gebhart/patrepeval huggingface dataset:
ProteinChip clinical proteomics: computational challenges and solutions. (2002)

ProteinChip technology, a suite of analytical tools that includes retentate chromatography, on-chip protein characterization, and multivariate analysis, allows researchers to examine patterns ofprotein expression and modification. Based on the surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) approach, ProteinChip technology has been pioneered by researchers at Ciphergen Biosystems (Fremont, CA, USA), as well as by users of Ciphergen's commercial embodiment of this technology the ProteinChip Biomarker System. This report will begin with a background of the technology and describe its applications in clinical proteomics and will then conclude with a discussion of tools and strategies to mine the large amounts of data generated during the course of a typical clinical proteomics study.
SOSUI: classification and secondary structure prediction system for membrane proteins. (1998)

sosui@biophys.bio.tuat. ac.jp.
Magnetic resonance image enhancement by reducing receptors' effective size and enabling multiple channel acquisition (2014)

Magnetic resonance imaging is empowered by parallel reading, which reduces acquisition time dramatically. The time saved by parallelization can be used to increase image quality or to enable specialized scanning protocols in clinical and research environments. In small animals, the sizing constraints render the use of multi-channeled approaches even more necessary, as they help to improve the typically low spatial resolution and lesser signal-to-noise ratio; however, the use of multiple channels also generates mutual induction (MI) effects that impairs imaging creation. Here, we created coils and used the shared capacitor technique to diminish first degree MI effects and pre-amplifiers to deal with higher order MI-related image deterioration. The constructed devices are tested by imaging phantoms that contain identical solutions; thus, creating the conditions for several statistical comparisons. We confirm that the shared capacitor strategy can recover the receptor capacity in compounded coils when working at the dimensions imposed by small animal imaging. Additionally, we demonstrate that the use of pre-amplifiers does not significantly reduce the quality of the images. Moreover, in light of our results, the two MI-avoiding techniques can be used together, therefore establishing the practical feasibility of flexible array coils populated with multiple loops for small animal imaging.
Regulation of voltage-gated K+ channel expression in the developing mammalian myocardium (1998)

As in neurons, depolarization-activated, Ca2+-independent outward K+ currents play prominent roles in shaping the waveforms of action potentials in myocardial cells. Several different types of voltage-gated K+ currents that contribute to the distinct phases of action potential repolarization have been characterized in myocardial cells isolated from different species, as well as in cells isolated from different regions of the heart in the same species. Important among these are the transient outward current, I(to), similar to the neuronal K+ current IA, and several components of delayed rectification, including I(Kr)[IK(rapid)], I(Ks)(IK(slow)], and I(Kur)[IK(ultrarapid)]. The properties of these currents in different species and cell types are remarkably similar, suggesting that the molecular correlates of functional voltage-gated K+ channel types are also the same. A number of voltage-gated K+ channel (Kv) pore-forming (alpha) and accessory (beta) subunits have now been cloned from heart cDNA libraries, and a variety of experimental approaches are being exploited to determine the molecular relationships between these subunits and functional voltage-gated myocardial K+ channels. Considerable progress has been made recently in defining these relationships, and the results obtained to date indeed suggest that distinct molecular entities underlie the different types of voltage-gated K+ channels characterized electrophysiologically in myocardial cells. Marked changes in the densities and/or the properties of voltage-gated K+ currents occur during normal cardiac development, as well as in conjunction with myocardial damage or disease, and there is considerable interest in understanding the molecular mechanisms underlying these changes. Although there is evidence for transcriptional, translational, and posttranslational regulation of functional voltage-gated K+ channel expression, we are only beginning to understand the underlying mechanisms; further studies focussed on delineating the molecular mechanisms controlling functional K+ channel expression are clearly warranted.
Chromatographic Hydrophobicity Index by Fast-Gradient RP-HPLC:  A High-Throughput Alternative to log P/log D (1997)

