gebhart/patrepeval huggingface dataset:
The ‘petite‐negative’ yeast Kluyveromyces lactis has a single gene expressing pyruvate decarboxylase activity (1996)

We cloned and sequenced the pyruvate decarboxylase (PDC; EC 4.1.1.1) structural gene KIPDCA in the yeast Kluyveromyces lactis and found it to be allelic to the previously isolated rag6 mutation. The putative amino acid sequence of the KIPdcAp appeared to be highly homologous to those of the yeast Pdc proteins identified so far. The disruption of KIPDCA indicated that it is the only PDC structural gene in K. lactis, as evidenced by the lack of PDC activity and ethanol production in the pdcA delta strains and by the absence of growth on glucose in the presence of respiratory inhibitors. It was observed that expression of the KIPDCA gene is induced by glucose at the transcriptional level. Transcription of the gene was reduced in the rag1, rag2, rag5 and rag8 mutants, which are defective for the low-affinity glucose permease, phosphoglucose isomerase, hexokinase, and a positive regulator of RAG1 expression, respectively.
Killing of Normal Melanocytes, Combined with Heat Shock Protein 70 and CD40L Expression, Cures Large Established Melanomas (2006)

Previously, we showed that nine intradermal injections of a plasmid in which the HSVtk suicide gene is expressed from a melanocyte-specific promoter (Tyr-HSVtk), combined with a plasmid expressing heat shock protein 70 (CMV-hsp70), along with systemic ganciclovir, kills normal melanocytes and raises a CD8+ T cell response that is potent enough to eradicate small, 3-day established B16 tumors. We show in this study that, in that regimen, hsp70 acts as a potent immune adjuvant through TLR-4 signaling and local induction of TNF-alpha. hsp70 is required for migration of APC resident in the skin to the draining lymph nodes to present Ags, derived from the killing of normal melanocytes, to naive T cells. The addition of a plasmid expressing CD40L increased therapeutic efficacy, such that only six plasmid injections were now required to cure large, 9-day established tumors. Generation of potent immunological memory against rechallenge in cured mice accompanied these therapeutic gains, as did induction of aggressive autoimmune symptoms. Expression of CD40L, along with hsp70, increased both the frequency and activity of T cells activated against melanocyte-derived Ags. In this way, addition of CD40L to the hsp70-induced inflammatory killing of melanocytes can be used to cure large established tumors and to confer immunological memory against tumor cells, although a concomitant increase in autoimmune sequelae also is produced.
Deriving Quantitative Crystallographic Information from the Wavelength-Resolved Neutron Transmission Analysis Performed in Imaging Mode (2017)

Current status of Bragg-edge/dip neutron transmission analysis/imaging methods is presented. The method can visualize real-space distributions of bulk crystallographic information in a crystalline material over a large area (~10 cm) with high spatial resolution (~100 μm). Furthermore, by using suitable spectrum analysis methods for wavelength-dependent neutron transmission data, quantitative visualization of the crystallographic information can be achieved. For example, crystallographic texture imaging, crystallite size imaging and crystalline phase imaging with texture/extinction corrections are carried out by the Rietveld-type (wide wavelength bandwidth) profile fitting analysis code, RITS (Rietveld Imaging of Transmission Spectra). By using the single Bragg-edge analysis mode of RITS, evaluations of crystal lattice plane spacing (d-spacing) relating to macro-strain and d-spacing distribution’s FWHM (full width at half maximum) relating to micro-strain can be achieved. Macro-strain tomography is performed by a new conceptual CT (computed tomography) image reconstruction algorithm, the tensor CT method. Crystalline grains and their orientations are visualized by a fast determination method of grain orientation for Bragg-dip neutron transmission spectrum. In this paper, these imaging examples with the spectrum analysis methods and the reliabilities evaluated by optical/electron microscope and X-ray/neutron diffraction, are presented. In addition, the status at compact accelerator driven pulsed neutron sources is also presented.
IL-6 polymorphism associated with fatal outcome in patients with severe traumatic brain injury (2011)

The findings indicate that genetic variation regarding inflammatory response has significant impact on the short-term outcome for patients after acute severe TBI.
EspE, a novel secreted protein of attaching and effacing bacteria, is directly translocated into infected host cells, where it appears as a tyrosine‐phosphorylated 90 kDa protein (1998)

