gebhart/patrepeval huggingface dataset:
Identification of a DOCK180-related Guanine Nucleotide Exchange Factor That Is Capable of Mediating a Positive Feedback Activation of Cdc42 (2006)

Cdc42, a member of the Rho subfamily of small GTPases, influences a wide range of activities including the establishment of cell polarity, migration, and the regulation of cell growth and differentiation. Here we describe the identification of an approximately 220-kDa protein that formed a stable complex with activated forms of Cdc42 and thereby showed characteristics of a downstream target/effector for this GTPase. However, molecular cloning of the cDNA encoding this protein (p220) revealed that it was highly related to Zizimin-1 and identical in sequence to a gene product in the data base designated DOCK11, which are members of the DOCK180 family of guanine nucleotide exchange factors (GEFs) for Cdc42 and Rac. Biochemical characterization shows that p220 is a specific GEF for Cdc42, with the GEF activity originating from its DHR2 (for DOCK homology region 2) domain. Nucleotide-depleted Cdc42 forms a stable complex with the DHR2 domain, whereas the binding of activated Cdc42 requires both the DHR2 domain and residues 66-126 within the amino-terminal portion of p220. Moreover, the full-length protein shows markedly higher GEF activity than the isolated DHR2 domain, whereas removal of the amino-terminal 126 amino acids necessary for binding-activated Cdc42 dramatically diminishes the activity. These and other results point to activated Cdc42 providing a positive feedback regulation of the GEF activity of p220. Thus, we refer to p220/DOCK11 as activated Cdc42-associated GEF, befitting its functional activity.
The ATPase and protease domains of yeast mitochondrial Lon: Roles in proteolysis and respiration-dependent growth (1998)

The ATP-dependent Lon protease of Saccharomyces cerevisiae mitochondria is required for selective proteolysis in the matrix, maintenance of mitochondrial DNA, and respiration-dependent growth. Lon may also possess a chaperone-like function that facilitates protein degradation and protein-complex assembly. To understand the influence of Lon's ATPase and protease activities on these functions, we examined several Lon mutants for their ability to complement defects of Lon-deleted yeast cells. We also developed a rapid procedure for purifying yeast Lon to homogeneity to study the enzyme's activities and oligomeric state. A point mutation in either the ATPase or the protease site strongly inhibited the corresponding activity of the pure protein but did not alter the protein's oligomerization; when expressed at normal low levels neither of these mutant enzymes supported respiration-dependent growth of Lon-deleted cells. When the ATPase- or the protease-containing regions of Lon were expressed as separate truncated proteins, neither could support respiration-dependent growth of Lon-deleted cells; however, coexpression of these two separated regions sustained wild-type growth. These results suggest that yeast Lon contains two catalytic domains that can interact with one another even as separate proteins, and that both are essential for the different functions of Lon.
The Search for Congenital Malformations in Newborns With Fetal Cocaine Exposure (2001)

This prospective, large-scale, blinded, systematic evaluation for congenital anomalies in prenatally cocaine-exposed children did not identify an increased number or consistent pattern of abnormalities.
Alternating zinc-finger motifs in the human male-associated protein ZFY (1990)

ZFY, a putative transcription factor encoded by the human Y chromosome, contains a distinctive two-finger repeat: odd-numbered and even-numbered CC/HH metal-binding motifs exhibit systematic alternation in sequence pattern. Such alternation, which is not generally observed in zinc-finger proteins, has also been described in an extensive family of Kruppel-like genes in Xenopus laevis and in the AIDS-associated human DNA-binding protein HIV-EP1. The strict conservation of a two-finger repeat among ZFY-, Kruppel- and HIV-related zinc-finger proteins suggests distinct mechanisms of protein-nucleic acid recognition. To test whether this sequence pattern reflects an underlying alternation in domain structure, we have synthesized and characterized single-finger peptides from the human ZFY gene. Remarkably, systematic differences in metal-dependent folding are observed in the circular dichroism spectra of even- and odd-numbered domains. Our results suggest the existence of distinct CC/HH finger submotifs, which may play different roles in nucleic acid recognition.
Lacto-N-fucopentaose III (Lewis x), a target of the antibody response in mice vaccinated with irradiated cercariae of Schistosoma mansoni (1996)