A new chromatographic hydrophobicity index (CHI) is described which can be used as part of a protocol for high-throughput (50-100 compounds/day) physicochemical property profiling for rational drug design. The index is derived from retention times (t(R)) observed in a fast gradient reversed-phase HPLC method. The isocratic retention factors (log k') were measured for a series of 76 structurally unrelated compounds by using various concentrations of acetonitrile in the mobile phase. By plotting the log k' as a function of the acetonitrile concentration, the slope (S) and the intercept (log k'(w)) values were calculated. The previously validated index of hydrophobicity φ(0) was calculated as -log k'(w)/S. A good linear correlation was obtained between the gradient retention time values, t(R) and the isocratically determined φ(0) values for the 76 compounds. The constants of this linear correlation can be used to calculate CHI. For most compounds, CHI is between 0 and 100 and in this range it approximates to the percentage (by volume) of acetonitrile required to achieve an equal distribution of compound between the mobile and the stationary phases. CHI values can be measured using acidic, neutral, or slightly basic eluents. Values corresponding to the neutral form of molecules could be measured for 52 of the compounds and showed good correlation (r = 0.851) to the calculated octanol/water partition coefficient (c log P) values.
Synthesis and SAR of 2-Aryloxy-4-alkoxy-pyridines as Potent Orally Active Corticotropin-Releasing Factor 1 Receptor Antagonists (2008)

A series of 2-aryloxy-4-alkoxy-pyridines ( 1) was identified as novel, selective, and orally active antagonists of the corticotropin-releasing factor 1 (CRF 1) receptor. Among these, compound 2 (CP-316311) is a potent and selective CRF 1 receptor antagonist with an IC 50 value of 6.8 nM in receptor binding and demonstrates oral efficacy in central nervous system (CNS) in vivo models. The regiochemistry of compounds in this series was determined by an X-ray structural analysis. A method to control regioselectivity via pyridine- N-oxides was developed. The synthesis of compounds in series 1 (Figure ) and [ (3)H]- 2 as well as the structure-activity relationship (SAR) are discussed. The in vitro, ex vivo, and in vivo properties of representative compounds are described herein. Compound 2 was advanced to phase II depression trials to test the hypothesis that CRF 1 antagonists could be used clinically as antidepressant drugs.
Stochastic resonance and the dithering effect in threshold physical systems (1995)

There is a wide class of phenomena which can be interpreted by using a dynamical system with a threshold as a model. Examples of these systems can be found in fields as diverse as digital communication and neurobiology. In this paper we discuss the dynamical behavior of threshold systems in the presence of noise. We show that both the dithering effect, well known to electronic engineers since the 1950s, and the phenomenon of stochastic resonance in threshold systems, recently introduced in the physical literature, can be described within the same scheme of noise activated processes. For these phenomena, in the absence of any frequency matching condition, the use of the term resonance is questionable and the notion of noice induced threshold crossings is more appropriate.
A dual-band RF front-end for WCDMA and GSM applications (2002)

An RF front-end for dual-band, dual-mode operation is presented in this paper. The front-end consumes 22.5 mW from a 1.8 V supply and is designed to be used in direct conversion WCDMA and GSM receivers. The measured noise figure, gain, and IIP3 are 2.3 dB, 39.5 dB, and -19 dBm for GSM and 4.3 dB, 33 dB, and -14.5 dBm for WCDMA, respectively. The front-end has 27 dB gain control range in both systems.
MÍDIA, POLÍTICA E SEXUALIDADE: COMO DESCONSTRUIR UMA IMAGEM PÚBLICA (2018)

O artigo se propoe analisar a abordagem do genero em veiculos midiaticos no que tange a politica no Brasil, mais especificamente durante a campanha presidencial de 2010 e 2014 com enfoque nas candidaturas de Dilma Rousseff, Marina Silva e Jose Serra e nos episodios que seguiram ate o processo de impeachment ocorrido em agosto de 2016. Procuramos analisar criticamente as assimetrias presentes nas pautas e maneiras como se dao os debates acerca da imagem publica dos tres, por ocasiao das referidas campanhas politicas e toda uma performance de odio dirigidas a Presidenta Dilma que eclodiram com o seu afastamento definitivo da Presidencia do Brasil. Alem disso, propomos uma reflexao acerca da nocividade que presente na essencializacao de identidades, bem como dos mecanismos do dispositivo da sexualidade em diversos âmbitos da vida social.
Human RNase H1 Activity Is Regulated by a Unique Redox Switch Formed between Adjacent Cysteines (2003)