Shiga toxin-producing Escherichia coli (STEC), enteropathogenic E. coli (EPEC) and some strains of Hafnia alvei are capable of inducing attaching and effacing (A/E) lesions, characterized by tight apposition of the bacteria to the eukaryotic membrane and formation of actin-based pedestals. In this study, we report on the identification of EspE, a novel secreted 80 kDa protein of A/E bacteria. During infection, EspE is delivered into the cytoplasm of the infected host cell, where it is detected as a higher-molecular-weight form of 90 kDa. We present evidence that translocated EspE becomes tyrosine phosphorylated and that this modified form of EspE may be identical to Hp90, the putative receptor of EPEC intimin. Bacteria of the classic enterohaemorrhagic E. coli (EHEC) serotype O157:H7 fail to induce a tyrosine phosphorylation of EspE and differ in this respect from other A/E bacteria. Translocated EspE, whether tyrosine phosphorylated or not, becomes incorporated into the bacteria-induced cytoskeletal structures, where it normally colocalizes with filamentous actin. EPEC are also able to induce 'pseudopods', elongated pedestals that have recently been implicated in a novel kind of actin-based motility. EspE is enriched at the tip of these structures, suggesting its involvement in the process of actin dynamics, which is triggered during the attaching and effacing process.
Microbial oxidation of aromatics in enantiocontrolled synthesis. Part 1. Expedient and general asymmetric synthesis of inositols and carbohydrates via an unusual oxidation of a polarized diene with potassium permanganate (1994)

This paper reports on the details of a general design of carbohydrates and cyclitols from biocatalytically derived synthons. Homochiral 1-halogenocyclohexa-4,6-diene-2,3-diols 1a and 1b have been generated from chloro- and bromo-benzene, respectively, by means of bacterial dioxygenase of Pseudomonas putida 39D. These chiral synthons have been manipulated to cyclitols and carbohydrates by further stereoselective functionalizations. The preparation of D-chiro-inositol, neo-inositol, muco-inositol, and allo-inositol exemplifies their use in enantiocontrolled synthesis. A novel oxidation of polarized dienes with KMnO4 resulted in the synthesis of α-halogeno epoxy diols, which proved unexpectedly stable. A mechanism is proposed for this transformation and placed in context with the only four reported examples of this reaction in the literature. In addition to the application of this new chemistry to the synthesis of cyclitols, chloro epoxy diol 21a has been transformed into a series of cyclitol synthons by reductive or hydrolytic operations. Reaction of 21a with ammonia led to the preparation of highly oxygenated pyrazines, whose structures were proven by X-ray crystallography. The use of 21a in the preparation of D-chiro-3-inosose, a hitherto unreported cyclitol derivative, is also reported. In addition, chloro epoxy diol 21a was transformed into D-erythruronolactone, completing the synthesis of this important chiral pool reagent in two operations from chlorobenzene. Oxidative cleavage of tetrol 20 yielded D-mannosolactone identical with an authentic sample.
Reexpression of neu-encoded oncoprotein counteracts the tumor-suppressing but not the metastasis-suppressing function of E1A. (1993)

By transfecting the adenovirus 5 E1A gene into neu-transformed NIH3T3 cells, we previously showed that E1A can dramatically repress neu-encoded p185 expression and, concomitantly, suppress the features of transformation and metastasis of neu+E1A transfectants. From these results we concluded that suppression of transformation and metastasis by E1A in neu-transformed cells may be through repression of neu gene expression. However, E1A has recently been shown to also repress the transformation features of other human cancer cells that do not overexpress neu. This observation raised a possibility that repression of neu gene expression in our neu+E1A cells might not be the only mechanism for transformation and metastasis suppression. To study whether other molecular mechanisms might be involved in suppression of transformation and metastasis by E1A in our neu+E1A cells, we reexpressed p185 oncoprotein in the neu+E1A cells by transfecting them with a plasmid containing activated rat neu complementary DNA and we examined whether E1A can suppress transformation and metastasis when the neu-encoded p185 protein is reexpressed. All the features of transformed cells including cell morphology, DNA synthesis rate, colony formation in soft agar, and tumorigenicity in nu/nu mice were restored in the cell lines that reexpressed neu. In addition, the levels of neu reexpression corresponded to the degree of malignant transformation. However, the in vivo metastatic tumor formation by these p185 reexpressing cells was still significantly inhibited by E1A. When metastasis-associated properties were examined in the cell lines that reexpressed p185, we found that cell motility was recovered by reexpression of p185 to the degree corresponding to the p185 reexpression level, but secretion of membrane-degrading gelatinases and invasion through the basement membrane preparation Matrigel by these cells were still inhibited by E1A. The data demonstrated that reexpression of p185 in neu+E1A cells can counteract the tumor-suppressing function of E1A but not completely recover the neu-induced metastatic phenotype. We conclude from these results that (a) repression of neu oncogene expression was indeed the molecular mechanism by which E1A suppressed tumor formation in neu-transformed 3T3 cells, and (b) suppression of metastasis by E1A in neu-transformed 3T3 cells was via multiple molecular mechanisms in addition to repressing neu. Our model system clearly demonstrated that tumorigenicity and metastasis are related but separable phenomena.
A Graphical Similarity Measure for Time Series Models. (1985)

