gebhart/patrepeval huggingface dataset:
Plasma Amino Acids in Relation to Cerebrospinal Fluid Monoamine Metabolites in Schizophrenic Patients and Healthy Controls (1985)

Compared to healthy controls, unmedicated schizophrenic patients had significantly higher plasma concentrations of taurine, methionine, valine, isoleucine, leucine, phenylalanine, and lysine. Except for taurine, these amino acids share the L-transport system for neutral amino acids. In the patients, homovanillic (HVA) acid levels in CSF were decreased and the plasma levels of the amino acids competing with tyrosine and tryptophan for transport into the brain, were all negatively correlated to the CSF concentrations of HVA and 5-HIAA. These findings could be explained by a change in the affinity of the L-system or by a decrease in its overall capacity in schizophrenia. Raised plasma levels of the competing amino acids may limit the brain uptake of tyrosine, leading to a diminished dopamine turnover, and resulting in a compensatory development of supersensitive dopamine receptors.
Chemokines Meet Defensins: the Merging Concepts of Chemoattractants and Antimicrobial Peptides in Host Defense (2002)

The capacity of the immune system to respond appropriately and eradicate microbial infections depends on the production of peptide and small protein mediators with diverse structures and functions, many of which are induced by contact with pathogens or inflammatory stimuli. Based on their activities
Simulation and expected performance analysis of multiple processor Z-buffer systems (1980)

The results of expected performance analysis and simulation of three multiple processor Z-buffer architectures are presented. These architectures have been proposed as approaches to applying many processors, working in parallel, to the task of rapidly creating shaded raster images. These architectures are attractive since they offer potentially high performance, in terms of image update rate, at modest cost. All three approaches make use of multiple instances of identical processor modules. The analyses and simulations indicate that substantial gain is possible by applying multiple processors to the task. But, as more and more processors are added, additional gains in performance become smaller and smaller. This result suggests optimal system sizes. The performance of these architectures depends on the processors used, the number of processors, and certain characteristics of the image environments. Each architecture has its own performance characteristics and limitations.
Synthesis, Characterization, and Surface Morphology of Pendant Polyhedral Oligomeric Silsesquioxane Perfluorocyclobutyl Aryl Ether Copolymers (2007)

The synthesis and characterization of solution processable, semi-fluorinated perfluorocyclobutyl (PFCB) aryl ether polymers possessing covalently bound pendant polyhedral oligomeric silsesquioxanes (POSS) cages is reported. The synthesis of POSS aryl trifluorovinyl ether (TFVE) monomers was accomplished by the condensation of commercial monosilanolalkyl-POSS with a TFVE-functionalized chlorosilane. POSS TFVE monomers were elucidated by 1H, 19F, 13C, and 29Si NMR spectroscopy, ATR-FTIR analysis, and elemental (C, H, and F) combustion analysis. Bulk thermal copolymerization of POSS TFVE monomers afforded random and block PFCB aryl ether copolymers functionalized with various POSS loadings. Quantitative monomer conversion was monitored by 19F NMR, which produced copolymer number-average molecular weights (Mn) of (19.5−24.9) × 103 (in CHCl3 using polystyrene as standard) determined by gel permeation chromatography (GPC). Thermal properties of POSS PFCB aryl ether copolymers were evaluated by differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA). Transmission electron microscope (TEM) analysis of spin cast optically transparent, flexible POSS PFCB aryl ether copolymer films revealed the presence of 5−20 nm-sized POSS agglomerates. Optical profilometer analysis of spin and drop cast film surfaces exhibited a modest increase in surface roughness of POSS PFCB aryl ether copolymers as compared to PFCB aryl ether homopolymers without POSS inclusion. The POSS copolymers exhibited a modest increase in hydrophobicity as measured by static water contact angle analysis. Synthesis, characterization, thermal analysis, and unique surface features of POSS PFCB aryl ether copolymers are discussed.
Purification and characterization of transfer RNA (guanine-1)methyltransferase from Escherichia coli. (1983)