Human RNase H1 is active only under reduced conditions. Oxidation as well as N-ethylmaleimide (NEM) treatment of human RNase H1 ablates the cleavage activity. The oxidized and NEM alkylated forms of human RNase H1 exhibited binding affinities for the heteroduplex substrate comparable with the reduced form of the enzyme. Mutants of human RNase H1 in which the cysteines were either deleted or substituted with alanine exhibited cleavage rates comparable with the reduced form of the enzyme, suggesting that the cysteine residues were not required for catalysis. The cysteine residues responsible for the observed redox-dependent activity of human RNase H1 were determined by site-directed mutagenesis to involve Cys(147) and Cys(148). The redox states of the Cys(147) and Cys(148) residues were determined by digesting the reduced, oxidized, and NEM-treated forms of human RNase H1 with trypsin and analyzing the cysteine containing tryptic fragments by micro high performance liquid chromatography-electrospray ionization-Fourier transform ion cyclotron mass spectrometry. The tryptic fragment Asp(131)-Arg(153) containing Cys(147) and Cys(148) was identified. The mass spectra for the Asp(131)-Arg(153) peptides from the oxidized and reduced forms of human RNase H1 in the presence and absence of NEM showed peptide masses consistent with the formation of a disulfide bond between Cys(147) and Cys(148). These data show that the formation of a disulfide bond between adjacent Cys(147) and Cys(148) residues results in an inactive enzyme conformation and provides further insights into the interaction between human RNase H1 and the heteroduplex substrate.
Phosphorylation of the Integrin α4 Cytoplasmic Domain Regulates Paxillin Binding (2001)

alpha4 integrins are essential for embryogenesis, hematopoiesis, inflammation, and immune response possibly because alpha4 integrins have distinct signaling properties from other integrins. Specifically, the alpha4 cytoplasmic domain binds tightly to paxillin, a signaling adaptor protein, leading to increased cell migration and an altered cytoskeletal organization that results in reduced cell spreading. The alpha4 tail contains potential phosphorylation sites clustered in its core paxillin binding region. We now report that the alpha4 tail is phosphorylated in vitro and in vivo. Furthermore, Ser(988) is a major phosphorylation site. Using antibodies specific for Ser(988)-phosphorylated alpha4, we found the stoichiometry of alpha4 phosphorylation varied in different cells. However, >60% of alpha4 was phosphorylated in Jurkat T cells. Phosphorylation at Ser(988) blocked paxillin binding to the alpha4 tail. A phosphorylation-mimicking mutant of alpha4 (alpha4S988D) blocked paxillin binding and reversed the inhibitory effect of alpha4 on cell spreading. Consequently, alpha4 phosphorylation is a biochemical mechanism to modulate paxillin binding to alpha4 integrins with consequent regulation of alpha4 integrin-dependent cellular functions.
The impact of demographic and risk factor changes on coronary heart disease deaths in Beijing, 1999–2010 (2009)

CHD death rates are continuing to rise in Beijing. This reflects worsening risk factor levels, compounded by demographic trends. However, the adverse impact of population ageing on CHD burden could be completely offset by eminently feasible improvements in diet and smoking.
An empirical validation of software cost estimation models (1987)

Practitioners have expressed concern over their inability to accurately estimate costs associated with software development. This concern has become even more pressing as costs associated with development continue to increase. As a result, considerable research attention is now directed at gaining a better understanding of the software-development process as well as constructing and evaluating software cost estimating tools. This paper evaluates four of the most popular algorithmic models used to estimate software costs (SLIM, COCOMO, Function Points, and ESTIMACS). Data on 15 large completed business data-processing projects were collected and used to test the accuracy of the models' ex post effort estimation. One important result was that Albrecht's Function Points effort estimation model was validated by the independent data provided in this study [3]. The models not developed in business data-processing environments showed significant need for calibration. As models of the software-development process, all of the models tested failed to sufficiently reflect the underlying factors affecting productivity. Further research will be required to develop understanding in this area.
Factors demogràfics de l'envelliment a Catalunya (1987)

