gebhart/patrepeval huggingface dataset:
Tor-Mediated Induction of Autophagy via an Apg1 Protein Kinase Complex (2000)

Autophagy is a membrane trafficking to vacuole/lysosome induced by nutrient starvation. In Saccharomyces cerevisiae, Tor protein, a phosphatidylinositol kinase-related kinase, is involved in the repression of autophagy induction by a largely unknown mechanism. Here, we show that the protein kinase activity of Apg1 is enhanced by starvation or rapamycin treatment. In addition, we have also found that Apg13, which binds to and activates Apg1, is hyperphosphorylated in a Tor-dependent manner, reducing its affinity to Apg1. This Apg1-Apg13 association is required for autophagy, but not for the cytoplasm-to-vacuole targeting (Cvt) pathway, another vesicular transport mechanism in which factors essential for autophagy (Apg proteins) are also employed under vegetative growth conditions. Finally, other Apg1-associating proteins, such as Apg17 and Cvt9, are shown to function specifically in autophagy or the Cvt pathway, respectively, suggesting that the Apg1 complex plays an important role in switching between two distinct vesicular transport systems in a nutrient-dependent manner.
Parameter-based speech quality measures for GSM (2004)

This contribution introduces instrumental speech quality measures for the GSM system based only on transmission parameters. Certain combinations of GSM parameters which quantify the transmission quality in terms of bit error rate, received power level, etc., were shown be suitable for the prediction of the resulting speech quality. Neither the original nor the received speech signal is needed for this kind of prediction. The proposed speech quality measures have been validated by extensive link-level simulations which are based on measurements of transmission parameters collected in a GSM-1800 network. Speech samples were produced by bit-exact transmission simulations using the measured link parameters for channel modelling. The reference speech quality assessments of these samples were carried out with the PESQ algorithm Ref.3. The correlation of the presented parameter measures with the intrusive PESQ measure is remarkable.
Langmuir-Blodgett deposition and second-order non-linear optics of several azobenzene dye polymers (1996)

The Langmuir-Blodgett (LB) film-forming properties of a number of novel azobenzene dye polymers are reported. The linear and second-order non-linear optical properties of the films have been studied using ellipsometry, visible spectroscopy and Pockels effect measurements. As monolayers, the effective electro-optic r-coefficients ranged from 1 to 8.7 pm V.−1 When one of the polymers was combined in an alternate layer film (230 layers in total), an r13-coefficient of 13 pm V−1 was achieved. This is one of the highest values reported for a ‘thick’ LB film.
Clustering of relational data containing noise and outliers (2002)

The concept of noise clustering algorithm is applied to several fuzzy relational data clustering algorithms to make them more robust against noise and outliers. The methods considered include techniques proposed by Roubens (1978), Hathaway et al. (1994) and FANNY by Kaufman and Rouseeuw (1990). A new fuzzy relational data clustering (FRC) algorithm is proposed through generalization of FANNY. The FRC algorithm is shown to have the same objective functional as the relational fuzzy c-means algorithm. However, through use of direct objective function minimization based on the Lagrangian multiplier technique, the necessary conditions for minimization are derived without imposition of the restriction that the relational data is derived from Euclidean measure of distance from object data. Robustness of the new algorithm is demonstrated through several examples.
Spectral distribution of photoionization cross sections by photoconductivity measurements (1975)

A new technique for measuring the spectral distribution of photoionization cross sections in photoconductors is presented. The method makes use of the fact that the occupancy of an impurity level is not changed during illumination with photons of different energy if the photocurrent is kept constant. A constant photocurrent is achieved by adjusting the light intensity. The spectral distribution of the photoionization cross section is then given by the inverse of the photon flux as a function of the photon energy. To demonstrate the applicability of this measuring technique, measurements were performed on oxygen-doped GaAs samples. Three deep energy levels (two 0.46 and 0.79 eV below the conduction band and one 0.48 eV above the valence band) were investigated and the spectral distribution of five photoionization cross sections were measured. All of them are in good agreement with calculated values, and thus an accurate determination of the threshold energies is achieved. For comparison, similar investigations were performed with p+n junctions giving results which are in good agreement with the photoconductivity measurements.
Identification of candidate drugs for the treatment of ALS (2005)

