gebhart/patrepeval huggingface dataset:
Upregulation of p21Cip1 in activated glial cells (2008)

The cdk inhibitor p21(Cip1), also named p21(Cip1/Waf1), is intimately involved in coupling growth arrest to cellular differentiation in several cell types. p21(Cip1) is a multifunctional protein that might regulate cell-cycle progression at different levels. In a recent study, we found no differences in the rate of proliferation between glial cells from wild-type and p21(Cip1-/-) mice. In the present study, we examined differences in glial activation between glial cells from wild-type and p21(Cip1-/-) mice, using mixed glial cultures, microglia-enriched cultures, and astrocyte-enriched cultures. We compared the effect of lipopolysaccharide and two forms (oligomeric and fibrillar) of the 1-42 beta-amyloid peptide on glial activation. We observed an attenuation of nuclear translocation of the nuclear factor kappa-B in p21(Cip1-/-) glial cells, when compared with glial cells from wild-type mice. In contrast, tumor necrosis factor-alpha release was enhanced in p21(Cip1-/-)microglial cells. In addition glial activation induced by lipopolysaccharide and the fibrillar form of the 1-42 beta-amyloid peptide upregulated p21(Cip1). Our results support a role for p21(Cip1) in the activation of glial cells, particularly in microglia.
Effect of experimental zinc deficiency and repletion on some immunological variables in guinea-pigs (1988)

1. Cellular and humoral immune responses were studied in guinea-pigs fed on zinc-deficient (ZnD), Zn-adequate (control) and Zn-replete diets containing 1.25, 50 and 100 mg Zn/kg diet respectively. 2. It was found that the ZnD guinea-pigs had significantly decreased ability to elicit delayed-type hypersensitivity (DTH) response against sheep erythrocytes as compared with controls on the 9th day of immunization. This was further substantiated by histological examination of DTH-positive skin sections. 3. A significant reduction in direct splenic plaque-forming-cell response and haemagglutinating-antibody titre was also observed in ZnD guinea-pigs. 4. Serum electrophoretic studies revealed a highly disordered protein profile with a significantly depressed value for gamma-globulin. 5. Zn repletion of the previously ZnD group resulted in marked, though incomplete, restoration of immunological responses.
A Minimal Model for the Study of Polychronous Groups (2008)

A minimal model of polychronous groups in neural networks is presented. The model is computationally efficient and allows the study of polychronous groups independent of specific neuron models. Computational experiments were performed with the model in one- and two-dimensional neural architectures to determine the dependence of the number of polychronous groups on various connectivity options. The possibility of using polychronous groups as computational elements is also discussed.
Chapter 7 Use of Recombinant Vaccinia Virus Vectors for Cell Biology (1994)

This chapter describes the use of several of the recombinant vaccinia expression systems, focuses on the systems that are most useful for cell biologists, and discusses their advantages and limitations. Vaccinia-mediated expression can be used for assessing cellular localization, posttranslational modifications, oligomerization, and transport and turnover rates. The system provides a rapid method for screening mutant proteins for expression and targeting. It is an excellent way of quickly deciding which mutant proteins might be worth further studying using stable expression systems. Expression of foreign genes using Vaccinia virus is based on recombinant viruses constructed by insertion of complementary DNA (cDNA) into the nonessential thymidine kinase (TK) gene. Both direct and indirect methods of expression are possible. The foreign gene can be inserted into the vaccinia genome by homologous recombination using a plasmid with flanking regions of vaccinia DNA. The recombinant virus is selected, expanded, and used to infect cells, which then express high levels of the foreign protein. Recombinant vaccinia viruses are generated by subcloning the foreign gene into a plasmid transfer vector so it is flanked by DNA from the vaccinia (TK) gene, which is nonessential for growth of the virus in tissue culture. This plasmid is then transfected into vaccinia-infected cells. Homologous recombination of the plasmid and the vaccinia genome generates a recombinant virus with an inactive TK gene.
Influence of Sp1/Sp3 Expression on Corneal Epithelial Cells Proliferation and Differentiation Properties in Reconstructed Tissues (2003)