Abstract : The purpose of this document is to introduce a graphical device useful as a measure of similarity or as a goodness of fit criterion for hypothesized time series models. It is based on the actual oscillation observed in time series as depicted by axis-crossings and higher order crossings. Higher order crossings (HOC) are axis-crossings of differenced time series and are closely linked to the spectral content of the series. In fact under the Gaussian assumption, to which we shall adhere, HOC determine the finite dimensional distributions up to a scale parameter given that the mean is zero. The main advantage of HOC is that they are easily obtained from an observed series and that only very few of them are needed, as the dicriminatory power in HOC usually diminishes with their order. Higher order crossings in time series discrimination were discussed in Kedem and Slud (1981), (1982), where a certain goodness of fit criterion is suggested, Here however the emphasis is on a graphical device rather than a single test statistic. This graphical method may be shown useful in answering the question 'Does a given time series oscillate as a certain hypothesized model?' Some examples with real and simulated data demonstrate the use and potential of this method.
Isolation and localization of herpes simplex virus type 1 mRNA (1979)

Herpes simplex virus (HSV) DNA bound to cellulose has been used as a reagent to isolate viral mRNA for size analysis on denaturing agarose gels. Total viral polysomal polyadenylated RNA was isolated from cells late after infection when such RNA has sequences encoded by approximately 45% of the HSV DNA. This RNA has a size range of from 1.5 to greater than or equal to 8 kilobases, with certain sizes, such as 1.7 to 1.9 kilobases, being favored. We have used the restriction endonucleases HindIII and XbaI singly and together to generate various sized fragments covering the entire HSV-1 genome. These fragments have been bound to cellulose to allow isolation of HSV-1 mRNA annealing to different regions of the viral genome. Discrete sizes of viral mRNA are associated with certain regions of the genome, but the mRNA population hybridizing to even the smallest restriction fragments is complex. We used hybridization of size-fractionated RNA to Southern blots of restriction fragments of HSV-1 DNA generated by the BglII as well as HindIII and XbaI endonucleases to confirm the preparative hybridization data and to provide some overlap data for positioning transcripts. The data of blot and preparative hybridization agreed very well and were combined to construct a preliminary transcription map of HSV-1. Such a map revealed at least two areas of the long unique region of the HSV-1 genome which annealed to a large number of HSV-1 transcripts. Furthermore, discrete-sized mRNA species larger than 5 kilobases in length were found only in the middle of the long unique region. The implications of these data are discussed.
Extensive and selective mutation of a rearranged VH5 gene in human B cell chronic lymphocytic leukemia. (1992)

B cell chronic lymphocytic leukemia (CLL) is the malignant, monoclonal equivalent of a human CD5+ B cell. Previous studies have shown that the VH and VL genes rearranged and/or expressed in CLL have few and apparently random mutations. However, in this study, we have found that the rearranged VH251 gene, one of the three-membered VH5 family, has extensive and selective mutations in B-CLL cells. Somatic mutation at the nucleotide level is 6.03% in B-CLLs whereas the somatic mutation levels are much lower in CD5+ and CD5- cord B cells, adult peripheral blood B cells, and Epstein-Barr virus-transformed CD5+ B cell lines (0.45, 0.93, and 1.92%, respectively). Complementary determining region 1 (CDR1) mutation in CLLs is particularly prevalent, and interchanges in CDRs often lead to acquisition of charge. Analysis of somatic mutations and mutations to charged residues demonstrated that the mutations in CLLs are highly selected.
Vaccinia virus-specific human CD4+ cytotoxic T-lymphocyte clones (1992)

