gebhart/patrepeval huggingface dataset:
Primase, the dnaG protein of Escherichia coli. An enzyme which starts DNA chains. (1978)

Conversion of the viral DNA of phage G4 to the duplex form provided an opportunity to isolate and determine the function of the dnaG protein, the product of a gene known to be essential for replication of the Escherichia coli chromosome. This stage of G4 DNA replication requires action of three proteins: the E. coli DNA-binding protein, the dnaG protein, and the DNA polymerase III holoenzyme. The dnaG protein has been purified approximately 25,000-fold to near-homogeneity. The native protein contains a single polypeptide of 60,000 daltons. It has been assayed for its activity on G4 DNA in three ways: (a) RNA synthesis, (b) complementation for replication of an extract of a temperature-sensitive dnaG mutant, and (c) priming of DNA replication by DNA polymerase III holoenzyme. The dnaG protein is highly specific for G4 DNA and synthesizes a unique 29-residue RNA primer to be described in the suceeding paper. Other single-stranded and duplex DNA templates are inactive. RNA primer synthesis by the dnaG protein has an apparent Km for ribonucleoside triphosphates near 10 micrometer, and a narrow optimum for Mg2+. The sharp specificity of the dnaG protein in choice of template and the utilization of either deoxyribonucleotides or ribonucleotides to produce a hybrid piece only a few residues long (as described in a succeeding paper) suggests that the dnaG protein previously named RNA polymerase by renamed primase.
The Influence of HLA Class I Alleles and Heterozygosity on the Outcome of Human T Cell Lymphotropic Virus Type I Infection (2000)

The inflammatory disease human T cell lymphotropic virus type I (HTLV-I)-associated myelopathy (HAM/TSP) occurs in only 1-2% of HTLV-I-infected individuals and is associated with a high provirus load of HTLV-I. We hypothesize that a person's risk of developing HAM/TSP depends upon the efficiency of their immune response to the virus, which differs between individuals because of polymorphism in genes that influence this response. Previously we showed that the possession of HLA-A*02 was associated with a lower risk of HAM/TSP, and with a lower provirus load in healthy carriers of HTLV-I. However, HLA-A*02 did not account for all the observed difference in the risk of HAM/TSP. Here we present evidence, in the same study population in Japan, that HLA-Cw*08 was also associated with disease protection (probability value, two-tailed test = 0.002) and with a lower proviral load in healthy carriers. Possession of the A*02 and/or Cw*08 genes prevented 36% of potential HAM/TSP cases. In contrast, HLA-B*5401 was associated with a higher susceptibility to HAM/TSP (probability value, two-tailed test = 0.0003) and with a higher provirus load in HAM/TSP patients. At a given provirus load, B*5401 appeared to increase the risk of disease. The fraction of HAM/TSP cases attributable to B*5401 was 17%. Furthermore, individuals who were heterozygous at all three HLA class I loci have a lower HTLV-I provirus load than those who were homozygous at one or more loci. These results are consistent with the proposal that a strong class I-restricted CTL response to HTLV-I reduces the proviral load and hence the risk of disease.
Brain Tumor Immunotherapy: What have We Learned so Far? (2015)

High grade glioma is a rare brain cancer, incurable in spite of modern neurosurgery, radiotherapy, and chemotherapy. Novel approaches are in research, and immunotherapy emerges as a promising strategy. Clinical experiences with active specific immunotherapy demonstrate feasibility, safety and most importantly, but incompletely understood, prolonged long-term survival in a fraction of the patients. In relapsed patients, we developed an immunotherapy schedule and we categorized patients into clinically defined risk profiles. We learned how to combine immunotherapy with standard multimodal treatment strategies for newly diagnosed glioblastoma multiforme patients. The developmental program allows further improvements related to newest scientific insights. Finally, we developed a mode of care within academic centers to organize cell-based therapies for experimental clinical trials in a large number of patients.
Plant antitumor agents. 23. Synthesis and antileukemic activity of camptothecin analogs (1986)