Expression of Sp1/Sp3 may represent a good predictor for selecting HCECs that are most likely to proliferate, stratify, and differentiate properly when used for the production of reconstructed corneal substitutes.
CD33 target validation and sustained depletion of AML blasts in long-term cultures by the bispecific T-cell–engaging antibody AMG 330 (2013)

Antibody-based immunotherapy represents a promising strategy to target and eliminate chemoresistant leukemic cells. Here, we evaluated the CD33/CD3-bispecific T cell engaging (BiTE) antibody (AMG 330) for its suitability as a therapeutic agent in acute myeloid leukemia (AML). We first assessed CD33 expression levels by flow cytometry and found expression in >99% of patient samples (n = 621). CD33 was highest expressed in AMLs with NPM1 mutations (P < .001) and lower in AMLs with complex karyotypes and t(8;21) translocations (P < .001). Furthermore, leukemic stem cells within the CD34(+)/CD38(-) compartment displayed CD33 at higher levels than healthy donor stem cells (P = .047). In MS-5 feeder cell-based long-term cultures that supported the growth of primary AML blasts for up to 36 days, AMG 330 efficiently recruited and expanded residual CD3(+)/CD45RA(-)/CCR7(+) memory T cells within the patient sample. Even at low effector to target ratios, the recruited T cells lysed autologous blasts completely in the majority of samples and substantially in the remaining samples in a time-dependent manner. This study provides the first correlation of CD33 expression levels with AML genotype in a comprehensive analysis of adult patients. Targeting CD33 ex vivo using AMG 330 in primary AML samples led to T cell recruitment and expansion and remarkable antibody-mediated cytotoxicity, suggesting efficient therapeutic potential in vivo.
Characterization of the haemorrhagic enteritis virus genome and the sequence of the putative penton base and core protein genes (1996)

Haemorrhagic enteritis virus (HEV) is a member of a genetically ill-defined group within the genus Aviadenovirus which causes significant clinical disease in gallinaceous fowl. Using DNA obtained from a low virulence isolate of HEV passed in turkeys, we developed a genomic restriction map and estimated an apparent genomic length of 25.5 kb. No evidence for extensive DNA hybridization was found between the HEV genome and either the hexon or penton base genes of human adenovirus 2 (HAdV-2) and fowl adenovirus 10 (FAdV-10). The HEV penton base gene was identified by PCR using primers based on conserved adenoviral DNA sequences. The penton base gene was expressed in Escherichia coli as a fusion protein and detected by anti-HEV serum in both colony and denaturing gel immunoblots. DNA sequencing revealed a putative penton base ORF with a predicted amino acid sequence showing approximately 39.0%, 53.0% and 44.2% similarity with the penton base of HAdV-2, human adenovirus 40 (HAdV-40) and FAdV-10, respectively. The penton base gene was located at 43.3-48.6 m.u. on the HEV genome and had a remarkably low G+C content (33.8%). DNA sequencing also revealed ORFs for putative core proteins resembling pVII, p-mu and a partial ORF similar to pVI (hexon-associated protein) of HAdV-2 and HAdV-40. The results support the claim that HEV represents a distinct group of viruses within the genus Aviadenovirus.
Lasing wavelength of an asymmetric double quantum well laser diode (1987)

It is demonstrated that in an asymmetric coupled GaAs double quantum well structure, we are able to choose a lasing wavelength out of at least four quantum state transitions by cavity loss control. The assignments of the observed lasing transitions are determined by photoluminescence measurement for the laser wafer, as well as by calculations using an isolated potential well model. We propose that one can realize wide-range wavelength tuning and multistep wavelength switching functions by modifying the two-dimensional density of states.
Glioblastoma cells negative for the anti-CD133 antibody AC133 express a truncated variant of the CD133 protein (2010)