A consortium of investigators interested in neurodegenerative diseases collaborated to screen 1040 drugs in multiple neurodegenerative disease assays. One model of amyotrophic lateral sclerosis (ALS) pathogenesis in particular incorporated glutamate exposure in enriched primary rat motor neuron cultures. In this model 78 compounds decreased motor neuron death caused by 100 microM glutamate. Almost all these pharmacological agents act at one or more of the following cellular targets: 1) protein synthesis inhibition; 2) Cox inhibition; 3) regulation of anion flux; 4) modulation of GABA receptors; 5) antioxidant, and 6) cell cycle inhibition. The most prevalent mode of action was the regulation of intracellular calcium. These data extend the understanding of motor neuron degeneration and identify a number of cellular targets for the improvement of combined therapies for neurodegenerative disease.
Effect of the carbohydrate moiety on the secondary structure of .beta.2-glycoprotein. I. Implications for the biosynthesis and folding of glycoproteins (1990)

By use of six highly purified exoglycosidases with well-defined specificity, the oligosaccharide units of human plasma beta 2-glycoprotein I (beta 2I) were modified by sequential enzymatic degradation. The released monosaccharides (NeuAc, Gal, GlcNAc, and Man) were quantified, and the carbohydrate compositions of the resulting glycoprotein (gp) derivatives were determined. The gp was found to be both partially sialylated and galactosylated. These findings which are in agreement with earlier reports suggest that the carbohydrate moiety of beta 2I possesses more bi- than tri-antennas, probably three of the former and two of the latter carbohydrate units. Circular dichroic (CD) spectra of native beta 2I and its derivatives were measured in aqueous buffer and 2-chloroethanol (2-CE). Analysis of these spectra for elements of secondary structure showed beta 2I and most of the derivatives to contain predominantly beta-sheet and beta-turn structures. The lack of alpha-helical structures in aqueous buffer was noted. Removal of a large portion of the carbohydrate moiety did not alter the CD spectra or secondary structure of beta 2I in either aqueous buffer or in 2-CE. However, after enzymatic removal of approximately 96% of the carbohydrate moiety, large significant changes in the spectra and secondary structures were observed. In aqueous buffer a shift in the wavelength minimum occurred, accompanied by an increase in the magnitude of the molar ellipticity and the amount of beta-turn, with a reduction in random coil. One-third of the amino acids which were originally in random coil conformation assumed beta-turns after removal of 96% of the carbohydrate moiety.(ABSTRACT TRUNCATED AT 250 WORDS)
Introduction to Bioinformatics: A Theoretical and Practical Approach (2003)

The genomic revolution that has spawned microarrays and high throughput technologies has produced vast amounts of complex biological data that require integration and multidimensional analysis. In Introduction to Bioinformatics: A Theoretical and Practical Approach, leading researchers and experts introduce the key biological, mathematical, statistical, and computer concepts and tools necessary for physical and life scientists to understand and analyze these data. For physical and computer scientists, the book provides a sound biological framework for understanding the questions a life scientist would ask in the context of currently available computational tools. Here, the basic cellular structure and the biological decoding of the genome, the long-range regulation of the genome, the in silico detection of the elements that impact long-range control, and the molecular genetic basis of disease as a consequence of replication are explained.
The Inducible Nitric Oxide Synthase Locus Confers Protection against Aerogenic Challenge of Both Clinical and Laboratory Strains of<i>Mycobacterium tuberculosis</i>in Mice (2001)

