gebhart/patrepeval huggingface dataset:
Evaluation of comparative protein modeling by M<scp>ODELLER</scp> (1995)

We evaluate 3D models of human nucleoside diphosphate kinase, mouse cellular retinoic acid binding protein I, and human eosinophil neurotoxin that were calculated by MODELLER, a program for comparative protein modeling by satisfaction of spatial restraints. The models have good stereochemistry and are at least as similar to the crystallographic structures as the closest template structures. The largest errors occur in the regions that were not aligned correctly or where the template structures are not similar to the correct structure. These regions correspond predominantly to exposed loops, insertions of any length, and non-conserved side chains. When a template structure with more than 40% sequence identity to the target protein is available, the model is likely to have about 90% of the mainchain atoms modeled with an rms deviation from the X-ray structure of approximately 1 A, in large part because the templates are likely to be that similar to the X-ray structure of the target. This rms deviation is comparable to the overall differences between refined NMR and X-ray crystallography structures of the same protein.
Metamodeling: An Emerging Representation Paradigm for System-Level Design (2009)

Editor's note:The use of metamodeling in system design allows abstraction of concepts germane to a number of varying modeling domains, and provides the ability of exploiting meta-information for a variety of system design tasks such as analysis, verification, synthesis, and test generation. This article provides an overview of emerging metamodeling techniques and their applications.—Tim Cheng, IEEE Design & Test editor in chief
Cockpit Displayed Traffic Information and Distributed Management in Air Traffic Control (1980)

The technical feasibility of graphically displaying information such as surrounding aircraft and navigation routes in the cockpit on a cathode ray tube has been suggested as a viable method for improving the safety, orderliness, and expeditiousness of the air traffic control system by distributing some of its management to the pilots equipped with this cockpit displayed traffic and navigation information (CDTI). Several years of experimental study of this Concept, using a three-cab simulator facility at NASA-Ames, have produced several consistent findings relating to system performance and pilot and controller work loads and opinions. These findings generally agree with those from other studies. The most consistent result is a considerable reduction in controller verbal work load without any appreciable increase in pilot verbal work load, although they may report an increase in visual work load. However, pilots tend to prefer distributed management to centralized management, while this is generally reversed for controllers. The reduced response delays in the system obtainable using CDT/ permit pilots to maintain their own spacing more closely and precisely than when depending entirely upon controller-issued radar vectors and speed commands. As a result, time between successive aircraft landings and its variability can be reduced, thereby increasing runway utilization. Limited findings suggest that CDTI-based benefits do not detract from system safety. On balance, distributed management offers significant advantages for air traffic control.
Epidermal Growth Factor (1972)

Abstract The major physicochemical properties of epidermal growth factor are reported. The molecular weight of epidermal growth factor is estimated to be approximately 6100 by the methods of sedimentation equilibrium, gel filtration, and minimum molecular weight calculations from amino acid analyses. Epidermal growth factor is a single chain polypeptide having an asparagine amino-terminal residue and an arginine carboxyl-terminal residue. It is further characterized by the absence of 3 specific amino acid residues: lysine, alanine, and phenylalanine. No detectable free sulfhydryl groups, hexosamines, or neutral sugars were observed. Epidermal growth factor has an isoelectric point of pH 4.60. The ultraviolet absorption spectrum is typical for proteins, with an E1%1 cm at 280 nm of 30.9. The secondary structure, as judged by ultraviolet circular dichroism, is principally nonhelical.
Conducting polymer/carbon nanocoil composite electrodes for efficient supercapacitors (2012)

Herein, we report for the first time, conducting polymer (polyaniline (PANI) and polypyrrole (PPY)) coated carbon nanocoils (CNCs) as efficient binder-free electrode materials for supercapacitors. CNCs act as a perfect backbone for the uniform distribution of the conducting polymers in the composites. In two electrode configuration, the samples exhibited high specific capacitance with the values reaching up to 360 and 202 F g−1 for PANI/CNCs and PPY/CNCs respectively. The values obtained for specific capacitance and maximum storage energy per unit mass of the composites were found to be comparable to one of the best reported values for polymer coated multi-walled carbon nanotubes. In addition, the fabricated PANI/CNC based supercapacitors exhibited a high value of 44.61 Wh kg−1 for maximum storage energy per unit mass. Although the devices exhibit an initial capacitance loss due to the instability of the polymer, the specific capacitance stabilizes at a fixed value after 500 charge–discharge cycles.
Dietary and Ruminally Derived trans-18:1 Fatty Acids Alter Bovine Milk Lipids (1994)

