gebhart/patrepeval huggingface dataset:
Bexarotene-Induced Hypothyroidism: Bexarotene Stimulates the Peripheral Metabolism of Thyroid Hormones (2007)

In the present study, we demonstrate that increased peripheral degradation of thyroid hormones by a nondeiodinase-mediated pathway contributes to bexarotene induced-hypothyroidism.
Organoapatite growth on an orthopedic alloy surface (1999)

We report here a method to coat orthopedic metals with the artificial bone material organoapatite. The growth of organoapatite on titanium alloy surfaces of foils and porous cylinders involves sequential preadsorption of poly(L-lysine) and poly(L-glutamic acid) on metal, followed by exposure to organoapatite-precipitating solutions. The organoapatite characterization of the coating was carried out by transmission electron microscopy, electron diffraction, scanning electron microscopy, energy-dispersive X-ray scattering, powder X-ray diffraction, FT-IR, and elemental analysis. The preadsorbed poly(amino acids) in the form of a self-assembled bilayer of oppositely charged macromolecules can lead to a surface coverage of titanium alloy in the range of 70-90%. The deposition mechanisms could involve the surface capture of embryonic crystals and the nucleation of apatite on the bilayer. Bioabsorbable organoapatite could serve as a tissue-engineering scaffold for bone regeneration into porous implants.
The measurement and importance of red cell survival (2008)

The measurement of red blood cell survival in the circulation has progressed from the original differential agglutination technique of Ashby to current isotopic and flow cytometric methods. While occasionally useful in the clinic, these methods find widespread use in a number of important research areas, including the evaluation of new red cell storage media in transfusion medicine and studies of the pathophysiology of sickle cell disease and diabetes. In this review, measurement techniques are placed in historical perspective and examined for relative merits and suitable application.
Soybean Aphid in Minnesota (2017)

The soybean aphid (Aphis glycines) is an eastern Asian soybean pest that is rapidly invading the United States. A recent immigrant, it was first detected in nine midwestern states including Minnesotain the summer of 2000. The soybean aphid now occurs from Minnesota east to New York and south to Missouri and Kentucky. Significant aphid damage and soybean crop losses in 2000 were reported from Wisconsin, Illinois, and Michigan. In the summer of 2001, severe infestations were reported throughout southeastern Minnesota.
Multi-Scale Modeling of Organic Electro-Optic Materials (2012)

Development of organic materials for photonics applications requires simultaneous optimization of molecular and bulk properties to obtain acceptable performance in device applications. In developing organic electro-optic materials based on the Pockels effect, these properties include the molecular hyperpolarizability (β) of organic non-linear optical (ONLO) chromophores, the extent to which chromophores can be acentrically ordered in a material, the number density of chromophores (ρN), and the dielectric constant (ε) of the environment surrounding the chromophores. Furthermore, constraint of orientational degrees of freedom (reduced dimensionality) due to engineered non-covalent interactions and/or high chromophore loading can strongly affect acentric ordering of chromophores. This parameter space can be efficiently searched through theory-aided design, but the vast differences in the spatial scales needed to simulate each property require a multi-scale approach to computational modeling. Coarse-grained, rigid-body Monte Carlo (RBMC) calculations can be used to simulate large ensembles of chromophores and analyze the effects of steric anisotropy and dipole moment on ordering. Fully atomistic molecular dynamics (MD) calculations using classical force fields can be used to probe specific intermolecular interactions at the nanoscale, and electronic structure calculations at various levels (semi-empirical, DFT, and correlated, wavefunction-based methods such as MP2) can be used to calculate optical properties and provide parameters for lower-level (force field based) calculations. These techniques have been used to model the dielectric and phase behavior of strongly polar liquids such as acetonitrile, assist in the characterization of chomophore-containing complexes that exhibit a four-fold increase in poling efficiency compared to its parent chromophore, and in the molecular engineering of an OLNO dye for DNA-based biophotonics. Additionally, the importance of accounting for molecular shape, electrostatic boundary conditions, and choice of electronic structure methods are discussed and critically analyzed.
Disubstituted 1-Aryl-4-Aminopiperidine Library Synthesis Using Computational Drug Design and High-Throughput Batch and Flow Technologies (2013)