Murine macrophages effect potent antimycobacterial function via the production of nitric oxide by the inducible isoform of the enzyme nitric oxide synthase (NOS2). The protective role of reactive nitrogen intermediates (RNI) against Mycobacterium tuberculosis infection has been well established in various murine experimental tuberculosis models using laboratory strains of the tubercle bacillus to establish infection by the intravenous route. However, important questions remain about the in vivo importance of RNI in host defense against M. tuberculosis. There is some evidence that RNI play a lesser role following aerogenic, rather than intravenous, M. tuberculosis infection of mice. Furthermore, in vitro studies have demonstrated that different strains of M. tuberculosis, including clinical isolates, vary widely in their susceptibility to the antimycobacterial effects of RNI. Thus, we sought to test rigorously the protective role of RNI against infection with recent clinical isolates of M. tuberculosis following both aerogenic and intravenous challenges. Three recently isolated and unique M. tuberculosis strains were used to infect both wild-type (wt) C57BL/6 and NOS2 gene-disrupted mice. Regardless of the route of infection, NOS2(-/-) mice were much more susceptible than wt mice to any of the clinical isolates or to either the Erdman or H37Rv laboratory strain of M. tuberculosis. Mycobacteria replicated to much higher levels in the organs of NOS2(-/-) mice than in those of wt mice. Although the clinical isolates all exhibited enhanced virulence in NOS2(-/-) mice, they displayed distinct growth rates in vivo. The present study has provided results indicating that RNI are required for the control of murine tuberculous infection caused by both laboratory and clinical strains of M. tuberculosis. This protective role of RNI is essential for the control of infection established by either intravenous or aerogenic challenge.
ω-3 Fatty Acid Treatment in Multiple Sclerosis (OFAMS Study) (2012)

No beneficial effects on disease activity were detected from ω-3 fatty acids when compared with placebo as monotherapy or in combination with interferon beta-1a. Magnetic resonance imaging disease activity was reduced as expected by interferon beta-1a. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00360906.
Diet, nutrition, and avoidable cancer. (1995)

In a 1981 review, Doll and Peto estimated that approximately 35% of cancer deaths in the United States were potentially avoidable by the modification of diet but that this percentage might be as low as 10% or as high as 70%. Since that time, the epidemiologic literature on diet and cancer has grown greatly, as has understanding of the mechanisms of carcinogenesis. In general, this expanded literature has not provided reason to alter the Doll and Peto estimate substantially. For colon cancer, evidence has accumulated that some of the international differences that were attributed to diet are probably due to physical activity. For breast cancer, the concept that fat intake per se is the primary reason for differences in rates among countries has not been supported by prospective studies. Although several lines of evidence suggest that caloric restriction and slow growth rates may contribute importantly to the low rates of breast cancer found outside Western countries, this may not translate directly to practical means of prevention. In contrast to breast cancer, more recent data have supported a causative role for red meat in the development of colon and prostate cancers, although perhaps not entirely due to its fat content. Whereas earlier thinking about nutrition and cancer emphasized the adverse effects of fat and other components in the diet, the most compelling evidence of the last decade has indicated the importance of protective factors, largely unidentified, in fruits and vegetables. Considering the more recent evidence, it is roughly estimated that about 32% of cancer may be avoidable by changes in diet; however, it now seems unlikely that less than 20% or more than 42% of cancer deaths would be avoidable by dietary change.
Machine protection system (MPS) for the XFEL (2009)

For the operation of a machine like the 3 km long linear accelerator XFEL at DESY Hamburg, a safety system keeping the beam from damaging components is obligatory. This machine protection system (MPS) must detect failures of the RF system, magnets, and other critical components in various sections of the XFEL as well as monitor beam and dark current losses, and react in an appropriate way by limiting average beam power, dumping parts of the macropulse, or—in the worst case—shutting down the whole accelerator. It has to consider the influence of various machine modes selected by the timing system. The MPS provides the operators with clear indications of error sources, and offers the possibility to mask any input channel to facilitate the operation of the machine. In addition, redundant installation of critical MPS components will help to avoid unneccessary downtime. This document summarizes the requirements on the machine protection system and includes plans for its architecture and for needed hardware components.
<i>Babesia divergens</i>: cloning and biochemical characterization of Bd37 (2002)

