gebhart/patrepeval huggingface dataset:
Histidine 295 and Histidine 510 Are Crucial for the Enzymatic Degradation of Heparan Sulfate by Heparinase III (2000)

The heparinases from Flavobacterium heparinum are powerful tools in understanding how heparin-like glycosaminoglycans function biologically. Heparinase III is the unique member of the heparinase family of heparin-degrading lyases that recognizes the ubiquitous cell-surface heparan sulfate proteoglycans as its primary substrate. Given that both heparinase I and heparinase II contain catalytically critical histidines, we examined the role of histidine in heparinase III. Through a series of diethyl pyrocarbonate modification experiments, it was found that surface-exposed histidines are modified in a concentration-dependent fashion and that this modification results in inactivation of the enzyme (k(inact) = 0.20 +/- 0.04 min(-)(1) mM(-)(1)). The DEPC modification was pH dependent and reversible by hydroxylamine, indicating that histidines are the sole residue being modified. As previously observed for heparinases I and II, substrate protection experiments slowed the inactivation kinetics, suggesting that the modified residue(s) was (were) in or proximal to the active site of the enzyme. Proteolytic mapping experiments, taken together with site-directed mutagenesis studies, confirm the chemical modification experiments and point to two histidines, histidine 295 and histidine 510, as being essential for heparinase III enzymatic activity.
Nephroprotective effect of the HMG-CoA-reductase inhibitor cerivastatin in a mouse model of progressive renal fibrosis in Alport syndrome (2007)

Cerivastatin prolongs the lifespan of COL4A3 knockout mice, reduces proteinuria and delays uraemia. These effects are associated with decreased renal fibrosis and a reduction of inflammatory cell infiltration.
Postmortem Aviation Forensic Toxicology: An Overview (2010)

An overview of the subtopic aviation combustion toxicology of the field of aerospace toxicology has been published. In a continuation of the overview, the findings associated with postmortem aviation forensic toxicology are being summarized in the present overview. A literature search for the period of 1960-2007 was performed. The important findings related to postmortem toxicology were evaluated. In addition to a brief introduction, this overview is divided into the sections of analytical methods; carboxyhemoglobin and blood cyanide ion; ethanol; drugs; result interpretation; glucose and hemoglobin A(1c); and references. Specific details of the subject matter were discussed. It is anticipated that this overview will be an outline source for aviation forensic toxicology within the field of aerospace toxicology.
Frequency domain volume rendering (1993)

The Fourier projection-slice theorem allows projections of volume data to be generated in O(n 2 log n) time for a volume of size n 3 . The method operates by extracting and inverse Fourier transforming 2D slices from a 3D frequency domain representation of the volume. Unfortunately, these projections do not exhibit the occlusion that is characteristic of conventional volume renderings. We present a new frequency domain volume rendering algorithm that replaces much of the missing depth and shape cues by performing shading calculations in the frequency domain during slice extraction. In particular, we demonstrate frequency domain methods for computing linear or nonlinear depth cueing and directional diffuse reflection. The resulting images can be generated an order of magnitude faster than volume renderings and may be more useful for many applications.
Studies on Phenazines. III (1953)

The phenazine synthesis of Wohl-Aue was modified to utilize m-nitroanisole and aniline by which 1-methoxyphenazine, 2-methoxyphenazine 10-N-oxide, and 1-methoxyphenazine 5-N-oxide were obtained in 7:2:1 ratio. The use of m-anisidine and nitrobenzene gave 1-methoxyphenazine and 2-methoxyphenazine 5-N-oxide in 2:1 ratio. These results have shown that the Wohl-Aue reaction resulted in the condensation taking place more readily at the ortho position to the methoxyl group than at the para position. The product obtained by the condensation at the para position was found to be the mono-N-oxide compound.
Heterogeneously Integrated InP/Si Metal-oxide-semiconductor Capacitor Mach-Zehnder Modulator (2017)

We have developed a Mach-Zehnder modulator using a 700-m-long heterogeneously integrated InP/Si metal-oxide-semiconductor capacitor. It exhibits VπL and insertion loss of 0.41 Vcm and 1.0 dB, respectively. We also demonstrate 25-Gbit/s NRZ signal modulation.
EFFECT OF INDOLE-3-ACETIC ACID DERIVATIVES ON NEUROEPITHELIUM IN RAT EMBRYOS (2005)

