gebhart/patrepeval huggingface dataset:
Systematic review: the epidemiology and natural history of non‐alcoholic fatty liver disease and non‐alcoholic steatohepatitis in adults (2011)

Non-alcoholic fatty liver disease is the most common cause of elevated liver enzymes. Within the NAFLD spectrum, only NASH progresses to cirrhosis and hepatocellular carcinoma. With the growing epidemic of obesity, the prevalence and impact of NAFLD continues to increase, making NASH potentially the most common cause of advanced liver disease in coming decades.
A Novel Map-Based Dead-Reckoning Algorithm for Indoor Localization (2014)

Step counting-based dead-reckoning has been widely accepted as a cheap and effective solution for indoor pedestrian tracking using a hand-held device equipped with motion sensors. To compensate for the accumulating error in a dead-reckoning tracking system, extra techniques are always fused together to form a hybrid system. In this paper, we first propose a map matching (MM) enhanced particle filter (PF) as a robust localization solution, in which MM utilizes the corridor information to calibrate the step direction estimation and PF is applied to filter out impossible locations. To overcome the dependency on manually input corridor information in the MM algorithm, as well as the computational complexity in combining two such algorithms, an improved PF is proposed. By better modelling of the location error, the improved PF calibrates the location estimation, as well as step direction estimation when the map information is available, while keeping the computational complexity the same as the original PF. Experimental results show that in a quite dense map constraint environment with corridors, the proposed methods have similar accuracy, but outperform the original PF in terms of accuracy. When only partial map constraints are applied to simulate a new testbed, the improved PF obtains the most robust and accurate results. Therefore, the improved PF is the recommended DR solution, which is adaptive to various indoor environments.
The RNA Binding Protein Mex-3B Is Required for IL-33 Induction in the Development of Allergic Airway Inflammation (2016)

Allergic airway inflammation is one of the primary features of allergic asthma. Interleukin-33 (IL-33) is recognized as a key pro-inflammatory cytokine that mediates allergic airway inflammation, and its expression is elevated in this condition, but little is known about the regulatory mechanisms underlying IL-33 induction. Here, we show that the RNA binding protein Mex-3B plays a critical role in the induction of IL-33 in the development of allergic airway inflammation. We generated Mex3b(-/-) mice and found that they develop significantly less airway inflammation than wild-type mice due to reduced induction of IL-33. Furthermore, we show that Mex-3B directly upregulates IL-33 expression by inhibiting miR-487b-3p-mediated repression of IL-33. Moreover, we show that inhalation of an antisense oligonucleotide targeting Mex-3B suppresses allergic airway inflammation. Our data identify a signaling pathway that post-transcriptionally regulates IL-33 expression and suggest that Mex-3B could be a promising molecular target for the treatment of allergic asthma.
National Institutes of Health Consensus Development Conference Statement: Adjuvant Therapy for Breast Cancer, November 1-3, 2000 (2001)

The panel concludes that decisions regarding adjuvant hormonal therapy should be based on the presence of hormone receptor protein in tumor tissues. Adjuvant hormonal therapy should be offered only to women whose tumors express hormone receptor protein. Because adjuvant polychemotherapy improves survival, it should be recommended to the majority of women with localized breast cancer regardless of lymph node, menopausal, or hormone receptor status. The inclusion of anthracyclines in adjuvant chemotherapy regimens produces a small but statistically significant improvement in survival over non-anthracycline-containing regimens. Available data are currently inconclusive regarding the use of taxanes in adjuvant treatment of lymph node-positive breast cancer. The use of adjuvant dose-intensive chemotherapy regimens in high-risk breast cancer and of taxanes in lymph node-negative breast cancer should be restricted to randomized trials. Ongoing studies evaluating these treatment strategies should be supported to determine if such strategies have a role in adjuvant treatment. Studies to date have included few patients older than 70 years. There is a critical need for trials to evaluate the role of adjuvant chemotherapy in these women. There is evidence that women with a high risk of locoregional tumor recurrence after mastectomy benefit from postoperative radiotherapy. This high-risk group includes women with four or more positive lymph nodes or an advanced primary cancer. Currently, the role of postmastectomy radiotherapy for patients with one to three positive lymph nodes remains uncertain and should be tested in a randomized controlled trial. Individual patients differ in the importance they place on the risks and benefits of adjuvant treatments. Quality of life needs to be evaluated in selected randomized clinical trials to examine the impact of the major acute and long-term side effects of adjuvant treatments, particularly premature menopause, weight gain, mild memory loss, and fatigue. Methods to support shared decision-making between patients and their physicians have been successful in trials; they need to be tailored for diverse populations and should be tested for broader dissemination.
Helicobacter pylori infection promotes the invasion and metastasis of gastric cancer through increasing the expression of matrix metalloproteinase-1 and matrix metalloproteinase-10 (2014)

