gebhart/patrepeval huggingface dataset:
WNT Signaling in Stem Cell Biology and Regenerative Medicine (2008)

WNT family members are secreted-type glycoproteins to orchestrate embryogenesis, to maintain homeostasis, and to induce pathological conditions. FZD1, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, FZD10, LRP5, LRP6, and ROR2 are transmembrane receptors transducing WNT signals based on ligand-dependent preferentiality for caveolin- or clathrin-mediated endocytosis. WNT signals are transduced to canonical pathway for cell fate determination, and to non-canonical pathways for regulation of planar cell polarity, cell adhesion, and motility. MYC, CCND1, AXIN2, FGF20, WISP1, JAG1, DKK1 and Glucagon are target genes of canonical WNT signaling cascade, while CD44, Vimentin and STX5 are target genes of non-canonical WNT signaling cascades. However, target genes of WNT signaling cascades are determined in a context-dependent manner due to expression profile of transcription factors and epigenetic status. WNT signaling cascades network with Notch, FGF, BMP and Hedgehog signaling cascades to regulate the balance of stem cells and progenitor cells. Here WNT signaling in embryonic stem cells, neural stem cells, mesenchymal stem cells, hematopoietic stem cells, and intestinal stem cells will be reviewed. WNT3, WNT5A and WNT10B are expressed in undifferentiated human embryonic stem cells, while WNT6, WNT8B and WNT10B in endoderm precursor cells. Wnt6 is expressed in intestinal crypt region for stem or progenitor cells. TNF/alpha-WNT10B signaling is a negative feedback loop to maintain homeostasis of adipose tissue and gastrointestinal mucosa with chronic inflammation. Recombinant WNT protein or WNT mimetic (circular peptide, small molecule compound, or RNA aptamer) in combination with Notch mimetic, FGF protein, and BMP protein opens a new window to tissue engineering for regenerative medicine.
Mitochondria and Neuronal Survival (2000)

Mitochondria play a central role in the survival and death of neurons. The detailed bioenergetic mechanisms by which isolated mitochondria generate ATP, sequester Ca(2+), generate reactive oxygen species, and undergo Ca(2+)-dependent permeabilization of their inner membrane are currently being applied to the function of mitochondria in situ within neurons under physiological and pathophysiological conditions. Here we review the functional bioenergetics of isolated mitochondria, with emphasis on the chemiosmotic proton circuit and the application (and occasional misapplication) of these principles to intact neurons. Mitochondria play an integral role in both necrotic and apoptotic neuronal cell death, and the bioenergetic principles underlying current studies are reviewed.
Activation of Proglucagon Gene Transcription Through a Novel Promoter Element by the Caudal-Related Homeodomain Protein cdx-2/3 (1996)

The proglucagon gene is expressed in a highly restricted tissue-specific manner in the A cells of the pancreatic islet and the L cells of the small and large intestines. The results of previous experiments indicate that cell-specific expression of the proglucagon gene is mediated by proteins that interact with the proximal G1 promoter element. We show here that the G1 element contains several AT-rich subdomains that bind proteins present in islet and enteroendocrine cell extracts. Electrophoretic mobility shift assay experiments using specific antisera identified the homeobox protein cdx-2/3 (which designates the same homeobox protein called cdx-2 for mice and cdx-3 for hamsters) as a major component of the G1-Gc2 complex in islet and intestinal cells. Mutations of the Gc element that decreased cdx-2/3 binding also resulted in decreased proglucagon promoter activity in islet and intestinal cell lines. The finding that cdx-2/3 mediates activation of the proglucagon promoter in both islet and enteroendocrine cells is consistent with the common endodermal lineage of these tissues and provides new insight into the coordinate regulation of genes expressed in both pancreatic and intestinal endocrine cell types.
Pathogenesis of Experimental Ebola Virus Infection in Guinea Pigs (1999)

