gebhart/patrepeval huggingface dataset:
miR-17∼92 cooperates with RB pathway mutations to promote retinoblastoma (2011)

The miR-17~92 cluster is a potent microRNA-encoding oncogene. Here, we show that miR-17~92 synergizes with loss of Rb family members to promote retinoblastoma. We observed miR-17~92 genomic amplifications in murine retinoblastoma and high expression of miR-17~92 in human retinoblastoma. While miR-17~92 was dispensable for mouse retinal development, miR-17~92 overexpression, together with deletion of Rb and p107, led to rapid emergence of retinoblastoma with frequent metastasis to the brain. miR-17~92 oncogenic function in retinoblastoma was not mediated by a miR-19/PTEN axis toward apoptosis suppression, as found in lymphoma/leukemia models. Instead, miR-17~92 increased the proliferative capacity of Rb/p107-deficient retinal cells. We found that deletion of Rb family members led to compensatory up-regulation of the cyclin-dependent kinase inhibitor p21Cip1. miR-17~92 overexpression counteracted p21Cip1 up-regulation, promoted proliferation, and drove retinoblastoma formation. These results demonstrate that the oncogenic determinants of miR-17~92 are context-specific and provide new insights into miR-17~92 function as an RB-collaborating gene in cancer.
Generation of Novel Rapamycin Structures by Microbial Manipulations. (1995)

A new rapamycin producing culture was isolated and designated as Actinoplanes sp. N902-109. The addition of a cytochrome P-450 inhibitor and precursor feeding using this culture, and biotransformation approaches generated new rapamycin analogs with modifications at C-4, C-9, C-16, C-27, C-28 and/or C-39. The immunosuppressive activity of the resulting analogs was established in the mixed lymphocyte reaction assay.
Production of monoclonal antibodies to human IFN-? and their use for analysis of the antigenic composition of various natural interferons (1982)

We have established three hybridoma cell lines (designated EBI-1, -2, and -3) secreting immunoglobulin G (IgG) antibodies specific for human alpha-interferon (HuIFN-alpha) by fusing P3X63Ag8.6.5.3 myeloma cells with spleen cells of mice immunized with human "lymphoblastoid" (NC-37) interferon (IFN). The antibodies were used to study the antigenic diversity of a number of IFNs derived from blood leukocytes and lymphoid cell lines. When incubated with 10 U of IFN, EBI-1 antibodies completely neutralized the antiviral activity of HuIFN-alpha rA produced in E coli as well as of IFN produced spontaneously in several lymphoblastoid cell lines. In contrast, only 60-70% of alpha-interferon (IFN-alpha) induced in leukocytes, lymphoma, or lymphoblastoid cell lines by Sendai virus or poly (I):(C) could be neutralized by the antibody; furthermore, IFN-alpha produced spontaneously in bromodeoxyuridine-treated lymphoma cells was also only partially neutralized. EBI-2 and EBI-3 antibodies were tested against a smaller set of samples and found to react similarly. Our results indicate that human IFN-alpha subtypes can be grouped into at least two antigenically distinguishable subsets, one of which being represented by IFN-alpha A, and that these subsets can be expressed differently under different conditions in a given cell type.
Microbial Degradation of Liquid Polybutadiene (1978)

Acinetobacter sp. 351 isolated from soil grows well on butadiene oligomers and degrades 30 percent of a commercial sample of liquid polybutadiene (cis-1,4 type, Mn=650) in 3 days. From the gel permeation chromatography of the substrate after the degradation, the strain was shown to degrade butadiene oligomers with the degree of polymerization up to about 10, but not higher oligomers. The strain also grows on n-alkanes with carbon numbers from 9 to 40, and on some alkenes and fatty acid methyl esters. The assimilation and oxidation of butadiene oligomers were compared with those of n-alkanes and alkenes.
Syndecan-1 and E-cadherin expression in differentiated type of early gastric cancer (2005)

Loss of syndecan-1 plays a role in the growth of G-type cancers of DGCs at an early stage, and the reduction of syndecan-1 expression in IM surrounding the tumors may influence the growth of G-type cancer.
A framework for oligonucleotide microarray preprocessing (2010)

The oligo package is freely available through BioConductor, http://www.bioconductor.org.
Comparison of the Human Immunodeficiency Virus Type 1 and 2 Proteases by Hybrid Gene Construction and trans-Complementation (1989)

