gebhart/patrepeval huggingface dataset:
Four‐year stability of Der p I in house dust under simulated domestic conditions in vitro (1994)

For almost 4 years, the stability of Der p I was assessed by RAST inhibition in house-dust samples incubated under simulated domestic conditions (5 or 25 degrees C and 75% relative humidity). Der p I concentrations were determined before heating dust samples at 60 degrees C to kill the mites, and at 0, 6, 14, 21, and 47 months after heating. Heating at 60 degrees C for 24 h caused no significant change in Der p I concentration. After a 47-month incubation under simulated domestic conditions, reduction of Der p I was still not obvious. It is concluded that even after extermination of mites, home textiles remain allergen reservoirs for an extended period of time. Avoidance schemes should take this into account.
Some recommendations concerning primary isolation of Mycoplasma suipneumoniae and Mycoplasma flocculare a survey. (1975)

Two mycoplasma species of the porcine respiratory tract: Mycoplasma suipneumoniae and Mycoplasma flocculare, have been notoriously difficult to cultivate. In the present paper a description is given of a new medium with which primary isolation of these organisms is usually successful. The basal medium is made from commercial dehydrated products. Pig serum is added and phenol red used as pH indicator. Contrary to what is customary in the preparation of mycoplasma media, various inorganic salts (Hank's balanced salt solution) are included and penicillin-G replaced as a bacteriostatic by bacitracin and meticillin. The volume of water is adjusted so as to give isotonia. Various additives often recommended for mycoplasma cultivation have been examined for growth promoting effect; apparently, however, they were all without effect. Working procedures for primary isolation trials are briefly described.
Development of a New Optical Wavelength Rejection Filter: Demonstration of its Utility in Raman Spectroscopy (1984)

A new tunable optical filter has been developed which rejects a narrow wavelength interval (&lt;7.5 nm) in the near-UV, visible, or near-IR spectral region and allows adjacent wavelengths to pass ( T &gt; 90%). This filter will be useful in optics, in spectroscopy, and for laser applications. The active element of the filter is a crystalline colloidal array of polystyrene spheres. The rejected wavelengths are Bragg diffracted from this ordered array. For a particular sphere concentration and scattering from a particular set of lattice planes, tunability can be achieved by the altering of the angle between the filter and incident light beam. Bragg diffraction and light rejection of these filters are monitored by transmission measurements. The utility of this filter for spectroscopic measurements is demonstrated for Raman spectroscopy. Raman measurements are shown for polypropylene, a highly scattering material with numerous low-frequency modes. The filter selectively attenuates the elastically scattered light and allows the low frequency peaks to be observed. Use of this wavelength rejection filter to reject the Rayleigh scattered light simplifies the instrumentation, decreases the cost, and increases the sensitivity of Raman spectral measurements. This filter also has the potential to replace dispersive elements such as gratings and prisms in a variety of spectroscopic and optical applications.
Carcinogenicity of Tobacco-Specific N-Nitrosamines (TSNA): The Role of the Vascular Network in the Selection of Target Organs (1991)

Click to increase image sizeClick to decrease image sizeKey Words: tobacco-specific N-nitrosaminesvascular networkautoradiographymetabolic capabilitynasal cavityolfactory regionesthesioneuroepitheliomaalveolar adenocarcinomaexocrine pancreas tumortumors at site of applicationorgan-specific carcinogenicity
A review of issues related to measuring colonization of plant roots by bacteria (1992)