Des d'un punt de vista demogràfic, envelliment de la població significa augment del nombre i especialment de la proporció de persones grans a costa de la importància relativa dels altres grups d'edat. Per aixó el principal indicador d'envelliment és la variació del pes relatiu dels grups d'edats més vells de la població. En el cas de Catalunya, aquest augment de la població anciana ha estat molt superior al del conjunt de la població. Així, des de 1900 fins 1981, el nombre de persones de més de 65 anys s'ha multiplicat per 8, en tant que el total d'habitants no més s'ha triplicat. D'aquesta manera l'estructura per edats de la població catalana s'ha modificat substancialment, sobre tot en les edats joves i velles: la proporció de persones de més de 65 anys és, en 1981, del 11,5%, mentre que en 1900 era del 4,23%. Paral·lelament, la proporció de joves ha disminuit, passant del 32,02% al 24, 49%. Tanmateix, malgrat la proporció de persones de més de 65 anys ha crescut ininterrompudament des de 1900, el procés d'envelliment era molt més accelerat en la primera meitat del segle que a partir de l'any 1950. En aquest sentit, la població rejoveneix formidablement, entre 1950 i 1975, passant a ser el grup de joves el que experimenta un creixement anual més fort fins 1975. Amb tot, la proporció de persones de més de 65 anys segueix augmentant, fonamentalment per causa de la reducció de la fecunditat en els darrers anys, amb una taxa de natalitat que ha passat del 19, 98 en el període 1971-1975 al 12, 25 en el quinquenni 1976-1980 (envelliment per la base). En l'ultim període pel que es disposa d'informació, el quinquenni 1976-1981, es produeix un canvi important en aquesta tendència i es pot parlar d'envelliment tant per la cúspide com per la base de la piràmide. Efectivament, des 1975 a 1981, l'esperança de vida al nèixer passa de 74 a 77 anys i aquest augment és consecuència, fonamentalment, de la reducció de la mortalitat en les edats ancianes (envelliment per la cúspide) i d'una brusca reducció de la fecunditat en els darrers anys, amb una taxa de natalitat que ha passat del 19, 98 en el període 1971-1975 al 12, 25 en el quinquenni 1976-1980 (envelliment per la base).
Partial and Total Cell Retention in a Filtration‐Based Homogeneous Perfusion Reactor (1995)

Suspended mammalian cells can be cultivated in a variety of operational modes (pure chemostat, total cell retention, or partial cell retention) in a homogeneous perfusion bioreactor by varying the cell bleed rate. Hybridomas were grown in the reactor at a perfusion rate of 2.0 day-1 for over 10 weeks at different specific growth rates and viable cell densities achieved by varying the extent of cell retention. Cell metabolism in the reactor was found to vary with the extent of cell retention, which determined both cell density and specific growth rate. With partial cell retention, the nutrient consumption and metabolite production rates decreased with both increasing growth rate and increasing cell density. The specific and volumetric antibody production rates, however, increased dramatically with cell density (and to a lesser extent with decreasing growth rate). The specific MAb production rate was lower with total cell retention than with partial retention at the same growth rate. Since the reactor can be operated over a range of perfusion rates and extents of cell retention, the system can be used to culture cell lines with widely different productivity patterns.
Direct determination of polyglucose metabolites in plasma using anion-exchange chromatography with pulsed amperometric detection (1997)

High-performance anion-exchange chromatography with pulsed amperometric detection (HPAE-PAD) was evaluated for the quantitation of polyglucose metabolites (DP2-DP7) in human plasma. The method was investigated for accuracy, precision, specificity, linearity, range and analyte stability. Samples were prepared by dilution into the standard range (0.1-10 mg / ml) followed by deproteinization using a 30 000 molecular mass cut-off filtration device. The limit of detection was 0.05 mg / ml for all metabolites. Method precision for DP2-DP7 varied from approximately 2% R.S.D. in the upper range to approximately 15% R.S.D. at the limit of quantitation. Samples were stable following one or two freeze-thaw cycles and, after preparation, they could be refrigerated for up to 72 h. Application of this method to clinical plasma samples from continuous ambulatory peritoneal dialysis (CAPD) patients administered one daily night-time intraperitoneal exchange of 2 l of 7.5% polyglucose solution for four weeks indicated that plasma levels of DP2, DP3 and DP4 increased from baseline levels of ,0.01 g / l to steady-state levels of 1.26 0.3, 1.260.3 and 0.460.1 g / l (mean6S.D.), respectively. These steady state plasma levels for DP2 and DP3 are comparable to previously reported levels in patients administered daily overnight 7.5% polyglucose dialysis solution.
Advances in Variational Inference (2017)