The subtype Zaire of Ebola (EBO) virus (Mayinga strain) was adapted to produce lethal infections in guinea pigs. In many ways, the disease was similar to EBO infections in nonhuman primates and humans. The guinea pig model was used to investigate the pathologic events in EBO infection that lead to death. Analytical methods included immunohistochemistry, in situ hybridization, and electron microscopy. Cells of the mononuclear phagocyte system, primarily macrophages, were identified as the early and sustained targets of EBO virus. During later stages of infection, interstitial fibroblasts in various tissues were infected, and there was evidence of endothelial cell infection and fibrin deposition. The distribution of lesions, hematologic profiles, and increases in serum biochemical enzymes associated with EBO virus infection in guinea pigs was similar to reported findings in experimentally infected nonhuman primates and naturally infected humans.
Damascene copper electroplating for chip interconnections (1998)

Damascene Cu electroplating for on-chip metallization, which we conceived and developed in the early 1990s, has been central to IBM's Cu chip interconnection technology. We review here the challenges of filling trenches and vias with Cu without creating a void or seam, and the discovery that electrodeposition can be engineered to give filling performance significantly better than that achievable with conformal step coverage. This attribute of superconformal deposition, which we call superfilling, and its relation to plating additives are discussed, and we present a numerical model that represents the shape-change behavior of this system.
Preparation and characterization of antisera to electrophoretically purified SA11 virus polypeptides (1981)

Antisera to SA11 virus proteins were prepared by immunizing rabbits with individual polypeptides separated by polyacrylamide gel electrophoresis under reducing or nonreducing conditions; the resulting antisera were characterized by four immunological methods. Results of complement fixation tests with double-shelled rotavirus particles and sera raised against reduced or unreduced proteins of the outer shell of the virus suggested the presence of common antigenic determinants in the outer capsid layers of SA11 and the Northern Ireland strain of calf rotavirus. In this test, antisera to outer shell polypeptides gp34 (O2) and gp25 (O4) cross-reacted with calf rotavirions, whereas those to p62 (O1) and p26 (O3) reacted only with the homologous virus. Antisera to the reduced outer shell proteins of the virus did not neutralize viral infectivity, nor did they possess hemagglutination inhibition activity. Evidence suggesting the presence of type-specific antigenic determinant(s) in the major inner protein p42 (I4) of SA11 virus, capable of inducing neutralizing antibody, is presented and discussed. Antisera produced against unreduced gp34 and p26 polypeptides of the virus contained type-specific neutralizing antibodies. Polypeptide gp34 was also capable of inducing hemagglutination inhibiting antibody. All of the antisera to unreduced polypeptides had agglutinating activity against double-shelled particles of homologous and heterologous rotaviruses.
Inhibition of Invasion of Invasive Human Bladder Carcinoma Cells by Protein Kinase C Inhibitor Staurosporine (1990)

To study the effect of the protein kinase C (PKC) inhibitor staurosporine on invasion, we selected the invasive human bladder carcinoma cell line EJ. Total PKC activity was more than twofold higher in the EJ cells than in RT4 cells (superficial human bladder carcinoma cells), which do not pass through an artificial basement membrane. There was more PKC activity in the cytosol than in the membrane of EJ cells. Staurosporine, at nontoxic concentrations, inhibited the invasion of EJ cells through an artificial basement membrane in a dose-dependent manner. Staurosporine caused a dose-dependent inhibition of cell motility but did not inhibit cell attachment. Staurosporine represents a new agent for the inhibition of tumor cell invasion and may prove useful in studying the mechanisms responsible for this phenomenon.
Mutationally activated Rho GTPases in cancer (2013)

The Rho family of GTPases (members of the Ras superfamily) are best known for their roles in regulating cytoskeletal dynamics. It is also well established that misregulation of Rho proteins contributes to tumorigenesis and metastasis. Unlike Ras proteins, which are frequently mutated in cancer (around 30%), Rho proteins themselves are generally not found to be mutated in cancer. Rather, misregulation of Rho activity in cancer was thought to occur by overexpression of these proteins or by misregulation of molecules that control Rho activity, such as activation or overexpression of GEFs and inactivation or loss of GAPs or GDIs. Recent studies, enabled by next-generation tumor exome sequencing, report activating point mutations in Rho GTPases as driver mutations in melanoma, as well as breast, and head and neck cancers. The Rac1(P29L) mutation identified in these tumor studies was previously identified by our lab as an activating Rac mutation in C. elegans neuronal development, highlighting the conserved nature of this mutation. Furthermore, this finding supports the relevance of studying Rho GTPases in model organisms such as C. elegans to study the mechanisms that underlie carcinogenesis. This review will describe the recent findings that report activating Rho mutations in various cancer types, moving Rho GTPases from molecules misregulated in cancer to mutagenic targets that drive tumorigenesis.
X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis (2007)