Indole-3-acetic acid (IAA), a natural auxin, induces microencephaly in rats exposed to IAA during gestation days (Days) 12-14, corresponding to the early stage of cerebral cortex development. The purpose of this study was to examine the effects of 5 IAA derivatives administration in pregnant rats on neuroepithelial cells in the embryos. N-Methylindole-3-acetic acid (1Me-IAA), 2-Methylindole-3-acetic acid (2Me-IAA), 2-Methyl-5-methoxyindole-3-acetic acid (2Me-5MeO-IAA), 5-Methoxyindole-3-acetic acid (5MeO-IAA), Indole butyric acid (IBA), and IAA were administered at 1,000 mg/kg except for 2Me-IAA at 500 mg/kg on Days 12, 13 and 14, and then embryos/fetuses were harvested on Day 14.5 or 21. The dams in the 1Me-IAA and 2Me-IAA groups exhibited rigidity and a decrease in locomotor activity. Although a decrease in the absolute brain weight was observed in the 1Me-IAA, 5MeO-IAA, IBA and IAA groups, a decrease in the relative brain weight was observed in only the IAA group. Histopathologically, apoptotic cells were observed mainly in the medial and dorsal layer of the neuroepithelium in the 5MeO-IAA and IAA groups on Day 14.5. The degree of induced neuroepithelial cell apoptosis was less in the 5MeO-IAA group than in the IAA group. However, it was confirmed that the histopathological changes induced by 5MeO-IAA were quite similar to the lesions induced by IAA and may have resulted from the same mechanisms.
Bioelectrical Impedance Analysis Estimation of Water Compartments in Elderly Diseased Patients: The Source Study (2001)

BIA estimated TBW with a difference of 0.48 +/- 2.3 l (mean +/- SD) (50 kHz; p = .01) and 0.69 +/- 2.2 l (100 kHz; p < 0.001) compared with (18)O dilution. The difference was not affected by the hydration status. Estimates of ECW with BIA were systematically biased compared with Br dilution: 4.6 +/- 3.1 l (equation from Segal and colleagues; p < .001) and 3.4 +/- 2.9 l (equation from Visser and colleagues; p < .001). We propose a new, cross-validated equation. Conclusions. Body water spaces can be estimated accurately in geriatric patients with BIA.
Supermotifs enable natural invariant chain-derived peptides to interact with many major histocompatibility complex-class II molecules. (1995)

Class II-associated invariant chain peptides (CLIPs) compete with natural allele-specific ligands for binding to several purified HLA-DR molecules. Truncation and substitution analysis showed that a minimal sequence of 13 amino acids is sufficient for excellent binding to DR17 and DR1. Hydrophobic residues at relative positions 1 and 9 (P1 and P9) which are shared among these DR-ligands, and are found to be anchored in complementary pockets by x-ray crystallography allow specific binding. Two flanking residues at either end next to the specific contact sites Met107 and Met115 contribute to binding irrespective of their side chains, suggesting H-bonds to the major histocompatibility complex (MHC) molecule. Thus, CLIPs behave like conventional ligands, however, lack their allele-specific contact sites. Introduction of the DR17-specific contact site aspartate at P4 dramatically improves invariant chain-peptide binding to DR17, but reduces DR1 binding. By contrast, binding to DR1, but not DR17 is strongly improved after introduction of the DR1-specific contact site alanine at P6. In addition, analyzing the fine specificity of the hydrophobic contact sites at P1 and P9, CLIP variants reflected the allele-specific preferences of DR17- or DR1-ligands, respectively, for aliphatic or aromatic residues. Alignment studies suggest that CLIPs are designed for promiscuous binding in the groove of many MHC class II molecules by taking advantage of one or more supermotifs. One such supermotif, for example, does not include the DR17-specific contact site aspartate at P4, which in conventional natural ligands like Apolipoprotein (2877-94) is necessary to confer a stable conformation. Introduction of aspartate at P4 generates a CLIP variant that is stable in the presence of sodium dodecyl sulfate, such as allele-specific ligands. Studying the stability of class II-CLIP complexes at pH 5, we found that CLIPs, similar to anchor-amputated ligands, can be released from class II molecules, in contrast to conventional natural ligands, which were irreversibly bound. Taken together, our data provide compelling evidence that CLIP peptides bind into the class II groove.
Perspectives on the Amyloid-β Cascade Hypothesis (2004)