Root colonization by introduced bacteria is an important step in the interaction of beneficial bacteria with the host plant. Investigators attempting to measure root colonization by bacteria must face several issues. A clear concept or definition of root colonization should be stated in each research summary, as several different definitions have been proposed. We consider true root colonists to be those bacteria that colonize roots in competitive conditions, i.e., natural field soils. Different methods of processing root samples are required if one is measuring external root colonization alone, internal colonization alone, or both. Given that most beneficial bacterial strains currently under investigation as root colonists are members of taxa naturally found in soils, a marking system is required to differentiate the introduced strain from members of the indigenous rhizosphere community. Spontaneous antibiotic resistance, immunological approaches, and foreign DNA sequences are among the marking systems that have been used and each has some possible advantages and disadvantages. More research is needed in the development and comparison of marking systems. The design of experiments to measure root colonization should take into account several statistical issues. One must decide what constitutes the sample unit for each replication of a given treatment, e.g., whole root systems or root segments. Consideration should also be given to how best to express the estimated population of root colonists (e.g., cfu/g fresh or dry weight root, cfu/cm root, or cfu/surface area root). Statistical analysis by standard analysis of variance tests should be used whenever possible to separate treatment means of colonization levels; however, one must determine that the underlying assumptions of these tests are correct for each experiment. Finally, in quantification of populations on roots, one will almost certainly encounter replications with no bacteria, i.e., zeros. There are several options for how to calculate treatment means when one or more replications is a zero, and the implications of these options are discussed. Key words: bioluminescence, genetic markers, plant growth-promoting rhizobacteria, rhizosphere bacteria, root, colonization.
Synthesis and biological properties of side-chain-modified bleomycins (1987)

New side-chain-modified bleomycins (BLMs) 3a-k have been synthesized by the reaction of demethyl BLM A2 with alpha-bromoacetamides (2a-k). The structures of these BLM analogues have been established by comparison of their NMR spectra with the corresponding spectra of model thiazole derivatives. Mass spectra (FAB) of the modified BLMs are not informative, since the fragmentation patterns exhibit a loss of the modified chain moiety, presumably in the matrix. The purity of the compounds is attested by TLC and HPLC analyses. Biological evaluation of 3a-k in in vitro (survival of B16 melanoma cells) shows that the compounds are almost as effective as bleomycin. Examination of the effects of 3c, 3e, and 3f on lungs of male mice indicates that the analogues do not exhibit lower pulmonary toxicity than bleomycin.
Inhibition of Hepatitis B Virus Replication by Drug-Induced Depletion of Nucleocapsids (2003)

Chronic hepatitis B virus (HBV) infection is a major cause of liver disease. Only interferon-alpha and the nucleosidic inhibitors of the viral polymerase, 3TC and adefovir, are approved for therapy. However, these therapies are limited by the side effects of interferon and the substantial resistance of the virus to nucleosidic inhibitors. Potent new antiviral compounds suitable for monotherapy or combination therapy are highly desired. We describe non-nucleosidic inhibitors of HBV nucleocapsid maturation that possess in vitro and in vivo antiviral activity. These inhibitors have potential for future therapeutic regimens to combat chronic HBV infection.
DNA Methylation Analysis of Chromosome 21 Gene Promoters at Single Base Pair and Single Allele Resolution (2009)

Differential DNA methylation is an essential epigenetic signal for gene regulation, development, and disease processes. We mapped DNA methylation patterns of 190 gene promoter regions on chromosome 21 using bisulfite conversion and subclone sequencing in five human cell types. A total of 28,626 subclones were sequenced at high accuracy using (long-read) Sanger sequencing resulting in the measurement of the DNA methylation state of 580427 CpG sites. Our results show that average DNA methylation levels are distributed bimodally with enrichment of highly methylated and unmethylated sequences, both for amplicons and individual subclones, which represent single alleles from individual cells. Within CpG-rich sequences, DNA methylation was found to be anti-correlated with CpG dinucleotide density and GC content, and methylated CpGs are more likely to be flanked by AT-rich sequences. We observed over-representation of CpG sites in distances of 9, 18, and 27 bps in highly methylated amplicons. However, DNA sequence alone is not sufficient to predict an amplicon's DNA methylation status, since 43% of all amplicons are differentially methylated between the cell types studied here. DNA methylation in promoter regions is strongly correlated with the absence of gene expression and low levels of activating epigenetic marks like H3K4 methylation and H3K9 and K14 acetylation. Utilizing the single base pair and single allele resolution of our data, we found that i) amplicons from different parts of a CpG island frequently differ in their DNA methylation level, ii) methylation levels of individual cells in one tissue are very similar, and iii) methylation patterns follow a relaxed site-specific distribution. Furthermore, iv) we identified three cases of allele-specific DNA methylation on chromosome 21. Our data shed new light on the nature of methylation patterns in human cells, the sequence dependence of DNA methylation, and its function as epigenetic signal in gene regulation. Further, we illustrate genotype-epigenotype interactions by showing novel examples of allele-specific methylation.
Quantification of Propionic Acid in the Bovine Spinal Disk After Infection of the Tissue With Propionibacteria acnes Bacteria (2017)