Carbohydrates on soluble egg antigens are major epitopes for the antibody responses of patients and mice infected with Schistosoma mansoni. Recently, protective sera of mice vaccinated with irradiated cercariae were shown to recognize carbohydrate epitopes on schistosomal glutathione S-transferase. The present study demonstrates that carbohydrate epitopes are major targets of sera from C57BL/6J and CBA/J mice vaccinated with 15- or 50-kilorad-irradiated cercariae of S. mansoni. Antibody titers to carbohydrate epitopes increased with the number of vaccinations and were considerably higher in C57BL/6J mice than in CBA/J mice. The specificity of this anticarbohydrate response was determined by measuring antibody binding to defined oligosaccharide residues known to be present on the parasite. A predominant target of the humoral anticarbohydrate response of vaccinated mice was lacto-N-fucopentaose III, a molecule relevant for cell trafficking. We observed no binding to its nonfucosylated homolog, lacto-N-neotetraose, or to oligosaccharides present on keyhole limpet hemocyanin. The strongest antibody response to lacto-N-fucopentaose III was observed for C57BL/6J and CBA/J mice repeatedly vaccinated with 15-kilorad-irradiated cercariae, which also achieve the highest levels of protection. Immunoglobulin M was the predominant antibody class binding to lacto-N-fucopentaose III. We conclude that in the irradiated-cercariae vaccine model, C57BL/6J and CBA/J mice produce anticarbohydrate antibodies against various stages of S. mansoni and that the oligosaccharide lacto-N-fucopentaose III is one target of this response. Lacto-N-fucopentaose III and its specific antibodies may profoundly affect host resistance and parasite homing.
The Biology of Glucagon and the Consequences of Hyperglucagonemia (2016)

The proglucagon-derived peptide hormone, glucagon, comprises 29 amino acids. Its secretion from the pancreatic α cells is regulated by several factors. Glucagon increases blood glucose levels through gluconeogenesis and glycogenolysis. Elevated plasma concentrations of glucagon, hyperglucagonemia, may contribute to diabetes. However, hyperglucagonemia is also observed in other clinical conditions than diabetes, including nonalcoholic fatty liver disease, glucagon-producing tumors and after gastric bypass surgery. Here, we review the current literature on hyperglucagonemia in disease with a particular focus on diabetes, and finally speculate that the primary physiological importance of glucagon may not reside in glucose homeostasis but in regulation of amino acid metabolism exerted via a hitherto unrecognized hepato-pancreatic feedback loop.
Transdermal dopaminergic D<sub>2</sub> receptor agonist therapy in Parkinson's disease with N‐0923 TDS: A double‐blind, placebo‐controlled study (2001)

N-0923 is a non-ergot, dopaminergic D(2) agonist designed to be transdermally available. It has anti-parkinsonian effects when infused intravenously. An adhesive matrix patch was developed to deliver N-0923 transdermally (N-0923 TDS). In this phase II trial, we evaluated the effectiveness of various doses of N-0923 TDS at replacing levodopa. Eighty-five Parkinson's disease (PD) patients were randomized to placebo or one of four doses of N-0923 TDS for 21 days. Change in daily levodopa dose was the primary efficacy measure. Significantly greater reductions in levodopa dose were achieved as compared to placebo for the two highest doses of N-0923 TDS. Patients treated with 33.5 mg and 67 mg N-0923 TDS decreased levodopa use by 26% and 28%, vs. 7% for placebo. N-0923 TDS was safe and well tolerated.
Principles of soldering and brazing (1994)

