gebhart/patrepeval huggingface dataset:
The Na+/glucose cotransporter (SGLT1). (1992)

An important class of Na+ transport proteins is the cotransporters. They exist in bacteria and animal cells and are responsible for the "active" accumulation of sugars, amino acids, carboxylic acids and some ions, e.g., I-, Cl-, and PO-4, in cells. In the small intestine and renal proximal tubule the cotransporters play an important role in the transport of salt and water across the epithelia. The most well known and best characterized Na+ cotransporter is the intestinal brush border Na+/glucose cotransporter. We have cloned, sequenced, and expressed both the rabbit and human Na+/glucose cotransporters. The cDNAs code for 73kDa proteins with 662-664 residues (86% identity). Secondary structure analysis suggests a 12 membrane-spanning helical model with the N- and C-termini in the cytoplasm. A single N-linked glycosylation site is utilized at Asn248. These sugars are not required for function. Two essential residues for functional expression in oocytes have been identified, Asp28 and Arg300. In two sisters with glucose-galactose malabsorption the transport defect is caused by a missense mutation changing Asp28 to Asn28, and we have found that changing Arg300 to Cys300 eliminated transport. Current research is directed to finding residues and domains essential for ligand binding and transport, and we are using electrophysiological techniques to correlate structure and function.
NMR and Quantum Chemical Study on the OH···π and CH···O Interactions between Trehalose and Unsaturated Fatty Acids:  Implication for the Mechanism of Antioxidant Function of Trehalose (2003)

Trehalose is a disaccharide that attracts much attention as a stress protectant. In this study, we investigated the mechanism of the antioxidant function of trehalose. The spin-lattice relaxation times (T(1)) of (1)H and (13)C NMR spectra were measured to investigate the interaction between trehalose and unsaturated fatty acid (UFA). We selected several kinds of UFA that differ in the number of double bonds and in their configurations (cis or trans). Several other disaccharides (sucrose, maltose, neotrehalose, maltitol, and sorbitol) were also analyzed by NMR. The T(1) values for the (1)H and (13)C signals assigned to the olefin double bonds in UFA decrease with increasing concentration of trehalose and the changes reaches plateaus at integer ratios of trehalose to UFA. The characteristic T(1) change is observed only for the combination of trehalose and UFA with cis double bond(s). On the other hand, from the (13)C-T(1) measurements for trehalose, the T(1) values of the C-3 (C-3') and C-6' (C-6) are found to change remarkably by addition of UFA. (1)H[bond](1)H NOESY measurements provide direct evidence for complexation of trehalose with linoleic acid. These results indicate that one trehalose molecule stoichiometrically interacts with one cis-olefin double bond of UFA. Computer modeling study indicates that trehalose forms a stable complex with an olefin double bond through OH...pi and CH...O types of hydrogen bonding. Furthermore, a significant increase in the activation energy is found for hydrogen abstraction reaction from the methylene group located between the double bonds that are both interacting with the trehalose molecules. Therefore, trehalose has a significant depression effect on the oxidation of UFA through the weak interaction with the double bond(s). This is the first study to elucidate the antioxidant function of trehalose.
Bactericidal Effect of Acidic Electrolyzed Water-Comparison of Chemical Acidic Sodium Hydrochloride (NaOCl) Solution (1996)

Acidic electrolyzed water is made recently by various kinds of machines and is widely utilized. In this study, we intended to clarify the relationship between the concentration of chloride and pH in the bactericidal effects with acidic electrolyzed water. The effects of weak or strong acidic electrolyzed water were compared with a pseudo-acidic water of pH adjusted by diluted hydrochloric acid and sodium hydroxide, on Staphylococcus aureus, Staphylococcus epidermidis and Pseudomononas aeruginosa. At pH 5.0 approximately 6.0, 3 bacterial strains were killed soon after being exposed to the acidic water containing chloride 50 mg/liter, and the amount of chloride did not change after allowing to stand open for 6 hours. At pH 2.67 approximately 2.80, the bactericidal effects was observed at the concentration of chloride 5 mg/liter, and 80% of chloride remained after allowing to stand for 6 hours. These results indicated that newly made strong acidic water is more effective under a smaller amount of chloride at pH 2.7, and that weak acidic electrolyzed water should be used, if stable bactericidal effect is expected in cleaning the surroundings.
El alimento vivo en el cultivo del camarón: investigaciones aplicadas al sector productivo (2007)