The tRNA modifying enzyme, tRNA (guanine-1)methyltransferase has been purified to near homogeneity from an overproducing Escherichia coli strain harboring a multicopy plasmid carrying the structural gene of the enzyme. The preparation gives a single major band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme is probably a single polypeptide chain of molecular weight 32,000. The amino acid composition is presented and the NH2-terminal amino acid sequence was established to be H2N-Met-Trp-Ile-Gly-Ile-Ile-Ser-Leu-Phe-Pro. The enzyme has a pI of 5.2. The tRNA (guanine-1)-methyltransferase has a pH optimum of 8.0-8.5, an apparent Km of 5 microM for S-adenosylmethionine. S-adenosylhomocysteine is a competitive inhibitor for the enzyme with an apparent Ki of 6 microM. Spermidine or putrescine are not required for activity, but they stimulate the rate of methylation 1.2-fold with optima at 2 and 6 mM, respectively. Ammonium ion is not required and is inhibitory at concentrations above 0.15 M. Magnesium ion inhibited the activity at a concentration as low as 2 mM. Sodium and potassium ions were inhibitory at concentrations above 0.1 M. The molecular activity of tRNA (guanine-1)-methyltransferase was calculated to 10.0 min-1. It was estimated that the enzyme is present at 80 molecules/genome in cells growing with a specific growth rate of 1.0.
Self-Assembly of Discoidal Phospholipid Bilayer Nanoparticles with Membrane Scaffold Proteins (2002)

Nanoparticulate phospholipid bilayer disks were assembled from phospholipid and a class of amphipathic helical proteins termed membrane scaffold proteins (MSP). Several different MSPs were produced in high yield using a synthetic gene and a heterologous expression system and purified to homogeneity by a one-step purification. The self-assembly process begins with a mixture of the phospholipid and MSP in the presence of a detergent. Upon removal of detergent, 10-nm diameter particles form containing either saturated or unsaturated phospholipid. The ratio of components in the initial mixture was found to be crucial for formation of a monodisperse population of nanoparticles. Exploration of the phase diagram of the lamellar to phospholipid−detergent mixed micelle transition reveals that self-assembly proceeds from the mixed micellar phase. In this case a homogeneous and monodisperse population is formed. In contrast, particle formation from the detergent−phospholipid lamellar phase results in altered size, yield, composition, and heterogeneity of the resultant particles. The nanodisks contain approximately 160 saturated or 125 unsaturated lipids and can be formed from designed amphipathic α-helical scaffold proteins. The 10-nm particles can thus contain two molecules of MSP1 or a single molecule of an MSP1 fusion (MSP2). The phospholipid bilayer main phase transition temperature is preserved in the nanodisks as determined by fluorescence spectroscopy. Scanning probe microscopy shows a monolayer of nanodisks on a mica surface with a diameter of 10 nm and the thickness of a single phospholipid bilayer (5.7 nm), confirming the presence of a bilayer domain. The gentle method of self-assembly and robustness of the resulting nanodisks provides a means for generating soluble lipid bilayer membranes on the nanometer scale and opens the possibility of using these nanostructures to incorporate single membrane proteins into a native-like environment.
Efficacy of low and high dose inhaled corticosteroid in smokers versus non-smokers with mild asthma (2005)

Compared with non-smokers, smokers with mild persistent asthma are insensitive to the therapeutic effect of low dose inhaled corticosteroid treatment administered for a 12 week period. The disparity of the response between smokers and non-smokers appears to be reduced with high dose inhaled corticosteroid. These findings have important implications for the management of individuals with mild asthma who smoke.
Cervical Aortic Arch (1997)

Cervical aortic arch is a rare type of aortic arch anomaly that is presumed to result from persistence of the third aortic arch and regression of the normal fourth arch. Most of the patients with this anomaly are asymptomatic, but symptoms of dysphagia and respiratory distress due to the compression by the vascular ring have been reported. Other findings such as a supraclavicular pulsatile mass, blood pressure discrepancies between the upper limbs, and loss of femoral or opposite-upper-limb pulses with compression of the cervical mass may also be present. In this article a twenty-two-year-old woman with symptomatic cervical aortic arch is presented. The patient had a left cervical pulsatile mass and elevated blood pressure on her right upper limb and was treated surgically with reanastomosis of the aorta.
Synthesis and properties of flame‐retardant benzoxazines by three approaches (2006)