The transmembrane glycoprotein CD133 is a marker commonly used for isolation and analysis of putative cancer stem-like cells. However, analysis of CD133 expression is potentially confounded by the fact that two of the commonly used anti-CD133 antibodies, AC133 and 293C, only recognize CD133 that has undergone glycosylation. Therefore, our aim was to thoroughly examine antibody recognition and mRNA expression of CD133 in glioblastoma multiforme. Glioblastoma cell lines and primary cultures obtained from resected tumor tissue were analyzed by real-time PCR, Western blot analysis, and flow cytometry for CD133, and immunofluorescence was used to determine cellular localization. The AC133 and 293C antibodies did not detect any CD133 on the surface of the glioblastoma cells despite the fact that a protein was detected using C24B9, an anti-CD133 antibody that recognizes an unglycosylated epitope. This CD133 variant was truncated ( approximately 16 kDa) and, unlike typical expression of full-length CD133 protein, was found throughout the cytoplasm instead of localized to the plasma membrane. Levels of mRNA and protein for the variant increased with stress, indicating potential for it to be a functional molecule. Because AC133 and 293C antibodies do not detect all CD133 variants in glioblastoma cells, alternate detection methods need to be utilized for complete analysis of CD133 expression and for accurately determining the relationship between CD133 and cancer stem-like cells.
Diagnosis of gastric cancers with fluorescein‐labeled monoclonal antibodies to carcinoembryonic antigen (1989)

Forty gastric adenocarcinomas in 30 resected stomachs were examined by an endoscopic immunofluorescent technique using fluorescein isothiocyanate (FITC)-labeled antibodies to carcinoembryonic antigen (CEA). Fluorescence images of the tumors were obtained with a newly developed endoscopic television system for detecting faint fluorescence. Computer-assisted processing was used to enhance the detection and localization of the tumors visualized by the immunofluorescent technique. Twenty seven (90%) of 30 tumors showed positive fluorescence after treatment with FITC-labeled antibodies for 60 minutes, whereas only two (40%) of five cancers could be detected by the immunofluorescent technique after treatment with antibodies for less than 60 minutes. There was no significant relationship between positive fluorescence and the gross and histological types or the stages of the tumors. In contrast, no positive fluorescence could be demonstrated in cases of benign gastric lesions or after pretreatment with FITC-labeled alpha-fetoprotein. This study therefore suggests that the immunofluorescent technique using FITC-labeled anti-CEA antibodies can be useful in detecting the early stages of gastric cancer.
Novel Gain-of-function Mutations of Platelet Glycoprotein Ibα by Valine Mutagenesis in the Cys209–Cys248 Disulfide Loop (2000)

Platelet-type von Willebrand disease is a bleeding disorder resulting from gain-of-function mutations of glycoprotein (GP) Ibalpha that increase its affinity for von Willebrand factor (vWf). The two known naturally occurring mutations, G233V and M239V, both enrich the valine content of an already valine-rich region within the Cys(209)-Cys(248) disulfide loop. We tested the effect of converting other non-valine residues in this region to valine. Of 10 mutants expressed in CHO cells as components of GP Ib-IX complexes, four displayed a gain-of-function phenotype (G233V, D235V, K237V, and M239V) based on (125)I-vWf binding and adhesion to immobilized vWf. The remainder displayed loss-of-function phenotypes. The gain-of-function mutants bound vWf spontaneously and had a heightened response to low concentrations of ristocetin or botrocetin, whereas the loss-of-function mutants bound vWf more poorly than wild-type GP Ibalpha. No distinct gain- or loss-of-function conformations were identified with conformation-sensitive antibodies. Compared with cells expressing wild-type GP Ibalpha, cells expressing the gain-of-function mutants rolled significantly more slowly over immobilized vWf under flow than wild-type cells and were able to adhere to vWf coated at lower densities. In aggregate, these data indicate that the region of GP Ibalpha bounded by Asn(226) and Ala(244) regulates the affinity for vWf.
Site-directed mutagenesis of a conserved domain in vaccinia virus thymidine kinase. Evidence for a potential role in magnesium binding. (1992)