A platform that incorporates computational library design, parallel solution-phase synthesis, continuous flow hydrogenation, and automated high throughput purification and reformatting technologies was applied to the production of a 120-member library of 1-aryl-4-aminopiperidine analogues for drug discovery screening. The application described herein demonstrates the advantages of computational library design coupled with a flexible, modular approach to library synthesis. The enabling technologies described can be readily adopted by the traditional medicinal chemist without extensive training and lengthy process development times.
Genotype may correlate with liver carcinogenesis and tumor characteristics in cirrhotic patients infected with hepatitis B virus subtype adw (2001)

To identify the influence of hepatitis B virus (HBV) genotype on development of hepatocellular carcinoma (HCC) and clinical outcome in chronic HBV infection, 26 consecutive cirrhotic patients infected with HBV subtype adw were investigated prospectively. HBV serology was undertaken using subtype-specific antibodies against hepatitis B surface antigens. The HBV genotype was determined by sequencing directly the polymerase chain reaction products of the HBV S gene. When HCC occurred, patients underwent transcatheter arterial embolization therapy. If tumor necrosis was incomplete, additional embolization therapy was carried out after a 3- to 4-month interval. At a median follow-up of 14.1 years (range 2.2 to 31.7), HCC occurred in 9 (35%) of 26 patients. Nineteen patients were infected with genotype B and 7 with genotype C. Four of the 19 genotype B patients (21%) and 5 of the 7 genotype C patients (71%) developed HCC (P = 0.058). Patient age (<45 years or 45 < or = ) at diagnosis of cirrhosis was the only significant independent factor influencing liver carcinogenesis by multiple logistic regression analysis and Cox's regression analysis (P = 0.0069 and 0.029, respectively). When analysis was limited to the age of 45 years or more at the last visit, genotype was the only contributory factor to HCC development by univariate analysis (P = 0.038). Whereas genotype B patients responded well to embolization therapy and had no recurrence of HCC for a prolonged period of time, genotype C patients showed poor responses and died of hepatic failure due to rapid HCC progression despite embolization therapy. The cumulative incidence of survival was significantly higher in the genotype B group (P = 0.0049). The HBV genotype correlated with the development of HCC, response to embolization therapy, and recurrence of HCC. Determination of HBV genotype may be useful in predicting outcomes in HBV subtype adw-related cirrhosis.
Attenuation of the Inflammatory Response in an Animal Colitis Model by Neutrophil Inhibitory Factor, a Novel β2-Integrin Antagonist (1996)

These results suggest that blockade of CD11b/CD18-mediated mucosal neutrophil recruitment may form part of a strategy for targeted therapeutic intervention in inflammatory bowel disease.
p53, p21, Rb and mdm2 oncoproteins. Expression in normal placenta, partial and complete mole, and choriocarcinoma. (1998)

Altered expression of p53, p21, Rb and mdm2 may be important in the pathogenesis of both complete mole and choriocarcinoma. However, unlike complete molar pregnancy, partial mole is not characterized by overexpression of p53. Overexpression of p53 and mdm2 proteins in complete mole and choriocarcinoma may be associated with more aggressive behavior in gestational trophoblastic disease.
Dynamic motor exhaust gas analysis using a fast laser-TOF-mass spectrometer (1994)

Most emissions of pollutants from combustion engines take place in the first minute after starting of the cold engine and in the instationary motor phases such as rapid load or speed changes. Thus, the optimization of the dynamic motor operation is one of the main efforts to reduce the emission of pollutants and to comply with future legislative limitations. In a joint development project, a system has been developed which in principle meets the requirements of the dynamic exhaust gas analysis.
Identification of a Polymyxin Synthetase Gene Cluster of Paenibacillus polymyxa and Heterologous Expression of the Gene in Bacillus subtilis (2009)