Eight optically active and nine racemic ring A modified analogues of 20(S)-camptothecin were prepared and evaluated for antitumor activity in the L-1210 leukemia system. The ring A mono- and disubstituted analogues displayed a wide variance in activity and potency. It was found that monosubstitution by NH2 or OH at positions 9, 10, or 11 yielded compounds with activity much higher than the parent compound, camptothecin, whereas substitution at position 12 greatly reduced activity. In general, disubstitution in ring A greatly reduced antileukemic activity. Replacement of ring A by heterocyclic rings (thiophene or pyridine) leads to analogues with only moderate activity.
Shewanella olleyana sp. nov., a marine species isolated from a temperate estuary which produces high levels of polyunsaturated fatty acids (2002)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Tumor endothelial marker 1–specific DNA vaccination targets tumor vasculature (2014)

Tumor endothelial marker 1 (TEM1; also known as endosialin or CD248) is a protein found on tumor vasculature and in tumor stroma. Here, we tested whether TEM1 has potential as a therapeutic target for cancer immunotherapy by immunizing immunocompetent mice with Tem1 cDNA fused to the minimal domain of the C fragment of tetanus toxoid (referred to herein as Tem1-TT vaccine). Tem1-TT vaccination elicited CD8+ and/or CD4+ T cell responses against immunodominant TEM1 protein sequences. Prophylactic immunization of animals with Tem1-TT prevented or delayed tumor formation in several murine tumor models. Therapeutic vaccination of tumor-bearing mice reduced tumor vascularity, increased infiltration of CD3+ T cells into the tumor, and controlled progression of established tumors. Tem1-TT vaccination also elicited CD8+ cytotoxic T cell responses against murine tumor-specific antigens. Effective Tem1-TT vaccination did not affect angiogenesis-dependent physiological processes, including wound healing and reproduction. Based on these data and the widespread expression of TEM1 on the vasculature of different tumor types, we conclude that targeting TEM1 has therapeutic potential in cancer immunotherapy.
The Structure of Rat Preproatrial Natriuretic Factor as Defined by a Complementary DNA Clone (1984)

The structure of rat preproatrial natriuretic factor ( preproANF ) was determined by nucleotide sequence analysis of an ANF complementary DNA clone. PreproANF is composed of a hydrophobic leader segment (20 amino acids), a precursor containing one glycosylation site (106 amino acids), and ANF (24 amino acids). Atrial natriuretic factor is located at the carboxyl terminus of the precursor molecule. The human, mouse, and rat genomes each contain a single ANF gene which is highly conserved.
Antibody localization in human renal cell carcinoma: a phase I study of monoclonal antibody G250. (1993)

131I-mAbG250 localized specifically to G250 antigen-positive RCC and seems to have considerable potential as an imaging agent in RCC patients. 131I-mAbG250 uptake in the tumors, relative as well as absolute, are among the highest reported for tumor biopsies obtained 8 days after IV mAb administration. Based on the specific localization and high accumulation, mAb G250 may have therapeutic potential.
The V1/V2 Domain of gp120 Is a Global Regulator of the Sensitivity of Primary Human Immunodeficiency Virus Type 1 Isolates to Neutralization by Antibodies Commonly Induced upon Infection (2004)

ABSTRACT A major problem hampering the development of an effective vaccine against human immunodeficiency virus type 1 (HIV-1) is the resistance of many primary viral isolates to antibody-mediated neutralization. To identify factors responsible for this resistance, determinants of the large differences in neutralization sensitivities of HIV-1 pseudotyped with Env proteins derived from two prototypic clade B primary isolates were mapped. SF162 Env pseudotypes were neutralized very potently by a panel of sera from HIV-infected individuals, while JR-FL Env pseudotypes were neutralized by only a small fraction of these sera. This differential sensitivity to neutralization was also observed for a number of monoclonal antibodies (MAbs) directed against sites in the V2, V3, and CD4 binding domains, despite often similar binding affinities of these MAbs towards the two soluble rgp120s. The neutralization phenotypes were switched for chimeric Envs in which the V1/V2 domains of these two sequences were exchanged, indicating that the V1/V2 region regulated the overall neutralization sensitivity of these Envs. These results suggested that the inherent neutralization resistance of JR-FL, and presumably of related primary isolates, is to a great extent mediated by gp120 V1/V2 domain structure rather than by sequence variations at the target sites. Three MAbs (immunoglobulin G-b12, 2G12, and 2F5) previously reported to possess broad neutralizing activity for primary HIV-1 isolates neutralized JR-FL virus at least as well as SF162 virus and were not significantly affected by the V1/V2 domain exchanges. The rare antibodies capable of neutralizing a broad range of primary isolates thus appeared to be targeted to exceptional epitopes that are not sensitive to V1/V2 domain regulation of neutralization sensitivity.
Epithelial Progeny of Estrogen-Exposed Breast Progenitor Cells Display a Cancer-like Methylome (2008)