The aim of this study was to investigate the effect and mechanism of <i>Helicobacter pylori</i> infection in the invasion and metastasis of gastric cancer. Specimens from 80 patients with gastric cancer (of which 20 patients had metastatic gastric cancer) and 40 patients with chronic gastritis were included in this study. <i>H. pylori</i> infection was determined by ELISA and the expression of matrix metalloproteinase-1 (MMP-1) and MMP-10 was observed using immunohistochemistry. The correlation between <i>H. pylori</i> infection and the clinical pathological features of gastric cancer was analyzed by SPSS 13.0 software. The protein expression levels of MMP-1 and MMP-10 in MGC-803 cells infected with <i>H. pylori</i> were analyzed using western blotting. <i>H. pylori</i> infection was found in 62 of the 80 patients with gastric cancer and in 13 of the 40 patients with chronic gastritis. In addition, <i>H. pylori</i> infection was correlated with the staging and lymph node metastasis, but not with the gender, age and histological types of patients. <i>H. pylori</i> infection was also significantly correlated with the expression of MMP-1 and MMP-10 (r=0.8718, P<0.05 and r=0.5477, P<0.05, respectively). The expression of MMP-1 and MMP-10 was significantly upregulated following induction by <i>H. pylori</i> infection (P<0.05), with significant effects occurring following infection for 12 and 6 h, respectively. <i>H. pylori</i> infection may promote the invasion and metastasis of gastric cancer by increasing the expression of MMP-1 and MMP-10.
Preadsorption of polymers on glass and silica to reduce fibrinogen adsorption (1989)

Glass and silica beads were precoated with various polymers to obtain steric exclusion chromatography (SEC) supports which are nonadsorbant for hydrophilic macromolecules. The efficiency of this treatment was estimated by subsequent radiolabeled fibrinogen adsorption. The result obtained with a block copolymer was better than with various hydrophilic homopolymers. This ABA type block copolymer, where A is a poly(N-acetylethyleneimine) (PAEI) sequence and B a polyethylene oxide (PEO) sequence was preadsorbed at pH 4.5 and 25 degrees C; the fibrinogen adsorption was reduced to less than 5% of the value observed on untreated solid surfaces. Thus the hemocompatibility of solid supports should be increased by precoating with this block copolymer. Results for nonporous glass beads and porous silica particles were in good correlation.
Structure-activity analysis of the activation of pertussis toxin (1987)

Bordetella pertussis, the causative agent of whooping cough, releases pertussis toxin in an inactive form. The toxin consists of an A protomer containing one S1 peptide subunit and a B oligomer containing several other peptide subunits. The toxin binds to cells via the B oligomer, and the S1 subunit is activated and expresses ADP-ribosyltransferase and NAD glycohydrolase activities. Treatment of purified toxin with dithiothreitol (DTT) in vitro increases both activities. ATP and the detergent 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) synergistically reduce the A0.5 (activation constant) for DTT from greater than 100 mM to 200 microM. We studied the structure-activity relationships of activators of the toxin. In the presence of CHAPS (1%) and DTT (10 mM) the following compounds increased the NAD glycohydrolase activity of the toxin with the following A0.5's in microM and fraction of the ATP effect in parentheses: ATP, 0.2 (1.0); ADP, 6 (0.8); UTP, 15 (0.7); GTP, 35 (0.6); pyrophosphate, 45 (0.7); triphosphate, 60 (0.6); tetraphosphate, greater than or equal to 170 (greater than or equal to 0.4). Thus, the polyphosphate moiety is sufficient to stimulate the toxin, and the adenosine moiety confers upon ATP its extraordinary affinity for the toxin. Phospholipid and detergents could substitute for CHAPS in the activation of the toxin. Glutathione substituted for DTT with an A0.5 of 2 mM, a concentration within the range found in eucaryotic cells. Thus, membrane lipids and cellular concentrations of glutathione and ATP are sufficient to activate pertussis toxin without the need for a eucaryotic enzymatic process.
Routine identification of Mycobacterium tuberculosis complex isolates by automated hybridization (1994)