The immunoprotective potential of Babesia divergens antigens released in supernatants of in vitro cultures of the parasite is generally known. Among a number of parasite molecules, a 37 kDa protein has been found in the supernatants of Babesia divergens cultures. In this report the cloning and biochemical characterization of this protein, called Bd37, are described. In addition, the processing of the protein was studied in vitro. Results suggest that Bd37 is encoded by a single copy gene. Bd37 appears to be a merozoite-associated molecule attached to the surface by a glycosylphosphatidylinositol moiety containing a palmitate residue attached to the inositol ring. In addition, it is demonstrated that both extremities of the protein are linked by a disulphide bond. Results further indicate that a soluble, hydrophilic form of Bd37 can be released from the merozoite surface by GPI-specific phospholipase D. The potential role the Bd37 protein and the GPI anchor are discussed.
The mononuclear phagocyte system of the mouse defined by immunohistochemical localization of antigen F4/80. Relationship between macrophages, Langerhans cells, reticular cells, and dendritic cells in lymphoid and hematopoietic organs. (1983)

The macrophage-specific antigen F4/80 has been localized in mouse lymphoid and hematopoietic tissue and skin using immunoperoxidase staining. The antigen permits identification of early mononuclear phagocyte precursors in the bone marrow, and is present also on larger cells forming the center of hematopoietic islands and lining vascular sinuses. In thymus F4/80+ cells are numerous in both cortex and medulla and are particularly concentrated around the corticomedullary region. In spleen, lymph node, and gut-associated lymphoid areas the major F4/80+ populations are in the red pulp, the medulla and subcapsular sinus, and the adjacent lamina propria, respectively. F4/80+ cells are rarely seen in T-dependent areas of lymph nodes, spleen, or Peyer's patch, but are present in large numbers in these areas during bacillus Calmette-Guerin (BCG)-induced inflammation. Macrophage infiltration occurs also in lymph nodes from athymic nu/nu mice and is therefore T cell independent. The interdigitating cell of T-dependent areas is F4/80-, but the Langerhans cell of the epidermis of the skin, which bears some ultrastructural resemblance to the interdigitating cell, is F4/80+. We conclude that the two cell types are probably not related.
Fully functional perpendicular STT-MRAM macro embedded in 40 nm logic for energy-efficient IOT applications (2015)

We present for the first time a fully functional 40 nm perpendicular STT-MRAM macro (1 Mb, ×32/×64 IO) embedded into a foundry standard CMOS logic platform. We achieved target design specifications of 20 ns read access time and 20–100 ns write cycle time without redundancy repair at standard core and IO voltages. The full 1 Mb macro can be switched reliably with write pulse as short as 6 ns, which results in full-chip write power of ∼ 3.2 μW/Mbps at ×64. This is the lowest eNVM write power reported at a full-chip level and about three orders of magnitude smaller than that of eFLASH. The 0.5 Mbit high-density bitcell array also demonstrates good Rp distribution and 100 % STT switching. Our results demonstrate superior power-area-feature attributes of perpendicular STT-MRAM as a best-in-class unified eNVM solution for Internet-of-Things (IOT) applications at 40 nm as well as the scalability of these advantages to 28 nm and beyond.
6. Design development of a tandem breakwater system for Hammond Indiana (1992)

An innovative breakwater concept consisting of a conventional breakwater and a submerged-reef breakwater operating in tandem has been designed for the southern end of Lake Michigan. The tandem breakwater system was found to cost $1 million less to build than a single structure designed to meet the same operating criteria. Because of the depth-limiting behavior of the reef, the tandem design possesses a lower design risk for extreme events. This paper provides a summary of the design development and physical model testing results for the concept. SYNOPSIS INTRODUCTION DESIGN DEVELOPMENT FINAL DESIGN EFFECT OF RELATIVE REEF SUBMERGENCE EFFECT OF CREST WIDTH EFFECT OF REEF POROSITY COMPARISON OF DATA TO THEORIES BREAKWATER SPACING REEF STABILITY SUMMARY AND CONCLUSIONS REFERENCES
Surface-Emitting Laser with a Common-Anode Configuration for Application to the Photonic Parallel Memory (1994)