Estrogen imprinting is used to describe a phenomenon in which early developmental exposure to endocrine disruptors increases breast cancer risk later in adult life. We propose that long-lived, self-regenerating stem and progenitor cells are more susceptible to the exposure injury than terminally differentiated epithelial cells in the breast duct. Mammospheres, containing enriched breast progenitors, were used as an exposure system to simulate this imprinting phenomenon in vitro. Using MeDIP-chip, a methylation microarray screening method, we found that 0.5% (120 loci) of human CpG islands were hypermethylated in epithelial cells derived from estrogen-exposed progenitors compared with the non-estrogen-exposed control cells. This epigenetic event may lead to progressive silencing of tumor suppressor genes, including RUNX3, in these epithelial cells, which also occurred in primary breast tumors. Furthermore, normal tissue in close proximity to the tumor site also displayed RUNX3 hypermethylation, suggesting that this aberrant event occurs in early breast carcinogenesis. The high prevalence of estrogen-induced epigenetic changes in primary tumors and the surrounding histologically normal tissues provides the first empirical link between estrogen injury of breast stem/progenitor cells and carcinogenesis. This finding also offers a mechanistic explanation as to why a tumor suppressor gene, such as RUNX3, can be heritably silenced by epigenetic mechanisms in breast cancer.
Sampling methodologies and dosage assessment techniques for submicrometre and ultrafine virus aerosol particles (2005)

The data and methods presented here provide a fundamental basis for future studies of submicrometre and ultrafine airborne virus particles.
Range and forage research needs for red meat production in the north central region (1977)

The 12 contiguous states of the North Central Region constitute one of the most productive agricultural areas in the world. Before the region was settled, vegetation consisted primarily of forest in the east, grasses in the west, and an intermingling of grass and forest in the central portions. Although the region contains a high proportion of productive soils, there are great differences within the region in soils, as well as in climate, vegetation, and geology. The short-grass soils in the western areas are higher in pH, lighter in color, and thinner than the tail-grass soils in the central and west-central areas, which have thick, dark surface horizons. The more strongly leached soils of the eastern humid forested areas are more acid and have thin, dark surface (A) horizons and light-colored subsurface horizons, which are mixed when cultivated. Approximately 75% of all soils in the region is derived from glacial till and loess. A large proportion of the deposits of glacial origin was derived locally from underlying bedrock or from material laid down during previous glaciations. Most of these deposits range from a few to tens of feet thick, but occasionally are several hundred feet thick. Loess deposits deeper than 4 feet cover large areas of Illinois, Iowa, Missouri, Kansas, and Nebraska. There also are extensive areas where shallow loess deposits cover the land surface.
Interaction between antibodies to Z-form deoxyribonucleic acid and double-stranded polynucleotides (1982)

Antibodies to Z-DNA have been elicited in rabbits immunized with chloro(diethylenetriamine)platinum(II)chloride (Cl2dienPt) modified poly(dG-dC).poly(dG-dC). Under physiological conditions this polynucleotide in which 12% of the bases were substituted is in the Z form. The antibodies are mainly immunoglobulins G as shown by gel filtration of the antiserum and by ultracentrifugation of the antibodies purified on a Sepharose--poly(dG-dC).poly(dG-dC) column. From the quantitative precipitin curve, it is concluded that each binding site of the antibody covers four nucleotide residues. The Z-form DNA-antibody complex is stabilized by electrostatic interactions. There was no interaction between poly(dI-br5dC).poly(dI-br5dC) in the Z form and the antibodies, which strongly suggests that the exocyclic amino group of guanine residues in Z-poly(dG-dC).poly(dG-dC) interacts with the antibody binding site. The modification of poly(dG-dC).poly(dG-dC) by 2-(acetylamino)fluorene residues decreases but does not prevent the binding to the antibodies. It is also shown that the polynucleotide poly(dG-br5dC).poly(dG-br5dC) adopts the Z form over a large range of salt concentration [5 mM tris(hydroxymethyl)aminomethane hydrochloride, pH 7.5, to 3 M NaCl].
Corneal biomechanical measurements before and after laser in situ keratomileusis (2008)