To determine the cleavage specificity of the proteases of the type 1 and 2 human immunodeficiency viruses (HIV-1, HIV-2), we interchanged this domain of the polymerase (pol) genes and analyzed the maturation programs of the chimeric polyproteins in an Escherichia coli expression system. In both cases, release of reverse transcriptase and integrase was observed, together with the respective 10-kDa protease form resulting from autocatalysis, although the maturation proceeded less efficiently compared to the homologous system. In further experiments, the ability of both HIV-1 and HIV-2 proteases to release in vivo gag p24 from an in-frame fusion of the full length gag and protease precursors was analyzed. In either case, p24 was released, albeit with greater efficiency in the heterologous gene construction. In vitro mixed lysate experiments with the HIV-1 gag precursor furthermore demonstrate that both enzymes respond to the aspartyl proteinase inhibitor pepstatin A. Taken together, these results illustrate that although different cleavage recognition sequences exist for HIV-1 and -2, they are amenable to the proteases of both viruses, but additionally that subtle differences in the mode of action of both enzymes are observable.
Inhibition of allergen-induced airway obstruction and leukotriene generation in atopic asthmatic subjects by the leukotriene biosynthesis inhibitor BAYx 1005 (1997)

These results indicate that BAYx 1005 is a potent inhibitor of allergen-provoked leukotriene synthesis in asthmatic subjects and lend further support to the suggestion that leukotrienes are important mediators of allergen-induced bronchoconstriction.
Excision repair of cis-diamminedichloroplatinum(II)-induced damage to DNA of Chinese hamster cells. (1979)

Platinum was lost from the DNA of cis-diamminedichloroplatinum(II) [cis-Pt(II)]-treated exponentially growing Chinese hamster V79-379A cells with a half-life of 28 hr. By contrast, platinum was lost from the DNA of cells treated in stationary-phase culture with a half-life of 4 days. Cells treated in and allowed to remain as a stationary-phase culture maintained an intact and apparently viable appearance. When the stationary-phase culture was diluted with fresh medium, cell division occurred, and cell survival, as measured by colony-forming ability, could be determined. Dilution of cells immediately after treatment with 40 micron cis-Pt(II) resulted in 0.19% control survival. There was an increase in the ability of the stationary-phase cells to survive cis-Pt(II) damage with time after treatment. Thus, after 3 days, the survival had increased from 0.19 to 15.9%. We demonstrate that this increased ability of stationary-phase cells to survive with time after treatment is due to DNA excision repair and hence that survival is inversely related to the extent of reaction of cis-Pt(II) with the DNA.
Incontinentia Pigmeni with nail dystrophy (2003)

A case of incontinentia pigmenti, a rare genodermatosis, with nail dystrophy and onycholysis is being reported.
Synthesis and biological activity of a conformationally constrained chemotactic gamma-lactam formyl tetrapeptide. (1996)

The synthesis and biological activity on human neutrophils of for-Met-(gamma-lactam)-Leu-Phe-OMe [fM(gamma l)LP-OMe], an analogue of the chemotactic fMLP-OMe, are reported. The tetrapeptide evidences chemotactic activity as well as superoxide anion production and lysozyme release, although with lower efficacy when compared with the parent tripeptide.
Effects of local compression on peroneal nerve function in humans (1993)

A new apparatus was developed to compress the anterior compartment selectively and reproducibly in humans. Thirty-five normal volunteers were studied to determine short-term thresholds of local tissue pressure that produce significant neuromuscular dysfunction. Local tissue fluid pressure adjacent to the deep peroneal nerve was elevated by the compression apparatus and continuously monitored for 2-3 h by the slit catheter technique. Elevation of tissue fluid pressure to within 35-40 mm Hg of diastolic blood pressure (approximately 40 mm Hg of in situ pressure in our subjects) elicited a consistent progression of neuromuscular deterioration including, in order, (a) gradual loss of sensation, as assessed by Semmes-Weinstein monofilaments, (b) subjective complaints, (c) reduced nerve conduction velocity, (d) decreased action potential amplitude of the extensor digitorum brevis muscle, and (e) motor weakness of muscles within the anterior compartment. Generally, higher intracompartmental pressures caused more rapid deterioration of neuromuscular function. In two subjects, when in situ compression levels were 0 and 30 mm Hg, normal neuromuscular function was maintained for 3 h. Threshold pressures for significant dysfunction were not always the same for each functional parameter studied, and the magnitudes of each functional deficit did not always correlate with compression level. This variable tolerance to elevated pressure emphasizes the need to monitor clinical signs and symptoms carefully in the diagnosis of compartment syndromes. The nature of the present studies was short term; longer term compression of myoneural tissues may result in dysfunction at lower pressure thresholds.
Table-top x-ray lasing based on optical-field-induced ionization (1992)