N/A.
Sprouty: how does the branch manager work? (2003)

Since the discovery of the prototypical Sprouty (Spry) protein in Drosophila, there has been an effort to determine how these novel modulators of the Ras/MAP-kinase pathway function. A clue to their mechanism of action comes from the several highly conserved sequences within all the currently known Spry isoforms: an approximately 110-residue cysteine-rich sequence in the C-terminal half that directs Spry proteins to a concentration of signaling proteins at the plasma membrane; a small motif surrounding a tyrosine residue (Y55 in human Spry2) that is responsible for interaction with other proteins. In cultured mammalian cells, hSpry2 inhibits epidermal growth factor receptor (EGFR) endocytosis and subsequently sustains the activation of MAP kinase but negatively regulates the same pathway following stimulation of fibroblast growth factor receptors (FGFRs). Current evidence indicates that Cbl is a key protein that interacts directly with Spry2 following activation of receptor tyrosine kinases (RTKs). It appears to be the ability of Cbl to interact as an E3 ubiquitin ligase on specific target proteins and as a docking protein in other contexts that dictates the differential effects Spry2 has on the Ras/MAP-kinase pathway following EGFR and FGFR activation.
Component selection and smoothing in multivariate nonparametric regression (2006)

We propose a new method for model selection and model fitting in multivariate nonparametric regression models, in the framework of smoothing spline ANOVA. The “COSSO” is a method of regularization with the penalty functional being the sum of component norms, instead of the squared norm employed in the traditional smoothing spline method. The COSSO provides a unified framework for several recent proposals for model selection in linear models and smoothing spline ANOVA models. Theoretical properties, such as the existence and the rate of convergence of the COSSO estimator, are studied. In the special case of a tensor product design with periodic functions, a detailed analysis reveals that the COSSO does model selection by applying a novel soft thresholding type operation to the function components. We give an equivalent formulation of the COSSO estimator which leads naturally to an iterative algorithm. We compare the COSSO with MARS, a popular method that builds functional ANOVA models, in simulations and real examples. The COSSO method can be extended to classification problems and we compare its performance with those of a number of machine learning algorithms on real datasets. The COSSO gives very competitive performance in these studies.
Temporal and cell-type specific expression of c-fos and c-jun protooncogenes in the mouse uterus after estrogen stimulation (1996)

Employing immunohistochemistry and in situ hybridization, we studied the temporal and cell type specific localization of c-Fos and c-Jun proteins and the corresponding messenger RNAs (mRNAs) elicited by a single 17beta-estradiol (E2) injection in the uteri of castrated adult mice. Cellular expression of mRNAs was in parallel with the synthesis of proteins within 1 h. E2 stimulated the c-fos expression rapidly and transiently in the epithelium and vascular endothelium. A second small peak of c-Fos protein and c-fos mRNA expression occurred around 11-13 h in the epithelium. No detectable amount of c-fos transcript and protein was present throughout the time course (0-24 h) in the stromal and myometrial cells. E2 treatment caused differential c-jun expression in all uterine cell types. In the epithelium, c-jun mRNA and protein expression was decreased during 1-6 h post injection, and thereafter returned showing small peak around 11-13 h. Induction of c-Jun protein and c-jun mRNA was evident in the stromal and myometrial cells at 2-3 h, and then the expression gradually decreased and returned to nearly control level by 24 h. E2 treatment induced rapid and transient activation of c-jun in the vascular endothelium. Present results suggest that transient increase of c-Fos and decrease of c-Jun protein at the early phase and coexpression of these proteins at the late phase contribute the proliferation of endometrial epithelium in mature mice. Furthermore, c-Fos and c-Jun expression in the vascular endothelium at the early phase may participate in the uterine imbibition.
Angiogenesis Research: Guidelines for Translation to Clinical Application (2001)