Changes in CH and CRF after LASIK suggest alteration in corneal biomechanics correlating with attempted correction. The CRF parameter may be more useful than the CH parameter in assessing biomechanical changes resulting from LASIK.
Neutralisation of muscle tumour necrosis factor alpha does not attenuate exercise-induced muscle pain but does improve muscle strength in healthy male volunteers (2007)

TNFalpha does not affect muscle soreness associated with unaccustomed exercise, but may improve the recovery of muscle function.
Positron emission tomography and autoradiography (1985)

This a text on cerebral and myocardial imaging using positron emission tomography and autoradiography. Authorities in nuclear medicine and biophysics define the central principles of these complex and rapidly evolving imagine technologies-their theoretical foundations, the nature of the biochemical events being measured, the basis for constructing tracer kinetic models, the criteria governing radiopharmaceutical design, and the rationale for PET in the clinical setting. After reviewing the characteristics of cerebral and myocardial hemodynamics, transport, and metabolism, the contributors detail the theory of PET and autoradiography, the instrumentation required, and the procedures involved.
Nonparametric methods for identifying differentiallyexpressed genes in microarray data (2002)

All methods exhibit very low false positive rates and identify a large fraction of the differentially expressed genes in simulated data sets with noise level similar to that of actual data. Overall, the rank sum test appears most conservative, which may be advantageous when the computationally identified genes need to be tested biologically. However, if a more inclusive list of markers is desired, a higher p-value cutoff or the nonparametric t-test may be appropriate. When applied to data from lung tumor and lymphoma data sets, the methods identify biologically relevant differentially expressed genes that allow clear separation of groups in question. Thus the methods described and evaluated here provide a convenient and robust way to identify differentially expressed genes for further biological and clinical analysis.
Analysis of a Carcinogen, 4,4′-Methylenedianiline, from Thermosetting Polyurethane during Sterilization (1989)

Polyurethane (PU) is widely used in medical devices such as potting material in artificial dialysis devices, plasma separators, etc. Gamma-ray irradiation is frequently used for the sterilization of such devices. This paper reports that a carcinogen, 4,4'-methylenedianiline (MDA, p,p'-diaminodiphenylmethane), is produced from medical thermosetting PU by gamma-ray irradiation. Gamma-ray irradiated PU was immersed in methanol or equine serum. The serum was treated with a mixture of 5N HCIO4:acetonitrile (1:10) in order to deproteinate and recover MDA. It was found that MDA is formed from thermosetting PU at around a few ppm in the original sample. The production of MDA increased with increasing irradiation dose. The MDA amount formed was related to the irradiation dose by a second order equation. Results of methanol and serum extraction were similar. Pressurized steam (autoclave) sterilization in place of gamma-ray sterilization was also examined. MDA production was not found in autoclave sterilization procedures. Gel permeation chromatography (GPC) of methanol or N,N-dimethylformamide (DMF) extract of irradiated PU showed that the PU oligomers eluted. Time course of methanol extract of irradiated PU was detected at 245.5 nm. This showed an exponential decline regardless of doses of irradiation.
Epitaxial InSb for elevated temperature operation of large IR focal plane arrays (2003)

The use of epitaxially grown indium antimonide (InSb) has previously been demonstrated for the production of large 2D focal plane arrays. It confers several advantages over conventional, bulk InSb photo-voltaic detectors, such as reduced cross-talk, however here we focus on the improvement in operating temperature that can be achieved because more complex structures can be grown. Diode resistance, imaging, NETD and operability results are presented for a progression of structures that reduce the diode leakage current as the temperature is raised above 80K, compared with a basic p<sup>+</sup>-n-n<sup>+</sup> structure presented previously. These include addition of a thin region of InAlSb to reduce p-contact leakage current, and construction of the whole device from InAlSb to reduce thermal generation in the active region of the detector. An increase in temperature to 110K, whilst maintaining full 80K performance, is achieved, and imaging up to 130K is demonstrated. This gives the prospect of significant benefits for the cooling systems, including, for example, use of argon in Joule-Thomson coolers or an increase in the life and/or decrease in the cost; power consumption and cool-down time of Stirling engines by several tens of per cent.
Leptin and Ghrelin in Relation toHelicobacter pyloriStatus in Adult Males (2008)