Table-top x-ray laser schemes in H- and Li-like ions following optical-field-induced ionization are discussed. The use of ultrashort ({le}100 fsec) ionizing pulses is shown to be necessary to keep secondary heating mechanisms, e.g., stimulated Raman scattering, at acceptable levels. The combination of longitudinal pumping and ultrashort pulses gives modest energy requirements (E{sub in}{le}0.1 J for Li-like Ne). The effects of plasma dispersion and longitudinal pumping, on the relative speeds of the ionizing laser pulse and the x- ray photons, are included in our calculations. The x-ray laser scheme is calculated to have relatively high energy efficiencies (E{sub out}/E{sub in}{ge} 10{minus}5) in Li-like Ne at 98 {angstrom}. Two approaches for creating the initial high-density gas/plasma using a laser heated thin film and a high-density gas jet are described. Applications in material science and chemistry, e.g., photoelectron spectroscopy, requiring the high-repetition rate (10--100 Hz) of the proposed x-ray laser are discussed.
Mechanism of incision by an apurinic≤apyrimidinjc endonuclease present in human placenta (1989)

An apparently homogeneous enzyme preparation, containing an apurinic/apyrimidinic (AP) endonuclease from human placenta, was by DNA sequencing analysis found to act as a class I AP-endonuclease, i.e. produce a 3'-deoxyribose and 5'-phosphomonoester nucleotide termini.
Forensic Applications of Whole Genome Amplification (2011)

Whole genome amplification (WGA) has been touted as a possible technique to augment fragment analysis of STRs in amplifying low-levels of DNA recovered from crime scenes or items. Only LCN DNA analysis is routinely used as an additional amplification step; but this is not without problems, such as the increased incidents of stochastic variations.&#13;\nA review of the literature was carried out in order to assess the latest research and to identify a potentially fit for purpose whole genome amplification technique.&#13;\nThere are three potential alternative techniques which show promise, miPEP, dcDOP-PCR and MDA used in conjunction with a macromolecular crowder; with the majority of studies investigating the effect of non-crowded MDA on a variety of stains, including degraded, low-level and stains containing mixtures of DNA.&#13;\nA number of techniques are suggested for incorporation into STR analysis depending on the sample type as well as future strands of work.
ID-based authentication system for computer virus detection (1990)

Authentication systems for computer virus detection are presented. The systems are based on identity-based signature schemes which can simplify the system management. In the systems a software maker signs software with his own secret key and users verify whether the software is infected with computer virus or not using one public key. Users have only to keep the public key, instead of keys corresponding to each software maker. The key management can therefore be simplified by the use of ID-based authentication systems.
Immunogenic tumor cell death induced by chemoradiotherapy: molecular mechanisms and a clinical translation (2013)

Chemoradiotherapy can induce immunogenic cell death, triggering danger signals such as high-mobility group box 1 protein, and resulting in T-cell immunity. This concept can potentially be harnessed for clinical therapy to enhance tumor-specific immunity. There is however limited information to translate this theory directly in a clinical setting. In this review, we will discuss and summarize molecular and cellular mechanisms underlying immunogenic tumor cell death induced by chemoradiotherapy, with emphasis on a clinical translation.
A methodology for automatic intensity-modulated radiation treatment planning for lung cancer (2011)

