gebhart/patrepeval huggingface dataset:
TCDB: the Transporter Classification Database for membrane transport protein analyses and information (2005)

The Transporter Classification Database (TCDB) is a web accessible, curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from a variety of living organisms. TCDB is a curated repository for factual information compiled from >10,000 references, encompassing approximately 3000 representative transporters and putative transporters, classified into >400 families. The transporter classification (TC) system is an International Union of Biochemistry and Molecular Biology approved system of nomenclature for transport protein classification. TCDB is freely accessible at http://www.tcdb.org. The web interface provides several different methods for accessing the data, including step-by-step access to hierarchical classification, direct search by sequence or TC number and full-text searching. The functional ontology that underlies the database structure facilitates powerful query searches that yield valuable data in a quick and easy way. The TCDB website also offers several tools specifically designed for analyzing the unique characteristics of transport proteins. TCDB not only provides curated information and a tool for classifying newly identified membrane proteins, but also serves as a genome transporter-annotation tool.
Definition of an HLA-DPw2-restricted epitope on NS3, recognized by a dengue virus serotype-cross-reactive human CD4+ CD8- cytotoxic T-cell clone (1993)

We previously reported that the clone JK34 was cross-reactive for dengue virus types 1, 2, 3, and 4 and recognized NS3 (I. Kurane, M. A. Brinton, A. L. Samson, and F. A. Ennis, J. Virol. 65:1823-1828, 1991). In the present experiments, we defined the epitope at the amino acid level, with 93 15-mer overlapping peptides which cover the entire NS3. A peptide 4 which contains amino acids 251 to 265 of NS3 sensitized the autologous B lymphoblastoid cell line (LCL) to the lysis by JK34. The smallest peptide recognized by JK34 was a 10-mer peptide which contains amino acids 255 to 264 (EIVDLMCHAT). A monoclonal antibody to HLA-DP inhibited the lysis of epitope peptide-pulsed autologous LCL by JK34. Genotypic typing revealed that the HLA-DP of this donor is DPA1*01, DPB1*0201, which is serologically defined as HLA-DPw2. JK34 lysed peptide 4-pulsed allogeneic LCL which carried HLA-DPw2. These results indicate that HLA-DPw2 is the restriction allele for recognition of this epitope by JK34.
Salmonella Pathogenicity Island 2-Dependent Evasion of the Phagocyte NADPH Oxidase (2000)

A type III protein secretion system encoded by Salmonella pathogenicity island 2 (SPI2) has been found to be required for virulence and survival within macrophages. Here, SPI2 was shown to allow Salmonella typhimurium to avoid NADPH oxidase-dependent killing by macrophages. The ability of SPI2-mutant bacteria to survive in macrophages and to cause lethal infection in mice was restored by abrogation of the NADPH oxidase-dependent respiratory burst. Ultrastructural and immunofluorescence microscopy demonstrated efficient localization of the NADPH oxidase in the proximity of vacuoles containing SPI2-mutant but not wild-type bacteria, suggesting that SPI2 interferes with trafficking of oxidase-containing vesicles to the phagosome.
Semantic Parsing on Freebase from Question-Answer Pairs (2013)

In this paper, we train a semantic parser that scales up to Freebase.Instead of relying on annotated logical forms, which is especially expensive to obtain at large scale, we learn from question-answer pairs.The main challenge in this setting is narrowing down the huge number of possible logical predicates for a given question.We tackle this problem in two ways: First, we build a coarse mapping from phrases to predicates using a knowledge base and a large text corpus.Second, we use a bridging operation to generate additional predicates based on neighboring predicates.On the dataset of Cai and Yates (2013), despite not having annotated logical forms, our system outperforms their state-of-the-art parser.Additionally, we collected a more realistic and challenging dataset of question-answer pairs and improves over a natural baseline.
An efficient neural classification chain of SAR and optical urban images (2001)