Alignment of prokaryotic and vertebrate type II thymidine kinases (TK) (EC 2.7.1.21), such as that encoded by vaccinia virus (VVTK), reveals three conserved regions: designated domains I, III, and VII. Domains I and III of VVTK contain residues which closely resemble segments A (ATP) and B (Mg2+), respectively, of a Mg.ATP binding descriptor proposed previously (Walker, J.E., Saraster, M., Runswick, M-J., and Gay, N.J. (1982) EMBO J. 1, 945-951). In support of this hypothesis, domain I of the VVTK enzyme has previously been identified as the ATP binding site (Black and Hruby, 1990b). With regard to Mg2+ binding, several features of the VVTK domain III suggest that it may be responsible for this activity: 1) sequence similarity to a magnesium binding motif proposed previously (Walker, J.E., Saraster, M., Runswick, M-J., and Gay, N.J. (1982) EMBO J. 1, 945-951); 2) alignment of the predicted secondary structure of type II TK enzymes with other magnesium-binding enzymes such as adenylate kinase, EF-TU, and p21 reveals a conserved aspartic acid residue preceded by several hydrophobic residues with domain III; and 3) the conserved VVTK domain III aspartic acid residue (D82) aligns with D93 residue of adenylate kinase which is has been shown by NMR to participate in Mg2+ binding (Yan, H., and Tsai, M.-D., Biochemistry, in press). To directly examine the potential contribution of the conserved domain III D82 residue of VVTK in magnesium binding, site-directed mutagenesis was performed on positions D82 and G84 to generate four mutants, N82, L82, I82, and V84. Each mutant was analyzed for enzyme activity, divalent cation requirements, tetramer formation, and ATP binding ability. The results obtained were consistent with D82 playing a direct role in Mg2+ binding and suggest that while the aspartic acid does not appear to participate directly with ATP binding it may instead act to facilitate ATP hydrolysis by binding Mg2+ which aids to correctly position ATP for nucleophilic attack.
Detection of a broad range of human adenoviruses in respiratory tract samples using a sensitive multiplex real‐time PCR assay (2008)

Human adenoviruses (hAdVs) are associated with acute respiratory tract infections in pediatric populations and have been identified as a cause of outbreaks in institutional settings. Rapid diagnosis of hAdV infection is critical for appropriate and timely management. This study reports the design and validation of a sensitive and specific multiplex real-time PCR for the detection of a broad range of hAdV serotypes in respiratory samples. The assay targets the conserved region of the hAdV hexon gene and utilizes hydrolysis probes for the detection of amplified products. The assay was evaluated using retrospectively (n = 864) and prospectively (n = 11,451) collected samples from November 2005 to July 2006. Seasonality studies and analysis of outbreaks was conducted over a 2-year period from January 2005 to December 2006 (n = 33,067 samples). The assay gave a hAdV positive rate of 7.1% (n = 811) for specimens tested prospectively and was able to detect a broad range of hAdV serotypes with good sensitivity and specificity. A high rate of co-infection was noted (21.7%). Adenovirus infections were more prevalent in the young with a median age of 24 months for positive patients. Sequence analysis of hAdV positives showed that serotype 7 was the most prevalent followed by serotypes 2 and 3. Association of hAdVs with respiratory outbreaks was low at 2.3% (6 of 266 outbreaks tested) and no seasonal variation was observed for hAdV infections during the 2-year study period. This assay can improve the detection of hAdVs in respiratory samples and can be used to provide valuable epidemiological information.
Gli3-mediated hedgehog inhibition in human pluripotent stem cells initiates and augments developmental programming of adult hematopoiesis (2013)

Programs that control early lineage fate decisions and transitions from embryonic to adult human cell types during development are poorly understood. Using human pluripotent stem cells (hPSCs), in the present study, we reveal reduction of Hedgehog (Hh) signaling correlates to developmental progression of hematopoiesis throughout human ontogeny. Both chemical- and gene-targeting–mediated inactivation of Hh signaling augmented hematopoietic fate and initiated transitions from embryonic to adult hematopoiesis, as measured by globin regulation in hPSCs. Inhibition of the Hh pathway resulted in truncation of Gli3 to its repressor, Gli3R, and was shown to be necessary and sufficient for initiating this transition. Our results reveal an unprecedented role for Hh signaling in the regulation of adult hematopoietic specification, thereby demonstrating the ability to modulate the default embryonic programs of hPSCs.
Pathogenic Role of Macrophages in Intradermal Infection of Methicillin-Resistant Staphylococcus aureus in Thermally Injured Mice (2010)

