gebhart/patrepeval huggingface dataset:
Lack of TXNIP protects β-cells against glucotoxicity (2008)

Glucotoxicity plays a major role in pancreatic beta-cell apoptosis and diabetes progression, but the factors involved have remained largely unknown. Our recent studies have identified TXNIP (thioredoxin-interacting protein) as a novel pro-apoptotic beta-cell factor that is induced by glucose, suggesting that TXNIP may play a role in beta-cell glucotoxicity. Incubation of INS-1 beta-cells and isolated primary mouse and human islets at high glucose levels led to a significant increase in TXNIP as well as in apoptosis. Very similar results were obtained in vivo in islets of diabetic mice. To determine whether TXNIP plays a causative role in glucotoxic beta-cell death, we used TXNIP-deficient islets of HcB-19 mice harbouring a natural nonsense mutation in the TXNIP gene. We incubated islets of HcB-19 and C3H control mice at low and high glucose levels and assessed them for TXNIP expression and apoptosis. Interestingly, whereas in C3H islets, high glucose levels led again to significant elevation of TXNIP and apoptosis levels as measured by TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick-end labelling) and cleaved caspase 3, no increase in apoptosis was observed in TXNIP-deficient HcB-19 islets, indicating that TXNIP is required for beta-cell death caused by glucotoxicity. Thus inhibition of TXNIP protects against glucotoxic beta-cell apoptosis and therefore may represent a novel therapeutic approach to halt diabetes progression.
A networked system for self-management of drug therapy and wellness (2010)

Background: A networked wellness system is under development to document actual ingestions of oral medications, to differentiate types/doses of drugs taken simultaneously, and to provide these data along with other metrics to patients and providers for individually tailored care. Methods: After ingestion, an edible sensor (embedded in drug) is activated by stomach fluid and communicates to a wearable monitor that identifies the sensor as unique and records ingestion time/date. The monitor also collects physiologic data and communicates via mobile phone to a secure server that integrates the data with other wireless devices (e.g. blood pressure, weight). Summary reports are generated periodically for patient and physician review. Results: No adverse effects were observed in animals using repeated, exaggerated doses of sensors. Two drug-sensor form factors have been tested in 3392 human ingestions with no major and very few minor adverse effects. Sensitivity was 97.0% and specificity was 97.7% when compared to directly observed ingestion. The system identified and differentiated up to 4 simultaneously ingested sensors with an identification accuracy of 100%. Data integration with multiple devices and report generation have been piloted successfully. Conclusions: Pre-clinical and early clinical system safety appear satisfactory; data integration and communication appear to be feasible. By providing context-rich information and fostering communication, this system may enhance patient-provider relationship and care coordination.
Controlled Switching of HVAC Circuit Breakers: Application Examples and Benefits (2008)

Controlled switching technology, that is, predefined controlled strategies for closing and/or opening each independent circuit breaker pole, is an effective way to reduce switching transients, prevent equipment failures, and improve power quality. The paper presents a tutorial on controlled switching of high-voltage ac (HVAC) circuit breakers and describes the controlled switching theory and technology that is in use today. The paper discusses the benefits of controlled switching and shares one utility's applications and experiences with the controlled switching of shunt capacitors, shunt reactors, transformers, and lines, using modern protective relays and control devices. The paper also discusses how to select the optimum controlled switching times to reduce switching transients.
Aberration in DNA Methylation in B-Cell Lymphomas Has a Complex Origin and Increases with Disease Severity (2013)

Despite mounting evidence that epigenetic abnormalities play a key role in cancer biology, their contributions to the malignant phenotype remain poorly understood. Here we studied genome-wide DNA methylation in normal B-cell populations and subtypes of B-cell non-Hodgkin lymphoma: follicular lymphoma and diffuse large B-cell lymphomas. These lymphomas display striking and progressive intra-tumor heterogeneity and also inter-patient heterogeneity in their cytosine methylation patterns. Epigenetic heterogeneity is initiated in normal germinal center B-cells, increases markedly with disease aggressiveness, and is associated with unfavorable clinical outcome. Moreover, patterns of abnormal methylation vary depending upon chromosomal regions, gene density and the status of neighboring genes. DNA methylation abnormalities arise via two distinct processes: i) lymphomagenic transcriptional regulators perturb promoter DNA methylation in a target gene-specific manner, and ii) aberrant epigenetic states tend to spread to neighboring promoters in the absence of CTCF insulator binding sites.
Function of Cytochrome P450 Enzymes RosC and RosD in the Biosynthesis of Rosamicin Macrolide Antibiotic Produced by Micromonospora rosaria (2012)

