gebhart/patrepeval huggingface dataset:
Mapping of human chromosome Xq28 by two-color fluorescence in situ hybridization of DNA sequences to interphase cell nuclei. (1991)

We have used the proximity of probe hybridization sites in interphase chromatin to derive the order of DNA sequences in a 2-3-Mbp region of human chromosome Xq28. The map generated bridges the results of genetic and pulsed-field gel electrophoresis mapping to produce a more complete map of Xq28 than possible with either of these other techniques alone. Two-color fluorescence in situ hybridization (FISH) was used to detect the positions of two or more probes in G1 male interphase nuclei. We show that cosmids that are 50 kbp to 2-3 Mbp apart can be ordered rapidly with two alternative approaches: (1) by comparing the average measured distance between two probes and (2) simply by scoring the order of red and green fluorescent dots after detection of three or more probes with two fluorochromes. The validity of these approaches is demonstrated using five cosmids from a region spanning approximately 800 kbp that includes the factor VIII (F8), glucose-6-phosphate dehydrogenase (G6PD), and color-vision pigment (CV) genes. The cosmid map derived from interphase mapping is consistent with the map determined by restriction-fragment analysis. The two interphase mapping approaches were then used (1) to orient the F8/CV cluster relative to two markers, c1A1 and st14c, which we show by metaphase mapping to be proximal to the F8/CV cluster, (2) to position st14c (DXS52) between c1A1 and F8, and (3) to orient the CV gene cluster relative to G6PD by using two CV-flanking cosmids, 18b41 and fr7. The probe order in Xq28 derived from interphase proximity is cen-c1A1-st14c-5'F8 (p624-p542-p625)-G6PD-18b41-3' green-green-red-fr7-tel. We also show that, to determine their order by using metaphase chromosomes, sequences must be at least 1 Mbp apart, an order of magnitude greater than required in interphase chromatin. The data show that FISH mapping is a simple way to order sequences separated by greater than or equal to 50 kbp for the construction of long-range maps of mammalian genomes.
Early Epidemiological and Clinical Characteristics of 28 Cases of Coronavirus Disease in South Korea (2020)

COVID-19 in Korea was spread by 16 infected individuals traveling from other countries, leading to second-generation cases. The initial symptoms were mostly minor, but the disease was infectious at this stage, resulting from close contact, particularly at home. Establishing an early detection strategy for COVID-19 is crucial for managing the transmission of the disease.
Comprehensive genomic characterization of squamous cell lung cancers (2012)

Lung squamous cell carcinoma is a common type of lung cancer, causing approximately 400,000 deaths per year worldwide. Genomic alterations in squamous cell lung cancers have not been comprehensively characterized, and no molecularly targeted agents have been specifically developed for its treatment. As part of The Cancer Genome Atlas, here we profile 178 lung squamous cell carcinomas to provide a comprehensive landscape of genomic and epigenomic alterations. We show that the tumour type is characterized by complex genomic alterations, with a mean of 360 exonic mutations, 165 genomic rearrangements, and 323 segments of copy number alteration per tumour. We find statistically recurrent mutations in 11 genes, including mutation of TP53 in nearly all specimens. Previously unreported loss-of-function mutations are seen in the HLA-A class I major histocompatibility gene. Significantly altered pathways included NFE2L2 and KEAP1 in 34%, squamous differentiation genes in 44%, phosphatidylinositol-3-OH kinase pathway genes in 47%, and CDKN2A and RB1 in 72% of tumours. We identified a potential therapeutic target in most tumours, offering new avenues of investigation for the treatment of squamous cell lung cancers.
The Structure of l-Aspartate Ammonia-Lyase from Escherichia coli, (1997)

The X-ray crystal structure of l-aspartate ammonia-lyase has been determined to 2.8 A resolution. The enzyme contains three domains, and each domain is composed almost completely of alpha helices. The central domain is composed of five long helices. In the tetramer, these five helices form a 20-helix cluster. Such clusters have also been seen in delta-crystallin and in fumarase. The active site of aspartase has been located in a region that contains side chains from three different subunits. The structure of the apoenzyme has made it possible to identify some of the residues that are involved in binding the substrate. These residues have been examined by site-directed mutagenesis, and their putative roles have been assigned [Jayasekera, M. M. K., Shi, W., Farber, G. K., & Viola, R. E. (1997) Biochemistry 36, 9145-9150].
Inhibition of Listeria innocua in Cheddar Cheese by Addition of Nisin Z in Liposomes or by In Situ Production in Mixed Culture (2002)