In this paper a suitable neural classification algorithm, based on the use of Adaptive Resonance Theory (ART) networks, is applied to the fusion and classification of optical and SAR urban images. ART networks provide a flexible tool for classification, but are ruled by a large number of parameters. Therefore, the simplified ART2-A algorithm is used in this paper, and the neural approach is integrated into a classification chain where fuzzy clustering for merging of classes is also considered. The interaction between the two methods leads to encouraging results in less CPU time than classification with fuzzy clustering alone or other classical approaches (ISODATA). Examples of classification are provided using C-band total power AIRSAR data and optical images of Santa Monica, Los Angeles.
Mammalian Caspases: Structure, Activation, Substrates, and Functions During Apoptosis (1999)

Apoptosis is a genetically programmed, morphologically distinct form of cell death that can be triggered by a variety of physiological and pathological stimuli. Studies performed over the past 10 years have demonstrated that proteases play critical roles in initiation and execution of this process. The caspases, a family of cysteine-dependent aspartate-directed proteases, are prominent among the death proteases. Caspases are synthesized as relatively inactive zymogens that become activated by scaffold-mediated transactivation or by cleavage via upstream proteases in an intracellular cascade. Regulation of caspase activation and activity occurs at several different levels: (a) Zymogen gene transcription is regulated; (b) antiapoptotic members of the Bcl-2 family and other cellular polypeptides block proximity-induced activation of certain procaspases; and (c) certain cellular inhibitor of apoptosis proteins (cIAPs) can bind to and inhibit active caspases. Once activated, caspases cleave a variety of intracellular polypeptides, including major structural elements of the cytoplasm and nucleus, components of the DNA repair machinery, and a number of protein kinases. Collectively, these scissions disrupt survival pathways and disassemble important architectural components of the cell, contributing to the stereotypic morphological and biochemical changes that characterize apoptotic cell death.
Local Expression of C-Type Natriuretic Peptide Markedly Suppresses Neointimal Formation in Rat Injured Arteries Through an Autocrine/Paracrine Loop (1997)

Our results showed that CNP, a secreted multifactorial molecule, was indeed effective in suppressing fibroproliferative response in injured arteries and suggest that the potent antiproliferation effect may not be the most critical factor for the effective suppression of neointimal formation. An adenovirus-mediated expression of CNP could be an effective and site-specific form of molecular intervention in proliferative arterial diseases.
Dynamic analysis of metabolic network for ethanol production in Saccharomyces cerevisiae (2007)

Application of metabolic engineering principles to the systematic design of ethanol production process crucially depends on the ability to describe quantitatively the dynamic kinetics for enzymes that related biosynthesis network. Goal of this investigation is the development of an essential dynamic model for ethanol production of Saccharomyces cerevisiae and the characterization of simulation results to probe its characteristic behavior[1, 2]. The results of this research provided a way to achieve more exact analysis of systemic approach in Saccharomyces cerevisiae metabolism and also this technique could be applied to other species.
B cell, heal thyself (2015)

![Figure][1] 

When B cell plasma membranes are wounded, lipid rafts (marked by cholera toxin B, black dots) are internalized into long tubular structures.



[Miller et al.][2] reveal that B cells are able to repair damage to their plasma membranes, but this process may inhibit their ability
Insect Population Control Using a Dominant, Repressible, Lethal Genetic System (2000)

A major modification to the sterile insect technique is described, in which transgenic insects homozygous for a dominant, repressible, female-specific lethal gene system are used. We demonstrate two methods that give the required genetic characteristics in an otherwise wild-type genetic background. The first system uses a sex-specific promoter or enhancer to drive the expression of a repressible transcription factor, which in turn controls the expression of a toxic gene product. The second system uses non-sex-specific expression of the repressible transcription factor to regulate a selectively lethal gene product. Both methods work efficiently in Drosophila melanogaster, and we expect these principles to be widely applicable to more economically important organisms.
Akt Phosphorylation at Ser473 Predicts Benefit of Paclitaxel Chemotherapy in Node-Positive Breast Cancer (2010)

pAkt significantly predicts disease-free benefit from the sequential addition of paclitaxel to AC chemotherapy in patients with node-positive breast cancer. Patients with pAkt-negative breast tumors do not appear to benefit from the addition of paclitaxel.
Ethanol production during batch fermentation with Saccharomyces cerevisiae: changes in glycolytic enzymes and internal pH (1987)

