gebhart/patrepeval huggingface dataset:
Molecular cloning and characterization of Escherichia coli K12 ygjG gene (2003)

Expression of E. coli K12 ygjG coding region revealed sigma54-depended ORF which encodes a 459-amino acid protein with putrescine:2-OG aminotransferase activity. The enzyme also was able to transaminate cadaverine and, in lower extent, spermidine.
Evaluation of S9788 as a potential modulator of drug resistance against human tumour sublines expressing differing resistance mechanisms In Vitro (1993)

Significant activity has been identified using S9788, a triazineaminopiperidine derivative, as a new modulator of multi-drug resistance against a series of drug-resistant human tumour-cell lines in vitro. Maximal non-cytotoxic concentrations (i.e., those resulting in < or = 10% cytotoxicity) of S9788 or verapamil were tested in combination with vinblastine, Adriamycin or vincristine and cytotoxicity was evaluated using a clonogenic assay, or the metabolic dye reduction MTT assay, or by monitoring growth inhibition. Under these conditions, the extent of resistance modulation by verapamil and by S9788 was comparable in the various tumour cell lines tested, although a definite concentration-dependent modulation was noted with both compounds. The highest dose-modification factors were noted in the highly vinblastine-resistant classic multi-drug-resistant subline CEM/VLB100, although resistance reversal was only partial. Resistance modulation by both verapamil and S9788 was noted in 4 drug-selected resistant sublines and 4 "intrinsically" resistant human tumour cell lines, which all exhibited significant P-glycoprotein expression. In contrast, in 2 drug-resistant human tumour sublines (GLC4/ADR and CEM/VM-1) characterized by altered topoisomerase-II activity and proving to be P-glycoprotein-negative, no resistance modulation relative to parental cells was observed. These data are consistent with the proposal that resistance modulation is mediated by interaction between S9788 and P-glycoprotein and support its clinical evaluation in patients with P-glycoprotein-positive tumours.
Purification and characterization of type II heat-labile enterotoxin of Escherichia coli (1986)

Type II heat-labile enterotoxin (LT-II) of Escherichia coli has several biologic activities similar to cholera toxin (CT) and E. coli type I heat-labile enterotoxin (LT-I), but it is not neutralized by antiserum prepared against CT or LT-I. LT-II was purified from E. coli SA53 and from E. coli HB101(pCP3837), a strain that contains the cloned LT-II genes in a hybrid plasmid and produces up to 600 times more LT-II than does SA53. Purification involved sonic disruption of bacterial cells, ammonium sulfate fractionation, chromatography on Affi-Gel Blue, chromatofocusing, and gel filtration on Sephadex G-100. The LT-II purified to apparent homogeneity from HB101(pCP3837) had an isoelectric point of 6.8, induced increased vascular permeability in rabbit intracutaneous tests, caused rounding of cultured Y1 adrenal cells accompanied by increased intracellular cyclic AMP, and was 25 to 50 times more potent than CT or LT-I in the Y1 adrenal-cell assay. In contrast, purified LT-II did not cause secretion in ligated rabbit ileal segments at doses corresponding to CT controls that gave strongly positive reactions. LT-II was composed of two different polypeptides with MrS of 28,000 (A) and 11,800 (B); treatment of LT-II with trypsin cleaved the A polypeptide to fragments A1 (Mr, 21,000) and A2 (Mr, 7,000). The activity of LT-II was not blocked by ganglioside GM1 at concentrations that inactivated LT-I or CT. Antiserum against the LT-II from E. coli HB101(pCP3837) completely neutralized purified LT-II and the LT-II in crude extracts of SA53, but it did not neutralize purified LT-I or CT.
Generation of auxotrophic mutants of Enterococcus faecalis (1995)