The effect of addition of purified nisin Z in liposomes to cheese milk and of in situ production of nisin Z by Lactococcus lactis subsp. lactis biovar diacetylactis UL719 in the mixed starter on the inhibition of Listeria innocua in cheddar cheese was evaluated during 6 months of ripening. A cheese mixed starter culture containing Lactococcus lactis subsp. lactis biovar diacetylactis UL719 was selected for high-level nisin Z and acid production. Experimental cheddar cheeses were produced on a pilot scale, using the selected starter culture, from milk with added L. innocua (10(5) to 10(6) CFU/ml). Liposomes with purified nisin Z were prepared from proliposome H and added to cheese milk prior to renneting to give a final concentration of 300 IU/g of cheese. The nisin Z-producing strain and nisin Z-containing liposomes did not significantly affect cheese production and gross chemical composition of the cheeses. Immediately after cheese production, 3- and 1.5-log-unit reductions in viable counts of L. innocua were obtained in cheeses with encapsulated nisin and the nisinogenic starter, respectively. After 6 months, cheeses made with encapsulated nisin contained less than 10 CFU of L. innocua per g and 90% of the initial nisin activity, compared with 10(4) CFU/g and only 12% of initial activity in cheeses made with the nisinogenic starter. This study showed that encapsulation of nisin Z in liposomes can provide a powerful tool to improve nisin stability and inhibitory action in the cheese matrix while protecting the cheese starter from the detrimental action of nisin during cheese production.
Control of nucleation in the crystallization of lysozyme (1993)

This work investigates the influence of storage of lysozyme in solution on its crystallization. The crystallization of hen egg-white lysozyme exhibits a storage effect (aging) that depends on the length of time the lysozyme solution is stored, after dissolving from freeze-dried powder, before being brought to crystallization conditions. The number of crystals obtained increases, while their size decreases, as the solution ages. Observations suggest that this effect is due to the presence of fungi that multiply in the stored protein solution. This aging effect was used to control nucleation and determine the number and size of lysozyme crystals to be formed in a given sample.
Fabrication of arrays of nanometer size test structures for scanning probe microscope tips characterization* (1994)

A problem in scanning probe microscopy (SPM) is the unknown shape of the probing tip. Generally, the image is a convolution between the shape of the tip and the surface. Information of the shape of the probe may be gained by imaging very sharp tips. Here we present a method for making two-dimensional arrays of very sharp tips. The tip arrays were made of silicon using electron beam lithography with subsequent ion-beam etching. To achieve the best possible resolution, ultrasonic excitation was used during development of the bilayered PMMA resist. Thus, openings in the resist with size nearly equal to the spot size of the writing e-beam have been obtained. A further decrease of the radius of the tips was obtained by the choice of appropriate thickness for the masking NiCr layer. The tips were conical with a height up to 100 nm with a radius of the tip down to 10 nm. The tips were suitable for study of the shape of AFM probe tips, under condition that the tip array samples were rinsed in water prior to the measurement. Without the rinsing procedure, strong sticking forces between the probe and the sample would have eroded both of them. The regularity of the array provided an easy way to calibrate the lateral motion of the scanner.
[Changes in 1H-MRS in glioma patients before and after irradiation: the significance of quantitative analysis of choline-containing compounds]. (2003)