The objectives of this study were to determine whether dietary fish oil enhances production of trans-18:1 isomers in the bovine rumen and whether flow of ruminally derived and/or dietary trans-18:1 to the small intestine is correlated with milk fat production. Four lactating Holstein cows with cannulas in the rumen and proximal duodenum were fed diets with 0% supplemental fat (control diet), 3% hydrogenated tallow fatty acids (HTFA diet), 1.5% menhaden oil plus 1.5% stearic acid (MO+SA diet), or 1.5% soybean oil plus 1.5% partially hydrogenated soybean oil (SBO+HSBO diet) in a 4 x 4 Latin square design. Intakes of trans-18:1 were 0, 12, 0 and 69 g/d when cows were fed the control, HTFA, MO+SA and SBO+HSBO diets, respectively. However, the extent of 18:1 + 18:2(n-6) + 18: 3(n-3) biohydrogenation in the rumen was reduced by consumption of the MO+SA and SBO+HSBO diets. As a result, flow of trans-18:1 to the duodenum was 163 g/d for MO+SA-fed cows and 152 g/d for SBO+HSBO-fed cows compared with 38 g/d for cows fed the HTFA and control diets. Incomplete biohydrogenation accounted for all of the trans-18:1 flow when the MO+SA diet was fed. Compared with results when the HTFA and control diets were fed, milk fat percentage was lower and concentration of trans-18:1 in milk fat was higher when the MO+SA and SBO+HSBO diets were fed. Across all treatments, milk fat percentage decreased linearly with the amount of trans-18:1 flowing to the duodenum and the concentration of trans-18:1 in milk fat. Results indicate that bovine milk fat percentage is depressed by trans-18:1, whether derived from the diet or from incomplete biohydrogenation of unsaturated fatty acids.
Peptide binding characteristics of the non-classical class Ib MHC molecule HLA-E assessed by a recombinant random peptide approach (2001)

Compared to the results obtained with rat classical class Ia MHC molecules, RT1-A1c and RT1-Au, HLA-E appears to refold around a random peptide library to reduced but detectable levels, suggesting that this molecule's specificity is tight but probably not as exquisite as has been previously suggested. This, and a previous report that it can associate with synthetic peptides carrying a viral sequence, suggests that HLA-E, similar to its mouse counterpart (Qa-1b), could possibly bind peptides different from MHC class I leader peptides and present them to T lymphocytes.
Reviews (2011)

This is the latest in a series of practical books published by Kogan Page in the field of education by Professor Phil Race in collaboration with various others. Phil Race, Emeritus Professor of Educational Development at the University of Glamorgan, has had a varied and inspirational career in higher education, and at present is Programme Director for the University of Durham Certificate in Teaching in Higher Education. Steve McDowell lectures in IT at Gateshead College and the Open UniversityDOI:10.1080/0968776970050113
Whisker Growth during Epitaxy of GaAs by Molecular Beam Epitaxy (1982)

GaAs whiskers, many of them originating from one point, were observed on GaAs epitaxial layers grown by molecular beam epitaxy. Very small pools of Ga and/or In are believed to precipitate the whiskers which grow at a relatively rapid rate. This whisker growth process is similar to the vapor-liquid-solid (VLS) growth and may not necessarily be a result of any particular substrate defect.
<title>Automated labeling of bibliographic data extracted from biomedical online journals</title> (2003)

A prototype system has been designed to automate the extraction of bibliographic data (e.g., article title, authors, abstract, affiliation and others) from online biomedical journals to populate the National Library of Medicine’s MEDLINE database. This paper describes a key module in this system: the labeling module that employs statistics and fuzzy rule-based algorithms to identify segmented zones in an article’s HTML pages as specific bibliographic data. Results from experiments conducted with 1,149 medical articles from forty-seven journal issues are presented.
Sustained spheromaks with ideal <i>n</i> = 1 kink stability and pressure confinement (2014)