Methodologies for biochemical identification of mycobacteria isolated from clinical samples are still cumbersome, taking skilled technicians 3 to 6 weeks. We describe here a 2-h identification system for mycobacterial isolates belonging to the Mycobacterium tuberculosis complex using a DNA probe. After 30 min of hands-off sample preparation, the 1.5-h hybridization test is totally automated in the newly developed VIDAS system (bioMérieux, Marcyl'Etoile, France), which performs solid-phase specific hybridization of 16S rRNA at 37 degrees C. The strain collection of actinomycetes tested was composed of 662 isolates from 27 species: 461 members of the M. tuberculosis complex (443 M. tuberculosis, 10 M. bovis, and 8 M. bovis BCG isolates) and 201 isolates of other species, including 55 M. avium-intracellulare isolates). They were identified by traditional methods: growth rate, colonial morphology, pigmentation, and biochemical profiles. The automated probe assay displayed an excellent correlation with the reference results. The four members of the Nocardia and Rhodococcus genera tested did not cross-hybridize. This flexible random-access and automated technology was shown to suit the routine context of the laboratory by rapidly delivering the results.
Novel nonseparation sandwich-type electrochemical enzyme immunoassay system for detecting marker proteins in undiluted blood (1995)

A novel nonseparation electrochemical enzyme immunoassay (NEEIA) for detecting marker proteins in undiluted blood is described. The approach is based on preferential electrochemical measurement of surface-bound enzyme-labeled reporter antibody (E-Ab), relative to an excess of this reagent in the sample solution. NEEIAs are carried out on microporous membranes coated with a thin, circular area of gold. The gold serves simultaneously as a working electrode and solid phase for immobilized capture anti-protein antibodies. In the assay, analyte protein is incubated concurrently with the Ab-coated gold surface and excess E-Ab conjugate. Detection of bound E-Ab is achieved by introducing the substrate for the enzyme through the back side of the membrane. The product of bound E-Ab is detected immediately by oxidation or reduction at the gold electrode, and the resulting current is proportional to the concentration of protein in the sample. The feasibility of the NEEIA approach is demonstrated via the detection of prostate-specific antigen in undiluted plasma samples (n = 64), with alkaline phosphatase as the label. Use of multiple gold films deposited on the same porous membrane to perform simultaneous NEEIAs is also described.
Epitope analysis following active immunization with tau proteins reveals immunogens implicated in tau pathogenesis (2014)

Our study identifies five previously unknown immunogenic motifs of wild-type and mutated (P301L) tau protein. Immunization with both proteins resulted in reduced tau pathology and neuroinflammation in a tau transgenic model, supporting the efficacy of tau immunotherapy in tauopathy.
Dehydration of fructose to 5-hydroxymethylfurfural in sub- and supercritical acetone (2003)

The dehydration of D-fructose (1) to 5-hydroxymethylfurfural (HMF, 2) is a well known reaction (acid-induced elimination of three moles of water), performed by many investigators during the last three decades. HMF and its oxidation product 2,5-furandicarboxylic acid are so called ‘sleeping giants’ in the field of intermediate chemicals from regrowing resources. HMF is a key substance between carbohydrate chemistry and mineral oil-based industrial chemistry and it has the potential of a commodity like terephthalic acid. Surprisingly, no technical process has been constructed until now. The reason is that high selectivities (in this context selectivity means yield divided by conversion in mol%) can only be obtained in high boiling polar solvents like dimethyl sulfoxide, dimethylformamide, acetonitrile, poly(glycol ether) etc. so that separation procedures are very expensive. Unfortunately, in aqueous systems (supercritical water), only low selectivities can be achieved. Considering the specifications for a modern sustainable and economical process, the use of green solvents like acetone, methanol or acetic acid in their sub- or supercritical states should be accounted for. The results for this reaction performed in sub- and supercritical acetone are presented here.
Replicating and host-restricted non-replicating vaccinia virus vectors for vaccine development. (1994)