These findings provide evidence that H. pylori status affects leptin and ghrelin homeostasis, presumably via intragastric interactions.
Green tea catechin EGCG inhibits ileal apical sodium bile acid transporter ASBT (2010)

Green tea catechins exhibit hypocholesterolemic effects probably via their inhibitory effects on intestinal bile acid absorption. Ileal apical sodium-dependent bile acid transporter (ASBT) is responsible for reabsorption of bile acids. The present studies were, therefore, designed to investigate the modulation of ASBT function and membrane expression by green tea catechins in human embryonic kidney HEK-293 cells stably transfected with ASBT-V5 fusion protein and intestinal Caco-2 monolayers. Our data showed that ASBT activity was significantly decreased by (-)-epigallocatechin-3-gallate (EGCG) but not other green tea catechins. Inhibition of PKC, phosphatidylinositol 3-kinase, and MAPK-dependent pathways failed to block the reduction in ASBT activity by EGCG. Kinetics studies showed a significant decrease in the V(max) of the transporter, whereas total ASBT content on the plasma membrane was unaltered by EGCG. Concomitant with the decrease in ASBT function, EGCG significantly reduced ASBT pool in the detergent-insoluble fraction, while increasing its presence in the detergent-soluble fraction of plasma membrane. Furthermore, EGCG decreased the association of ASBT with floating lipid raft fractions of cellular membrane on Optiprep density gradient. In conclusion, our data demonstrate a novel role of lipid rafts in the modulation of ASBT function by the dietary component EGCG, which may underlie the hypocholesterolemic effects of green tea.
1-μm-pumped OPO based on orientation-patterned GaP (2015)

Orientation patterned gallium phosphide (OP-GaP) is a new nonlinear optical (NLO) crystal which exhibits the highest nonlinear coefficient (d<sub>14</sub>=70.6 pm/V) and the longest infrared cut-off (12.5 &mu;m) of any quasi-phase-matched (QPM) material that can be pumped at 1-&mu;m without significant two-photon absorption. Here we report the first 1064nm-pumped OPO based on bulk OP-GaP. Multi-grating OP-GaP QPM structures were grown by producing an inverted GaP layer by polar-on-nonpolar molecular beam epitaxy (MBE), lithographically patterning, reactive ion etching, and regrowing by MBE to yield templates for subsequent bulk growth by low-pressure hydride vapor phase epitaxy (LP-HVPE). The pump source was a diode-end-pumped Nd:YVO<sub>4</sub> monoblock laser with an RTP high-voltage Q-switch (1064 nm, 1W, 10kHz, 3.3 ns) which was linearly polarized along the &lt;100&gt; orientation of the AR-coated 16.5 x 6.3 x 1.1 mm<sup>3</sup> OP-GaP crystal (800-&mu;m thick HVPE layer, 20.8 &mu;m grating period only 150 &mu;m thick) mounted on a copper blocked maintained at 20°C by a thermo-electric cooler. The OPO cavity was a linear resonator with 10-cm ROC mirrors coated for DRO operation (85%R at signal, 55%R at idler). The pump 4&sigma;-diameter at the crystal face was 175 &mu;m. The observed OPO signal (idler) threshold was 533 mW (508 mW) with a slope efficiency of 4% (1%) and maximum output power 15 mW (4 mW). The signal (1342 nm) and idler (4624 nm) output wavelengths agreed well with sellemier predictions. Orange parasitic output at 601.7nm corresponded to 9<sup>th</sup> order QPM sum frequency mixing of the 1064-nm pump and the 1385-nm signal.
A hidden markov model framework for traffic event detection using video features (2005)

A novel approach for highway traffic event detection in video is presented. The proposed algorithm extracts event features directly from compressed video and detects traffic event using a Gaussian mixture hidden Markov model (GMHMM). First, an invariant feature vector is extracted from discrete cosine transform (DCT) domain and macro-block vectors after MPEG video stream is parsed. The extracted feature vector accurately describes the change of traffic state and is robust towards different camera setups and illumination situations, such as sunny, cloud, and night. Six traffic patterns are studied and a GMHMM is trained to model these patterns in offline stage. Then, Viterbi algorithm is used to determine the most likely traffic condition. The proposed algorithm is efficient both in terms of computational complexity and memory requirement. The experimental results prove the system has a high detection rate. The presented model based system can be easily extended for detection of similar traffic events.