Improve your current joining processes Examine new techniques for unique applications Accurately troubleshoot joining problems Select the best joining method for specific needs Includes separate bibliography. This detailed, yet easy-to-understand ASM book critically examines the key physical principles of soldering and brazing, and explains their relevance to making jointsuproviding you with new insights. The relationships between processing conditions, filler materials, base materials, joint geometry and their influence on integrity are thoroughly explained and illustrated. By understanding these principles, you will know what materials and processing conditions to use and how to achieve the best joints. In addition, a special chapter is devoted to case studies of problem solving and process development. You will see prime examples of how to develop effective soldering and brazing solutions and identify failure modes. Equilibrium phase diagrams illustrate the metallurgical reactions and chances in physical properties that take place during joining. When not available, a methodology for determining an alloy systemAs critical characteristics enables you to specify the best filler for a particular application. In addition, the book covers the latest developments in joining, including composite solders, diffusion soldering and brazing, and advances in techniques for joining non-metals. Contents: Filler Alloys and Their Metallurgy Applications of Phase Diagrams to Soldering and Brazing The Role of Materials in Defining Process Constraints The Joining Environment Assessment of Joining Quality Characterization and Process Development in Soldering and Brazing: Selected Case Studies.
Continuous Purification of Proteins by Selective Nonadsorptive Preparative Chromatography (1993)

Continuous forms of chromatography are important to the biotechnology industry for the production of therapeutic proteins. Selective non-adsorption preparative (SNAP) chromatography may be used in a cross-current, simulated moving bed to produce a continuous purification system. It has the advantages of speed, efficient use of packing material, scalability, decrease cost of pumping systems, gentleness with regard to protein denaturation, and reduced dilution of the sample. An immobilized metal affinity chromatography (IMAC) column may be added in tandem with SNAP to concentrate as well as purify the protein.
Association of distinct α <sub>2</sub> adrenoceptor and serotonin transporter polymorphisms with constipation and somatic symptoms in functional gastrointestinal disorders (2004)

Functionally distinct alpha(2A) and alpha(2C) adrenoceptor and serotonin transporter polymorphisms are associated with constipation and high somatic symptoms in patients with lower functional gastrointestinal disorders, although the strength of the genetic contribution to the phenotype is unclear.
The active principle of Caro's acid, HSO<sub>5</sub><sup>–</sup>: X-ray crystal structure of KHSO<sub>5</sub>·H<sub>2</sub>O (1984)

The structure of HSO5–, the active component in Caro's acid, in the title compound, and in the triple salt K5(HSO5)2(HSO4)(SO4), has been determined and the location of the proton on the peroxo group established.
All-dielectric photonic-assisted wireless receiver (2008)

High Power Microwave (HPM) weapons and other sources of intense microwave power pose a growing threat to modern RF receivers. To address this problem, all-dielectric photonic-assisted receivers have been proposed and demonstrated. Here, we describe a new configuration of this type with 15 dB better sensitivity over prior designs. The complete lack of metal and electronics in the front-end offers immunity against damage from intense electromagnetic radiation. In this experiment, detection of C band electromagnetic signal at 6.54 GHz with a sensitivity of -112 dBm/Hz is demonstrated.
Actin-Bundling Protein L-Plastin Regulates T Cell Activation (2010)

Engagement of TCRs induces actin rearrangements, which are critical for T cell activation. T cell responses require new actin polymerization, but the significance of higher-order actin structures, such as microfilament bundles, is unknown. To determine the role of the actin-bundling protein leukocyte-plastin (L-plastin; LPL) in this process, T cells from LPL(-/-) mice were studied. LPL(-/-) T cells were markedly defective in TCR-mediated cytokine production and proliferation. LPL(-/-) T cells also spread inefficiently on surfaces with immobilized TCR ligands and formed smaller immunological synapses with APCs, likely due to defective formation of lamellipodia. LPL(-/-) mice showed delayed rejection of skin allografts after release from immunosuppression. Moreover, LPL(-/-) mice developed much less severe neurologic symptoms in experimental autoimmune encephalomyelitis, which correlated with impaired T cell responses to Ag, manifested by reduced proliferation and production of IFN-γ and IL-17. Thus, LPL-dependent actin bundling facilitates the formation of lamellipodia and normal immunological synapses and thereby enables T cell activation.
Parametric conversion with distributedly modulated capacitors (DMC) for low-noise and non-reciprocal RF front-ends (2013)