Polymyxin, a long-known peptide antibiotic, has recently been reintroduced in clinical practice because it is sometimes the only available antibiotic for the treatment of multidrug-resistant gram-negative pathogenic bacteria. Lack of information on the biosynthetic genes of polymyxin, however, has limited the study of structure-function relationships and the development of improved polymyxins. During whole genome sequencing of Paenibacillus polymyxa E681, a plant growth-promoting rhizobacterium, we identified a gene cluster encoding polymyxin synthetase. Here, we report the complete sequence of the gene cluster and its function in polymyxin biosynthesis. The gene cluster spanning the 40.6-kb region consists of five open reading frames, designated pmxA, pmxB, pmxC, pmxD, and pmxE. The pmxC and pmxD genes are similar to genes that encode transport proteins, while pmxA, pmxB, and pmxE encode polymyxin synthetases. The insertional disruption of pmxE led to a loss of the ability to produce polymyxin. Introduction of the pmx gene cluster into the amyE locus of the Bacillus subtilis chromosome resulted in the production of polymyxin in the presence of extracellularly added L-2,4-diaminobutyric acid. Taken together, our findings demonstrate that the pmx gene cluster is responsible for polymyxin biosynthesis.
A simple technique to measure stress in ultrathin films during growth (1995)

We demonstrate an easy implementation of the cantilever bending beam approach to measure stress during film growth in ultrahigh vacuum. Using a simple and compact optical deflection technique, film stress with sub-monolayer sensitivity can be detected. A stress measurement during FeSi2 formation on Si(111) is presented.
Automatic Evaluation and Uniform Filter Cascades for Inducing N-Best Translation Lexicons (1995)

This paper shows how to induce an N-best translation lexicon from a bilingual text corpus using statistical properties of the corpus together with four external knowledge sources. The knowledge sources are cast as filters, so that any subset of them can be cascaded in a uniform framework. A new objective evaluation measure is used to compare the quality of lexicons induced with different filter cascades. The best filter cascades improve lexicon quality by up to 137% over the plain vanilla statistical method, and approach human performance. Drastically reducing the size of the training corpus has a much smaller impact on lexicon quality when these knowledge sources are used. This makes it practical to train on small hand-built corpora for language pairs where large bilingual corpora are unavailable. Moreover, three of the four filters prove useful even when used with large training corpora.
A novel point mutation (G-1 to T) in a 5' splice donor site of intron 13 of the dystrophin gene results in exon skipping and is responsible for Becker muscular dystrophy. (1994)

The mutations in one-third of Duchenne and Becker muscular dystrophy patients remain unknown, as they do not involve gross rearrangements of the dystrophin gene. We now report a defect in the splicing of precursor mRNA (pre-mRNA), resulting from a maternally inherited mutation of the dystrophin gene in a patient with Becker muscular dystrophy. This defect results from a G-to-T transversion at the terminal nucleotide of exon 13, within the 5' splice site of intron 13, and causes complete skipping of exon 13 during processing of dystrophin pre-mRNA. The predicted polypeptide encoded by the aberrant mRNA is a truncated dystrophin lacking 40 amino acids from the amino-proximal end of the rod domain. This is the first report of an intraexon point mutation that completely inactivates a 5' splice donor site in dystrophin pre-mRNA. Analysis of the genomic context of the G-1-to-T mutation at the 5' splice site supports the exon-definition model of pre-mRNA splicing and contributes to the understanding of splice-site selection.
Isolation and characterization of a species-specific DNA fragment for detection of Candida albicans by polymerase chain reaction (1992)

A 2-kbp DNA fragment, EO3, that was present in multiple copies in the Candida albicans genome was isolated for use in developing a detection method for C. albicans by polymerase chain reaction (PCR). Dot blot hybridization revealed that EO3 was specific for the 40 isolates of C. albicans serotypes A and B used. Using a set of primers (20-mer each) derived from the nucleotide sequence of EO3, we performed specific amplification of a 1.8-kbp DNA fragment within EO3 by PCR. All 40 isolates belonging to C. albicans serotypes A and B contained amplifiable 1.8-bkp fragments, although the DNA of the amplified products exhibited small variations in size, yielding three different fragment groups. Southern blot hybridization probed with EO3 showed that these 1.8-kbp fragments were derived from the EO3 region. Conversely, the 1.8-kbp fragment was not amplified from 38 isolates belonging to seven other medically important Candida species or from isolates of Cryptococcus neoformans, Saccharomyces cerevisiae, various bacteria, and a human cell line. The detection limit of the PCR assay for C. albicans with the EO3 fragment was shown to be approximately 2 to 10 cells and 100 cells in saline and human urine, respectively, by ethidium bromide staining and 2 and 10 cells, respectively, by Southern blot analysis. In addition, EO3 was assumed to originate from mitochondrial DNA on the basis of the results of its characterizations. These results indicate that the PCR system using the 1.8-kbp fragment as a target is a reliable method for identifying C. albicans isolates, thereby suggesting its potentials for specific and sensitive detection of C. albicans in samples from patients with candidiasis.
Recombinant vaccinia virus/Venezuelan equine encephalitis (VEE) virus protects mice from peripheral VEE virus challenge (1988)

