gebhart/patrepeval huggingface dataset:
Normalizing tweets with edit scripts and recurrent neural embeddings (2014)

Tweets often contain a large proportion of abbreviations, alternative spellings, novel words and other non-canonical language. These features are problematic for standard language analysis tools and it can be desirable to convert them to canonical form. We propose a novel text normalization model based on learning edit operations from labeled data while incorporating features induced from unlabeled data via character-level neural text embeddings. The text embeddings are generated using an Simple Recurrent Network. We find that enriching the feature set with text embeddings substantially lowers word error rates on an English tweet normalization dataset. Our model improves on stateof-the-art with little training data and without any lexical resources.
Purification, Molecular Cloning, and Expression of a Human Stratum Corneum Trypsin-like Serine Protease with Possible Function in Desquamation (1999)

A new human 33-kDa serine protease was purified from human epidermis, and its cDNA was cloned from a keratinocyte library, from mRNA from a human keratinocyte line (HaCat) and from mRNA from human skin. Polyclonal antibodies specific for the new protein detected three groups of proteins in partially purified extracts of cornified eptihelium of human plantar skin. The three components are proposed to correspond to proenzyme, active enzyme, and proteolytically modified active enzyme. After N-deglycosylation, there was a decrease in apparent molecular mass of all detected components. Expression of the cloned cDNA in a eukaryotic virus-derived system yielded a recombinant protein that could be converted to an active protease by treatment with trypsin. Polymerase chain reaction analyses of cDNA from a number of human tissues showed high expression of the new enzyme in the skin and low expression in brain, placenta, and kidney. Homology searches yielded the highest score for porcine enamel matrix protease (55% amino acid sequence homology). High scores were also obtained for human and mouse neuropsin and for human stratum corneum chymotryptic enzyme. The function of this new protease, tentatively named stratum corneum tryptic enzyme, may be related to stratum corneum turnover and desquamation in the epidermis.
Influenza A penetrates host mucus by cleaving sialic acids with neuraminidase (2013)

IAV interacts with human mucus on frozen tissue sections and mucus-coated beads. Inhibition of IAV infection by sialylated human mucus is dose-dependent, and enhanced when NA is inhibited with oseltamivir. Thus NA cleaves sialylated decoys during initial stages of infection. Understanding IAV interactions with host mucins is a promising new avenue for drug development.
Major histocompatibility complex (MHC) class I KbDb−/− deficient mice possess functional CD8+ T cells and natural killer cells (1998)

We obtained mice deficient for major histocompatibility complex (MHC) molecules encoded by the H-2K and H-2D genes. H-2 KbDb -/- mice express no detectable classical MHC class I-region associated (Ia) heavy chains, although beta2-microglobulin and the nonclassical class Ib proteins examined are expressed normally. KbDb -/- mice have greatly reduced numbers of mature CD8+ T cells, indicating that selection of the vast majority (>90%) of CD8+ T cells cannot be compensated for by beta2-microglobulin-associated molecules other than classical H-2K and D locus products. In accord with the greatly reduced number of CD8+ T cells, spleen cells from KbDb -/- mice do not generate cytotoxic responses in primary mixed-lymphocyte cultures against MHC-disparate (allogeneic) cells. However, in vivo priming of KbDb -/- mice with allogeneic cells resulted in strong CD8+ MHC class Ia-specific allogeneic responses. Thus, a minor population of functionally competent peripheral CD8+ T cells capable of strong cytotoxic activity arises in the complete absence of classical MHC class Ia molecules. KbDb -/- animals also have natural killer cells that retain their cytotoxic potential.
An unusual pagC::TnphoA mutation leads to an invasion- and virulence-defective phenotype in Salmonellae (1992)