Abstract We propose three approaches to obtain flame‐retardant benzoxazines. In the first approach, we synthesize a novel benzoxazine (dopot‐m) from a phosphorus‐containing triphenol (dopotriol), formaldehyde, and methyl amine. Dopot‐m is copolymerized with a commercial benzoxazine [6′,6‐bis(3‐phenyl‐3,4‐dihydro‐2 H ‐1,3‐benzoxazineyl)methane (F‐a)] or diglycidyl ether of bisphenol A (DGEBA). The thermal properties and flame retardancy of the F‐a/dopot‐m copolymers increase with the content of dopot‐m. As for the dopot‐m/DGEBA curing system, the glass‐transition temperature of the dopot‐m/DGEBA copolymer is 252 °C, which is higher than that of poly(dopot‐m). The 5% decomposition temperature of the dopot‐m/DGEBA copolymer increases from 323 to 351 °C because of the higher crosslinking density caused by the reaction of phenolic OH and epoxy. In the second approach, we incorporate the element phosphorus into benzoxazine via the curing reaction of dopotriol and F‐a. After the curing, the thermal properties of the F‐a/dopotriol copolymers are almost the same as those of neat poly(F‐a), and this implies that we can incorporate the flame‐retardant element phosphorus into the polybenzoxazine without sacrificing any thermal properties. In the third approach, we react dopo with electron‐deficient benzoxazine to incorporate the element phosphorus. After the curing, the glass‐transition temperatures of polybenzoxazines decrease slightly with the content of dopo, mainly because of the smaller crosslinking density of the resultant polybenzoxazines. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 3454–3468, 2006
Late‐onset frontotemporal dementia with a novel exon 1 (Arg5His) tau gene mutation (2002)

We report a case of frontotemporal dementia and parkinsonism linked to chromosome 17 of 5 years' duration in an 81-year-old man whose brother had died at age 86 years with dementia. In this patient, we found frontal and temporal neuronal loss, glial-predominant tau deposits, progressive supranuclear palsy-like straight tubules, accumulation of 4-repeat-predominant Sarkosyl-insoluble tau, and a novel exon 1 (Arg5His) tau gene mutation. This mutation decreased microtubule-promoting capacity and increased fibrillation of tau in vitro. Thus, we consider that the Arg5His mutation is an authentic tau gene abnormality responsible for the patient's tau pathology and late-onset dementia.
Pharmacogenetics of Uridine Diphosphoglucuronosyltransferase (UGT) 1A Family Members and its Role in Patient Response to Irinotecan (2006)

Glucuronidation, catalyzed by the glucuronosyltransferase (UGT) superfamily, is a major biotransformation pathway for several drugs, including irinotecan. Irinotecan is commonly used in colorectal cancer chemotherapy. Irinotecan undergoes metabolism in humans and is converted to its active metabolite SN-38, a topoisomerase I inhibitor. SN-38 is inactivated via glucuronidation catalyzed by various hepatic and extrahepatic UGT1A isozymes. Although the role of the UGT1A1 *28 genetic variant has received much attention in altered toxicity upon irinotecan treatment, other UGT1A enzymes also play an important role. This review summarizes pharmacokinetic, toxicologic, and pharmacogenetic studies carried out to date in irinotecan and SN-38 disposition.
Hypercolumns for object segmentation and fine-grained localization (2015)

Recognition algorithms based on convolutional networks (CNNs) typically use the output of the last layer as a feature representation. However, the information in this layer may be too coarse spatially to allow precise localization. On the contrary, earlier layers may be precise in localization but will not capture semantics. To get the best of both worlds, we define the hypercolumn at a pixel as the vector of activations of all CNN units above that pixel. Using hypercolumns as pixel descriptors, we show results on three fine-grained localization tasks: simultaneous detection and segmentation [22], where we improve state-of-the-art from 49.7 mean AP <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r</sup> [22] to 60.0, keypoint localization, where we get a 3.3 point boost over [20], and part labeling, where we show a 6.6 point gain over a strong baseline.
An Automated Liquid Chromatography-Mass Spectrometry Process to Determine Metabolic Stability Half-Life and Intrinsic Clearance of Drug Candidates by Substrate Depletion (2008)