The evaluation of the response to radiation therapy in brain tumor patients is a major and an important issue. Although CT and MRI can measure changes in tumor size, it is difficult to use these imaging methods to evaluate the viability or the proliferation activity of a tumor. In this study, we investigated the metabolite changes in glioma patients using 1H-MRS from before to after radiation therapy, to see whether or not early metabolic changes occur during therapy. Seven patients with histologically proven glioma (1 astrocytoma, 1 anaplastic astrocytoma, 2 oligoastrocytoma, 1 oligodendroglioma, 2 glioblastoma) were examined by means of 1H-MRS using a point-resolved spectroscopy (PRESS) sequence with a repetition time of 2,000 ms and echo times of 68 ms, 136 ms and 272 ms. The 1H-MRS was evaluated by both the spectrum pattern and the quantification of the metabolites. As to radiation therapy, each patient received a total dose of 64.8 Gy (1.8 Gy/fraction) with a 10-MeV linear accelerator. The results revealed that the concentration of choline-containing compounds (Cho) was 4.55 +/- 1.08 mmol/kg wet weight before radiation therapy and was reduced to 2.69 +/- 0.56 mmol/kg wet weight (p < 0.01) after radiation therapy. Moreover, both the N-acetylaspartate (NAA) peak and creatine/phosphocreatine (t-Cr) peak were lower after radiation therapy than before. The peaks of both the lipids (Lip) and lactate (Lac) were higher after radiation therapy than before. In conclusion, Cho concentration is thought to be a useful marker for the evaluation of early post-radiation response. The effect of radiation therapy can be evaluated according to the value of Cho. Further long-term MRS study is needed to prove whether or not the decrease of the Cho value in the present study will change before recurrence at later stages.
Molecularly Mediated Thin Film Assembly of Nanoparticles on Flexible Devices: Electrical Conductivity versus Device Strains in Different Gas/Vapor Environment (2011)

The ability to precisely control nanoparticle-enabled electrical devices for applications involving conformal wrapping/bending adaptability in various complex sensing environments requires an understanding of the electrical correlation with the device strain and exposure to the molecular environment. This report describes novel findings of an investigation of molecularly mediated thin film assembly of gold nanoparticles on flexible chemiresistor devices under different device strains and exposure molecules. Both theoretical and experimental data have revealed that the electrical conductivity of the nanoparticle assembly depends on a combination of the device strain and the exposure molecules. Under no device strain, the electrical conductivity is sensitive to the molecular nature in the exposure environment, revealing a clear increase in electrical conductivity with the dielectric constant of vapor molecules. Under small device strains, the electrical conductivity is shown to respond sensitively to the strain directions (tensile vs compressive strain) and also to the dielectric constant of the vapor molecules in a way resembling the characteristic under no device strain. Under large device strains, the electrical conductivity is shown to respond to the difference in dielectric constant of the vapor molecules but, more significantly, to the device tensile and compressive strains than those under small device strains. This combination of device strain and dielectric characteristic is also dependent on the orientation of the microelectrode patterns with respect to the device strain direction, a finding that has important implications to the design of flexible arrays for a complex sensing environment.
Oat beta-glucan reduces blood cholesterol concentration in hypercholesterolemic subjects. (1994)

The main component of the soluble fibre of oats, beta-glucan, significantly reduced the total and LDL cholesterol levels of hypercholesterolemic adults without changing HDL cholesterol.
IFN-αβ-Mediated Inflammatory Responses and Antiviral Defense in Liver Is TLR9-Independent but MyD88-Dependent during Murine Cytomegalovirus Infection (2007)

Chemokine responses critical for inflammation and promotion of effective innate control of murine CMV (MCMV) in liver have been shown to be dependent on immunoregulatory functions elicited by IFN-alphabeta. However, it remains to be determined whether upstream factors that promote viral sensing resulting in the rapid secretion of IFN-alphabeta in liver differ from those described in other tissues. Because plasmacytoid dendritic cells (pDCs) are known producers of high levels of systemic IFN-alpha in response to MCMV, this study examines the in vivo contribution of pDCs to IFN-alpha production in the liver, and whether production of the cytokine and ensuing inflammatory events are dependent on TLR9, MyD88, or both. We demonstrate that whereas MyD88 deficiency markedly impaired secretion of IFN-alpha, production of the cytokine was largely independent of TLR9 signaling, in the liver. MyD88 and TLR9 were needed for IFN-alpha production in the spleen. Moreover, hepatic but not splenic pDCs produced significant amounts of intracellular IFN-alpha in the absence of TLR9 function during infection. Furthermore, production of CCL2, CCL3, and IFN-gamma, as well as the accumulation of macrophages and NK cells, was not affected in the absence of functional TLR9 in the liver. In contrast, these responses were dramatically reduced in MyD88(-/-) mice. Additionally, MyD88(-/-) but not TLR9(-/-) mice exhibited increased sensitivity to virus infection in liver. Collectively, our results define contrasting compartmental functions for TLR9 and MyD88, and suggest that the infected tissue site uniquely contributes to the process of virus sensing and regulation of localized antiviral responses.
Increased serum concentrations of interleukin-1 beta in patients with coronary artery disease. (1996)