In intensity-modulated radiotherapy (IMRT), the quality of the treatment plan, which is highly dependent upon the treatment planner's level of experience, greatly affects the potential benefits of the radiotherapy (RT). Furthermore, the planning process is complicated and requires a great deal of iteration, and is often the most time-consuming aspect of the RT process. In this paper, we describe a methodology to automate the IMRT planning process in lung cancer cases, the goal being to improve the quality and consistency of treatment planning. This methodology (1) automatically sets beam angles based on a beam angle automation algorithm, (2) judiciously designs the planning structures, which were shown to be effective for all the lung cancer cases we studied, and (3) automatically adjusts the objectives of the objective function based on a parameter automation algorithm. We compared treatment plans created in this system (mdaccAutoPlan) based on the overall methodology with plans from a clinical trial of IMRT for lung cancer run at our institution. The 'autoplans' were consistently better, or no worse, than the plans produced by experienced medical dosimetrists in terms of tumor coverage and normal tissue sparing. We conclude that the mdaccAutoPlan system can potentially improve the quality and consistency of treatment planning for lung cancer.
Human motion: modeling and recognition of actions and interactions (2004)

Processing of image sequences has progressed from simple structure from motion paradigm to the recognition of actions/interactions as events. Understanding human activities in video has many potential applications including automated surveillance, video archival/retrieval, medical diagnosis, sports analysis, and human-computer interaction. Understanding human activities involves various steps of low-level vision processing such as segmentation, tracking, pose recovery, and trajectory estimation as well as high-level processing tasks such as body modeling and representation of action. While low-level processing has been actively studied, high-level processing is just beginning to receive attention. This is partly because high-level processing depends on the results of low-level processing. However, high-level processing also requires some independent and additional approaches and methodologies. We focus on the following aspects of high-level processing: (1) human body modeling, (2) level of detail needed to understand human actions, (3) approaches to human action recognition, and (4) high-level recognition schemes with domain knowledge. The review is illustrated by examples of each of the areas discussed, including recent developments in our work on understanding human activities.
Developmental changes of hematoside of rat small intestine. Postnatal hydroxylation of fatty acids and sialic acid. (1983)

The hematoside of rat intestine is analyzed from 1 day to 60 days of age. During the first 3 weeks of life, GM3 (N-acetylneuraminylgalactosylglucosylceramide) contains only nonhydroxylated fatty acids and accounts for 80-90% of the ganglioside sialic acid. Its concentration is maximum at 6 days (315 micrograms of NeuAc/g of intestine) and falls abruptly over the next 2 weeks. It reaches 45 micrograms of NeuAc/g of intestine at 60 days. Between 28 and 60 days, GM3 accounts for 72% of the total intestinal gangliosides. From 21 days on, structural modifications of GM3 are observed. N-Acetylneuraminic acid is replaced progressively by N-glycolylneuraminic acid and nonhydroxylated fatty acids are replaced by alpha-hydroxylated fatty acids. Both changes are interpreted as the result of hydroxylations of GM3 components which are triggered at the time of weaning. These hydroxylations take place chiefly in epithelial cells and to a much lesser extent in nonepithelial residue, as shown by the separate analysis of both compartments of rat intestine at 38 and 60 days. In epithelial cells, the highest percentage of alpha-hydroxylated fatty acids and of N-glycolylneuraminic acid is found at 60 days. In addition, 4 D-hydroxysphinganine is the major base of the GM3 of intestinal cells from birth to adulthood.
Evidence for a second cell cycle block at G2/M by p53. (1995)

Wild type p53 can induce cell cycle arrest at specific points in the cell cycle, in particular G1/S, an ability lost by most p53 mutants. We have previously reported that p53 mutant genes can rescue REF52 cells from ras-induced growth arrest and that over expression of wild type p53 inhibits cell growth in these cells. In this paper we examined whether p53 can also induce cell cycle arrest at the G2/M boundary of the cell cycle. To accomplish this we used the REF52 cell line and the temperature sensitive p53val135 mutant allele. Cells were enriched in the late G1 and early S phases before the temperature shift. REF52 cells expressing mutant-p53val135 alone with an activated H-ras gene arrest primarily at the G1/S and G2/M parts of the cell cycle at the restrictive temperature, as determined by flow cytometry analysis. These results suggest that the anti-proliferative activity of p53 may be involved in regulation of the cell cycle at the G2/M restriction point as well as transit through G1/S and initiation of DNA synthesis.
Multimodal Magnetic‐Resonance/Optical‐Imaging Contrast Agent Sensitive to NADH (2009)