For the better part of the past two decades, studies on the molecular, biochemical and cellular mechanisms of Alzheimer disease have focused on amyloid-beta protein, the major proteinaceous component of senile plaques. In fact, the Amyloid Cascade Hypothesis has come to dominate the field both in terms of proposed disease mechanism as well as potential for therapeutic intervention. In this review, we look at the Amyloid Cascade Hypothesis from the perspective of pathology, cell biology, and genetics. In all cases, alternate interpretations of old data as well as new evidence indicates that amyloid-beta, far from being the harbinger of disease, actually occurs secondary to more fundamental pathological changes and may even play a protective role in the diseased brain. These findings bring into serious doubt the validity of the Amyloid Cascade Hypothesis as the central cause of Alzheimer disease and, consequently, the potential usefulness of therapeutic targets against amyloid-beta.
Finding Substance in the FCC's Policy of "Substantial Service" (2004)

An FCC license for the use of the electromagnetic spectrum is a valuable asset, but it exists only for a limited duration. Therefore, obtaining a license renewal is vital to a licensee, especially one who has participated in an auction and made substantial investments in order to obtain the rights the license confers. This Note describes the mechanisms by which licensees obtain greater certainty that their licenses will be renewed, including the concept of renewal expectancy. One form of such expectancy is the ambiguous "substantial service" requirement. This Note explains the origins of the term, discusses its current uses, and shows how this requirement is linked to the FCC's policy of flexible use. This Note explores how, when the policy of substantial service is used to promote flexible use, potential problems arise. Specifically, this Note asks whether substantial service, as applied to licenses issued under broad service rules designed to promote the widest possible variety of use, creates too ambiguous a standard for licensees to know with sufficient certainty that their licenses will be renewed. Additionally, this Note questions whether the substantial service standard, as it is currently applied, consistent with the goals of the Communications Act of 1934, as amended.\nThe Author argues that these problems can be solved by either the FCC returning to the policy of specifically announcing service benchmarks or through legislative change that would eliminate the requirement that a licensee must demonstrate compliance with service requirements.
Vipp1 deletion mutant of Synechocystis : A connection between bacterial phage shock and thylakoid biogenesis? (2001)

Plant chloroplasts originated from an endosymbiotic event by which an ancestor of contemporary cyanobacteria was engulfed by an early eukaryotic cell and then transformed into an organelle. Oxygenic photosynthesis is the specific feature of cyanobacteria and chloroplasts, and the photosynthetic machinery resides in an internal membrane system, the thylakoids. The origin and genesis of thylakoid membranes, which are essential for oxygenic photosynthesis, are still an enigma. Vipp1 (vesicle-inducing protein in plastids 1) is a protein located in both the inner envelope and the thylakoids of Pisum sativum and Arabidopsis thaliana. In Arabidopsis disruption of the VIPP1 gene severely affects the plant's ability to form properly structured thylakoids and as a consequence to carry out photosynthesis. In contrast, Vipp1 in Synechocystis appears to be located exclusively in the plasma membrane. Yet, as in higher plants, disruption of the VIPP1 gene locus leads to the complete loss of thylakoid formation. So far VIPP1 genes are found only in organisms carrying out oxygenic photosynthesis. They share sequence homology with a subunit encoded by the bacterial phage shock operon (PspA) but differ from PspA by a C-terminal extension of about 30 amino acids. In two cyanobacteria, Synechocystis and Anabaena, both a VIPP1 and a pspA gene are present, and phylogenetic analysis indicates that VIPP1 originated from a gene duplication of the latter and thereafter acquired its new function. It also appears that the C-terminal extension that discriminates VIPP1 proteins from PspA is important for its function in thylakoid formation.
Inducible nitric oxide synthase in pulmonary alveolar macrophages from patients with tuberculosis. (1996)