Una de las actividades comerciales que mas ha avanzado en la actualidad es el cultivo del camaron, sin embargo, esta biotecnologia carece de un control de calidad eficaz, sobre todo con el uso del alimento vivo (produccion y calidad). En el departamento del DICTUS un grupo de investigadores ha trabajado con los cultivos a nivel masivo desde 1990 hasta el 2006 para estudiar las principales tecnicas aplicadas en el manejo comercial, la calidad nutricia de las microalgas y la optimizacion de los cultivos masivos al exterior, ademas de la contaminacion bacteriana en los mismos cultivos
BASING KNOWLEDGE ACQUISITION TOOLS IN PERSONAL CONSTRUCT PSYCHOLOGY (1991)

Personal construct psychology is a theory of individual and group psychological and social processes that has been used extensively in knowledge acquisition research to model the cognitive processes of human experts. The psychology has the advantage of taking a constructivist position appropriate to the modeling of specialist human knowledge but basing this on a positivist scientific position that characterizes human conceptual structures in axiomatic terms that translate directly to computational form. The repertory grid knowledge elicitation methodology is directly derived from personal construct psychology. In its original form, this methodology was based on the notion of dichotomous constructs and did not encompass the ordinal relations between them captured in semantic net elicitation. However, it was extended in successive tools developed for applied knowledge acquisition and tested in a wide variety of applications. This paper gives an overview of personal construct psychology and its expression as an intensional logic describing the cognitive processes of anticipatory agents, and uses this to survey knowledge acquisition tools deriving from personal construct psychology and to suggest how future tool architectures may be designed in an integrated fashion within this framework.
Size-Selective Dispersion of Dodecanethiol-Coated Nanocrystals in Liquid and Supercritical Ethane by Density Tuning (2002)

Silver and gold nanocrystals, sterically stabilized with dodecanethiol ligands, were dispersed in supercritical ethane. Nanocrystal dispersibility was measured as a function of solvent densitywith pressures and temperatures ranging from 138 to 414 bar and 25 °C to 65 °C, respectivelyusing UV/visible absorbance spectroscopy and transmission electron microscopy (TEM). Dispersibility depends strongly on the nanocrystal size and solvent density. Higher density reduces the effective χ interaction parameter for dodecane in ethane, which leads directly to increased steric repulsion between nanocrystals. Since the van der Waals attraction between the nanocrystal cores increases significantly with size, an increase in ethane density and thus solvent strength disperses larger nanocrystals with size selectivity. A reduction in ethane density precipitates the nanocrystals, again with size selectivity. Furthermore, the ethane density could be cycled to reversibly precipitate and disperse sterically stabilized nanocrystals selectively. Calculations of ligand tail solvation in terms of the cohesive energy densities of ethane and dodecane capture the essential physics of density tuning of the size of the dispersed nanocrystals.
Photocurrent estimation from multiple nondestructive samples in CMOS image sensor (2001)

CMOS image sensors generally suffer form lower dynamic range than CCDs due to their higher readout noise. Their high speed readout capability and the potential of integrating memory and signal processing with the sensor on the same chip, open up many possibilities for enhancing their dynamic range. Earlier work have demonstrated the use of multiple non-destructive samples to enhance dynamic range, while achieving higher SNR than using other dynamic range enhancement schemes. The high dynamic range image is constructed by appropriately scaling each pixel's last sample before saturation. Conventional CDS is used to reduce offset FPN and reset noise. This simple high dynamic range image construction scheme, however, does not take full advantage of the multiple samples. Readout noise power, which doubles as a result of performing CDS, remain as high as in conventional sensor operation. As a result dynamic range is only extended at the high illumination end. The paper explores the use of linear mean-square-error estimation to more fully exploit the multiple pixel samples to reduce readout noise and thus extend dynamic range at the low illumination end. We present three estimation algorithms: (1) a recursive estimator when reset noise and offset FPN are ignored, (2) a non-recursive algorithm when reset noise and FPN are considered, and (3) a recursive estimation algorithm for case (2), which achieves mean square error close to the non-recursive algorithm without the need to store all the samples. The later recursive algorithm is attractive since it requires the storage of only a few pixel values per pixel, which makes its implementation in a single chip digital imaging system feasible.
Human T-lymphocyte growth factor: regulation of growth and function of T lymphocytes (1981)