Two phenotypes believed to contribute to the pathogenesis of Salmonella infections are macrophage survival and invasion of epithelial cells. It was recently observed that the Salmonella macrophage survival factor PagC has significant amino acid similarity to the Yersinia invasion factor Ail. This observation raised the possibilities that macrophage survival is in part determined by the pathway of entry and that PagC confers an entry mechanism that does not trigger the microbicidal activities of the macrophage. Thus, we sought to investigate the role of PagC in invasion by examining (i) the invasion phenotype of pagC mutants and (ii) the invasion phenotype of Escherichia coli carrying pagC. A previously identified invasion-defective TnphoA insertion mutant of Salmonella enteritidis was found to have TnphoA inserted into the signal sequence-encoding region of pagC; the pagC allele from this mutant, SM5T, was designated pagC64. In contrast, Salmonella typhimurium carrying the pagC1 allele (a TnphoA insertion mutation, downstream of the region encoding the signal sequence) was not defective for invasion. Further analysis of these two pagC alleles suggested that the invasion-defective phenotype associated with pagC64 is not due to the loss of PagC function but rather is due to the synthesis of a hybrid PagC-alkaline phosphatase protein that is aberrantly localized, most likely to the inner membrane, and thus may prevent proper localization or function of a factor(s) required for efficient invasion. The observation that pagC did not confer an invasive phenotype to E. coli further suggests that PagC is not an invasion factor. A cloned pagC gene complemented the macrophage survival defect of S. typhimurium pagC1 mutants, but the cloned ail gene did not. Together these results suggest that the structural similarity between PagC and Ail may not extend to a similarity in function. Interestingly, S. enteritidis carrying the pagC64 allele that results in both an invasion defect and a macrophage survival defect was less virulent for mice infected intragastrically or intraperitoneally than was S. enteritidis carrying the pagC1 allele that results only in a macrophage survival defect.
Increased spatiotemporal resolution reveals highly dynamic dense tubular matrices in the peripheral ER (2016)

The endoplasmic reticulum (ER) is an expansive, membrane-enclosed organelle that plays crucial roles in numerous cellular functions. We used emerging superresolution imaging technologies to clarify the morphology and dynamics of the peripheral ER, which contacts and modulates most other intracellular organelles. Peripheral components of the ER have classically been described as comprising both tubules and flat sheets. We show that this system consists almost exclusively of tubules at varying densities, including structures that we term ER matrices. Conventional optical imaging technologies had led to misidentification of these structures as sheets because of the dense clustering of tubular junctions and a previously uncharacterized rapid form of ER motion. The existence of ER matrices explains previous confounding evidence that had indicated the occurrence of ER "sheet" proliferation after overexpression of tubular junction-forming proteins.
Quality control of anti human CD3 and CD4 monoclonal antibodies. (1990)

By testing two monoclonal antibodies (MoAb), we tried out two methods, which might be suitable for quality control of anti human T cell MoAb. RIV6 and RIV9 were investigated by flow cytometry and Enzyme-linked Immunosorbent Assay (ELISA). The characteristics, specificity and biological activity of RIV6 and RIV 9 were determined and compared respectively with other CD4 specific MoAb, OKT4, OKT4a, LEU3a and the CD3 specific MoAb OKT3 and LEU4 by flow cytometry. An ELISA was set up to quantify mouse IgG3 antibody. Specificity, plate variability and day to day effects were determined. The results illustrate that ELISA and flow cytometry are valuable tools in the quality control of these antibodies.
Methods of inference and learning for performance modeling of parallel applications (2007)

Increasing system and algorithmic complexity combined with a growing number of tunable application parameters pose significant challenges for analytical performance modeling. We propose a series of robust techniques to address these challenges. In particular, we apply statistical techniques such as clustering, association, and correlation analysis, to understand the application parameter space better. We construct and compare two classes of effective predictive models: piecewise polynomial regression and artifical neural networks. We compare these techniques with theoretical analyses and experimental results. Overall, both regression and neural networks are accurate with median error rates ranging from 2.2 to 10.5 percent. The comparable accuracy of these models suggest differentiating features will arise from ease of use, transparency, and computational efficiency.
Vascular endothelial growth factor is an autocrine growth factor, signaling through neuropilin-1 in non-small cell lung cancer (2015)

Our data demonstrate that VEGF is an autocrine growth factor in NSCLC signaling, at least in part, through NP1. Targeting this VEGF receptor may offer potential as a novel therapeutic approach and also support the evaluation of the role of NP1 as a biomarker predicting sensitivity or resistance to VEGF and VEGFR-targeted therapies in the clinical arena.
Comparison of Piperazine and Tetramisole in Treatment of Ascariasis (1968)