Increasing the helicity injector drive frequency up to 68.5 kHz on the Helicity Injected Torus-Steady Inductive (HIT-SI) experiment has produced spheromaks with current amplifications of 3.8, ideal n = 1 kink stability, improved toroidal symmetry and pressure confinement. Current centroid calculations from surface magnetic probes show an outward shift in the magnetic field at frequencies above 50 kHz. Grad-Shafranov equilibria indicate pressure confinement at higher injector operating frequencies. The minimum characteristic frequency needed to achieve this confining effect on HIT-SI plasmas is found to be approximately 30 kHz by analysis of the density fluctuations.
High-speed and low-power implementation of hash message authentication code through partially unrolled techniques (2005)

In this paper an efficient implementation, in terms of performance, of the keyed-hash message authentication code (HMAC) using the SHA-256 hash function is presented. This mechanism is used for message authentication in combination with a shared secret key. The proposed hardware implementation, invokes a partially unrolled implementation for the underlying hash function leading to a high-throughput and low-power implementation for the whole HMAC construction. Special care has been taken so that the proposed implementation doesn't introduce extra design complexity; while in parallel functionality was kept to the required levels.
The Culture Brand and Radical Alterities (2011)

A noted feature of the postcolonial environment is how the anthropological termculture has entered the demotic narratives of the disciplines former subjects. Notions ofculture are now set to perform many tasks, and Indigenous claims that particular practices,attributes or things constitute examples of a discreet culture are frequent. This paper arguesthat such claims are not necessarily cultural in the way supposed, but rather form part of aninternational discourse of rights now utilised by minorities and indigenes in settler nationsas a way of asserting authority and of proclaiming identity and resistance. It concludes bynoting that much contemporary postcolonial (and other) scholarships respect for differenceand need for radical alterities as the basis of a critique of western hegemony weakens the will for analysis of these issues, leading at times to contradictory argument.
The development of a new measure of quality of life for young people with diabetes mellitus: the ADDQoL-Teen. (2004)

The ADDQoL-Teen is a new measure of perceived impact of diabetes and its treatment on QoL of teenagers. It will help healthcare professionals and parents consider QoL issues as well as medical outcomes when caring for young people with diabetes. It may be used in clinical trials and for routine clinical monitoring in a context of continuing evaluation.
Depot-Specific Hormonal Characteristics of Subcutaneous and Visceral Adipose Tissue and their Relation to the Metabolic Syndrome (2002)

Visceral adipose tissue (VAT) imaged by computed tomography (CT) or magnetic resonance imaging (MRI) is associated with the metabolic syndrome features, being morphologically and functionally different from subcutaneous adipose tissue (SAT). Insulin effect is lower and catecholamine effect higher in visceral adipose tissue, with its metabolites and its secretions draining through portal system, partially at least, to the liver. Thus, visceral cells transfer and release fatty acids more extensively, have increased glucocorticoid and reduced thiazolidinedione responses, produce more angiotensinogen, interleukin-6 and plasminogen activator inhibitor-1, and secrete less leptin and adiponectin than SAT. Furthermore, there are regional differences in the intrinsic characteristics of the preadipocytes, with those of SAT presenting greater differentiation and fat cell gene expression but less apoptosis than that of VAT. All features contribute to the morbidity associated with increased VAT. To evaluate the relationship between VAT and components of the metabolic syndrome, 55 non-diabetic women, 11 lean (VAT < 68 cm 2) and 44 obese were studied. The obese with VAT within the normal range (VAT < or = 68 cm 2) had higher BMI, WHR, BP and resistance to FFA suppression during oGTT in comparison to the lean controls. The obese with VAT > 68 cm 2 compared to those with VAT < or = 68 cm 2 had similar body mass index (BMI) but significantly higher in vivo homeostasis model assessment for insulin resistance (HOMA IR ) results and triglycerides. By pooling all data, correlation analysis indicated that VAT contributes more to insulin resistance (HOMA IR ) than SAT does, but not when insulin-suppressed plasma free fatty acids during oral glucose tolerance test as an index of insulin resistance are taken into consideration.
DNA BINDING TO ELECTROPOLYMERIZED POLYPYRROLE: THE DEPENDENCE ON FILM CHARACTERISTICS (2001)