The discovery of T-cell growth factor (TCGF) has made it possible to now routinely grow in tissue culture normal and neoplastic human T cells for long periods and in large amounts. TCGF has been recently purified. It is a small protein released by a subset of mature T cells following lectin-antigen activation, which in turn acts upon other T-cell subsets that have developed specific receptors for TCGF after lectin-antigen stimulation. Thus, release of TCGF and development of receptors for it appear to be obligatory for the clonal expansion of all activated T cells. Unlike normal T cells, neoplastic T cells respond directly to TCGF, requiring no prior in vitro lectin-antigen activation. This has led to the development of several new cell lines from patients with T-cell leukemias and lymphomas. In some cases, these cells become independent of exogenous TCGF by producing their own growth factor, implying a role for TCGF in the continuous proliferation of these cells. These developments necessitate a reevaluation of some concepts of immunoregulation of T-cell activities in terms of production and response to TCGF. In addition, this information has clinical implications. Recent results have shown that a major defect of the athymic nude mouse is the inability to produce TCGF and that some immunosuppressive agents, such as glucocorticosteroids and cyclosporin-A, exert their effects on T cells by disrupting the TCGF-T-cell interaction. Some human immune deficiencies might be due to a failure to respond to or to produce TCGF, which in some cases might be corrected by exogenous TCGF.
Second round robin for plasma hepcidin methods: First steps toward harmonization (2012)

Measurements of the iron regulatory hormone hepcidin by various methodologies and laboratories are not harmonized. As a result different numeric results are obtained for the same clinical sample. We investigated whether better agreement between plasma hepcidin methods can be achieved by harmonization. Native plasma pools (n = 11) of a variety of hepcidin concentrations and blank plasma spiked with three different quantities of synthetic hepcidin-25 purchased from two different commercial sources (n = 6), were distributed in duplicate among 21 methods worldwide. We assessed commutability by comparing results from synthetic hepcidin with those from native samples in various method couples by Bland-Altman plots. Methods differed substantially in absolute values and reproducibility. For the majority of methods we found that samples with synthetic hepcidin-25 were noncommutable with the native samples. In an attempt to harmonize by using native hepcidin results, we selected two methods that showed good mutual agreement of native results and calculated consensus values as the medians for the 11 duplicate native samples obtained by these two methods. Finally, we constructed algorithms enabling the laboratories to calculate the hepcidin consensus (HEPCON) value using their own native hepcidin results. We found that the use of these algorithms substantially reduced the between-method CV. Until commutable materials are defined, hepcidin harmonization can be achieved by exploiting specific algorithms, allowing each lab to report their native hepcidin concentrations in HEPCON values. This study represents the first step toward harmonization of plasma hepcidin methods and facilitates aggregation of hepcidin data from different research investigations.
Chronic Pruritus (2013)

Chronic pruritus requires careful evaluation for primary dermatologic or systemic causes. In addition to treatment of the underlying cause, when identified, various topical and systemic therapies may be used, although supporting data from randomized trials are scarce.
Deep Learning for Genomics: A Concise Overview (2018)

Advancements in genomic research such as high-throughput sequencing techniques have driven modern genomic studies into "big data" disciplines. This data explosion is constantly challenging conventional methods used in genomics. In parallel with the urgent demand for robust algorithms, deep learning has succeeded in a variety of fields such as vision, speech, and text processing. Yet genomics entails unique challenges to deep learning since we are expecting from deep learning a superhuman intelligence that explores beyond our knowledge to interpret the genome. A powerful deep learning model should rely on insightful utilization of task-specific knowledge. In this paper, we briefly discuss the strengths of different deep learning models from a genomic perspective so as to fit each particular task with a proper deep architecture, and remark on practical considerations of developing modern deep learning architectures for genomics. We also provide a concise review of deep learning applications in various aspects of genomic research, as well as pointing out potential opportunities and obstacles for future genomics applications.
Functions and specificity of T cells following nucleic acid vaccination of mice against Mycobacterium tuberculosis infection (1997)