Mice immunized with recombinant vaccinia virus (VACC) expressing Venezuelan equine encephalitis (VEE) virus capsid protein and glycoproteins E1 and E2 or with attenuated VEE TC-83 virus vaccine developed VEE-specific neutralizing antibody and survived intraperitoneal challenge with virulent VEE virus strains including Trinidad donkey (subtype 1AB), P676 (subtype 1C), 3880 (subtype 1D), and Everglades (subtype 2). However, unlike immunization with TC-83 virus, immunization with the recombinant VACC/VEE virus did not protect mice from intranasal challenge with VEE Trinidad donkey virus. These results suggest that recombinant VACC/VEE virus is a vaccine candidate for equines and humans at risk of mosquito-transmitted VEE disease but not for laboratory workers at risk of accidental exposure to aerosol infection with VEE virus.
Young's Modulus, Shear Modulus, and Poisson's Ratio in Silicon and Germanium (1965)

The elastic coefficients for an arbitrary rectangular coordinate system are calculated as a function of direction cosines in the crystal. Young's modulus, shear modulus, and Poisson's ratio are defined in general and values tabulated for some of the more important directions in the crystal. Graphs of these moduli are also plotted as a function of crystal direction for orientations in the (100) and (110) planes as well as planes determined by the [110] direction and any perpendicular direction.
Design, Synthesis, and Conformational Analysis of a Proposed Type I β-Turn Mimic (1998)

In an effort to design a dipeptide structural mimic of protein and peptide β-turns, we have prepared and evaluated the conformation of derivatives of the novel, highly constrained ten-membered lactam, (3S,10S)-(6E)-2-azacyclodec-6-enone (1). A synthetic route utilizing ring-closing olefin metathesis (RCM) has been used to prepare this novel ten-membered ring in high yield. X-ray crystallography and 1H NMR analysis have established that ring closure proceeds to give the trans-olefin and that 1 exists in two conformations, that of a chair−chair and chair−boat. Monte Carlo-molecular mechanics conformational searching has indicated that this ring system would be a good mimic of a type I β-turn. The synthesis of model tri- and tetrapeptide analogues based on 1 is reported. NMR studies indicate that the tetrapeptide derivatives constrain the i+1 and i+2 torsion angles to within 30° of those predicted for an ideal type I β-turn (φ1 = −82°, ψ1 = −20°, φ2 = −107°, ψ2 = −18°) and that this conformation was shown to be stable in both hydrogen-bonding solvents as well as non-hydrogen bonding solvents at various temperatures.
T cell receptor repertoire in polymyositis: clonal expansion of autoaggressive CD8+ T cells. (1995)

In polymyositis (PM), CD8+ T cell receptor (TCR) alpha/beta + cells invade and destroy major histocompatibility complex class I-positive muscle fibers. We combined polymerase chain reaction (PCR) and double-fluorescence immunocytochemistry to analyze the T cell receptor (TCR) repertoire expressed in muscle of PM patients. In patient 1, inverse PCR revealed a preferential usage of TCR V alpha 33.1, V beta 13.1, and V beta 5.1. Six of six TCR V alpha 33.1+ clones and five of seven V beta 13.1+ clones had identical nucleotide sequences. In contrast, the V beta 5.1+ TCRs were more heterogeneous. Similar results were obtained with an independent PCR method using primers specific for TCR V alpha 33, V beta 13, or V beta 5. No TCR sequences could be amplified from noninflammatory control muscle. Furthermore, none of the TCR sequences found in PM muscle could be detected in blood from the same patient or from a normal control subject. Immunohistochemistry confirmed that V beta 5.1 and V beta 13.1 were overrepresented in the muscle lesions of this patient. 32% of all CD8+ T cells were V beta 13.1+, and 16% were V beta 5.1+. However, approximately 60% of the CD8+ T cells that invaded muscle fibers were V beta 13.1+, whereas 10% were V beta 5.1+. In patient 2, 50% of the T cells were V beta 5.1+, and as in patient 1, these T cells were mainly located in interstitial areas. In patient 3, > 75% of the autoinvasive T cells stained with an anti-V beta 3 mAb. Sequence analysis of 15 PCR clones amplified with a V beta 3-specific primer showed that 9 (60%) sequences were identical. The results suggest that (a) a strikingly limited TCR repertoire is expressed in PM muscle; (b) there is a dissociation between the TCR usage of autoinvasive and interstitial T cells; and (c) the autoinvasive T cells are clonally expanded.
CINRG randomized controlled trial of creatine and glutamine in Duchenne muscular dystrophy (2005)