The high-output pathway of nitric oxide production helps protect mice from infection by several pathogens, including Mycobacterium tuberculosis. However, based on studies of cells cultured from blood, it is controversial whether human mononuclear phagocytes can express the corresponding inducible nitric oxide synthase (iNOS;NOS2). The present study examined alveolar macrophages fixed directly after bronchopulmonary lavage. An average of 65% of the macrophages from 11 of 11 patients with untreated, culture-positive pulmonary tuberculosis reacted with an antibody documented herein to be monospecific for human NOS2. In contrast, a mean of 10% of bronchoalveolar lavage cells were positive from each of five clinically normal subjects. Tuberculosis patients' macrophages displayed diaphorase activity in the same proportion that they stained for NOS2, under assay conditions wherein the diaphorase reaction was strictly dependent on NOS2 expression. Bronchoalveolar lavage specimens also contained NOS2 mRNA. Thus, macrophages in the lungs of people with clinically active Mycobacterium tuberculosis infection often express catalytically competent NOS2.
Electrical properties of heavily doped polycrystalline silicon-germanium films (1994)

The electrical properties of polycrystalline silicon-germanium (poly-Si/sub 1/spl minus/x/Ge/sub x/) films with germanium mole fractions up to 0.56 doped by high-dose ion implantation are presented. The resistivity of heavily doped p-type (P/sup +/) poly-Si/sub 1/spl minus/x/Ge/sub x/ is much lower than that of comparably doped poly-Si, because higher levels of boron activation and higher hole mobilities are achieved in poly-Si/sub 1/spl minus/x/Ge/sub x/. The resistivity of heavily doped n-type (N/sup +/) poly-S/sub 1/spl minus/x/Ge/sub x/ is similar to that of comparably doped poly-Si for x<0.45; however, it is considerably higher for larger Ge mole fractions due to significant reductions in phosphorus activation. Lower temperatures (/spl sim/500/spl deg/C), as well as lower implant doses, are sufficient to achieve low resistivities in boron-implanted poly-Si/sub 1/spl minus/x/Ge/sub x/ films, compared to poly-Si films. The work function of P/sup +/ poly-Si/sub 1/spl minus/x/Ge/sub x/ decreases significantly (by up to /spl sim/0.4 Volts), whereas the work function of N/sup +/ poly-Si/sub 1/spl minus/x/Ge/sub x/ decreases only slightly, as Ge content is increased. Estimates of the energy bandgap of poly-Si/sub 1/spl minus/x/Ge/sub x/ show a reduction (relative to the bandgap of poly-Si) similar to that observed for unstrained single-crystalline Si/sub 1/spl minus/x/Ge/sub x/ for a 26% Ge film, and a reduction closer to that observed for strained single-crystalline Si/sub 1/spl minus/x/Ge/sub x/ for a 56% Ge film. The electrical properties of poly-Si/sub 1/spl minus/x/Ge/sub x/ make it a potentially favorable alternative to poly-Si for P/sup +/ gate-material applications in metal-oxide-semiconductor technologies and also for p-channel thin-film transistor applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A terahertz time-domain spectrometer for simultaneous transmission and reflection measurements at normal incidence (2009)

We present a versatile terahertz time-domain spectrometer which allows reflection measurements at normal incidence and double pass transmission measurements in a single experimental setup. Two different modes for transmission measurements are demonstrated for precise measurements of transparent high or low refractive index materials, respectively. The refractive indices and absorption coefficients of cesium iodide, potassium bromide, sodium chloride, polytetrafluoroethylene (PTFE, Teflon), and silicon have been measured in the frequency range between 1.4 and 4.7 THz. The parameters of the Lorentz oscillator functions describing the phonon polariton dispersions of CsI and KBr have been determined.
Recent Androgen Receptor Antagonists in Prostate Cancer (2014)

Androgen receptor has been shown to promote prostate cell growth and carcinogenesis of prostate cancer by up-regulating its target genes. Testosterone and dihydrotestosterone are two major hormones which bind to and activate androgen receptor. Targeting both the androgen receptor and the enzymes catalyzing the biosynthesis of testosterone and dihydrotestosterone has been shown to be clinically beneficial in the treatment of prostate cancer. Prostate cancer can become castration-resistant after long term treatment with chemo drugs, so efforts in finding compounds with improved efficiency to castration-resistant prostate cancer are urgently needed. In this review we summarized the studies on recent progress in the development of small molecular AR antagonists for the treatment of prostate cancer.
MRI-guided gas bubble enhanced ultrasound heating inin vivorabbit thigh (2003)