Vaccinia virus, effectively used for immunization against smallpox, now serves as a recombinant vector for the development of vaccines against other infectious agents and cancer. Recent advances have led to increased gene expression, enhanced immunogenicity, and greater safety. Both replicating and host-restricted non-replicating vectors are available.
Overproduction and dissection of proteins by the expression-cassette polymerase chain reaction. (1990)

We report an efficient, general approach for the construction of protein-overproducing strains of Escherichia coli. The method, expression-cassette polymerase chain reaction (ECPCR), allows the insertion of virtually any contiguous coding sequence between sequences that direct high-level protein biosynthesis in E. coli. The gene expression cassettes obtained by ECPCR are inserted into a regulated overexpression plasmid, and the resulting construct is used to transform E. coli. By effecting simultaneous 5' and 3' modification of a coding sequence, ECPCR permits the facile generation of mutant proteins having N- and/or C-terminal truncations. The method is a highly efficient way to dissect a multidomain protein into its component domains. The efficiency of the ECPCR approach is demonstrated in this study by construction of permuted overexpression vectors for the first two extracellular domains of the human CD4 protein.
Immunological and molecular characterization of Helicobacter felis urease (1994)

Urease activity has recently been shown to be an important virulence determinant for Helicobacter pylori, allowing it to survive the low pH of the stomach during colonization. Experimental murine infection with Helicobacter felis is now being used as a model for H. pylori infection to study the effects of vaccines, antibiotics, and urease inhibitors on colonization. However, little information comparing the ureases of H. felis and H. pylori is available. Urease was partially purified from the cell surface of H. felis ATCC 49179 by A-5M agarose chromatography, resulting in an eightfold increase in specific activity over that of crude urease. The apparent Km for urea for the partially purified urease was 0.4 mM, and the enzyme was inhibited in a competitive manner by flurofamide (50% inhibitory concentration = 0.12 microM). Antiserum to whole cells of H. pylori recognized both H. pylori and H. felis urease B subunits. Antiserum raised against H. felis whole cells recognized the large and small autologous urease subunits and the cpn60 heat shock molecule in both H. felis and H. pylori. However, this antiserum showed only a weak reaction with the B subunit of H. pylori urease. Two oligomeric DNA sequences were used as probes to evaluate the relatedness of H. felis and H. pylori urease gene sequences. One 30-mer from the ureA sequence, which had been shown previously to be specific for H. pylori, failed to hybridize to H. felis genomic DNA. A probe to the putative coding sequence for the active site of the H. pylori ureB subunit hybridized at low intensity to a 2.8-kb fragment of BamHI-HindIII-digested H. felis DNA, suggesting that the sequences were homologous but not identical, a result confirmed from the recently published sequences of ureA and ureB from H. felis.
On the design of clone-based haplotyping (2013)

Our results provide practical guidelines for the development and design of clone-based methods to achieve long range, high-resolution and accurate haplotypes.
Total Synthesis of an Antitumor Agent RA-VII via an Efficient Preparation of Cycloisodityrosine (1999)