The cytochrome P450 enzyme-encoding genes rosC and rosD were cloned from the rosamicin biosynthetic gene cluster of Micromonospora rosaria IFO13697. The functions of RosC and RosD were demonstrated by gene disruption and complementation with M. rosaria and bioconversion of rosamicin biosynthetic intermediates with Escherichia coli expressing RosC and RosD. It is proposed that M. rosaria IFO13697 has two pathway branches that lead from the first desosaminyl rosamicin intermediate, 20-deoxo-20-dihydro-12,13-deepoxyrosamicin, to rosamicin.
[Surveys of the epidemiological team of the French Rheumatology Society (RESFR) on the prescription of D-penicillamine in the treatment of rheumatoid polyarthritis]. (1986)

Two surveys carried out by the Epidemiology Team of the French Rheumatology Society (RESFR) were used to assess the treatment of rheumatoid arthritis (RA) by means of D-penicillamine (DP). In the initial survey, which is described in this article, 119 rheumatologists throughout France were asked to give their opinion as to the place of DP: they use this drug in cases of severe RA, usually after gold salts and synthetic antimalarials have proved ineffective. The dosage is generally 600 mg per day, with a maximum dosage of 900 mg per day. The rheumatologists consider DP an effective treatment with good or fair clinical safety. The most frequent adverse reactions are proteinuria and skin eruptions.
Genetic Analysis of Human Traits In Vitro: Drug Response and Gene Expression in Lymphoblastoid Cell Lines (2008)

Lymphoblastoid cell lines (LCLs), originally collected as renewable sources of DNA, are now being used as a model system to study genotype-phenotype relationships in human cells, including searches for QTLs influencing levels of individual mRNAs and responses to drugs and radiation. In the course of attempting to map genes for drug response using 269 LCLs from the International HapMap Project, we evaluated the extent to which biological noise and non-genetic confounders contribute to trait variability in LCLs. While drug responses could be technically well measured on a given day, we observed significant day-to-day variability and substantial correlation to non-genetic confounders, such as baseline growth rates and metabolic state in culture. After correcting for these confounders, we were unable to detect any QTLs with genome-wide significance for drug response. A much higher proportion of variance in mRNA levels may be attributed to non-genetic factors (intra-individual variance--i.e., biological noise, levels of the EBV virus used to transform the cells, ATP levels) than to detectable eQTLs. Finally, in an attempt to improve power, we focused analysis on those genes that had both detectable eQTLs and correlation to drug response; we were unable to detect evidence that eQTL SNPs are convincingly associated with drug response in the model. While LCLs are a promising model for pharmacogenetic experiments, biological noise and in vitro artifacts may reduce power and have the potential to create spurious association due to confounding.
Assessment of infection in diabetic foot ulcers (2000)

Typical signs of infection in diabetic foot ulcers are often absent or late. This literature review outlines the factors practitioners must take into account when assessing for and managing such infections.
A novel and comprehensive mouse model of human non-alcoholic steatohepatitis with the full range of dysmetabolic and histological abnormalities induced by gold thioglucose and a high-fat diet (2011)

Treatment with GTG and HF diet induce, in mice, a comprehensive model of human NASH, with the full range of dysmetabolic and histological abnormalities.
Beta1 integrin-mediated adhesion between renal tubular cells after anoxic injury. (1997)