Tetramisole, a new synthetic anthelmintic, was compared with piperazine in the treatment of ascariasis in African children. Of 100 children receiving tetramisole 94 were cured, and of 100 given piperazine 85 were cured (0.05>P>0.02). Tetramisole was free of side-effects.
Plasminogen activator inhibitor type-1 protein, mRNA and gene transcription are increased by phorbol esters in human rhabdomyosarcoma cells. (1988)

By use of an enzyme-linked immunosorbent assay, we have found that phorbol 12-myristate 13-acetate (PMA) causes an approximately 10-fold increase in the level of type-1 plasminogen activator inhibitor (PAI-1) accumulated in conditioned medium of the human rhabdomyosarcoma cell line. Half-maximal stimulation occurred at approximately equal to 15 nM PMA. The effect was only observed with phorbol esters that are tumor promoting. Maximal levels of secreted PAI-1 were observed 24 h after PMA addition. The increase in secreted PAI-1 was preceded by a transient approximately 10-fold increase in intracellular PAI-1 content, maximal at 8 h after PMA addition. There was a 20-fold increase in the cellular level of two 2.3- and 3.4-kilobase PAI-1 mRNAs and a more than 5-fold increase in the PAI-1 gene transcription rate. The protein synthesis inhibitor cycloheximide (10 micrograms/ml) also increased the level of PAI-1 mRNA, and when both cycloheximide and PMA were used, an additive effect was observed. Cycloheximide changed the ratio between the two PAI-1 mRNAs in favor of the 3.4-kilobase species. Overall, the data show that transcriptional activation of the PAI-1 gene forms part of the pleiotropic responses to tumor-promoting phorbol esters.
Lipoarabinomannan. Multiglycosylated form of the mycobacterial mannosylphosphatidylinositols. (1992)

The lipopolysaccharides of mycobacteria, lipoarabinomannan (LAM) and lipomannan (LM), of key importance in host-pathogen interaction, were recently shown to contain a phosphatidylinositol "anchoring domain." We now have established that LAM and LM are based on the phosphatidylinositol mannosides, the characteristic glycophospholipids of mycobacteria. Digestion of the arabinose-free LM with an endo-alpha 1----6-mannosidase yielded evidence for the presence of the 1-(sn-glycerol-3-phospho)-D-myo-inositol-2,6-bis-alpha-D-mannopyranoside unit, indistinguishable from that derived from phosphatidylinositol dimannoside. This same inositol substitution pattern was shown to be present in LAM by methylation analysis before and after dephosphorylation. Positions C-2 and C-6 of the inositol unit of LAM are occupied by mannosyl residues and C-1 by a phosphoryl group. Partial acid hydrolysis of per-O-methylated LAM and comparison by gas chromatography-mass spectrometry of the resulting derivatized oligosaccharides with like products from phosphatidylinositol hexamannoside demonstrated that the C-6 of inositol is the point of attachment of the mannan core of LAM, which consists of an alpha 1----6-linked backbone with considerable alpha-1----2 side chains. Thus, a structural and presumably biosynthetic relationship is established between some of the membranous mannosylphosphatidylinositols described some 25 years ago and the newly emerging, biologically active lipopolysaccharides of mycobacteria.
A Surveillance System Regulates Selective Entry of RNA into the Shoot Apex (2002)

Phloem-mobile endogenous RNA is trafficked selectively into the shoot apex. In contrast, most viruses and long-distance post-transcriptional gene silencing (PTGS) signals are excluded from the shoot apex. These observations suggest the operation of an underlying regulatory mechanism. To examine this possibility, a potexvirus movement protein, known to modify cell-to-cell trafficking and PTGS, was expressed ectopically in transgenic plants. These plants were found to be compromised in their capacity to exclude both viral RNA and silencing signals from the shoot apex. The transgenic plants also displayed various degrees of abnormal leaf polarity depending on transgene expression level. Normal patterns of organ development were restored by either virus- or Agrobacterium tumefaciens-mediated induction of PTGS. This revealed the presence of an RNA signal surveillance system that acts to allow the selective entry of RNA into the shoot apex. We propose that this surveillance system regulates signaling and protects the shoot apex, in particular the cells that give rise to reproductive structures, from viral invasion.
Activation of human T lymphocyte subsets: helper and suppressor/cytotoxic T cells recognize and respond to distinct histocompatibility antigens. (1981)