During batch fermentation, the rate of ethanol production per milligram of cell protein is maximal for a brief period early in this process and declines progressively as ethanol accumulates in the surrounding broth. Our studies demonstrate that the removal of this accumulated ethanol does not immediately restore fermentative activity, and they provide evidence that the decline in metabolic rate is due to physiological changes (including possible ethanol damage) rather than to the presence of ethanol. Several potential causes for the decline in fermentative activity have been investigated. Viability remained at or above 90%, internal pH remained near neutrality, and the specific activities of the glycolytic and alcohologenic enzymes (measured in vitro) remained high throughout batch fermentation. None of these factors appears to be causally related to the fall in fermentative activity during batch fermentation.
Characterization of a zinc-dependent transcriptional activator from Arabidopsis (1996)

The C2-H2 zinc-finger is a widely occurring DNA binding motif, usually present as tandem repeats. The majority of C2-H2 zinc-finger proteins that have been studied are derived from animals. Here, we characterize a member of a distinct class of plant C2-H2 zinc-finger proteins in detail. A cDNA clone encoding a DNA binding protein from Arabidopsis was isolated by SouthWestern screening. The protein, termed ZAP1 (Zinc-dependent Activator Protein-1), is encoded by a single copy gene, which is expressed to similar levels in root and flower, to a somewhat lower level in stem and to low levels in leaf and siliques. The optimal binding site was determined by random binding site selection, and the consensus sequence found is CGTTGACCGAG. The homology between ZAP1 and other DNA binding proteins is restricted to a repeated region of a stretch of 24 highly conserved amino acids followed by a zinc-finger motif (C-X4-C-X22-23-H-X1-H). The C-terminal zinc-finger region is essential for DNA binding, whereas deletion of the N-terminal one resulted in 2.5-fold reduced binding affinity. Binding of ZAP1 to DNA was abolished by metal-chelating agents. The activation domain as determined in yeast is adjacent to and possibly overlapping with the DNA binding domain. Particle bombardment experiments with plant cells showed that ZAP1 increases expression of a gusA reporter gene that is under control of ZAP1 binding sites. We conclude that ZAP1 is a plant transcriptional activator with a C2-H2 zinc-finger DNA binding domain.
Filaggrin failure - from ichthyosis vulgaris to atopic eczema and beyond (2016)

The main proteinaceous component of the keratohyalin granules within the granular layer keratinocytes of the epidermis is the giant, repetitive polyprotein profilaggrin. When granular layer cells commit to terminal differentiation to form the flattened squames of the stratum corneum, profilaggrin is rapidly cleaved into multiple copies of the 37 kDa filaggrin monomer, which binds to and condenses the keratin cytoskeleton, thereby facilitating cellular compression. Within the stratum corneum, filaggrin is broken down to form natural moisturising factor, a pool of amino acids and derivatives thereof that exerts multiple effects. Filaggrin is therefore essential for normal stratum corneum biogenesis and physiology. In 2006, the McLean group identified the first loss-of-function mutations in the filaggrin gene (FLG) as the cause of the common monogenic genodermatosis ichthyosis vulgaris (IV). In parallel, they showed by multiple methods that these mutations, carried by up to 10% of various human populations are the major genetic predisposing factor for atopic dermatitis (eczema) and all of the associated allergic phenotypes that constitute the atopic diathesis. This paradigm-shifting work showed that skin barrier deficiency is a major early event in the pathophysiology of eczema and allergy.
Mast Cell Blocking Reduces Brain Edema and Hematoma Volume and Improves Outcome after Experimental Intracerebral Hemorrhage (2006)