Angiogenesis research is being translated to the clinic. Certain guidelines may facilitate this effort. Recruitment of endothelial cells by a tumor is an early event in angiogenesis, a process regulated at genetic and epigenetic levels. The microvascular endothelial cell has become an important second target in cancer therapy. Angiogenesis inhibitors are either "direct" or "indirect" and their optimal dosing depends on a different logic than conventional chemotherapy. Conversely, antiangiogenic scheduling of chemotherapy can by-pass drug resistance. Like all solid tumors, hematologic malignancies are angiogenesis-dependent. Further, angiogenesis is modulated by proteins and cells from the hematopoietic and hemostatic systems. Clinical testing of angiogenesis inhibitors has accentuated the need for surrogate markers of tumor angiogenesis activity. Microvessel density, so valuable as a prognostic indicator of metastatic risk, cannot determine efficacy of an angiogenesis inhibitor. In the future, angiogenesis inhibitors may be added to chemotherapy or to radiotherapy, or to other modalities. Also, combinations of angiogenesis inhibitors may be administered together.
Structural alterations of faecal and mucosa‐associated bacterial communities in irritable bowel syndrome (2012)

Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disorder in western countries. Previous studies on IBS, mostly based on faecal samples, suggest alterations in the intestinal microbiota. However, no consensus has been reached regarding the association between specific bacteria and IBS. We explore the alterations of intestinal bacterial communities in IBS using massive sequencing of amplified 16S rRNA genes. Mucosal biopsies of the ascending and descending colon and faeces from 16 IBS patients and 9 healthy controls were analysed. Strong inter-individual variation was observed in the composition of the bacterial communities in both patients and controls. These communities showed less diversity in IBS cases. There were larger differences in the microbiota composition between biopsies and faeces than between patients and controls. We found a few over-represented and under-represented taxa in IBS cases with respect to controls. The detected alterations varied by site, with no changes being consistent across sample types.
Clinical and microbiological features of subjects with adult periodontitis who responded poorly to scaling and root planing (1997)

In a previous report, it was shown that scaling and root planing (SRP) decreased mean pocket depth and attachment level in subjects with adult periodontitis, as well as the levels and prevalence of Bacteroides forsythus, Porphyromonas gingivalis and Treponema denticola. However, a subset of subjects in that study exhibited mean loss of attachment following SRP. The purpose of the present investigation was to seek clinical and microbiological differences between subjects who responded well or poorly to SRP. 57 subjects with adult periodontitis were treated by full-mouth SRP under local anaesthetic. Clinical assessments of plaque, redness, suppuration, BOP, pocket depth and attachment level were made at 6 sites per tooth prior to and 3 months post-SRP. Attachment level measurements were repeated at each visit and differences in means between visits used to assess change. 18 subjects showed mean attachment loss 3 months post-SRP (poor response group), while 39 showed mean attachment level gain (good response group). The prevalence and levels of 40 subgingival taxa in subgingival plaque samples from the mesiobuccal site of each tooth (maximum 28 sites) in each subject prior to and 3 months post-SRP were assessed using checker-board DNA-DNA hybridization. The prevalence of each species was computed for each subject and averaged across subjects in the 2 treatment-response groups at each visit. Differences between groups were sought using the Mann-Whitney test. There were no statistically significant differences between the 2 response groups in any clinical parameter prior to therapy. Subjects in the good response group showed more attachment level gain at sites with baseline pocket depths of < 4 mm, 4-6 and > 6 mm than poor response subjects. Of 40 species evaluated, A. naeslundii genospecies 2 (A. viscosus), T. denticola, C. gracilis and C. rectus were significantly higher and more prevalent pre-therapy in the good response subjects. Mean attachment level change post SRP could be predicted using multiple linear regression with A. naeslundii genospecies 2 (A. viscosus) and T. denticola as the predictor variables (r2 = 0.373, p < 0.00001). Sites that gained > or = 2 mm of attachment post therapy showed a significant decrease in the counts of P. gingivalis (7.5 +/- 3.5 to 0.2 +/- 0.2 x 10(5)), T. denticola (8.2 +/- 3.5 to 1.8 +/- 1.1 x 10(5)) and B. forsythus (11.1 +/- 5.7 to 0.3 +/- 0.2 x 10(5)). The data of the present investigation indicate that SRP is most effective in subjects and sites with high levels of the subgingival species that this therapy affects.
Growth of Agricultural Journalism and Agricultural Research Information Centre at ICAR (1998)