Intradermal infection of methicillin-resistant Staphylococcus aureus (MRSA) in burned mice was pathogenically analyzed. An abscess was formed in normal mice intradermally infected with 10(8) CFU/mouse of MRSA, and all of these mice survived after the infection; however, abscess formation was not demonstrated to occur in burned mice similarly exposed to the pathogen, and all of these mice died within 5 days of infection. In burned mice, MRSA infected at the burn site intradermal tissues spread quickly throughout the whole body, while in normal mice, the pathogen remained localized at the infection site. Macrophages (Mφ) isolated from the infection site tissues of normal mice produced interleukin-12 (IL-12) but not IL-10 and were characterized as M1Mφ. These M1Mφ were not isolated from the infection site tissues of burned mice. When normal-mouse infection site tissue Mφ were adoptively transferred to burned mice at the MRSA infection site, an abscess formed, and the infection did not develop into sepsis. In contrast, an abscess did not form and sepsis developed in normal mice that were inoculated with burned-mouse infection site tissue Mφ. These Mφ produced IL-10 but not IL-12 and were characterized as M2Mφ. These results indicate that abscess formation is a major mechanism of host resistance against intradermal MRSA infection. M1Mφ in the tissues surrounding the infection site play a pivotal role in abscess formation; however, the abscess is not formed in burned mice where M2Mφ predominate. M2Mφ have been described as inhibitor cells for Mφ conversion from resident Mφ to M1Mφ.
Medical Treatment of Peripheral Arterial Disease and Claudication (2001)

Peripheral arterial disease, which is caused by atherosclerotic occlusion of the arteries to the legs, is an important manifestation of systemic atherosclerosis. The age-adjusted prevalence of peripheral arterial disease is approximately 12 percent, and the disorder affects men and women equally (Table 1).7,8 Patients with peripheral arterial disease, even in the absence of a history of myocardial infarction or ischemic stroke, have approximately the same relative risk of death from cardiovascular causes as do patients with a history of coronary or cerebrovascular disease (Table 2).12,15 In patients with peripheral arterial disease, the rate of death from all causes . . .
Biochemical and immunochemical study of lysyl oxidase in experimental hepatic fibrosis in the rat. (1978)

Lysyl oxidase catalyzes the crosslinking of collagen and elastin. Lysyl oxidase activity was measured and localized in rat liver during the evolution of hepatic fibrosis induced by CCl4. Enzyme activity measured with DL-[6-3H]-lysine-labeled collagen substrates in liver and plasma increased sharply after approximately 3 wk of injection, reached a maximum at 6 wk, and then decreased. The increase in activity correlated histologically with early connective tissue septa formation, and the magnitude of increase was significantly greater than that found for the intracellular collagen biosynthetic enzymes protocollagen prolyl hydroxylase and lysyl hydroxylase. Indirect immunofluorescence studies showed that lysyl oxidase was present in association with collagen in the extracellular space. However, it was not possible to correlate the distribution pattern with a particular liver cell type. These observations suggest that serial measurements of lysyl oxidase activity in liver or plasma may be useful for correlating changes in connective tissue formation with histologic connective tissue deposition.
Induction of Adrenal Suppression by Megestrol Acetate in Patients with AIDS (1995)

Prolonged administration of megestrol acetate can induce clinically significant secondary adrenal suppression, and abrupt withdrawal of megestrol acetate after prolonged administration can cause adrenal insufficiency.
Scanner identification using sensor pattern noise (2007)

Digital images can be captured or generated by a variety of sources including digital cameras and scanners. In many cases it is important to be able to determine the source of a digital image. This paper presents methods for authenticating images that have been acquired using flatbed desktop scanners. The method is based on using the pattern noise of the imaging sensor as a fingerprint for the scanner, similar to methods that have been reported for identifying digital cameras. To identify the source scanner of an image a reference pattern is estimated for each scanner and is treated as a unique fingerprint of the scanner. An anisotropic local polynomial estimator is used for obtaining the reference patterns. To further improve the classification accuracy a feature vector based approach using an SVM classifier is used to classify the pattern noise. This feature vector based approach is shown to achieve a high classification accuracy.