Intracerebral hemorrhage (ICH) is associated with high mortality and disability, and there is no widely approved clinical therapy. Poor outcome after ICH results mostly from a mass effect owing to enlargement of the hematoma and brain swelling, leading to displacement and disruption of brain structures. Cerebral mast cells (MC) are resident inflammatory cells that are located perivascularly and contain potent vasoactive, proteolytic, and fibrinolytic substances. We previously found pharmacological MC stabilization and genetic MC deficiency to be associated with up to 50% reduction of postischemic brain swelling in rats. Here, we studied the role of MC and MC stabilization in ICH using in vivo magnetic resonance imaging and ex vivo digital imaging for calculating brain edema and hematoma volume. In a rat ICH model of autologous blood injection into the basal ganglia, four groups of Wistar rats received either saline or sodium cromoglycate (MC stabilizer, two groups) or compound 48/80 (MC degranulator). Evaluated 24 h later, MC stabilization had resulted in highly significantly better neurologic scores (P<0.001), decrease mortality (P=0.002), less brain swelling (P<0.001), and smaller hematoma volume growth (P<0.001) compared with saline and compound 48/80. Moreover, to support our hypothesis, we induced ICH in MC-deficient rats and their wild-type littermates (WT). MC-deficient rats responded with significantly better neurologic scores (P<0.001), decrease mortality (0% versus 25%), less brain swelling (P<0.05), and smaller hematoma growth (P<0.05) than WT. The role of MC deserves a close evaluation as a potential target in the development of novel forms of ICH therapy.
A 1.2 ns GaAs 4 K read only memory (2003)

The first commercially available GaAs 4 K ROM (read-only memory) has been designed and manufactured using the 3-level metal HMED (high-margin enhancement/depletion) process. The access time of 1.2 ns is obtained with a power dissipation of 1.9 W. It is concluded that extra margin in the circuit design for a wide range of power supply variation and processing window has contributed to good processing yield. The design criteria also allow the target pinch-off voltage to be changed for a particular application need in power/speed combination.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A multifunctional androgen receptor screening assay using the high‐throughput Hypercyt® flow cytometry system (2008)

The androgen receptor (AR) is a steroid hormone receptor which regulates transcription of androgen-sensitive genes and is responsible for the development and maintenance of male secondary sexual characteristics. Chemicals that interfere with AR activity may lead to pathological conditions in androgen-sensitive tissues. A variety of reporter systems have been developed, driven by androgen-sensitive promoters, which screen for chemicals that modulate androgenic activity. We have developed a flexible, high-throughput AR transcriptional activation assay, designated the Multifunctional Androgen Receptor Screening (MARS) assay, to facilitate the identification of novel modulators of AR transcriptional activity using flow cytometry. Androgen-independent human prostate cancer-derived PC3 cells were transiently cotransfected with an expression vector for the wild-type human AR and an androgen-sensitive promoter regulating the expression of destabilized enhanced GFP (dsEGFP). The transfected cells were stimulated with established androgenic and antiandrogenic compounds and assessed for increased or decreased dsEGFP expression. To screen for antagonists of AR transcription, the AR agonist R1881 was coadministered at submaximal concentrations with potential AR antagonists. The assay was formatted for high-throughput screening using the HyperCyt flow cytometry system. Agents with established androgenic and antiandrogenic activity were used for validation of the MARS assay. AR agonists were found to potently induce dsEGFP. Furthermore, AR agonists induced dsEGFP expression in a dose-dependent manner. Alternatively, AR antagonists blocked dsEGFP expression when coadministered with low-dose R1881, which also occurred in a dose-dependent manner. Modulators of AR transcriptional activity can be successfully identified by the MARS assay, utilizing a rapid, flexible, sensitive, and high-throughput format. Dose-response curves can be successfully generated for these compounds, allowing for an assessment of potency. Because of its simplicity and high-throughput compatibility, the MARS assay and HyperCyt system combined with flow cytometric analysis represents a valuable and novel addition to the current repertoire of AR transcriptional activation screening assays.
Human Interferon γ is encoded by a single class of mRNA (1982)

Polyadenylated RNA from human peripheral blood lymphocytes and spleen cells, treated with different inducers for IFN-gamma production, was fractionated on denaturing sucrose gradients. Two IFN-gamma mRNA peaks at 12S and 16S were consistently observed. Nucleotide sequence analysis of cDNA clones showed that the 12S IFN-gamma mRNA from the different sources is identical to the gel fractionated 18S IFN-gamma mRNA which gave rise to the IFN-gamma cDNA clone p69 (1). Nucleotide sequence analysis of several IFN-gamma cDNA clones showed the presence of a CGA (Arg) codon at position 140 of mature IFN-gamma in contrast with the CAA (Gln) codon, which is found in p69 (1). Specifically primed cDNA extension on total induced polyadenylated RNA revealed the presence of a single mRNA species having a 5' untranslated region of 125-130 nucleotides. The nucleotide sequence of this region has been obtained. These data suggest that a single human IFN-gamma gene, which has very little polymorphism, gives rise to a single size class of mRNA.
Intermolecular homologous recombination between transfected sequences in mammalian cells is primarily nonconservative. (1987)