A novel structure of a vertical-cavity surface-emitting laser (VCSEL) was proposed and demonstrated. Using a common-anode configuration, lower mesa height and lower electrical resistance were realized. The threshold current was 6 mA for a 10-µm-diameter device under room-temperature pulsed operation. The lasing wavelength was 939 nm. This configuration is suitable for large-scale integration. We also propose an optoelectronic integrated circuit (OEIC) with the common-anode configuration, which consists of a VCSEL and a heterostructure phototransistor (HPT) for optical parallel processing.
Recombinant Fibronectin Matrix Mimetics Specify Integrin Adhesion and Extracellular Matrix Assembly (2012)

Tissue engineering seeks to create functional tissues and organs by integrating natural or synthetic scaffolds with bioactive factors and cells. Creating biologically active scaffolds that support key aspects of tissue regeneration, including the re-establishment of a functional extracellular matrix (ECM), is a challenge currently facing this field. During tissue repair, fibronectin is converted from an inactive soluble form into biologically active ECM fibrils through a cell-dependent process. ECM fibronectin promotes cell processes critical to tissue regeneration and regulates the deposition and organization of other ECM proteins. We previously developed biomimetics of ECM fibronectin by directly coupling the heparin-binding fragment of the first type III repeat of fibronectin (FNIII1H) to the integrin-binding repeats (FNIII8-10). As adhesive substrates, fibronectin matrix mimetics promote cell growth, migration, and contractility through a FNIII1H-dependent mechanism. Here, we analyzed fibronectin matrix mimetic variants designed to include all or part of the integrin-binding domain for their ability to support new ECM assembly. We found that specific modifications of the integrin-binding domain produced adhesive substrates that selectively engage different integrin receptors to, in turn, regulate the amount of fibronectin and collagen deposited into the ECM. The ability of fibronectin matrix mimetics to direct cell-substrate interactions and regulate ECM assembly makes them promising candidates for use as bioactive surfaces, where precise control over integrin-binding specificity and ECM deposition are required.
FATTENING CATTLE WITH SUGAR CANE: THE EFFECT OF DIFFERENT PROPORTIONS OF STALK AND TOPS 3 (1976)

2.51X; feed conversion (kg DM/kg gain) = 7.71 +.0134X. The content of dry matter and of Brix in the juice both of tops and stalk increased during the progress of the trial. The voluntary consumption index also decreased with time on experiment, this effect being more noticeable for the diets with higher proportion of stalk. There was a negative relationship between voluntary consumption index and Brix in juice for the 100% stalk ration (b = -.134 ±.054), this tendency being less marked with the 100% tops ration (b = -.0024 ±.058).
Effect of Octreotide on Intestinal Motility and Bacterial Overgrowth in Scleroderma (1991)

Octreotide stimulates intestinal motility in normal subjects and in patients with scleroderma. In such patients, the short-term administration of octreotide reduces bacterial overgrowth and improves abdominal symptoms. This agent may be useful for the treatment of intestinal dysmotility in patients with scleroderma.
Suppression of a broad spectrum of liver autoimmune pathologies by single peptide-MHC-based nanomedicines (2019)

Peptide-major histocompatibility complex class II (pMHCII)-based nanomedicines displaying tissue-specific autoantigenic epitopes can blunt specific autoimmune conditions by re-programming cognate antigen-experienced CD4+ T-cells into disease-suppressing T-regulatory type 1 (TR1) cells. Here, we show that single pMHCII-based nanomedicines displaying epitopes from mitochondrial, endoplasmic reticulum or cytoplasmic antigens associated with primary biliary cholangitis (PBC) or autoimmune hepatitis (AIH) can broadly blunt PBC, AIH and Primary Sclerosing Cholangitis in various murine models in an organ- rather than disease-specific manner, without suppressing general or local immunity against infection or metastatic tumors. Therapeutic activity is associated with cognate TR1 cell formation and expansion, TR1 cell recruitment to the liver and draining lymph nodes, local B-regulatory cell formation and profound suppression of the pro-inflammatory capacity of liver and liver-proximal myeloid dendritic cells and Kupffer cells. Thus, autoreactivity against liver-enriched autoantigens in liver autoimmunity is not disease-specific and can be harnessed to treat various liver autoimmune diseases broadly.