In this study, we propose a focused ultrasound surgery protocol that induces and then uses gas bubbles at the focus to enhance the ultrasound absorption and ultimately create larger lesions in vivo. MRI and ultrasound visualization and monitoring methods for this heating method are also investigated. Larger lesions created with a carefully monitored single ultrasound exposure could greatly improve the speed of tumour coagulation with focused ultrasound. All experiments were performed under MRI (clinical, 1.5 T) guidance with one of two eight-sector, spherically curved piezoelectric transducers. The transducer, either a 1.1 or 1.7 MHz array, was driven by a multi-channel RF driving system. The transducer was mounted in an MRI-compatible manual positioning system and the rabbit was situated on top of the system. An ultrasound detector ring was fixed with the therapy transducer to monitor gas bubble activity during treatment. Focused ultrasound surgery exposures were delivered to the thighs of seven New Zealand while rabbits. The experimental, gas-bubble-enhanced heating exposures consisted of a high amplitude 300 acoustic watt, half second pulse followed by a 7 W, 14 W or 21 W continuous wave exposure for 19.5 s. The respective control sonications were 20 s exposures of 14 W, 21 W and 28 W. During the exposures, MR thermometry was obtained from the temperature dependency of the proton resonance frequency shift. MRT2-enhanced imaging was used to evaluate the resulting lesions. Specific metrics were used to evaluate the differences between the gas-bubble-enhanced exposures and their respective control sonications: temperatures with respect to time and space, lesion size and shape, and their agreement with thermal dose predictions. The bubble-enhanced exposures showed a faster temperature rise within the first 4 s and higher overall temperatures than the sonications without bubble formation. The spatial temperature maps and the thermal dose maps derived from the MRI thermometry closely correlated with the resulting lesion as examined by T2-weighted imaging. The lesions created with the gas-bubble-enhanced heating exposures were 2-3 times larger by volume, consistently more spherical in shape and closer to the transducer than the control exposures. The study demonstrates that gas bubbles can reliably be used to create significantly larger lesions in vivo. MRI thermometry techniques were successfully used to monitor the thermal effects mediated by the bubble-enhanced exposures.
A convenient synthesis of 2‐substituted 4‐amino‐5‐pyrimidinecarbonitriles (1987)

Abstract Synthesis of the novel 2‐halogenated 4‐amino‐5‐pyrimidinecarbonitriles 3a,b starting from ethoxy‐methylenemalononitrile 1 and cyanamide is described. Nucleophilic substitution of the reactive halogen atom leads to the derivatives 5a‐g, 6 and 7a‐h.
Biologic and immunologic characteristics of cold-adapted influenza virus. (1969)

Summary Cold variants of influenza virus showed an impaired capacity to reproduce at acid pH (5.7 to 6.3) and elevated temperature (41°C). These features were used as markers to differentiate the cold variant from the original “wild” strain. After eight consecutive passages in mice, the viral strains recovered from the lungs of infected mice could still be identified by these selective markers as the cold variants. They showed no reversion to virulence upon ten consecutive passages in mice and retained their capacity to elicit a good antibody response. Ferrets responded as did mice to infection with the cold variants; the animals showed no evidence of disease and developed good HI antibody response. In addition, ferrets that possessed circulating antibody showed a heightened antibody response after they were reinoculated intranasally with cold variant virus.
New approaches for treating staphylococcal biofilm infections (2011)

Bacteria of the genus Staphylococcus are a prominent cause of acute and chronic infections. The ability of the staphylococci to establish biofilms has been linked to the persistence of chronic infections, which has drawn considerable interest from researchers over the past decade. Biofilms can be defined as sessile communities of surface-attached cells encased in an extracellular matrix, and treatment of bacteria in this mode of growth is challenging due to the resistance of biofilm structures to both antimicrobials and host defenses. In this review of the literature, we introduce Staphylococcus aureus and Staphylococcus epidermidis biofilms and summarize current antibiotic treatment approaches for staphylococcal biofilm infections. We also review recent studies on alternative strategies for preventing biofilm formation and dispersing established biofilms, including matrix-degrading enzymes, small-molecule approaches, and manipulation of natural staphylococcal disassembly mechanisms. While research on staphylococcal biofilm development is still in its early stages, new discoveries in the field hold promise for improved therapies that target staphylococcal biofilm infections.