beta 1 integrin-mediated adhesion between renal tubular cells after anoxic injury. This study examined the effect of sublethal injury, induced by ATP depletion (5 mM cyanide in the absence of dextrose), on the distribution and function of beta 1 integrins in primary cultures of mouse proximal tubular (MPT) cells. It was shown in this study that sublethal injury results in loss of focal contacts present in uninjured MPT cells, and that the beta 1 integrin molecule becomes redistributed to the apical membrane domain of sublethally injured cells. Polystyrene beads coated with Arg-Gly-Asp (RGD)-containing peptide adhere to the surface of sublethally injured MPT cells but not to control, dextrose-treated cells, indicating that the beta 1 integrins present on the apical surface of the cell remain functional. The presence of an excess of free RGD-containing peptide reduces binding of RGD-coated beads to sublethally injured MPT cells by approximately 50%. It was also demonstrated that adherence of MPT cells in suspension to cyanide-treated monolayers is increased more than 300% above adhesion to control, uninjured monolayers. This abnormal cell-cell adhesion is ameliorated by the presence of an excess of RGD-containing peptide and is reversed if cyanide-treated cells are allowed to recover for 1 h. It was concluded that the beta 1 integrin becomes expressed on the apical surface of MPT cells after sublethal injury. These apically expressed integrins remain functional and mediate aberrant adhesion between MPT cells.
<title>Melody retrieval on the web</title> (2001)

This paper explores issues involved in a web-based query-by-humming system, which can find a piece of music in the digital music repository based on hummed melodies. Melody representation, melody matching, melody extraction and query construction are critical for an efficient and robust query-by-humming system and thus the focuses of this paper. Compared to previous systems, a new and more effective melody representation and corresponding melody matching methods which combined both pitch and rhythmic information were adopted, a whole set of tools and deliverable software were implemented, and experiments were conducted to evaluate the system. The experimental results demonstrate that our methods are more effective for most users than other existing methods.
Assessment of serum CYFRA 21-1 in lung cancer (1996)

These findings suggest that serum assays of CYFRA 21-1 are clinically useful for the diagnosis of lung carcinoma.
Combinations of BRAF, MEK, and PI3K/mTOR Inhibitors Overcome Acquired Resistance to the BRAF Inhibitor GSK2118436 Dabrafenib, Mediated by NRAS or MEK Mutations (2012)

Recent results from clinical trials with the BRAF inhibitors GSK2118436 (dabrafenib) and PLX4032 (vemurafenib) have shown encouraging response rates; however, the duration of response has been limited. To identify determinants of acquired resistance to GSK2118436 and strategies to overcome the resistance, we isolated GSK2118436 drug-resistant clones from the A375 BRAF(V600E) and the YUSIT1 BRAF(V600K) melanoma cell lines. These clones also showed reduced sensitivity to the allosteric mitogen-activated protein/extracellular signal-regulated kinase (MEK) inhibitor GSK1120212 (trametinib). Genetic characterization of these clones identified an in-frame deletion in MEK1 (MEK1(K59del)) or NRAS mutation (NRAS(Q61K) and/or NRAS(A146T)) with and without MEK1(P387S) in the BRAF(V600E) background and NRAS(Q61K) in the BRAF(V600K) background. Stable knockdown of NRAS with short hairpin RNA partially restored GSK2118436 sensitivity in mutant NRAS clones, whereas expression of NRAS(Q61K) or NRAS(A146T) in the A375 parental cells decreased sensitivity to GSK2118436. Similarly, expression of MEK1(K59del), but not MEK1(P387S), decreased sensitivity of A375 cells to GSK2118436. The combination of GSK2118436 and GSK1120212 effectively inhibited cell growth, decreased ERK phosphorylation, decreased cyclin D1 protein, and increased p27(kip1) protein in the resistant clones. Moreover, the combination of GSK2118436 or GSK1120212 with the phosphoinositide 3-kinase/mTOR inhibitor GSK2126458 enhanced cell growth inhibition and decreased S6 ribosomal protein phosphorylation in these clones. Our results show that NRAS and/or MEK mutations contribute to BRAF inhibitor resistance in vitro, and the combination of GSK2118436 and GSK1120212 overcomes this resistance. In addition, these resistant clones respond to the combination of GSK2126458 with GSK2118436 or GSK1120212. Clinical trials are ongoing or planned to test these combinations.
Photolabile Linkers for Solid-Phase Synthesis (2018)