A 22-kb segment of chromosomal DNA from Enterococcus faecalis OG1RF containing the pyrimidine biosynthesis genes pyrC and pyrD was previously detected as complementing Escherichia coli pyrC and pyrD mutations. In the present study, it was found that the E. faecalis pyrimidine biosynthetic genes in this clone (designated pKV48) are part of a larger cluster resembling that seen in Bacillus spp. Transposon insertions were isolated at a number of sites throughout the cluster and resulted in loss of the ability to complement E. coli auxotrophs. The DNA sequences of the entire pyrD gene of E. faecalis and selected parts of the rest of the cluster were determined, and computer analyses found these to be similar to genes from Bacillus subtilis and Bacillus caldolyticus pyrimidine biosynthesis operons. Five of the transposon insertions were introduced back into the E. faecalis chromosome, and all except insertions in pyrD resulted in pyrimidine auxotrophy. The prototrophy of pyrD knockouts was observed for two different insertions and suggests that E. faecalis is similar to Lactococcus lactis, which has been shown to possess two pyrD genes. A similar analysis was performed with the purL gene from E. faecalis, contained in another cosmid clone, and purine auxotrophs were isolated. In addition, a pool of random transposon insertions in pKV48, isolated in E. coli, was introduced into the E. faecalis chromosome en masse, and an auxotroph was obtained. These results demonstrate a new methodology for constructing defined knockout mutations in E. faecalis.
New concept for long-acting insulin: spontaneous conversion of an inactive modified insulin to the active hormone in circulation: 9-fluorenylmethoxycarbonyl derivative of insulin. (1999)

Insulin is a short-lived species in the circulatory system. After binding to its receptor sites and transmission of its biological signals, bound insulin undergoes receptor-mediated endocytosis and consequent degradation. An inactive insulin derivative that is not recognized by the receptor has a longer circulation life, but obviously is biologically impotent. (Fmoc)2 insulin is an insulin derivative purified through high-performance liquid chromatography in which two 9-fluorenylmethoxycarbonyl (Fmoc) moieties are covalently linked to the (alpha-amino group of phenylalanine B1 and the epsilon-amino group of lysine B29. It has 1-2% of the biological potency and receptor binding capacity of the native hormone. After incubation, (Fmoc)2 insulin undergoes a time-dependent spontaneous conversion to fully active insulin in aqueous solution at 37 degrees C and a pH range of 7-8.5. At pH 7.4, the conversion proceeds slowly (t1/2 = 12 +/- 1 days) and biological activity is generated gradually. A single subcutaneous administration of (Fmoc)2 insulin to streptozocin-treated diabetic rats normalized their blood glucose levels and maintained the animals in an anabolic state over 2-3 days. A broad shallow peak of immunoreactive insulin was found to persist in circulation over this period. To confirm further that the long-acting effect of (Fmoc)2 insulin proceeds via slow release in the blood circulation itself, we administered native insulin, NPH insulin, or the (Fmoc)2 derivative intraperitoneally. The rats recovered from hypoglycemia at t1/2 = 8.0 +/- 0.3 and 10 +/- 0.4 h after administration of native and NPH insulin, respectively. In contrast, (Fmoc)2 insulin was active for a significantly longer time, with an extended onset of t1/2 = 26 +/- 1h, and a glucose-lowering effect even 40 h after administration. (Fmoc)2 insulin was also found to be more resistant to proteolysis. Finally, we found that (Fmoc)2 insulin does not induce antigenic effects. In summary, we present here a new concept for prolonging the half-life of insulin in the circulatory system, in which receptor-mediated endocytosis and degradation is delayed and accompanied by a time-dependent generation of basal insulin.
Vascular Permeability Precedes Spontaneous Intracerebral Hemorrhage in Stroke-Prone Spontaneously Hypertensive Rats (2007)

Salt-loaded SHRsp rats have increased vascular permeability up to 2 weeks before ICH, predicting hemorrhage both in space and time. These results suggest that hypertensive ICH is preceded by focal vasculopathy detectable by Gd leak.
T Helper 17/Regulatory T Cell Balance and Experimental Models of Peritoneal Dialysis-Induced Damage (2015)

Fibrosis is a general complication in many diseases. It is the main complication during peritoneal dialysis (PD) treatment, a therapy for renal failure disease. Local inflammation and mesothelial to mesenchymal transition (MMT) are well known key phenomena in peritoneal damage during PD. New data suggest that, in the peritoneal cavity, inflammatory changes may be regulated at least in part by a delicate balance between T helper 17 and regulatory T cells. This paper briefly reviews the implication of the Th17/Treg-axis in fibrotic diseases. Moreover, it compares current evidences described in PD animal experimental models, indicating a loss of Th17/Treg balance (Th17 predominance) leading to peritoneal damage during PD. In addition, considering the new clinical and animal experimental data, new therapeutic strategies to reduce the Th17 response and increase the regulatory T response are proposed. Thus, future goals should be to develop new clinical biomarkers to reverse this immune misbalance and reduce peritoneal fibrosis in PD.
Localization of distinct F2-isoprostanes in human atherosclerotic lesions. (1997)