Intermolecular recombination in mammalian cells was studied by coinfecting African green monkey cells in culture with two shuttle vector plasmids, each carrying an incomplete but overlapping portion of the gene for neomycin resistance. The region of homology between the two plasmids was about 0.6 kilobases. Recombination between the homology regions could reconstruct the neomycin resistance gene, which was monitored by analysis of progeny plasmids in bacteria. The individual plasmids carried additional markers which, in combination with restriction analysis, allowed the determination of the frequency of formation of the heterodimeric plasmid which would be formed in a conservative recombination reaction between the homologous sequences. Reconstruction of the neomycin resistance gene was readily observed, but only 1 to 2% of the neomycin resistance plasmids had the structure of the conservative heterodimer. Treatment of the plasmids which enhanced the frequency of the neomycin resistance gene reconstruction reaction did not significantly increase the relative frequency of conservative product plasmids. The results support nonconservative models for recombination of these sequences.
Normal-incidence guided-mode resonant grating filters:?design and experimental demonstration (1998)

Guided-mode resonant grating filters have numerous applications. However, in weakly modulated gratings designed for use at normal incidence, the filtering resonance of these subwavelength-period devices splits for angles of incidence that are even slightly off normal incidence. Strongly modulated gratings are designed that essentially overcome this practical problem near normal incidence. In addition, these gratings can have, by design, either broad or narrow spectral characteristics. An experimental demonstration (1.5-2.0-mu m wavelength range) of such a normal-incidence guided-mode resonant silicon grating upon a sapphire substrate is presented. The measured reflection resonance had a FWHM of 67-100 nm for angles of incidence of 0-8 degrees and peak efficiency of ~80% .
A 5′ Noncoding Exon Containing Engineered Intron Enhances Transgene Expression from Recombinant AAV Vectors in vivo (2016)

We previously developed a mini-intronic plasmid (MIP) expression system in which the essential bacterial elements for plasmid replication and selection are placed within an engineered intron contained within a universal 5' UTR noncoding exon. Like minicircle DNA plasmids (devoid of bacterial backbone sequences), MIP plasmids overcome transcriptional silencing of the transgene. However, in addition MIP plasmids increase transgene expression by 2 and often >10 times higher than minicircle vectors in vivo and in vitro. Based on these findings, we examined the effects of the MIP intronic sequences in a recombinant adeno-associated virus (AAV) vector system. Recombinant AAV vectors containing an intron with a bacterial replication origin and bacterial selectable marker increased transgene expression by 40 to 100 times in vivo when compared with conventional AAV vectors. Therefore, inclusion of this noncoding exon/intron sequence upstream of the coding region can substantially enhance AAV-mediated gene expression in vivo.
Heart-Rate Recovery Immediately after Exercise as a Predictor of Mortality (1999)

A delayed decrease in the heart rate during the first minute after graded exercise, which may be a reflection of decreased vagal activity, is a powerful predictor of overall mortality, independent of workload, the presence or absence of myocardial perfusion defects, and changes in heart rate during exercise.
A Simple and Complete Purification of Single-Walled Carbon Nanotube Materials (1999)

Carbon single-walled nanotubes (SWNTs) need to be highly pure for use in various applications. A simple and efficient purification method is reported here to provide >98 % pure SWNTs (see Figure) in a three-step process involving dilute nitric acid reflux and oxidation in air. The method also provides an analytical technique for the determination of the SWNT content in the crude and purified samples.
Self-healing algorithm forlogical mesh connection on ring networks (1994)

A self-healing algorithm is proposed for a ring network connected as a logical mesh. It offers good performance in terms of protection line capacity, restoration time, and survivability against multiple failures.