Agents get smart: A macrocycle-based gadolinium complex undergoes an isomerization in the presence of NADH, leading to an r1 relaxivity increase of 54 %, while the intense fluorescence disappears (see scheme). This agent could facilitate the use of magnetic resonance imaging (MRI) for probing tissue redox status. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Polymorphisms inPPARGenes (PPARD,PPARG, andPPARGC1A) and the Risk of Chronic Kidney Disease in Japanese: Cross-Sectional Data from the J-MICC Study (2013)

Chronic kidney disease (CKD) is well known as a strong risk factor for both end stage renal disease and cardiovascular disease. To clarify the association of polymorphisms in the PPAR genes (PPARD, PPARG, and PPARGC1A) with the risk of CKD in Japanese, we examined this association among the Japanese subjects using the cross-sectional data of J-MICC (Japan Multi-Institutional Collaborative Cohort) Study. The subjects for this analysis were 3,285 men and women, aged 35-69 years, selected from J-MICC Study participants; genotyping was conducted by multiplex polymerase chain reaction-based Invader assay. The prevalence of CKD was determined for CKD stages 3-5 (defined as eGFR < 60 ml/min/1.73 m(2)). Participants with CKD accounted for 17.3% of the study population. When those with PPARD T-842C T/T were defined as reference, those with PPARD T-842C T/C and C/C demonstrated the OR for CKD of 1.26 (95%CI 1.04-1.53) and 1.31 (95%CI 0.83-2.06), respectively. There were no significant associations between the polymorphisms in other PPAR genes and the risk of CKD. The present study found a significantly increased risk of CKD in those with the C allele of PPARD T-842C, which may suggest the possibility of personalized risk estimation of this life-limiting disease in the near future.
Measurement of Glial Fibrillary Acidic Protein in Human Blood: Analytical Method and Preliminary Clinical Results (1999)

girls (n 110; r 0.426; P 0.0001), and in boys and girls together (n 230; r 0.306; P 0.0001).
Copper-Catalyzed, Palladium-Free Carbonylative Sonogashira Coupling Reaction of Aliphatic and Aromatic Alkynes with Iodoaryls (2008)

Copper bis(2,2,6,6-tetramethyl-3,5-heptanedionate) catalyzed carbonylative Sonogashira coupling reactions of aliphatic/aromatic alkynes with iodoaryls are reported for the first time. The protocol eliminates the use of a toxic, air-sensitive, and expensive Pd-phosphine-based catalytic system, and provides high yields of desired products.
Heat acclimation in rats: modulation via lipid polyunsaturation (2002)

Heat acclimation of rats has been shown to enhance endurance of rat hearts to ischemic insult and acute heat stress. Common protective features have been shown to be operative during both these stress-inducing conditions. To explore the role of membrane lipid composition in the adaptive response, we analyzed two major parameters that impact membrane dynamics and order, the nonesterified cholesterol levels and the acyl chain composition of phospholipids, in rat heart and salivary glands, both major thermoregulatory organs, in short- and long-term heat-acclimated rats. Before exposure to heat, control salivary gland tissue has a higher cholesterol-to-phospholipid mole ratio (0.32 +/- 0.02) than heart (0.14 +/- 0.01), and the acyl chains of its phospholipids are 50% more saturated. The remodeling strategies of the tissues after exposure to heat differed. Heart cholesterol levels increased after short-term heat acclimation (approximately 50%), whereas salivary gland cholesterol levels decreased in acute heat stress and long-term heat acclimation (approximately 32%). Remodeling of phospholipid acyl chains, particularly an increase in docosahexaenoic acid, was a protective strategy in both tissues (57% in heart and >100% in salivary glands). Modifying membrane lipid composition by treating rats with liposomes composed of egg phosphatidylcholine (PC) before exposure to heat resulted in a 38% increase in endurance to thermal stress. The density and affinity of muscarinic receptors of submaxillary salivary glands, involved in the acclimation response, were measured in control and PC liposome-treated rats, and then both groups were subjected to short-term heat acclimation. After PC treatment the well-established compensatory upregulation of the muscarinic receptors and concomitant decrease in their affinity was blunted. The substantial increase in the thermal endurance of heat-challenged intact rats after treatment with PC liposomes (600 vs. 200 min) suggests that membrane lipid composition plays a role in the ability of these tissues to respond to heat stress.