Photolabile linkers are the subjects of intense research because they allow the release of the target molecule simply by irradiation. Photochemical release of synthesis products is often facilitated without additional reagents under mild reaction conditions, which may even be environmentally friendly and appealing in the context of greener chemistry. The mild conditions also allow for applications of released material in subsequent biological screening experiments, where contamination with cleavage reagents would be detrimental. This Review pays attention to the increasing number of photolabile linkers developed for solid-phase synthesis and release and covers: (i) o-nitrobenzyloxy linkers, (ii) o-nitrobenzylamino linkers, (iii) α-substituted o-nitrobenzyl linkers, (iv) o-nitroveratryl linkers, (v) phenacyl linkers, (vi) p-alkoxyphenacyl linkers, (vii) benzoin linkers, (viii) pivaloyl linkers, and (ix) other photolabile linkers.
Oxidative decarboxylation of retinoic acid in microsomes of rat liver and kidney (1968)

Liver and kidney microsomes have been found to catalyze a rapid decarboxylation of retinoic acid in vitro. The reaction requires NADPH and Fe(2+), and is further stimulated by the presence of pyrophosphate. Thiamine pyrophosphate contained sufficient iron as an impurity to provide strong enhancement of the reaction in the absence of added iron. The decarboxylation could also be shown to occur nonenzymatically in the presence of ascorbate, Fe(2+), and boiled microsomes, but there was little autoxidation resulting in decarboxylation. The reaction was strongly inhibited by chelating agents, N,N'-diphenyl-p-phenylene diamine, phenazine methosulfate, and ferricyanide, and resembled lipid peroxidation in both its cofactor requirements and response to inhibitors. The product of the reaction appeared to lack only the C-15 of the original retinoic acid molecule. It was not retained by diethylaminoethyl cellulose, was more polar than retinoic acid upon silicic acid chromatography, had a lower UV absorption maximum (295 m micro ) than the starting product, and seemed to have an aldehyde group at C-14. The physiological significance of the decarboxylation remains to be assessed, but its rapidity makes it important to in vitro work on retinoic acid.
Disease-specific motifs can be identified in circulating nucleic acids from live elk and cattle infected with transmissible spongiform encephalopathies (2008)

To gain insight into the disease progression of transmissible spongiform encephalopathies (TSE), we searched for disease-specific patterns in circulating nucleic acids (CNA) in elk and cattle. In a 25-month time-course experiment, CNAs were isolated from blood samples of 24 elk (Cervus elaphus) orally challenged with chronic wasting disease (CWD) infectious material. In a separate experiment, blood-sample CNAs from 29 experimental cattle (Bos taurus) 40 months post-inoculation with clinical bovine spongiform encephalopathy (BSE) were analyzed according to the same protocol. Next-generation sequencing provided broad elucidation of sample CNAs: we detected infection-specific sequences as early as 11 months in elk (i.e. at least 3 months before the appearance of the first clinical signs) and we established CNA patterns related to BSE in cattle at least 4 months prior to clinical signs. In elk, a progression of CNA sequence patterns was found to precede and correlate with macro-observable disease progression, including delayed CWD progression in elk with PrP genotype LM. Some of the patterns identified contain transcription-factor-binding sites linked to endogenous retroviral integration. These patterns suggest that retroviruses may be connected to the manifestation of TSEs. Our results may become useful for the early diagnosis of TSE in live elk and cattle.
Noninvasive volumetric quality evaluation of post-surgical clear corneal incision via high-resolution Fourier-domain optical coherence tomography (2010)

A novel approach for post-surgical evaluation of clear corneal incision quality is presented. The complete volumetric information of an ex-vivo bovine cornea with incision and suture is obtained by high-resolution Fourier-domain optical coherence tomography and illustrated by various computer graphics technologies. This method provides more comprehensive information to evaluate surgery quality and monitor the healing process.
Surface Self-Assembled PEGylation of Fluoro-Based PVDF Membranes via Hydrophobic-Driven Copolymer Anchoring for Ultra-Stable Biofouling Resistance (2013)