F2-Isoprostanes are prostaglandin (PG) isomers formed in situ in cell membranes by peroxidation of arachidonic acid. 8-epi PGF2alpha and IPF2alpha-I are F2-isoprostanes produced in humans which circulate in plasma and are excreted in urine. Measurement of F2-isoprostanes may offer a sensitive, specific, and noninvasive method for measuring oxidant stress in clinical settings where reactive oxygen species are putatively involved. We determined whether isoprostanes were present in human atherosclerotic lesions, where lipid peroxidation is thought to occur in vivo. 8-epi PGF2alpha ranged from 1.310-3.450 pmol/micromol phospholipid in atherectomy specimens compared with 0.045-0.115 pmol/micromol phospholipid (P < 0.001) in vascular tissue devoid of atherosclerosis. Corresponding values of IPF2alpha-I were 5.6-13.8 vs. 0.16-0.44 pmol/micromol phospholipid (P < 0.001). Levels of the two isoprostanes in vascular tissue were highly correlated (r = 0.80, P < 0.0001). Immunohistochemical studies confirmed that foam cells adjacent to the lipid necrotic core of the plaque were markedly positive for 8-epi PGF2alpha. These cells were also reactive with anti-CD68, an epitope specific for human monocyte/macrophages. 8-epi PGF2alpha immunoreactivity was also detected in cells positive for anti-alpha-smooth muscle actin antibody, which specifically recognizes vascular smooth muscle cells. Our results indicate that 8-epi PGF2alpha and IPF2alpha-I, two distinct F2-isoprostanes and markers of oxidative stress in vivo, are present in human atherosclerotic plaque. Quantitation of these chemically stable products of lipid peroxidation in target tissues, as well as in biological fluids, may aid in the rational development of antioxidant drugs in humans.
Clinical Aspects of Nutrition in Advanced Cancer (1992)

Nutritional assessments of our patients with disseminated malignancies have revealed that the incidences of reported anorexia, decreased food intake, and weight loss range between 49 and 64%. It is therefore essential that a planned approach to the nutritional needs of patients with advanced cancer be part of routine oncology care. Our first step is a clinical assessment of the patient's nutritional state and diet, and a determination of caloric and nutrient needs. The potential tools available to the oncologist in the management of the undernourished cancer patient are many and include dietary counseling, food supplements (which contain vitamins and other micronutrients), stimulation of appetite, enteral nutrition, total parenteral nutrition, or a combination of these. The dietitian can be an invaluable component of the cancer care team, both in the inpatient and outpatient settings. An understanding of the role of each intervention will enable the physician to use available resources rationally and efficiently.
Target size study for one-handed thumb use on small touchscreen devices (2006)

This paper describes a two-phase study conducted to determine optimal target sizes for one-handed thumb use of mobile handheld devices equipped with a touch-sensitive screen. Similar studies have provided recommendations for target sizes when using a mobile device with two hands plus a stylus, and interacting with a desktop-sized display with an index finger, but never for thumbs when holding a small device in a single hand. The first phase explored the required target size for single-target (discrete) pointing tasks, such as activating buttons, radio buttons or checkboxes. The second phase investigated optimal sizes for widgets used for tasks that involve a sequence of taps (serial), such as text entry. Since holding a device in one hand constrains thumb movement, we varied target positions to determine if performance depended on screen location. The results showed that while speed generally improved as targets grew, there were no significant differences in error rate between target sizes =9.6 mm in discrete tasks and targets =7.7 mm in serial tasks. Along with subjective ratings and the findings on hit response variability, we found that target size of 9.2 mm for discrete tasks and targets of 9.6 mm for serial tasks should be sufficiently large for one-handed thumb use on touchscreen-based handhelds without degrading performance and preference.
Benchmarking of a full-body inertial motion capture system for clinical gait analysis (2008)