Many modern unsupervised or semi-supervised machine learning algorithms rely on Bayesian probabilistic models. These models are usually intractable and thus require approximate inference. Variational inference (VI) lets us approximate a high-dimensional Bayesian posterior with a simpler variational distribution by solving an optimization problem. This approach has been successfully used in various models and large-scale applications. In this review, we give an overview of recent trends in variational inference. We first introduce standard mean field variational inference, then review recent advances focusing on the following aspects: (a) scalable VI, which includes stochastic approximations, (b) generic VI, which extends the applicability of VI to a large class of otherwise intractable models, such as non-conjugate models, (c) accurate VI, which includes variational models beyond the mean field approximation or with atypical divergences, and (d) amortized VI, which implements the inference over local latent variables with inference networks. Finally, we provide a summary of promising future research directions.
Characterization of a unique corticosterone-binding protein in Candida albicans. (1982)

This paper further characterizes a protein we have demonstrated in Candida albicans which has the ability to bind corticosterone and related steroid hormones. Fungal cells are disrupted and cytosol is incubated with [3H]corticosterone for 3 h at which time peak steady state binding is achieved. Bound hormone is separated from free using Sephadex G-50 minicolumns or dextran-coated charcoal. Binding was found to be a linear function of protein concentration. The bound hormone co-migrates with authentic corticosterone in thin layer chromatographic systems indicating no metabolism of the radioprobe. Scatchard analysis of the binding in the pseudohyphal form of C. albicans yielded values of 6.3 nM for the Kd and a binding capacity of about 650 fmol/mg of cytosol protein; both determinations are comparable to our findings in the yeast form of this organism. A series of sterols were tested for their ability to displace [3H]corticosterone from the yeast binder, and the results show that the binder is remarkably selective and stereo specific. Physical-chemical studies show the binder to be degraded at high temperatures and that binding is destroyed by trypsin and sulfhydryl blockers. The protein sediments at 4 S on sucrose gradients and does not exhibit ionic dependent aggregation. The molecular weight is estimated to be approximately 43,000 daltons by gel chromatography. We hypothesize that this intracellular protein may represent a primitive form of either the mammalian glucocorticoid receptor or the plasma corticosteroid-binding globulin.
Time reversal of ultrasonic fields. I. Basic principles (1992)

Time reversal of ultrasonic fields represents a way to focus through an inhomogeneous medium. This may be accomplished by a time-reversal mirror (TRM) made from an array of transmit-receive transducers that respond linearly and allow the incident acoustic pressure to be sampled. The pressure field is then time-reversed and re-emitted. This process can be used to focus through inhomogeneous media on a reflective target that behaves as an acoustic source after being insonified. The time-reversal approach is introduced in a discussion of the classical techniques used for focusing pulsed waves through inhomogeneous media (adaptive time-delay techniques). Pulsed wave time-reversal focusing is shown using reciprocity valid in inhomogeneous medium to be optimal in the sense that it realizes the spatial-temporal matched filter to the inhomogeneous propagation transfer function between the array and the target. The research on time-reversed wave fields has also led to the development of new concepts that are described: time-reversal cavity that extends the concept of the TRM, and iterative time-reversal processing for automatic sorting of targets according to their reflectivity and resonating of extended targets.
Expression of ricin B chain in <i>Escherichia coli</i> (1989)

DNA encoding ricin B chain was fused to that encoding the E. coli OmpA signal peptide using the expression secretion vector pIN-111-ompA. When induced, E. coli cells transformed with the recombinant plasmid express ricin B chain. The recombinant product accumulates in the periplasmic space in a soluble, biologically active form.