Stable biofouling resistance is significant for general filtration requirements, especially for the improvement of membrane lifetime. A systematic group of hyper-brush PEGylated diblock copolymers containing poly(ethylene glycol) methacrylate (PEGMA) and polystyrene (PS) was synthesized using an atom transfer radical polymerization (ATRP) method and varying PEGMA lengths. This study demonstrates the antibiofouling membrane surfaces by self-assembled anchoring PEGylated diblock copolymers of PS-b-PEGMA on the microporous poly(vinylidene fluoride) (PVDF) membrane. Two types of copolymers are used to modify the PVDF surface, one with different PS/PEGMA molar ratios in a range from 0.3 to 2.7 but the same PS molecular weights (MWs, ∼5.7 kDa), the other with different copolymer MWs (∼11.4, 19.9, and 34.1 kDa) but the similar PS/PEGMA ratio (∼1.7 ± 0.2). It was found that the adsorption capacities of diblock copolymers on PVDF membranes decreased as molar mass ratios of PS/PEGMA ratio reduced or molecular weights of PS-b-PEGMA increased because of steric hindrance. The increase in styrene content in copolymer enhanced the stability of polymer anchoring on the membrane, and the increase in PEGMA content enhanced the protein resistance of membranes. The optimum PS/PEGMA ratio was found to be in the range between 1.5 and 2.0 with copolymer MWs above 20.0 kDa for the ultrastable resistance of protein adsorption on the PEGylated PVDF membranes. The PVDF membrane coated with such a diblock copolymer owned excellent biofouling resistance to proteins of BSA and lysozyme as well as bacterium of Escherichia coli and Staphylococcus epidermidis and high stable microfiltration operated with domestic wastewater solution in a membrane bioreactor.
Regulation of gene transcription by estrogen and progesterone. Lack of hormonal effects on transcription by Escherichia coli RNA polymerase. (1980)

Estrogen and progesterone markedly stimulate transcription of ovalbumin and conalbumin (transferrin) genes in chick oviduct as measured by hybridization of labeled RNA synthesized in isolated nuclei to immobilized plasmid DNA containing these gene sequences. Using this direct assay for specific gene transcription, we explored the basis of previous reports indicating that steroid hormones also cause changes in oviduct chromatin structure that can be detected by Escherichia coli RNA polymerase. We observed no effect of these hormones on the ability of E. coli RNA polymerase to transcribe specifically the conalbumin and ovalbumin genes 8 1/2 h after hormone administration when transcription of these genes by endogenous RNA polymerase was elevated 5- and 30-fold, respectively. Furthermore, we were unable to detect any significant effect of either of these hormones on the total number of E. coli RNA polymerase binding sites in oviduct nuclei or chromatin. In contrast, after several days of hormone administration, we detected an apparent preferential ovalbumin RNA synthesis by E. coli RNA polymerase and this effect could be transferred to unstimulated nuclei by a 0.35 M salt extract of active nuclei. However, further experiments revealed that this preferential ovalbumin RNA synthesis is an artifact produced by transcription from contaminating ovalbumin mRNA. We conclude that E. coli RNA polymerase does not recognize steroid hormone-induced changes in oviduct chromatin.
Visualizing the kinetics of tumor-cell clearance in living animals (1999)

Evaluation of potential antineoplastic therapies would be enhanced by noninvasive detection of tumor cells in living animals. Because light is transmitted through mammalian tissues, it was possible to use bioluminescence to monitor (both externally and quantitatively) growth and regression of labeled human cervical carcinoma (HeLa) cells engrafted into immunodeficient mice. The efficacy of both chemotherapy and immunotherapeutic treatment with ex vivo expanded human T cell-derived effector cells was evaluated. In the absence of therapy, animals showed progressive increases in signal intensity over time. Animals treated with cisplatin had marked reductions in tumor signal; 5'-fluorouracil was less effective, and cyclophosphamide was ineffective. Immunotherapy dramatically reduced signals at high effector-to-target cell ratios, and significant decreases were observed with lower ratios. This model system allowed sensitive, quantitative, real-time spatiotemporal analyses of the dynamics of neoplastic cell growth and facilitated rapid optimization of effective treatment regimens.
Spectral measurement of absorption by spectroscopic frequency-domain optical coherence tomography (2000)

A new method of measurement that essentially combines Fourier-domain optical coherence tomography with spectroscopy is introduced. By use of a windowed Fourier transform it is possible to obtain, in addition to the object structure, spectroscopic information such as the absorption properties of materials. The feasibility of this new method for performing depth-resolved spectroscopy is demonstrated with a glass filter plate. The results are compared with theoretically calculated spectra by use of the well-known spectral characteristics of the light source and the filter plate.