Evidence is presented that suggests the binding of DNA to electropolymerized polypyrrole (PPy) is directly related to the presence of positive charge carriers in PPy. The adsorption rate of short radiolabelled ∅X174 DNA fragments (average size 300 bp) onto thin films of electroxidized PPy doped with p-toluene sulfonate was found to vary as a function of: film storage conditions, film age, electrochemical reduction, but not synthesis current density. DNA bound more readily to films stored under dry conditions. DNA binding varied only slightly with the current density used during PPy electropolymerization. The DNA binding levels were significantly reduced with increasing PPy film age. This observation correlated qualitatively, but not quantitatively, with the known loss of PPy conductivity and charge defects with aging. DNA adsorption levels fell off far more rapidly with film age than does conductivity. Oxidized PPy films bound DNA at a higher rate than films which had been reduced subsequent to electroxidative synthesis, thereby removing a large fraction of the surface positive charge defects. These results support the idea that DNA binding is brought about by the presence of positive charge defect carriers in the PPy film.
Why do bell plates ring (2003)

Abstract: Bell plates are polygonal plates which, when held in the hand and struck with a beater, produce an initial transient followed by a sustained, pure tone. The presence of the sustained tone depends sensitively on the shape. This paper addresses the question: why does a particular shape ring so well, while slightly different shapes do not? We show that, in the standard ringing shape, the nodal lines of one of the lowest modes of vibration fuse in the handle to produce a region that exerts neither vibrational force nor torque on the hand, and therefore does not transfer vibrational energy to the hand. 1.
New Hybrids between<i>Saccharomyces</i>Sensu Stricto Yeast Species Found among Wine and Cider Production Strains (1998)

Two yeast isolates, a wine-making yeast first identified as a Mel+ strain (ex. S. uvarum) and a cider-making yeast, were characterized for their nuclear and mitochondrial genomes. Electrophoretic karyotyping analyses, restriction fragment length polymorphism maps of PCR-amplified MET2 gene fragments, and the sequence analysis of a part of the two MET2 gene alleles found support the notion that these two strains constitute hybrids between Saccharomyces cerevisiae and Saccharomyces bayanus. The two hybrid strains had completely different restriction patterns of mitochondrial DNA as well as different sequences of the OLI1 gene. The sequence of the OLI1 gene from the wine hybrid strain appeared to be the same as that of the S. cerevisiae gene, whereas the OLI1 gene of the cider hybrid strain is equally divergent from both putative parents, S. bayanus and S. cerevisiae. Some fermentative properties were also examined, and one phenotype was found to reflect the hybrid nature of these two strains. The origin and nature of such hybridization events are discussed.
Manufacturing Processes for Design Professionals (2007)

Introduction: Design for Manufacture Forming Technology Plastics and Rubber Metal Glass Ceramics Wood Composites Layered Manufacturing Cutting Technology Thermal Mechanical Joining Technology Thermal Mechanical Finishing Technology Additive Processes Subtractive Processes Printing Material Profiles Wood Plastic Metal Glass and Ceramics.
Soluciones prácticas para la eficacia en España de un convenio de gestación por encargo: de nuevo a propósito de la STS de 6 de febrero de 2014 (2014)

Ante la pasividad del legislador, y a la luz de la aparentemente contraria STS de 6 de febrero de 2014 y de las consideraciones extraidas de la nueva Ley 20/2011, de 21 de julio, del Registro Civil �y que entrara en vigor el proximo 22 de julio de este ano�, se proponen una serie de soluciones practicas para la efectividad de un convenio de gestacion por encargo hecho por espanoles en Espana o en pais que lo permita.
Impaired Nitric Oxide Synthase Pathway in Diabetes Mellitus (2002)

A glucose-induced impairment of DDAH causes ADMA accumulation and may contribute to endothelial vasodilator dysfunction in DM.
Antioxidant N-acetyl-L-cysteine ameliorates symptoms of premature aging associated with the deficiency of the circadian protein BMAL1 (2009)