Vaccinia virus-specific cytotoxic T-lymphocyte (CTL) clones were established from a healthy donor, who had been immunized with vaccinia virus vaccine, by stimulation of peripheral blood lymphocytes with UV-inactivated vaccinia virus antigen. The phenotype of all of the clones established was CD3+ CD4+ CD8- Leu11-. We used a panel of allogenic vaccinia virus-infected B-lymphoblastoid cell lines and demonstrated that some of the clones recognized vaccinia virus epitopes presented by human leukocyte antigen (HLA) class II molecules. Monoclonal antibodies specific for either HLA-DP or HLA-DR determinant reduced the cytotoxicity of specific clones. The HLA-restricted cytotoxicity of the clones is vaccinia virus specific, because vaccinia virus-infected but not influenza virus-infected autologous target cells were lysed. Using vaccinia virus deletion mutants, we found that some of the CTL clones recognize an epitope(s) that lies within the HindIII KF regions of the vaccinia virus genome. These results indicate that heterogeneous CD4+ CTL clones specific for vaccinia virus are induced in response to infection and may be important in recovery from and protection against poxvirus infections.
Detection of epidermal growth factor receptor in the serum of gastric carcinoma patients (1997)

BACKGROUND Epidermal growth factor receptor (EGFR) is overexpressed in various malignancies including carcinoma of the breast, lung, esophagus, cervix, and stomach. In patients with gastric carcinoma, its overexpression may be associated with advanced stage and poor prognosis. METHODS The levels of EGFR extracellular domain were determined in serum from 40 gastric carcinoma patients using enzyme-linked immunosorbent assay. Serum EGFR levels were measured in 5 Stage I, 2 Stage II, 6 Stage III, and 27 Stage IV patients, and 29 healthy controls. RESULTS The mean serum level for EGFR in the gastric carcinoma patients was significantly elevated compared with that of healthy controls (681 ± 226 fmol/mL vs. 440 ± 46 fmol/mL; P < 0.0001). Thirty-one patients with gastric carcinoma (77.5%) showed elevated EGFR levels above a cutoff value of 532 fmol/mL (defined as 2 standard deviations above the mean of the controls). No significant association was noted between positivity of EGFR and gender, age, stage, and tumor differentiation. CONCLUSIONS The authors believe that serum EGFR could be useful as a tumor marker of gastric carcinoma for diagnosis, prognosis, follow-up after surgery, and monitoring patient response to chemotherapy. Cancer 1997; 79:1879-83. © 1997 American Cancer Society.
Molecular beam epitaxial growth of high quality HgTe and Hg1−xCdxTe onto GaAs(001) substrates (1984)

HgTe and Hg1−xCdxTe epilayers have been grown for the first time onto GaAs (001) substrates by molecular beam epitaxy (MBE). A thin MBE CdTe buffer has been first deposited. The (001) orientation of the substrate is conserved during the growth. Despite the important lattice mismatch in situ electron diffraction experiments showed that the films have a high crystal quality. Hall measurements carried out on these layers confirm their high quality because they exhibited high electron Hall mobilities. We have shown also, using a Hall mobility profiling etching technique, that the interfacial disorder zone in a HgCdTe layer deposited on a 0.4-μm CdTe buffer layer could be less than 1 μm. This first report of very good electrical performances for Hg1−xCdxTe layers grown onto GaAs substrates is highly promising for growth and device applications regarding this material and related superlattices.
Decreased Ethylene Biosynthesis, and Induction of Aerenchyma, by Nitrogen- or Phosphate-Starvation in Adventitious Roots of Zea mays L. (1989)

