer simulator of sensor errors. The simulator, a component of a larger simulation platform approved by the Food and Drug Administration in January 2008 for pre-clinical testing of closed-loop strategies, has been successfully applied to in silico testing of closed-loop control algorithms, resulting in an investigational device exemption for closed-loop trials at the University of Virginia.
An Aluminum Heat Sink and Radiator for Electrophoresis Capillaries (1996)

An aluminum heat sink and radiator are used with forced air cooling of an electrophoresis capillary. Theoretical analyses of the operating limits and heat dissipation characteristics are presented. A system designed for power dissipation as high as 5 W is shown to dissipate heat efficiently and to operate without arcing at voltages higher than 30 kV.
Phase I trial of D2C7 immunotoxin (D2C7-IT) administered intratumorally via convection-enhanced delivery (CED) for recurrent malignant glioma (MG). (2020)

2566 Background: D2C7-IT is a recombinant immunotoxin comprised of a dual-specific antibody fragment targeting EGFRwt and EGFRvIII and a genetically engineered form of the Pseudomonas exotoxin, PE38-KDEL. We report the results of a phase I trial evaluating D2C7-IT delivered intratumorally by CED. Methods: Eligible patients were adults with recurrent supratentorial WHO grade III or IV MG; solitary tumor; ≥4 weeks after chemotherapy, bevacizumab or study drug; adequate organ function; and KPS>70%. Two patients per dose level (DL) were to enroll in the dose escalation portion (dose range: 40ng/mL to 23,354ng/mL). Results: From May 2015 to May 2018, 43 patients enrolled on study. Observed dose limiting toxicities include: grade 4 seizure (n=1) on DL3, grade 3 confusion and pyramidal tract syndrome (n=1) on DL13, and grade 4 cerebral edema (n=1) and grade 3 dysphasia (n=1) on DL17. Grade 3 or higher adverse events possibly related to D2C7-IT include: seizure (grade 4, n=2; grade 3, n=3), cerebral edema (grade 4, n=1), hydrocephalus (grade 3, n=5), headache (grade 3, n=4), hemiparesis (grade 3, n=4), dysphasia (grade 3, n=3), lymphopenia (grade 3, n=4), thromboembolic event (grade 3, n=3); and one each of grade 3 elevated ALT, urinary tract infection, fall, wound complication, generalized muscle weakness, confusion, encephalopathy, and somnolence. As of February 2020, four patients remain alive, with three patients demonstrating persistent radiographic partial response more than 54, 34 and 28 months after a single infusion of D2C7-IT. Conclusions: Dose level 13 (6,920ng/mL) was selected as the optimal phase II dose. Accrual in a dose expansion phase II trial is ongoing, and we are initiating a combination trial of D2C7-IT with checkpoint inhibitior. Clinical trial information: NCT02303678 .
Preclinical Pharmacological Evaluation of Letrozole as a Novel Treatment for Gliomas (2015)

We present data that letrozole, an extensively used aromatase inhibitor in the treatment of estrogen receptor-positive breast tumors in postmenopausal women, may be potentially used in the treatment of glioblastomas. First, we measured the in vitro cytotoxicity of letrozole and aromatase (CYP19A1) expression and activity in human LN229, T98G, U373MG, U251MG, and U87MG, and rat C6 glioma cell lines. Estrogen receptor (ER)-positive MCF-7 and ER-negative MDA-MB-231 cells served as controls. Cytotoxicity was determined employing the MTT assay, and aromatase activity using an immunoassay that measures the conversion of testosterone to estrogen. Second, in vivo activity of letrozole was assessed in Sprague-Dawley rats orthotopically implanted with C6 gliomas. The changes in tumor volume with letrozole treatment (4 mg/kg/day) were assessed employing μPET/CT imaging, employing [(18)F]-fluorodeoxyglucose (F18-FDG) as the radiotracer. Brain tissues were collected for histologic evaluations. All glioma cell lines included here expressed CYP19A1 and letrozole exerted considerable cytotoxicity and decrease in aromatase activity against these cells (IC50, 0.1-3.5 μmol/L). Imaging analysis employing F18-FDG μPET/CT demonstrated a marked reduction of active tumor volume (>75%) after 8 days of letrozole treatment. Immunohistochemical analysis revealed marked reduction in aromatase expression in tumoral regions of the brain after letrozole treatment. Thus, employing multifaceted tools, we demonstrate that aromatase may be a novel target for the treatment of gliomas and that letrozole, an FDA-approved drug with an outstanding record of safety may be repurposed for the treatment of such primary brain tumors, which currently have few therapeutic options.
Parameterization of Temporal Structure in the Single-Dielectric-Barrier Aerodynamic Plasma Actuator (2006)

We present the results of two measurements that describe the interaction of an aerodynamic plasma actuator (a dielectric barrier discharge plasma in which an asymmetric arrangement of electrodes leads to momentum coupling into neutral air) with the surrounding atmosphere. We show that the presence of oxygen in the Earth's atmosphere plays a substantial role in the efficiency of the actuator. We measure the time-resolved neutral air density in the vicinity of the actuator using a laser beam probe. We show that the effect of the actuator is to establish a region of increased neutral density in the vicinity of its exposed electrode's edge, and we show that the actuator couples directed momentum into the air by pulling air up this density gradient, against the corresponding pressure, and releasing it in the downstream direction when the plasma quenches, replacing it with air from the volume above the actuator. These measurements harmonize previously contradictory measurements of the actuator's behavior.
Visions & Reflections (Minireview) New insights into the mechanism of heat shock response activation (2008)

Heat shock (HS) response is a universal mechanism of protection against adverse environ- mental conditions. It is manifested mainly by rapid and robust induction of molecular chaperones and other cytoprotective proteins. In higher eukaryotes the activation of the HS response is mediated by a master regulator, heat shock transcription factor 1 (HSF1). Here we outline recent progress in under- standing the early steps in HSF1 activation by heat in the context of existing models of HSF1 regulation.