Serum IL-1 beta concentrations are raised in patients with ischaemic heart disease, in particular in those with minimal coronary artery disease and angina. The precise role of IL-1 beta in coronary artery disease remains to be determined.
Infectivity and glycoprotein processing of herpes simplex virus type 1 grown in a ricin-resistant cell line deficient in N-acetylglucosaminyl transferase I (1982)

We report on the replication of herpes simplex virus type 1 (HSV-1) and viral glycoprotein processing in RicR14 cells, a mutant ricin-resistant cell line defective in N-acetylglucosaminyl transferase I activity. In these cells HSV-1(MP) and (F) replicated to yields very similar to those in parental BHK cells. The kinetics of HSV-1 adsorption in mutant and in parent cells was also essentially identical. Progeny virions from ricin-resistant and wild-type cells displayed comparable specific infectivities. However, in the mutant cells the efficiency of plating of progeny virus from both RicR14 and BHK cells was reduced. HSV-1(MP) failed to induce syncytia in RicR14 cells either in a plaque assay or after a high-multiplicity infection. Moreover, the fully glycosylated forms of glycoproteins (gB, gC, and gD) were totally absent, and only the partially glycosylated precursors (pgC, pgD. and a triplet in the gB-gA region) accumulated in HSV-1-infected ricin-resistant cells and in herpesvirions made in these cells. Consistent with these results analysis of pronase glycopeptides from cells labeled with [14C]glucosamine showed a strong decrease of sialylated complex-type oligosaccharides and a dramatic accumulation of the neutral mannose-rich chains. The latter chains predominate in partially glycosylated precursors, whereas the complex acidic chains predominate in the fully processed forms of HSV glycoproteins. These results taken together indicate that (i) host-cell N-acetylglucosaminyl transferase I participates in the processing of HSV glycoproteins; and (ii) infectivity of herpesvirions does not necessarily require the mature form of gB. The absence of HSV-1(MP)-induced fusion in RicR14 cells is discussed.
Enzymes of the Isoleucine-Valine Pathway in Acinetobacter (1972)

Regulation of four of the enzymes required for isoleucine and valine biosynthesis in Acinetobacter was studied. A three- to fourfold derepression of acetohydroxyacid synthetase was routinely observed in two different wild-type strains when grown in minimal medium relative to cells grown in minimal medium supplemented with leucine, valine, and isoleucine. A similar degree of synthetase derepression was observed in appropriately grown isoleucine or leucine auxotrophs. No significant derepression of threonine deaminase or transaminase B occurred in either wild-type or mutant cells grown under a variety of conditions. Three amino acid analogues were tested with wild-type cells; except for a two- to threefold derepression of dihydroxyacid dehydrase when high concentrations of aminobutyric acid were added to the medium, essentially the same results were obtained. Experiments showed that threonine deaminase is subject to feedback inhibition by isoleucine and that valine reverses this inhibition. Cooperative effects in threonine deaminase were demonstrated with crude extracts. The data indicate that the synthesis of isoleucine and valine in Acinetobacter is regulated by repression control of acetohydroxyacid synthetase and feedback inhibition of threonine deaminase and acetohydroxyacid synthetase.
Design and Synthesis of Potent and Selective α4β7Integrin Antagonists (2001)

Interactions of the integrins alpha(4)beta(7) with its cognate ligand mucosal addressin cell adhesion molecule-1 (MAdCAM-1) play a crucial role in the development of mucosa-associated lymphoid organs, in the generation of mucosal immune responses, and in diverse pathological processes such as chronic inflammatory bowel disease and type I diabetes. Using a previously developed spatial screening technique we describe the development of potent and selective alpha(4)beta(7) integrin antagonists based on the domain 1 Leu-Asp-Thr (LDT) sequence of MAdCAM-1 that is essential for alpha(4)beta(7) integrin binding. A library of homodetic cyclic penta- and hexapeptides was synthesized presenting the pharmacophoric LDT-sequence in different conformations. The cyclic hexapeptide P10 cyclo(Leu-Asp-Thr-Ala-D-Pro-Ala) inhibits alpha(4)beta(7) integrin mediated cell adhesion to MAdCAM-1 effectively. Further optimization of the lead structure P10 resulted in cyclic hexapeptides with enhanced activity. The compounds P25 cyclo(Leu-Asp-Thr-Ala-D-Pro-Phe), P28 cyclo(Leu-Asp-Thr-Asp-D-Pro-Phe), P29 cyclo(Leu-Asp-Thr-Asp-D-Pro-His), and P30 cyclo(Leu-Asp-Thr-Asp-D-Pro-Tyr) strongly inhibited alpha(4)beta(7) integrin mediated cell adhesion to MAdCAM-1, but they did not affect binding of the closely related alpha(4)beta(1) integrin to VCAM-1.
Conserved sites in the 5'-3' exonuclease domain ofEscherichia coliDNA polymerase (1993)