The 38-kDa glycolipoprotein of Mycobacterium tuberculosis has been known to evoke prominent T cell and Ab responses in patients with active tuberculosis. In this study, we investigated its protective capacity using plasmid DNA immunization in a mouse experimental model. Prior knowledge of several antigenic determinants has been beneficial for analyzing the phenotype and specificity of T cells, which determine the efficacy of this vaccination procedure. C57BL/6 mice responded to the 38-kDa gene-pcDNA3 plasmid with strong CD4+ Th1 and CD8+ cytotoxic T cell responses of the IFN-gamma-producing Tc1 phenotype. After challenge with virulent tubercle bacilli, the bacterial load in the spleens and lungs of vaccinated mice was reduced to a level similar to that imparted by Mycobacterium bovis Bacille Calmette-Guérin vaccination. Notably, the specificity of CD4+ and CD8+ T cells from DNA-vaccinated and tubercle-infected mice was found to be strikingly different in respect of several peptide epitopes. The identified peptides recognized by T cells from protected mice are of further interest for the development of subunit-based vaccines against tuberculosis.
Multiple Rare Alleles Contribute to Low Plasma Levels of HDL Cholesterol (2004)

Heritable variation in complex traits is generally considered to be conferred by common DNA sequence polymorphisms. We tested whether rare DNA sequence variants collectively contribute to variation in plasma levels of high density lipoprotein cholesterol (HDL-C). We sequenced three candidate genes (ABCA1, APOA1, and LCAT) that cause Mendelian forms of low HDL-C levels in individuals from a population-based study. Nonsynonymous sequence variants were significantly more common (16% versus 2%) in individuals with low HDL-C (<fifth percentile) than in those with high HDL-C (>95th percentile). Similar findings were obtained in an independent population, and biochemical studies indicated that most sequence variants in the low HDL-C group were functionally important. Thus, rare alleles with major phenotypic effects contribute significantly to low plasma HDL-C levels in the general population.
Shell-type micromechanical oscillator (2003)

Shell-type micromechanical resonators operating in radio frequency range were fabricated utilizing mechanical stress that is built into polysilicon thin films. Significant increase of the resonant frequency (in comparison with flat, plate-type resonators of the same size) and the rich variety of vibrating modes demonstrate great potential for "2.5-Dimensional" MEMS structures. A finite curvature of the shell also provides a mechanism for driving resonators by coupling in plane stress with out of plane deflection. By modulating the intensity of a low power laser beam (P~10&mu;Watts) focused on the resonator we introduced a time-variable, in-plane, thermomechanical stress. This stress modulation resulted in experimentally observed, large amplitude, out-of-plane, vibrations for a dome-type resonator. A double laser beam experimental setup was constructed where mechanical motion of a shell-type resonator was actuated by a modulated, sharply focused Ar<sup>+ </sup>ion (blue) laser beam and detected by a red HeNe laser using an interferometric setup. A positive feedback loop was implemented by amplifying the red laser signal (related to the oscillator deflection) and applying it to modulate the blue (driving) laser beam. Stable self-sustained vibrations were observed providing that the feedback gain was high enough. Employing a frequency selective amplifier in the feedback loop allowed excitation of different modes of vibrations. Fine frequency tuning was realized by adjusting the CW component of either lasers' intensity or a phase shift in the feedback loop. Frequency stability better than 1 ppm (10<sup>-6</sup>) at 9 MHz was demonstrated for self-sustained vibrations for certain modes of the dome-shaped oscillators.
RNA Interference Silencing of a Major Lipid Droplet Protein Affects Lipid Droplet Size in Chlamydomonas reinhardtii (2009)