We tested the efficacy and safety of glutamine (0.6 gm/kg/day) and creatine (5 gm/day) in 50 ambulant boys with Duchenne muscular dystrophy in a 6-month, double-blind, placebo-controlled clinical trial. Drug efficacy was tested by measuring muscle strength manually (34 muscle groups) and quantitatively (10 muscle groups). Timed functional tests, functional parameters, and pulmonary function tests were secondary outcome measures. Although there was no statistically significant effect of either therapy based on manual and quantitative measurements of muscle strength, a disease-modifying effect of creatine in older Duchenne muscular dystrophy and creatine and glutamine in younger Duchenne muscular dystrophy cannot be excluded. Creatine and glutamine were well tolerated.
THERAPEUTIC MONOCLONAL ANTIBODIES (1995)

Monoclonal antibodies have been used extensively over the last few years in clinical trials of rheumatoid arthritis (RA). Not only are they potential therapeutic agents, but they are also useful probes into the immunopathogenesis of RA. Anti-tumour necrosis factor alpha (TNF alpha) monoclonal antibodies have been shown to be clinically efficacious. Although they produced rapid disease amelioration, the duration of clinical improvement was limited to 4-6 weeks. Re-treatments were again effective but long-term studies are required to assess their therapeutic role in RA. So far, the therapeutic effects of lymphocyte-depleting antibodies have been disappointing. From the data, it is clear that synovial lymphocytes are more difficult to eliminate than peripheral blood lymphocytes and it is likely that in order to delete all synovial lymphocytes, high doses of depleting antibodies will be required which could lead to severe immunosuppression. Hence, lymphocyte depletion may not be a feasible therapeutic strategy. However, there are a number of clinical trials currently underway attempting to inhibit CD4 lymphocyte function by non-depleting antibodies. In animal models of RA, such antibodies have been shown to induce long-term disease remission. Another possibility is to combine several monoclonal antibodies in order to induce disease remission in RA. This strategy has been used in murine collagen-induced arthritis in which a combination of anti-CD4 and anti-TNF alpha monoclonal antibodies was shown to be synergistic.
Structure-guided redesign of d-fructose-6-phosphate aldolase from E. coli: remarkable activity and selectivity towards acceptor substrates by two-point mutation (2011)

Structure-guided re-design of the acceptor binding site of D-fructose-6-phosphate aldolase from E. coli leads to the construction of FSA A129S/A165G double mutant with an activity between 5- to >900-fold higher than that of wild-type towards N-Cbz-aminoaldehyde derivatives.
Volumetric blood flow via time-domain correlation: experimental verification (1990)

A novel ultrasonic volumetric flow measurement method using time-domain correlation of consecutive pairs of echoes has been developed. An ultrasonic data acquisition system determined the time shift between a pair of range gated echoes by searching for the time shift with the maximum correlation between the RF sampled waveforms. Experiments with a 5-MHz transducer indicate that the standard deviation of the estimate of steady fluid velocity through 6-mm-diameter tubes is less than 10% of the mean. Experimentally, Sephadex (G-50; 20-80 mum dia.) particles in water and fresh porcine blood have been used as ultrasound scattering fluids. Two-dimensional (2-D) flow velocity can be estimated by slowly sweeping the ultrasonic beam across the blood vessel phantom. Volumetric flow through the vessel is estimated by integrating the 2-D flow velocity field and then is compared to hydrodynamic flow measurements to assess the overall experimental accuracy of the time-domain method. Flow rates from 50-500 ml/min have been estimated with an accuracy better than 10% under the idealized characteristics used in this study, which include straight circular thin-walled tubes, laminar axially-symmetric steady flow, and no intervening tissues.