Plants of Zea mays L. cv TX5855 were grown in a complete, well oxygenated nutrient solution then subjected to nutrient starvation by omitting either nitrate and ammonium or phosphate from the solution. These treatments induced the formation of aerenchyma close to the apex of the adventitious roots that subsequently emerged from the base of the shoot, a response similar to that shown earlier to be induced by hypoxia. Compared with control plants supplied with all nutrients throughout, N- or P-starvation consistently depressed the rates of ethylene release by excised, 25 mm apical segments of adventitious roots. Some enzymes and substrates of the ethylene biosynthetic pathway were examined. The content of 1-amino cyclopropane-1-carboxylic acid (ACC) paralleled the differences in ethylene production rates, being depressed by N or P deficiency, while malonyl-ACC showed a similar trend. Activity of ACC synthase and of ethylene forming enzyme (g(-1) fresh weight) was also greater in control roots than in nutrient starved ones. These results indicate that much of the ethylene biosynthetic pathway is slowed under conditions of N- or P-starvation. Thus, by contrast to the effects of hypoxia, the induction of aerenchyma in roots of Zea mays by nutrient starvation is not related to an enhanced biosynthesis and/or accumulation of ethylene in the root tips.
Controlled Synthesis of Monodisperse Silver Nanocubes in Water (2004)

Monodisperse silver nanocubes with edge length of 55 +/- 5 nm were, for the first time, synthesized in water on the basis of HTAB-modified silver mirror reaction at 120 degrees C (HTAB, n-hexadecyltrimethylammonium bromide). The individual nanocube was crystallographically well defined with a single crystal bonded by six {200} facets. The nanocubes were soluble to form stable aqueous solutions and had a strong tendency to assemble into two-dimensional arrays with regular checked pattern on substrate.
Lyme Arthritis Synovial γδ T Cells Instruct Dendritic Cells via Fas Ligand (2005)

gammadelta T cells participate in the innate immune response to a variety of infectious microorganisms. They also link to the adaptive immune response through their induction of maturation of dendritic cells (DC) during the early phase of an immune response when the frequency of Ag-specific T cells is very low. We observe that in the presence of Borrelia burgdorferi, synovial Vdelta1 T cells from Lyme arthritis synovial fluid potently induce maturation of DC, including production of IL-12, and increased surface expression of CD40 and CD86. The activated DC are then able to stimulate the Vdelta1 T cells to up-regulate CD25. Both of these processes are initiated primarily by Fas stimulation rather than CD40 activation of DC via high expression of Fas ligand by the Vdelta1 T cells. DC are resistant to Fas-induced death due to expression of high levels of the Fas inhibitor c-FLIP. This effect serves to divert Fas-mediated signals from the caspase cascade to the ERK MAPK and NF-kappaB pathways. The findings affirm the importance of the interaction of certain T cell populations with DC during the early phases of the innate immune response. They also underscore the view that as levels of c-FLIP increase, Fas signaling can be diverted from induction of apoptosis to pathways leading to cell effector function.
Molecular cloning of the human cholecystokinin gene by use of a synthetic probe containing deoxyinosine. (1985)

A synthetic DNA based on the known amino acid sequence of the brain/gut peptide cholecystokinin (CCK) was synthesized. This DNA contained deoxyinosines at ambiguous codon positions and was used as a probe to isolate the CCK gene directly from a human genomic library. Nucleotide sequence analysis of the isolated gene revealed that human preprocholecystokinin consists of 115 amino acid residues, with 11 amino acids in common with the human gastrin precursor, another member of the gastrin-CCK family, and that the coding region is separated by a single, long intron. CCK appears to be encoded by a single-copy gene in the haploid human genome, as revealed by genomic Southern hybridization analysis, suggesting that the same gene is expressed both in gut and brain.
Cytotoxicity,radiosensitization, and chemosensitization of tumor cells by 2-deoxy-D-glucose In vitro (2009)

The glucose analog 2-deoxy-D-glucose (2-DG), an inhibitor of glucose transport and glycolytic ATP production, is the most widely investigated metabolic inhibitor for targeting glucose metabolism. Besides depleting energy in cells, 2-DG has also been found to alter N-linked glycosylation leading to unfolded protein responses and induce changes in gene expression and phosphorylation status of proteins involved in signaling, cell cycle control, DNA repair, calcium influx, and apoptosis. Inhibition of cell proliferation and induction of apoptosis have been observed as cytotoxic effects in a wide variety of tumor cells in vitro, while sensitization of tumor cells to ionizing radiation and certain chemotherapeutic drugs is associated with enhanced mitotic as well as apoptotic cell death induced by the primary therapeutic agent. Therefore, there has been a considerable amount of interest in developing 2-DG as a therapeutic agent or adjuvant in the radiotherapy and chemotherapy of tumors.
The GenusArtemisia: A Comprehensive Review (2010)

Various species of Artemisia seems to hold great potential for in-depth investigation for various biological activities, especially their effects on the central nervous and cardiovascular systems.