Eukaryotic cells store oils in the chemical form of triacylglycerols in distinct organelles, often called lipid droplets. These dynamic storage compartments have been intensely studied in the context of human health and also in plants as a source of vegetable oils for human consumption and for chemical or biofuel feedstocks. Many microalgae accumulate oils, particularly under conditions limiting to growth, and thus have gained renewed attention as a potentially sustainable feedstock for biofuel production. However, little is currently known at the cellular or molecular levels with regard to oil accumulation in microalgae, and the structural proteins and enzymes involved in the biogenesis, maintenance, and degradation of algal oil storage compartments are not well studied. Focusing on the model green alga Chlamydomonas reinhardtii, the accumulation of triacylglycerols and the formation of lipid droplets during nitrogen deprivation were investigated. Mass spectrometry identified 259 proteins in a lipid droplet-enriched fraction, among them a major protein, tentatively designated major lipid droplet protein (MLDP). This protein is specific to the green algal lineage of photosynthetic organisms. Repression of MLDP gene expression using an RNA interference approach led to increased lipid droplet size, but no change in triacylglycerol content or metabolism was observed.
Fabrication and characterization of a micromechanical sensor for differential detection of nanoscale motions (2002)

We have micromachined a mechanical sensor that uses interferometry to detect the differential and absolute deflections of two adjacent cantilevers. The overall geometry of the device allows simple fluidic delivery to each cantilever to immobilize molecules for biological and chemical detection. We show that differential sensing is 50 times less affected by ambient temperature changes than the absolute, thus enabling a more reliable differentiation between specific cantilever bending and background effects. We describe the fabrication process and show results related to the dynamic characterization of the device as a differential sensor. The root-mean-squared (r.m.s.) sensor noise in water and air is /spl sim/1 nm over the frequency range of 0.4-40 Hz. We also find that in air, the deflection resolution is limited only by the cantilever's thermomechanical noise level of 0.008 /spl Aring//Hz/sup 1/2/ over the frequency range of 40-1000 Hz.
Integrated Optoelectronic Devices Based on Conjugated Polymers (1998)

An all-polymer semiconductor integrated device is demonstrated with a high-mobility conjugated polymer field-effect transistor (FET) driving a polymer light-emitting diode (LED) of similar size. The FET uses regioregular poly(hexylthiophene). Its performance approaches that of inorganic amorphous silicon FETs, with field-effect mobilities of 0.05 to 0.1 square centimeters per volt second and ON-OFF current ratios of >10(6). The high mobility is attributed to the formation of extended polaron states as a result of local self-organization, in contrast to the variable-range hopping of self-localized polarons found in more disordered polymers. The FET-LED device represents a step toward all-polymer optoelectronic integrated circuits such as active-matrix polymer LED displays.
Role of the C-terminal propeptide in the activity and maturation of γ-interferon-inducible lysosomal thiol reductase (GILT) (2002)

gamma-Interferon-inducible lysosomal thiol reductase (GILT) is constitutively expressed in antigen-presenting cells. GILT facilitates unfolding of endocytosed antigens in MHC class II-containing compartments by enzymatically reducing disulfide bonds. The enzyme is synthesized as a 35-kDa precursor. Although a fraction of the precursor is secreted as a disulfide-linked dimer, the majority is directed via the mannose-6-phosphate receptor pathway to endocytic compartments where its N- and C-terminal propeptides are cleaved to generate the 30-kDa mature form. Both precursor and mature GILT reduce disulfide bonds with an acidic pH optimum. In this report, we show that the cysteine residues in the C-terminal propeptide, Cys-211 and Cys-222, serve key structural roles. Mutation of Cys-222 abolishes disulfide-linked dimerization of precursor GILT and decreases the efficiency of GILT maturation. Mutation of Cys-211 results in both impaired intracellular maturation and loss of enzymatic activity of the precursor form at an acidic pH. A similar phenotype was obtained upon mutation of Cys-200, which is retained in the mature form. Cys-200 and Cys-211 seem to form a disulfide bond that links the propeptide and the mature enzyme until reduction in the lysosome. This disulfide bridge is essential for stability of the enzyme at low pH and for its proper maturation in vivo.