Affymetrix exon arrays aim to target every known and predicted exon in the human, mouse or rat genomes, and have reporters that extend beyond protein coding regions to other areas of the transcribed genome. This combination of increased coverage and precision is important because a substantial proportion of protein coding genes are predicted to be alternatively spliced, and because many non-coding genes are known also to be of biological significance. In order to fully exploit these arrays, it is necessary to associate each reporter on the array with the features of the genome it is targeting, and to relate these to gene and genome structure. X:Map is a genome annotation database that provides this information. Data can be browsed using a novel Google-maps based interface, and analysed and further visualized through an associated BioConductor package. The database can be found at http://xmap.picr.man.ac.uk.
Expression and processing of bacterial beta-lactamase in the yeast Saccharomyces cerevisiae. (1981)

The mode of expression in Saccharomyces cerevisiae of the bacterial antibiotic resistance gene coding for beta-lactamase (EC 3.5.2.6) is described. Yeast transformants, containing hybrid plasmid pMP78-1 consisting of pBR325 in a 2-micrometers DNA vector, synthesize an active beta-lactamase protein. The enzyme was purified about 100-fold over crude extracts. With regard to activity, molecular weight, and binding to specific antibodies the yeast beta-lactamase was indistinguishable from the purified enzyme from Escherichia coli. Because the bacterial enzyme is synthesized as a preprotein with subsequent maturation, the results suggest that S. cerevisiae is able to convert the preprotein to the mature beta-lactamase. This was confirmed by in vitro experiments showing that the bacterial preprotein can be processed by crude extracts of S. cerevisiae.
Antibiotic Activity and Characterization of BB-3497, a Novel Peptide Deformylase Inhibitor (2001)

Peptide deformylase (PDF) is an essential bacterial metalloenzyme which deformylates the N-formylmethionine of newly synthesized polypeptides and as such represents a novel target for antibacterial chemotherapy. To identify novel PDF inhibitors, we screened a metalloenzyme inhibitor library and identified an N-formyl-hydroxylamine derivative, BB-3497, and a related natural hydroxamic acid antibiotic, actinonin, as potent and selective inhibitors of PDF. To elucidate the interactions that contribute to the binding affinity of these inhibitors, we determined the crystal structures of BB-3497 and actinonin bound to Escherichia coli PDF at resolutions of 2.1 and 1.75 A, respectively. In both complexes, the active-site metal atom was pentacoordinated by the side chains of Cys 90, His 132, and His 136 and the two oxygen atoms of N-formyl-hydroxylamine or hydroxamate. BB-3497 had activity against gram-positive bacteria, including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis, and activity against some gram-negative bacteria. Time-kill analysis showed that the mode of action of BB-3497 was primarily bacteriostatic. The mechanism of resistance was via mutations within the formyltransferase gene, as previously described for actinonin. While actinonin and its derivatives have not been used clinically because of their poor pharmacokinetic properties, BB-3497 was shown to be orally bioavailable. A single oral dose of BB-3497 given 1 h after intraperitoneal injection of S. aureus Smith or methicillin-resistant S. aureus protected mice from infection with median effective doses of 8 and 14 mg/kg of body weight, respectively. These data validate PDF as a novel target for the design of a new generation of antibacterial agents.
Proinflammatory and Anti-Inflammatory Cytokines Mediated by NF-κB Factor as Prognostic Markers in Mammary Tumors (2016)