In order for gait analysis to be established as part of routine clinical diagnoses, an accurate, flexible and user-friendly motion capture system is required. Commonly used optical, mechanical and acoustic systems offer acceptable accuracy and repeatability, but are often expensive and restricted to laboratory use. Inertial motion capture has seen great innovation in the last few years, but the technology is not yet considered mature enough for clinical gait analysis. In this paper we compare the kinematic reliability of inertial motion capture with optical motion capture during routine gait studies of eight able-bodied subjects. The root mean squared, RMS, and coefficient of correlation, R, was used to compare data sets. Saggital plane joint angles in the knee and hip compared very well. Corresponding transverse and frontal plane values were moderately accurate. The ankle joint angles calculated from the two systems were less accurate. This was believed to be due to the use of different rotation axis orientations used for calculation of angular rotations.
Lipoprotein Profile and High-Density Lipoproteins: Subfractions Distribution in Centenarians (1998)

In order to assess the role of HDL on longevity, we studied HDL subfraction distribution in centenarian women compared with a group of weight- and gender-matched healthy normolipidemic controls. We did not find any significant difference in the mean plasma lipid, apolipoprotein, and Lp(a) levels. On the contrary, in spite of similar HDL-cholesterol concentrations (1.32 +/- 0.41 mmol/l in centenarians vs. 1.32 +/- 0.25 mmol/l in controls, p = not significant), HDL2b and HDL3a levels were, respectively, significantly increased and significantly reduced in centenarians in comparison with controls (HDL2b 32.4 +/- 9.2% in centenarians vs. 23.4 +/- 7.7% in controls, p < 0.002, and HDL3a 26.3 +/- 9.8% in centenarians vs. 34.1 +/- 7.3% in controls, p < 0.01). Moreover, HDL2b levels were significantly raised and HDL3a levels were significantly reduced in centenarians in comparison with both 'middle-aged' and 'elderly' subjects, whereas no difference for any HDL subfraction was found between the two groups of controls of different ages. Age was significantly correlated with HDL2b and HDL3a (respectively, +0.452, p < 0.001, and -0.370, p < 0.01) in all subjects, but not with all the other lipid, lipoprotein and apolipoprotein parameters, but we observed a large overlapping of individual values of HDL2b between centenarians and controls. Since HDL2b levels were found to be inversely correlated with coronary heart disease risk, we could speculate that, in some cases, this may probably favor a healthy ageing, but long-term longitudinal studies are necessary to define the relative importance of HDL subfractions distribution as a marker of longevity. Probably other factors or clinical characteristics play a major role in the ageing process.
Model-based automated generation of user interfaces (1994)

User interface design and development for knowledgebased systems and most other types of applications is a resource-consuming activity. Thus, many attempts have been made to automate, to certain degrees, the construction of user interfaces. Current tools for automated design of user interfaces are able to generate the static layout of an interface from the application&amp;apos;s data model using an intelligent program that applies design rules. These tools, however, are not capable of generating the dynamic behavior of the interface, which must be specified programmatically, and which constitutes most of the effort of interface construction. Mecano is a model-based userinterface development environment that uses a domain model to generate both the static layout and the dynamic behavior of an interface. A knowledge-based system applies sets of dialog design and layout rules to produce interfaces from the domain model. Mecano has been used successfully to completely generate the layout and the dynamic behavior of relatively large and complex, domainspecific, form- and graph-based interfaces for applications in medicine and several other domains.
A comparison between continuum- and line source AAS for speciation analysis of butyl- and phenyltin compounds (2006)

The analytical potential of using instrumentation based on AAS for speciation analysis was investigated. Organic tin (OT) species were determined following gas chromatographic (GC) separation, atomization in a quartz tube (QT) and detection by line source AAS (LSAAS) and, for comparison, by state of the art continuum source AAS (CSAAS). For an unbiased comparison of the AAS instruments, their working conditions were individually optimized. For CSAAS, the linear range was limited by the GC column capacity (10–1600 ng g−1) and for LSAAS this range was limited by stray radiation (20–1000 ng g−1). With background correction, the instrumental LODs for OT were 6–22 pg as tin for CSAAS, while for LSAAS corresponding values were five to ten times poorer. Without background correction, the LOD of CSAAS was twice as good as that of LSAAS. For method validation, two certified reference materials, Harbour Sediment BCR-646 and Oyster Tissue BCR-710, were analysed.
Uncovering Therapeutic Targets FOR Glioblastoma: A Systems Biology Approach (2007)