Deficiency of the circadian clock protein BMAL1 leads to premature aging and increased levels of reactivate oxygen species in several tissues of mice. In order to investigate the role of oxidative stress in accelerated aging and development of age-related pathologies, we continuously administered the antioxidant N-acetyl-L-cysteine toBmal1-deficient mice through their entire lifespan by supplementing drinking water. We found that the life long treatment with antioxidant significantly increased average and maximal lifespan and reduced the rate of age-dependent weight loss and development of cataracts. At the same time, it had no effect on time of onset and severity of other age-related pathologies characteristic of Bmal1-/- mice, such as joint ossification, reduced hair regrowth and sarcopenia. We conclude that chronic oxidative stress affects longevity and contributes to the development of at least some age-associated pathology, although ROS-independent mechanisms may also play a role. Our bioinformatics analysis identified the presence of a conservative E box element in the promoter regions of several genes encoding major antioxidant enzymes. We speculate that BMAL1 controls antioxidant defense by regulating the expression of major antioxidant enzymes.
Flashlight Scene Detection for MPEG Videos (2005)

A new flashlight scene detection approach is presented. It focuses on two techniques: a new flashlight model based on the spatial-temporal characteristics of intensity value for the DC sequence, and a local threshold selection scheme using the sliding window. The advantages of this approach are its good performance for multi-frame and gradual flashlight scene cases, and local threshold selection. Experimental results show that the proposed algorithm is fast, robust and high accuracy
Insulin-Like Growth Factor-I as an Amplifier of Follicle- Stimulating Hormone Action: Studies on Mechanism(s) and Site(s) of Action in Cultured Rat Granulosa Cells* (1988)

The ovarian granulosa cell has recently been shown to be a site of insulin-like growth factor-I (IGF-I) production, reception, and action. In large measure, IGF-I action (in the rat) appears contingent upon its ability to synergize with FSH, a major promoter of granulosa cell differentiation. It is the objective of the in vitro studies reported herein to elucidate the cellular mechanism(s) whereby IGF-I amplifies FSH hormonal action, placing special emphasis on the potential role of the putative intracellular second messenger cAMP in this regard. Basal FSH binding (115.7 +/- 2.1 fmol/mg cell protein) to rat granulosa cells cultured under serum-free conditions remained unchanged after 72 h of treatment with IGF-I (50 ng/ml) by itself (107.1 +/- 1.0 fmol/mg cell protein). In contrast, treatment with FSH (20 ng/ml) resulted in a significant (P less than 0.05) decrease in FSH binding capacity (but not affinity) relative to controls in either the absence or presence of IGF-I. Whereas treatment with FSH resulted in a substantial increase in forskolin-stimulatable adenylate cyclase activity (10 +/- 1.7% conversion of [3H] ATP to [3H]cAMP), concurrent treatment with IGF-I resulted in 2.2-fold enhancement of FSH action. This IGF-I effect proved dose dependent with an apparent median effective dose of 3.6 +/- 0.8 ng/ml, a concentration in keeping with its granulosa cell receptor binding affinity. Significantly, however, IGF-I proved capable of enhancing Bt2cAMP-stimulated progesterone accumulation suggesting that IGF-I may be also acting at site(s) distal to cAMP generation. Taken together, these and previous studies indicate that nanomolar concentrations of exogenously added IGF-I may be interacting with the FSH transduction signal at multiple cellular site(s) to effect amplification of FSH action.
Matrix‐assisted laser desorption/ionization with an external ion source Fourier‐transform mass spectrometer (1994)

Mass spectra of several model oligopeptides (substance P, [Arg8]-vasopressin, tyrothricin, and the B-chain of bovine insulin) have been obtained with a matrix-assisted laser desorption/ionization (MALDI) source and a custom-designed Fourier-transform mass spectrometer (FTMS). The MALDI source is outside the magnetic field in a separately pumped external chamber, and ions are injected through the fringing fields of the magnet and into the FTMS analyzer cell by a long quadrupole mass filter that is operated in the RF-only mode. A large window on the ion source housing makes it easy to point and focus the laser beam onto the sample probe tip. A good quality mass spectrum is achieved for 0.5 pmol of substance P, and the mass resolution for the B-chain of bovine insulin is 19,000.