Inflammation results in the production of cytokines, such as interleukin- (IL-) 4 and IL-10 with immunosuppressive properties or IL-6 and TNF-α with procarcinogenic activity. Furthermore, NF-κB is the major link between inflammation and tumorigenesis. This study verified the interaction between active inflammatory cytokines in the tumor microenvironment and serum of female dogs with mammary tumors and their correlation with the clinicopathological characteristics and overall survival. Measurement of gene expression was performed by qPCR and protein levels by ELISA/Luminex. High gene and protein expression levels of NF-κB, IL-6, and TNF-α were found in association with characteristics that reflect worse prognosis and a negative correlation between TNF-α protein expression and survival time was observed (p < 0.05). In contrast, high gene and protein expression levels of IL-4 and IL-10 were associated with characteristics of better prognosis and an increased level of IL-4 and a longer survival time of animals were obtained (p < 0.05). In addition, there was a positive correlation between TNF-α and IL-6 expression in association with NF-κB. The results show a significant correlation of these cytokines with tumor development, associated with NF-κB expression and cytokines promodulation, showing that these biological factors could be used as predictive and prognostic markers in breast cancer.
Vitamin A and reproduction in rats (1964)

Abstract Retinoic acid (vitamin A acid), the carboxylic acid corresponding to the primary alcohol retinol (vitamin A), has previously been thought to fulfil all the functions of vitamin A except in vision, since rats fed a diet deficient in retinol but supplemented with retinoic acid grow well, outwardly appearing healthy, yet become blind. This paper reports that female rats on such a diet had normal oestrous cycles and became pregnant when mated, but always resorbed the foetuses and no litters were born. The first abnormalities detected were necrosis and slight polymorph infiltration around the periphery of the placental disk about the sixteenth day of pregnancy. Supplementation with retinol as late as the tenth day resulted in the birth of a healthy litter. Retinoic acid therefore maintained the early but not the later stages of gestation. When very small amounts of retinol were given during pregnancy, dead or weak young were born; on higher supplements of the vitamin, litters were weaned successfully. By this means young rats were produced with negligible stores of retinol. Male rats fed retinoic acid but not retinol had small and often oedematous testes. The germinal epithelium sloughed off and in some tubules the lumen was obliterated, but in others the lumen remained, and in these some spermatocytes and spermatogonia were held tenaciously. The seminal vesicles were smaller than in controls given retinol. In rats born with negligible stores of retinol—see above—and maintained on retinoic acid, the testes remained infantile; spermatids were never formed. Feeding retinol restored spermatogenesis in degenerate testes and promoted the normal development of testes that had remained infantile; it also ensured the growth of the seminal vesicles. Retinoic acid did not therefore serve in reproduction, although it replaced the true vitamin in maintaining life, growth and general health. Besides the latter so-called systemic function, vitamin A must have a discrete and specific role in reproduction, viz. that performed by retinol but not by retinoic acid. From among the many previously reported features of disordered reproduction in vitamin A-deficient animals, it was possible to distinguish which had arisen from a failure of this specifically ‘reproductive’ role and which from a ‘systemic’ deficiency. The inactivity of retinoic acid in reproduction demonstrates that in rats vitamin A has not two, as previously thought, but three dissociable modes of action: (1) systemic; (2) in vision; and (3) in reproduction.
Disease-associated Bias in T Helper Type 1 (Th1)/Th2 CD4+ T Cell Responses Against MAGE-6 in HLA-DRB10401+ Patients With Renal Cell Carcinoma or Melanoma (2002)