Even though glioblastoma, WHO grade IV (GBM) is one of the most devastating adult cancers, current treatment regimens have not led to any improvements in patient life expectancy or quality of life. The constitutively active EGFRvIII receptor is one of the most commonly mutated proteins in GBM and has been linked to radiation and chemotherapeutic resistance. To define the mechanisms by which this protein alters cell physiology, we have recently performed a phosphoproteomic analysis of EGFRvIII signaling networks in GBM cells. The results of this study provided important insights into the biology of this mutated receptor, including oncogene dose effects and differential utilization of signaling pathways. Moreover, clustering of the phosphoproteomic data set revealed a previously undescribed crosstalk between EGFRvIII and the c-Met receptor. Treatment of the cells with a combination employing both EGFR and c-Met kinase inhibitors dramatically decreased cell viability in vitro. In this perspective, we highlight the use of systems biology as a tool to better understand the molecular basis of GBM tumor biology as well as to uncover non-intuitive candidates for therapeutic target validation.
Genome-Wide Analysis of mRNA Decay Rates and Their Determinants in Arabidopsis thaliana (2007)

To gain a global view of mRNA decay in Arabidopsis thaliana, suspension cell cultures were treated with a transcriptional inhibitor, and microarrays were used to measure transcript abundance over time. The deduced mRNA half-lives varied widely, from minutes to >24 h. Three features of the transcript displayed a correlation with decay rates: (1) genes possessing at least one intron produce mRNA transcripts significantly more stable than those of intronless genes, and this was not related to overall length, sequence composition, or number of introns; (2) various sequence elements in the 3' untranslated region are enriched among short- and long-lived transcripts, and their multiple occurrence suggests combinatorial control of transcript decay; and (3) transcripts that are microRNA targets generally have short half-lives. The decay rate of transcripts correlated with subcellular localization and function of the encoded proteins. Analysis of transcript decay rates for genes encoding orthologous proteins between Arabidopsis, yeast, and humans indicated that yeast and humans had a higher percentage of transcripts with shorter half-lives and that the relative stability of transcripts from genes encoding proteins involved in cell cycle, transcription, translation, and energy metabolism is conserved. Comparison of decay rates with changes in transcript abundance under a variety of abiotic stresses reveal that a set of transcription factors are downregulated with similar kinetics to decay rates, suggesting that inhibition of their transcription is an important early response to abiotic stress.
100-K superconducting phases in the Tl-Ca-Ba-Cu-O system (1988)

Two superconducting phases, ${\mathrm{Tl}}_{2}$${\mathrm{Ca}}_{2}$${\mathrm{Ba}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{10+\mathrm{\ensuremath{\delta}}}$ (2223) and ${\mathrm{Tl}}_{2}$${\mathrm{Ca}}_{1}$${\mathrm{Ba}}_{2}$${\mathrm{Cu}}_{2}$${)}_{8+\mathrm{\ensuremath{\delta}}}$ (2122), both with onset ${\mathrm{T}}_{\mathrm{c}}$ near 120 K and zero resistivity at 100 K, have been isolated from samples in the Tl-Ca-Ba-Cu-O system. The new 2223 superconductor has a 5.40\ifmmode\times\else\texttimes\fi{}5.40\ifmmode\times\else\texttimes\fi{}36.25-A${\mathrm{\r{}}}^{3}$ pseudotetragonal unit cell. The 2122 superconductor, which appears to be structurally related to ${\mathrm{Bi}}_{2}$${\mathrm{CaSr}}_{2}$${\mathrm{Cu}}_{2}$${\mathrm{O}}_{8+\mathrm{\ensuremath{\delta}}}$, has a 5.44\ifmmode\times\else\texttimes\fi{}5.44\ifmmode\times\else\texttimes\fi{}29.55-A${\mathrm{\r{}}}^{3}$ pseudotetragonal subcell. The 2223 phase is probably related to 2122 by the addition of extra calcium and copper layers.