An automated process is described for the detailed assessment of the in vitro metabolic stability properties of drug candidates in support of pharmaceutical property profiling. Compounds are incubated with liver microsomes using a robotic liquid handler. Aliquots are taken at various time points, and the resulting samples are quantitatively analyzed by liquid chromatography-mass spectrometry utilizing ion trap mass spectrometers to determine the amount of compound remaining. From these data metabolism rates can be calculated. A high degree of automation is achieved through custom software, which is employed for instrument setup, data processing, and results reporting. The assay setup is highly configurable, allowing for any combination of up to six user-selected time points, variable substrate concentration, and microsomes or other biologically active media. The data, based on relative substrate depletion, affords an estimate of metabolic stability through the calculation of half-life (t(1/2)) and intrinsic clearance, which are used to differentiate and rank order drug leads. In general, t(1/2) is the time necessary for the metabolism, following first-order kinetics, of 50% of the initial compound. Intrinsic clearance is the proportionality constant between rate of metabolism of a compound and its concentration at the enzyme site. Described here is the setup of the assay, and data from assay test compounds are presented.
Subnuclear Distribution of Progesterone Receptors A and B in Normal and Malignant Endometrium (2004)

The nuclear progesterone receptor (PR), which is expressed as two proteins with different functions (PRA and PRB), is expressed in the normal endometrium and endometrial cancer. Our previous work has shown that there is a disruption to the relative PR isoform expression in progression to malignancy in endometrial cancer in which expression of a single isoform is common. A consistent feature in these studies was discrete punctate distribution of PRA and PRB in the nuclei of endometrial cancer cells. In this study PRA and PRB distribution within the nucleus was examined in vivo in the normal endometrium during the menstrual cycle, and in endometrial cancer, by dual immunofluorescence and confocal microscopy using cohorts in which PRA and PRB expression levels have previously been characterized. In the normal endometrium, PR was distributed evenly within the nucleus and also localized in discrete subnuclear foci. In the proliferative phase, even PR distribution was predominant and both PR isoforms were colocated and distributed evenly. In the secretory phase, there was a marked increase in the proportion of nuclei containing PR distributed into discrete foci, and PRB was the predominant isoform in nuclear foci. There was an inverse relationship between even and focal PR distribution in the menstrual cycle, suggesting that hormonal fluctuations were involved in movement of PR into focal nuclear locations. In endometrial cancers colocalization of PRA and PRB was infrequent, and there was no relationship between even and focal PR isoform distribution, unlike the normal endometrium. PRA was predominantly evenly distributed in endometrial cancers, whereas PRB was focal. Even PRB distribution in endometrial cancer was not often noted. Multivariate analysis showed that PRA expression was highly predictive of even nuclear distribution in endometrial cancers and PRB expression of distribution into foci, and these associations were independent of total PRA and PRB levels. Nuclear distribution of PR isoforms was associated with clinical grade, where tumors of high grade had significantly fewer nuclei containing even PRA distribution and focal PRB distribution, compared with tumors of low grade. In the normal endometrium, localization of PR into nuclear foci coincides with high progesterone levels, suggesting that altered intranuclear PR distribution is hormonally regulated. Nuclear distribution may be an important component of gene regulation in target tissues, and disruptions in PR distribution in endometrial cancer could affect the function of PR and contribute to aberrant hormonal responses.
Stable single-mode compound-ring erbium-doped fiber laser (1996)