Transmission lines with time-varying reactance exhibit interesting behaviors such as parametric amplification and mixing [1]. In this paper, such a transmission line realized with distributedly modulated capacitors (DMC) is demonstrated with its active conversion gain, low noise figure as well as non-reciprocity. DMC is offered a great potential to operate in an RF front-end either as a broadband low-noise amplifier (LNA) or an integrated circulator. A practical implementation is presented with varactors and microstrip lines connected in double-balanced fashion. DMC shows in simulations that 9 dB gain with below 0.5 dB noise figure over the input signal frequency of 1 to 6 GHz is achievable when it is optimized for gain and noise performance. Alternatively when the circuit is optimized for isolation, greater than 13 dB isolation can be achieved from 500 MHz to 1.8 GHz, which has been verified with the experiment.
Echo-state conditional variational autoencoder for anomaly detection (2016)

Anomaly detection involves identifying the events which do not conform to an expected pattern in data. A common approach to anomaly detection is to identify outliers in a latent space learned from data. For instance, PCA has been successfully used for anomaly detection. Variational autoencoder (VAE) is a recently-developed deep generative model which has established itself as a powerful method for learning representation from data in a nonlinear way. However, the VAE does not take the temporal dependence in data into account, so it limits its applicability to time series. In this paper we combine the echo-state network, which is a simple training method for recurrent networks, with the VAE, in order to learn representation from multivariate time series data. We present an echo-state conditional variational autoencoder (ES-CVAE) and demonstrate its useful behavior in the task of anomaly detection in multivariate time series data.
A Mobile PTS2 Receptor for Peroxisomal Protein Import in <i>Pichia pastoris </i> (1998)

Using a new screening procedure for the isolation of peroxisomal import mutants in Pichia pastoris, we have isolated a mutant (pex7) that is specifically disturbed in the peroxisomal import of proteins containing a peroxisomal targeting signal type II (PTS2). Like its Saccharomyces cerevisiae homologue, PpPex7p interacted with the PTS2 in the two-hybrid system, suggesting that Pex7p functions as a receptor. The pex7Delta mutant was not impaired for growth on methanol, indicating that there are no PTS2-containing enzymes involved in peroxisomal methanol metabolism. In contrast, pex7Delta cells failed to grow on oleate, but growth on oleate could be partially restored by expressing thiolase (a PTS2-containing enzyme) fused to the PTS1. Because the subcellular location and mechanism of action of this protein are controversial, we used various methods to demonstrate that Pex7p is both cytosolic and intraperoxisomal. This suggests that Pex7p functions as a mobile receptor, shuttling PTS2-containing proteins from the cytosol to the peroxisomes. In addition, we used PpPex7p as a model protein to understand the effect of the Pex7p mutations found in human patients with rhizomelic chondrodysplasia punctata. The corresponding PpPex7p mutant proteins were stably expressed in P. pastoris, but they failed to complement the pex7Delta mutant and were impaired in binding to the PTS2 sequence.
Automatic lighthouse generation for directed state space search (2000)

Previous researchers have suggested the use of "lighthouses" to act as guides in directed state space search. The drawback of using lighthouses is that the user has to manually derive them, through a potentially laborious examination of the design. Additionally, specifying a large number of lighthouses results in wasted effort during the search. We present approaches to automatically generate high-quality lighthouses for hard-to-cover targets.
A Meta‐analysis of Letters of Recommendation in College and Graduate Admissions: Reasons for hope (2014)

Letters of recommendation are used extensively in academic admissions and personnel selection. Despite their prominence, comparatively little is known about their predictive power for multiple outcomes. This meta‐analysis combine the existing literature for college grade point average ( GPA ), academic outcomes of GPA , performance ratings, degree attainment, and research productivity for nonmedical school graduate programs, and GPA and internship performance ratings for medical school students. Intercorrelations with other commonly used predictors are also estimated and used to estimate incremental predictive power. Overall, letters of recommendation, in their current form, are generally positively but weakly correlated with multiple aspects of performance in post‐secondary education. However, letters do appear to provide incremental information about degree attainment, a difficult and heavily motivationally determined outcome.
Syzygium impressum (Myrtaceae), A New Species from Hong Kong (2008)