This study was directed at determining the major histocompatibility complex (MHC) antigens recognized by helper (Leu-3) and suppressor-cytotoxic (Leu-2) T lymphocyte subsets in man. These 2 subsets were isolated from peripheral blood with monoclonal antibodies and challenged in vitro with various stimuli. Only Leu-3 cells proliferated in response to autologous nonrosetting cells and soluble antigens, suggesting that helper but not suppressor-cytotoxic T cells recognize autologous HLA-DR antigen. Furthermore, only Leu-3 T cells responded to allogeneic DR antigen; this was shown in reactions between 2 siblings who were HLA-identical except for a single disparity at HLA-DR caused by a crossover event. Leu-3 cells activated in primary allogeneic mixed leukocyte reactions (MLR) responded equally in secondary allogeneic MLR to the priming cells and to cells that were identical at HLA-DR but discordant at HLA-A, B, and C to the priming cell. The antigens responsible for stimulating Leu-2 cells in allogeneic MLR were not identified, although the results are compatible with a role for HLA-A and B antigens and exclude a dominant role for HLA-DR. These data indicate that the helper and suppressor-cytotoxic T cell subsets in man respond differentially to MHC antigens in a manner analogous to the murine Lyt-2- 3- and Lyt-2+ 3+ populations.
Storm- and Fair-Weather Combined Flow on the Central Texas Continental Shelf (1988)

ABSTRACT Examination of current meter measurements from fair-weather periods and storm events on the central Texas shelf provides information on the means by which sand is transported across the shelf to be deposited as thin ( Building upon observations from these smaller storms and available wind, tide, and wave data, a model of the kinematics of sand transport was developed for Hurricane Carla, which crossed the Texas shelf in September 1961. In this reconstruction, combined flow is oriented obliquely offshore on the immediate right and left side of the storm track (looking toward the coast) and onshore on the storm's far left side. This combined-flow transport pattern is consistent with the observed distribution of the sand bed deposited during the passage of the storm, as revealed by cores of the near-surface modern sediments. This model also differs considerably from an earlier explanation for the Carla sand bed which invoked turbidity currents generated during the ebb of the storm surge following hurr cane landfall.
Novel Subunit Composition of a Renal Epithelial KATPChannel (1998)

Unique ATP-inhibitable K+ channels (KATP) in the kidney determine the rate of urinary K+ excretion and play an essential role in extracellular K+ balance. Here, we demonstrate that functionally similar low sulfonylurea affinity KATP channels are formed by two heterologous molecules, products of Kir1.1a and cystic fibrosis transmembrane conductance regulator (CFTR) genes. Co-injection of CFTR and Kir1.1a cRNA into Xenopus oocytes lead to the expression of K+ selective channels that retained the high open probability behavior of Kir1.1a but acquired sulfonylurea sensitivity and ATP-dependent gating properties. Similar to the KATP channels in the kidney but different from KATP channels in excitable tissues, the Kir1.1a/CFTR channel was inhibited by glibenclamide with micromolar affinity. Since the expression of Kir1.1a and CFTR overlap at sites in the kidney where the low sulfonylurea affinity KATP are expressed, our study offers evidence that these native KATP channels are comprised of Kir1.1a and CFTR. The implication that Kir subunits can interact with ABC proteins beyond the subfamily of sulfonylurea receptors provides an intriguing explanation for functional diversity in KATP channels.
The underglycosylation of plasma alpha1-antitrypsin in congenital disorders of glycosylation type I is not random (2002)

Conditions under which the glycosylation capacity of cells is limited provide an opportunity for studying the efficiency of site-specific glycosylation and the role of glycosylation in the maturation of glycoproteins. Congenital disorders of glycosylation type 1 (CDG-I) provide such a system. CDG-I is characterized by underglycosylation of glycoproteins due to defects in the assembly or transfer of the common dolichol-pyrophosphate-linked oligosaccharide precursor of asparagine-linked glycans. Human plasma alpha1-antitrypsin is normally fully glycosylated at three asparagine residues (46, 83, and 247), but un-, mono-, di-, and fully glycosylated forms of alpha1-antitrypsin were detected by 2D PAGE in the plasma from patients with CDG-I. The state of glycosylation of the three asparagine residues was analyzed in all the underglycosylated forms of alpha1-antitrypsin by peptide mass fingerprinting using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. It was found that asparagine 46 was always glycosylated and that asparagine 83 was never glycosylated in the underglycosylated glycoforms of alpha1-antitrypsin. This showed that the asparagine residues are preferentially glycosylated in the order 46>247>83 in the mature underglycosylated forms of alpha1-antitrypsin found in plasma. It is concluded that the nonoccupancy of glycosylation sites is not random under conditions of decreased glycosylation capacity and that the efficiency of glycosylation site occupancy depends on structural features at each site. The implications of this observation for the intracellular transport and sorting of glycoproteins are discussed.
Identification of oligopeptides binding to peritoneal tumors of gastric cancer (2006)