In this paper we report the fabrication of a robust, tunable single-longitudinal-mode compound-ring Er/sup 3+/-doped fiber laser. The laser is fundamentally structured on an all-fiber compound-ring resonator in which a dual-coupler fiber ring is inserted into the main cavity. When combined in tandem with a mode-restricting intracavity tunable bandpass filter, the compound-ring resonator ensures single-longitudinal-mode laser oscillation. The laser can provide up to 20 mW output power over much of its 1525 to 1570 nm wavelength tuning range. The short-term linewidth of the laser output measured is less than 5 kHz. The laser frequency is actively stabilized for a long time by exploiting the inherent filter nature of the compound-ring resonator. The reduction of an associated frequency modulation is also discussed in detail.
Human Embryonic Stem Cell–Derived Cells Rescue Visual Function in Dystrophic RCS Rats (2006)

Embryonic stem cells promise to provide a well-characterized and reproducible source of replacement tissue for human clinical studies. An early potential application of this technology is the use of retinal pigment epithelium (RPE) for the treatment of retinal degenerative diseases such as macular degeneration. Here we show the reproducible generation of RPE (67 passageable cultures established from 18 different hES cell lines); batches of RPE derived from NIH-approved hES cells (H9) were tested and shown capable of extensive photoreceptor rescue in an animal model of retinal disease, the Royal College of Surgeons (RCS) rat, in which photoreceptor loss is caused by a defect in the adjacent retinal pigment epithelium. Improvement in visual performance was 100% over untreated controls (spatial acuity was approximately 70% that of normal nondystrophic rats) without evidence of untoward pathology. The use of somatic cell nuclear transfer (SCNT) and/or the creation of banks of reduced complexity human leucocyte antigen (HLA) hES-RPE lines could minimize or eliminate the need for immunosuppressive drugs and/or immunomodulatory protocols.
Repression of retrovirus-mediated transgene expression by interferons: implications for gene therapy (1997)

Retrovirus-mediated gene transfer is commonly used in gene therapy protocols and has the potential to provide long-term expression of the transgene. Although expression of a retrovirus-delivered transgene is satisfactory in cultured cells, it has been difficult to achieve consistent and high-level expression in vivo. In this investigation, we explored the possibility of modulating transgene expression by host-derived cytokines. Normal human keratinocytes and dermal fibroblasts were transduced with recombinant retroviruses expressing a reporter gene (lacZ). Treatment of transduced cells with a proinflammatory cytokine, gamma interferon (IFN-gamma), significantly reduced lacZ expression to less than 25% of that of nontreated cells. The inhibition was concentration dependent (peak at 5 ng/ml) and time dependent (maximal at 16 h for transcript and 24 h for protein); expression remained repressed in the continued presence of IFN-gamma but returned to normal levels 24 h after IFN-gamma withdrawal. The decrease in beta-galactosidase activity appeared to result from decrease in steady-state lacZ mRNA levels. Inhibitors of transcription and translation blocked IFN-gamma-induced repression, suggesting involvement of newly synthesized protein intermediates. Similar results were obtained by treatment of transduced cells with IFN-alpha but not with other proinflammatory cytokines, including tumor necrosis factor alpha, interleukin-2 (IL-1), IL-4, and granulocyte colony-stimulating factor. Although the level of lacZ mRNA was reduced by >70% following IFN treatment, the rate of lacZ transcription was not significantly different from that for nontreated cells. These results suggest that IFN-mediated regulation of transgene expression is at a posttranscriptional level. Interestingly, IFN-gamma also suppressed transgene expression driven by a cellular promoter (involucrin) inserted in an internal position in the retroviral vector. The presence of the overlapping 3' untranslated regions in transcripts initiated from the internal promoter and the long terminal repeat is suggestive of a posttranscriptional regulation, likely at the level of RNA stabilization. These results provide direct evidence for modulatory effects of IFNs on retrovirus-mediated transgene expression and suggest that gene therapy results may be altered by host inflammatory responses.
Extensions of H.264/AVC for Multiview Video Compression (2006)

We consider multiview video compression: the problem of jointly compressing multiple views of a scene recorded by different cameras. To take advantage of the correlation between views, we propose using disparity compensated view prediction and view synthesis and describe how these features can be implemented by extending the H.264/AVC compression standard. Finally, we discuss experimental results on the test sequences from the MPEG call for proposals on multiview video.