A new species of Syzygium Gaertner (Myrtaceae), S. impressum N. H. Xia, Y. F. Deng & K. L. Yip, is described and illustrated. The new species is similar to S. buxifolium Hook. & Arn., but differs by its obovate leaves, conspicuously impressed midveins, and smaller fruits.
Notch signaling induces cytoplasmic CD3ϵ expression in human differentiating NK cells (2007)

It has been proposed that heterogeneity in natural killer (NK)–cell phenotype and function can be achieved through distinct thymic and bone marrow pathways of NK-cell development. Here, we show a link between Notch signaling and the generation of intracellular CD3ϵ (cyCD3)–expressing NK cells, a cell population that can be detected in vivo. Differentiation of human CD34+ cord blood progenitors in IL-15–supplemented fetal thymus organ culture or OP9-Delta-like 1 (DL1) coculture resulted in a high percentage of cyCD3+ NK cells that was blocked by the γ-secretase inhibitor DAPT. The requirement for Notch signaling to generate cyCD3+ NK cells was further illustrated by transduction of CD34+ cord blood (CB) cells with either the active intracellular part of Notch or the dominant-negative mutant of mastermind-like protein 1 that resulted in the generation of NK cells with respectively high or low frequencies of cyCD3. Human thymic CD34+ progenitor cells displayed the potential to generate cyCD3+ NK cells, even in the absence of Notch/DL1 signaling. Peripheral blood NK cells were unable to induce cyCD3 expression after DL1 exposure, indicating that Notch-dependent cyCD3 expression can only be achieved during the early phase of NK-cell differentiation.
Type XXIII Collagen, a New Transmembrane Collagen Identified in Metastatic Tumor Cells (2003)

We have identified a transmembrane collagen, collagen XXIII, in rat prostate carcinoma cells. Differential display of mRNA expression in prostate carcinoma sublines with varying metastatic potential revealed overexpression of this transcript in the metastatic AT6.1 subline. cDNA cloning identified a 2733-bp transcript from AT6.1 RNA, encoding a protein of 532 amino acids, together with a 3067-bp human homologue, resulting in a 540-amino acid protein. Collagen XXIII is predicted to be a type II membrane protein consisting of an amino-terminal cytoplasmic domain, a transmembrane region, and three collagenous domains flanked by short noncollagenous domains. Collagen XXIII is a new member of the transmembrane collagen family, showing structural homology with the transmembrane collagens XIII and XXV. We present evidence that collagen XXIII is expressed as a approximately 75-kDa protein at the cell surface and that it can be cleaved by furin protease activity. Cleavage results in a approximately 60-kDa soluble protein that forms a multimeric complex and exhibits a low affinity interaction with heparin.
Effect of methyl substituents on permeability and permselectivity of gases in polyimides prepared from methyl‐substituted phenylenediamines (1992)

Abstract Permeability and solubility coefficients for H 2 , CO 2 , O 2 , CO, N 2 , and CH 4 in polyimides prepared from 6FDA and methyl‐substituted phenylenediamines were measured to investigate effects of the substituents on gas permeability and permselectivity. The methyl substituents restrict internal rotation around the bonds between the phenyl rings and the imide rings. The rigidity and nonplanar structure of the polymer chain, and the bulkiness of methyl groups make chain packing inefficient, resulting in increases in both diffusion and solubility coefficients of the gases. Polyimides from tetramethyl‐ p ‐phenylenediamine and trimethyl‐ m ‐phenylenediamine display very high permeability coefficients and very low permselectivity due to very high diffusion coefficients and very low diffusivity selectivity, as compared with the other polyimides having a similar fraction of free space. This suggests that these polyimides have high fractions of large‐size free spaces.
Oncogenic JAK1 and JAK2-activating mutations resistant to ATP-competitive inhibitors (2011)

Our data indicate that some activating mutations not only promote autonomous cell proliferation but also confer resistance to ATP-competitive inhibitors. In vivo, such a mutation can potentially occur as primary JAK-activating mutations but also as secondary mutations combining oncogenicity with drug resistance.