Journal Article Conserved sites in the 5'-3' exonuclease domain of Escherichia coli DNA polymerase Get access Psblo D. Gutman, Psblo D. Gutman Department of Pathology, F.E.Heébert School of Medicine, Uniformed Services University of the Heatlh sciences4301 jones Bridge Road, Bethesda, MD 20814-4799, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Kenneth W. minton Kenneth W. minton * Department of Pathology, F.E.Heébert School of Medicine, Uniformed Services University of the Heatlh sciences4301 jones Bridge Road, Bethesda, MD 20814-4799, USA * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 21, Issue 18, 11 September 1993, Pages 4406–4407, https://doi.org/10.1093/nar/21.18.4406 Published: 11 September 1993 Article history Received: 27 April 1993 Revision received: 27 July 1993 Accepted: 27 July 1993 Published: 11 September 1993
Topical delivery of interleukin‐13 antisense oligonucleotides with cationic elastic liposome for the treatment of atopic dermatitis (2008)

These data suggests that IL-13 ASO/cEL complex can provide a potential therapeutic tool for the treatment of AD and also be applied to other immune diseases associated with the production of Il-13.
Professional Entry and the Adviser Relationship (1991)

A longitudinal design was used to examine socialization of professional newcomers (n = 134) at entry into professional doctoral training and at the end of 1 year of training. Anticipatory and encounter experiences are related to commitment and research productivity within the program and for a 5-year period following. As hypothesized, a supportive adviser relationship was strongly and positively related to socialization outcomes and moderate socialization processes. Contrary to hypotheses, however, more supportive adviser relationships appear to offset other socialization processes or to be associated with negative outcomes from socialization.
Expressed sequence tag analysis of adult human iris for the NEIBank Project: steroid-response factors and similarities with retinal pigment epithelium. (2002)

The iris libraries are a rich source of novel as well as known genes, including molecular markers for pigmented cells that are also shared with RPE. A number of transcripts code for proteins involved in steroid response, with interesting implications for control of intraocular pressure. These sequence verified clones provide a nonredundant set for micro-array construction.
The Plastidic 2-Cysteine Peroxiredoxin Is a Target for a Thioredoxin Involved in the Protection of the Photosynthetic Apparatus against Oxidative Damage (2002)

The chloroplastic drought-induced stress protein of 32 kD (CDSP32) is composed of two thioredoxin modules and is induced by environmental and oxidative stress conditions. We investigated whether the plastidic protein BAS1, which is related to eubacterial 2-Cys peroxiredoxin, is a target for CDSP32. Using a CDSP32 active-site mutant, we showed that the BAS1 and CDSP32 proteins form a mixed disulfide complex in vitro. Moreover, affinity chromatography indicated that BAS1 is a major target for CDSP32 in chloroplasts. CDSP32 was able to reduce BAS1 in vitro, and BAS1 displayed CDSP32-dependent peroxidase activity. The function of CDSP32 was investigated in transgenic potato lines without detectable levels of the protein as a result of cosuppression. Under conditions of photooxidative stress induced by incubation with either methyl viologen or t-butyl hydroperoxide or by exposure to low temperature under high light, plants lacking CDSP32 exhibited decreased maximal photosystem II photochemical efficiencies compared with the wild type and transgenic controls. In addition, plants without CDSP32 retained much less chlorophyll than controls under stress, indicating increased damage to photosynthetic membranes. We conclude that CDSP32 is a thioredoxin with a critical role in plastid defense against oxidative damage and that this role is related to its function as a physiological electron donor to the BAS1 peroxiredoxin.