T helper type 1 (Th1)-type CD4+ antitumor T cell help appears critical to the induction and maintenance of antitumor cytotoxic T lymphocyte (CTL) responses in vivo. In contrast, Th2- or Th3/Tr-type CD4+ T cell responses may subvert Th1-type cell-mediated immunity, providing a microenvironment conducive to disease progression. We have recently identified helper T cell epitopes derived from the MAGE-6 gene product; a tumor-associated antigen expressed by most melanomas and renal cell carcinomas. In this study, we have assessed whether peripheral blood CD4+ T cells from human histocompatibility leukocyte antigens (HLA)-DRβ1*0401+ patients are Th1- or Th2-biased to MAGE-6 epitopes using interferon (IFN)-γ and interleukin (IL)-5 enzyme-linked immunospot assays, respectively. Strikingly, the vast majority of patients with active disease were highly-skewed toward Th2-type responses against MAGE-6–derived epitopes, regardless of their stage (stage I versus IV) of disease, but retained Th1-type responses against Epstein-Barr virus– or influenza-derived epitopes. In marked contrast, normal donors and cancer patients with no current evidence of disease tended to exhibit either mixed Th1/Th2 or strongly Th1-polarized responses to MAGE-6 peptides, respectively. CD4+ T cell secretion of IL-10 and transforming growth factor (TGF)-β1 against MAGE-6 peptides was not observed, suggesting that specific Th3/Tr-type CD4+ subsets were not common events in these patients. Our data suggest that immunotherapeutic approaches will likely have to overcome or complement systemic Th2-dominated, tumor-reactive CD4+ T cell responses to provide optimal clinical benefit.
Drug effects on the neovascularization response to silver nitrate cauterization of the rat cornea (1985)

Neovascular growth into the cornea induced by silver nitrate cauterization is the basis of this experimental model developed to test potential anti-inflammatory drugs for ocular use. Cauterization of the rat cornea with a silver nitrate applicator stick provides the stimulus for neovascularization, which is scored by a "blinded" investigator. Burn stimulus intensity is also scored to substantiate a consistent stimulus among the groups. Compounds showing activity in this model include topical dexamethasone, prednisolone, ticabesone propionate, ketorolac, and phenidone. This model is presented as a practical method for testing anti-inflammatory drugs in the eye.
Compiling to a VLIW fragment pipeline (2001)

The latest generation of graphics hardware supports fully programmable vertex and pixel/fragment operations, but programming this hardware at a low level is difficult and time consuming. To address this problem, we have developed a complete real-time procedural shading system that compiles a high-level shading language to programmable vertex and fragment hardware, as described in a separate publication. In this paper, we describe in detail the algorithms used by this system to generate and optimize fragment code for NVIDIA's register combiner architecture and show that our compiler generates efficient code. The register combiner architecture has some similarities to VLIW CPU architectures, so we compare our compilation algorithms to those described in the literature for VLIW CPU architectures. We also discuss some of the lessons we learned from building and using this compiler that may be useful to the designers of future programmable graphics hardware.
Neutralization sensitivity of human immunodeficiency virus type 1 is determined in part by the cell in which the virus is propagated (1994)

Neutralizing antibody responses to human immunodeficiency virus type 1 (HIV-1) vary widely and have not been reproducibly associated with prognosis or disease progression. We have found that both low-passage clinical isolates and laboratory-adapted strains of HIV-1 have different sensitivities to neutralization by the same antiserum, depending on the host cell in which the viral stock is prepared. One such isolate (VL069) grown in H9 cells was neutralized by 20 human sera at a geometric mean titer of 1:2,047; this same isolate prepared in peripheral blood mononuclear cell (PBMC) culture was neutralized at a mean titer of < 1:10 by the same sera. Adsorption and mixing experiments indicated that neither antibody to H9 cell components nor blocking by excess viral antigen was responsible for the differences observed. This host cell effect is rapidly reversible upon passage of the virus from PBMCs to H9 cells and back into PBMCs. In contrast, the neutralization characteristics remained remarkably stable over extended culture in PBMCs. Two laboratory strains and five clinical isolates were evaluated in expanded studies of this phenomenon. While the neutralization characteristics of most of the strains studied were affected by the host cell in which the strain was propagated, two of the strains (one clinical isolate and one laboratory strain) appeared antigenically unaffected by their cell of origin. Host cell effect was also evident in neutralization by monoclonal antibodies directed against the CD4-binding region and the V2, V3, and gp41 regions. Possible mechanisms for this host cell effect include (i) mutation during passaging; (ii) selection in different host cells of different subpopulations of the (uncloned) viral stock; and (iii) cell-specific posttranslational modifications. To explore these possibilities, the V3 through V5 region of gp120 was sequenced in preparations made by passing VL069 into H9 cells and into PBMCs; HIVMN grown in CEM-SS cells and in PBMCs was also sequenced. In both cases, a few amino acid changes outside the V3 region were found. Studies are currently under way to assess the significance of these changes.