Details of efficient syntheses of (9S,12S)-cycloisodityrosine (6) and a concise total synthesis of RA-VII (1) were described. An intramolecular SNAr-based cycloetherification reaction was employed as the key ring-closure step for construction of the illusive 14-membered m,p-cyclophane. Treatment of methyl N-[N-(tert-butyloxycarbonyl)-l-(3-hydroxy-4-methoxyphenylalanyl]-l-4-fluoro-3-nitrophenylalaninate ((9S,12S)-10) with potassium carbonate in DMSO at room temperature provided a mixture of two atropdiastereomers 20a and 20b in 75% yield that were transformed into cycloisodityrosine 6 in good overall yield. Furthermore, a size-selective ring-forming process was established for methyl N-[N-(tert-butyloxycarbonyl)-l-(3,4-dihydroxyphenylalanyl)]-l-4-fluoro-3-nitrophenylalaninate ((9S,12S)-11). Thus, cyclization of 11 (K2CO3, DMSO, rt), followed by in situ methylation, gave exclusively the 14-membered m,p-cyclphane 20a and 20b without competitive formation of the alternative 15-membered p,p-cyclophane. The selective ring-forming process allowed us to develop one of the shortest and the most efficient synthesis of cycloisodityrosine to date. Computational studies have shown that it was the elimination, but not the addition, step that determined the ring-size selectivity observed in the cyclization of substrate 11. Coupling of 6 with l-N-Boc-Ala (51) proceeded efficiently to provide the corresponding tripeptide 52 that, after removal of the N-Boc function, was allowed to react with another tripeptide 53 to afford the hexapeptide 50 in good overall yield. Saponification followed by liberation of amino function from 50 gave the seco-acid, whose cyclization (DPPA, DMF, NaHCO3) afforded the natural product RA-VII (1).
Annoyance from transportation noise: relationships with exposure metrics DNL and DENL and their confidence intervals. (2001)

We present a model of the distribution of noise annoyance with the mean varying as a function of the noise exposure. Day-night level (DNL) and day-evening-night level (DENL) were used as noise descriptors. Because the entire annoyance distribution has been modeled, any annoyance measure that summarizes this distribution can be calculated from the model. We fitted the model to data from noise annoyance studies for aircraft, road traffic, and railways separately. Polynomial approximations of relationships implied by the model for the combinations of the following exposure and annoyance measures are presented: DNL or DENL, and percentage "highly annoyed" (cutoff at 72 on a scale of 0-100), percentage "annoyed" (cutoff at 50 on a scale of 0-100), or percentage (at least) "a little annoyed" (cutoff at 28 on a scale of 0-100). These approximations are very good, and they are easier to use for practical calculations than the model itself, because the model involves a normal distribution. Our results are based on the same data set that was used earlier to establish relationships between DNL and percentage highly annoyed. In this paper we provide better estimates of the confidence intervals due to the improved model of the relationship between annoyance and noise exposure. Moreover, relationships using descriptors other than DNL and percentage highly annoyed, which are presented here, have not been established earlier on the basis of a large dataset.
Fabrication of frequency spectrum synthesiser consistingofarrayed-waveguide grating pair and thermo-optic amplitude and phase controllers (1999)

The fabrication is reported of an integrated-optic frequency spectrum synthesiser which is capable of shaping and encoding modelocked optical pulse waveforms by controlling the amplitude and phase of each line spectral component. The synthesiser consists of an arrayed-waveguide grating (AWG) pair for demultiplexing and multiplexing the spectral components and thermo-optic switches and phase shifters for arbitrarily patterning them. The dynamic range of the synthesiser is ~30 dB and the amplitude and phase resolutions are 0.1 – 0.2 dB and π/100, respectively.
Sequence analysis and regulation of thehtrA gene ofEscherichin coli:a σ32-independent mechanism of heat-inducible transcription (1988)

Previous work has established that the E. coli htrA gene product is essential for bacterial survival at temperatures above 42 degrees. We have sequenced the htrA gene region and found an open reading frame (ORF) coding for a protein of 491 amino acids with a calculated molecular weight of 51,163 daltons. This molecular weight corresponds well with that seen following electrophoresis on SDS-polyacrylamide gels. This protein has an amino-terminal sequence typical for a leader peptide and undergoes post-translational modification by cleavage of an amino-terminal portion. The insertional mutations which affect the function of the htrA gene map inside this ORF. The levels of htrA mRNA increase rapidly and transiently upon heat shock in a manner independent of the rpoH gene, which encodes the sigma 32 RNA polymerase subunit and is known to regulate transcription of typical heat shock genes. Using S1 mapping and RNA primer extension, we have identified the htrA promoter and found that it is similar to the P3 promoter of the rpoH gene. The P3 promoter is especially active at high temperatures and is recognized by a recently identified transcriptional factor, sigma E.