Modern agricultural journalism was born in lndia with the advent of printing when three books on modem methods were got translated by Sir Syed Ahmad Khan. Now, ICAR publishes four journals and two newdetters in English and three in Hindi. Overall, about 250 periodicals in lndia are devoted to agriculture. The paper also describes the Agricultural Research lnformation Centre (ARIC) at Indian Council of Agricultural Research Headquarters, India, the databases available, publications broughtout and services rendered by the centre. Besides the importance of ARIC in SAARC countries, the proposals for the ninth plan are also discussed. http://dx.doi.org/10.14429/dbit.18.2.3390
Quantitation of DNA from exfoliated colonocytes isolated from human stool surface as a novel noninvasive screening test for colorectal cancer. (1998)

The only widely used screening test for early detection of colorectal cancer, the fecal occult blood test, lacks both sensitivity and specificity because it relies upon incidental bleeding rather than the neoplastic process. With the purpose of developing a new noninvasive diagnostic approach, we quantified DNA extracted from cells isolated from the surface of human stools by a novel procedure. Stools collected from 28 healthy individuals, 17 colorectal cancer patients, and 11 colorectal polyp patients were analyzed. A stool DNA index (SDNAI), expressed as DNA amount in nanograms per gram of stool, had a remarkable 4.5-fold difference in mean values between colorectal cancer patients and healthy people of comparable age. SDNAI was 2133 +/- 407 in the cancer group versus 469 +/- 65 in healthy people of the older (> 50 years) age group (P = 0.0005). The difference was independent of tumor location and size. If 700 ng of DNA/g of stool was taken as a cutoff SDNAI value in discrimination between older healthy people and cancer patients, sensitivity and specificity values reached 1.00 and 0.81, respectively. Age dependence of SDNAI was demonstrated by substantially lower SDNAI values (mean, 227 +/- 41) in younger healthy individuals. Polyp patients sometimes displayed elevated SDNAI values, but considerable variation was observed (mean, 1215 +/- 548). These preliminary findings indicate that SDNAI provides a novel, simple, and powerful noninvasive test for colorectal cancer early detection and screening. The fundamental advantage of the SDNAI is that it directly characterizes colonic epithelium involved in carcinogenesis.
Structure-function relationships in the sodium-potassium ATPase .alpha. subunit: site-directed mutagenesis of glutamine-111 to arginine and asparagine-122 to aspartic acid generates a ouabain-resistant enzyme (1988)

Na,K-ATPases from various species differ greatly in their sensitivity to cardiac glycosides such as ouabain. The sheep and human enzymes are a thousand times more sensitive than the corresponding ones from rat and mouse. To define the region of the alpha 1 subunit responsible for this differential sensitivity, chimeric cDNAs of sheep and rat were constructed and expressed in ouabain-sensitive HeLa cells. The construct containing the amino-terminal half of the rat alpha 1 subunit coding region and carboxyl-terminal half of the sheep conferred the ouabain-resistant phenotype to HeLa cells while the reverse construct did not. This indicates that the determinants involved in ouabain sensitivity are located in the amino-terminal half of the Na,K-ATPase alpha subunit. By use of site-directed mutagenesis, the amino acid sequence of the first extracellular domain (H1-H2) of the sheep alpha 1 subunit, Gln-Ala-Ala-Thr-Glu-Glu-Glu-Pro-Gln-Asn-Asp-Asn, was changed to that of the rat, Arg-Ser-Ala-Thr-Glu-Glu-Glu-Pro-Pro-Asn-Asp-Asp. When expressed in HeLa cells, this mutated sheep alpha 1 construct, like the rat/sheep chimera, was able to confer ouabain resistance to these cells. Furthermore, similar results were observed when HeLa cells were transfected with a sheep alpha 1 cDNA containing only two amino acid substitutions. This double mutation was a Gln-111----Arg and Asn-122----Asp change at the amino terminus and carboxyl terminus, respectively, of the H1-H2 extracellular region. The resistant cells, whether transfected with the rat alpha 1 cDNA, the rat/sheep chimera, or the mutant sheep alpha 1 cDNAs, exhibited identical biochemical characteristics including ouabain-inhibitable cell growth, 86Rb+ uptake, and Na,K-ATPase activity.(ABSTRACT TRUNCATED AT 250 WORDS)