This is a report of in vivo intraperitoneal biopanning, and we successfully identified a novel peptide to target the multiple peritoneal tumors of gastric cancer. A phage display library was injected directly into the abdominal cavity of mice bearing peritoneal tumors of human gastric cancer, and phages associated with the tumors were subsequently reclaimed from isolated samples. The tumor-associated phages were amplified and the biopanning cycle was repeated five times to enrich for high affinity tumor-selective binding peptides. Finally, a tri-peptide motif, KLP, which showed homology with laminin 5 (a ligand for alpha3beta1 integrin), was identified as a binding peptide for peritoneal tumors of gastric cancer. Phage clones displaying the sequence KLP showed 64-fold higher binding to peritoneal tumors than control phage and were preferentially distributed in tumors rather than in normal organs after intraperitoneal injection into mice. In addition, the KLP phages were more likely to bind to cancer cells in malignant ascites derived from a patient with recurrent gastric cancer. Synthesized peptide containing the motif KLP (SWKLPPS) also showed a strong binding activity to peritoneal tumors without cancer growth effect. Liposomes conjugated with SWKLPPS peptide appeared significantly more often in tumors than control liposomes after intraperitoneal injection into mice. Furthermore, modification of liposomes with SWKLPPS peptide enhanced the antitumor activity of adriamycin on gastric cancer cells. The peptide motif KLP seems a potential targeting ligand for the treatment of peritoneal metastasis of gastric cancer.
Estimation of protective levels of anti-O-specific lipopolysaccharide immunoglobulin G antibody against experimental Escherichia coli infection (1993)

Serum obtained after immunization with an O18 polysaccharide-toxin A conjugate vaccine was evaluated for the estimation of protective levels of anti-O-specific lipopolysaccharide (LPS) immunoglobulin G (IgG) antibody against bacteremia and death caused by a homologous serotype of Escherichia coli K1 strains. Passive transfer of rabbit serum conferred significant protection from a lethal E. coli infection in a neonatal rat model. The overall incidence of bacteremia and mortality was 4% in rat pups receiving undiluted postvaccination serum, while that in control animals was 100% (P < 0.001). The overall incidences of bacteremia were 5 and 72% for animals with serum anti-O18 LPS IgG concentrations of > 1.0 and < 1.0 microgram/ml, respectively, while the overall incidences of mortality for animals with serum anti-O18 LPS IgG levels of > 1.0 and < 1.0 microgram/ml were 0 and 72%, respectively (P < 0.001). Protection against E. coli infection was also demonstrated with human anti-O18 polysaccharide IgG. None of the animals with human anti-O18 LPS IgG levels of > 1 microgram/ml had bacteremia after bacterial challenge, whereas all animals with bacteremia at 18 h had levels of < 1 microgram/ml. These findings suggest that serum anti-O18 LPS IgG concentrations of > 1.0 microgram/ml may provide protection against bacteremia and death caused by a homologous E. coli K1 infection.
Imaging Crystals, Polymers, and Processes in Water with the Atomic Force Microscope (1989)

The atomic force microscope (AFM) can be used to image the surface of both conductors and nonconductors even if they are covered with water or aqueous solutions. An AFM was used that combines microfabricated cantilevers with a previously described optical lever system to monitor deflection. Images of mica demonstrate that atomic resolution is possible on rigid materials, thus opening the possibility of atomic-scale corrosion experiments on nonconductors. Images of polyalanine, an amino acid polymer, show the potential of the AFM for revealing the structure of molecules important in biology and medicine. Finally, a series of ten images of the polymerization of fibrin, the basic component of blood clots, illustrate the potential of the AFM for revealing subtle details of biological processes as they occur in real time.