gebhart/patrepeval huggingface dataset:
Transcript of the Question and Answer Sessions from the Fifth International Symposium on Avian Influenza (2003)

Peter Woolcock. Did the amino acid sequence change from emu to chicken passes as IVPI increased? Paul Selleck. No changes were seen in a PCR product covering 200 bases around the HA cleavage site. Daniel Perez. During the serial passage of the H7 in chickens, were viruses passaged in eggs before going to chickens? (I mean ck to eggs to ck to eggs to ck or ck to ck to ck)? Paul Selleck. The virus used for the first IVPI had been passed twice in eggs and between each pass in chickens the virus was reisolated in eggs from cloacal swabs (i.e., egg-egg-ck-egg-ckegg-ck). David Swayne. Have surveys been done in wild birds to access the influenza subtypes they are carrying? You mentioned the wild birds several times in the presentation associated within the farms and area. Paul Selleck. Yes, immediately following the outbreak, a fairly stringent survey was done of the wild bird population in the area. Unfortunately, H7 viruses were not isolated from these birds. And in the past, surveys of other wild bird populations in Australia have also failed to yield any H7 viruses. Anonymous. Is there any new subtype of avian influenza now? And have any new methods been developed on evaluating pathogenicity of avian influenza viruses? Dennis Senne. I guess I lose this one to Dr. Alexander by default. Currently there are still only 15 subtypes of influenza that are recognized. I am not aware of any new subtypes that have been described in the literature. As far as methods for pathogenicity testing, the standard tests are being used. The tests are to determine the amino acid sequence at the cleavage site of the hemagglutinin protein and the chicken pathogenicity test that Dr. Alexander referred to earlier and promised to tell us about on Wednesday. If there are any specific questions regarding the specifics of the pathotyping tests, we would be glad to discuss those, but I don't know that this is the appropriate time. Hailu Kinde. The transmurial oviductal edema and fibrinous yolk peritirutis was also seen with H6N2 infection. However, we have not seen the severe tracheitis you saw with H7N2. Robert Eckroade. Okay, I was unaware that those lesions were occurring in your H6. Anonymous. In your opinion, what is the best
Combining textual and visual cues for content-based image retrieval on the World Wide Web (2002)

A system is proposed that combines textual and visual statistics in a single index vector for content-based search of a WWW image database. Textual statistics are captured in vector form using latent semantic indexing (LSI) based on text in the containing HTML document. Visual statistics are captured in vector form using color and orientation histograms. By using an integrated approach, it becomes possible to take advantage of possible statistical couplings between the content of the document (latent semantic content) and the contents of images (visual statistics). The combined approach allows improved performance in conducting content-based search. Search performance experiments are reported for a database containing 100,000 images collected from the WWW.
An investigation of tape spring fold curvature (2004)

Tape springs are being used with increasing frequency in today’s space industry to deploy small satellite aerials and array areas. However, to accurately model the deployment of an appendage mounted with tape spring hinges, it is necessary to accurately model the opening moments produced from the material strains in the tape spring fold. These moments are primarily a function of curvature. This paper uses a photographic method to study the post buckling curvatures at the fold location for both two and three dimensional tape spring folds. The results are finally compared to determine the overall data trends.
Reductive methylation of proteins with sodium cyanoborohydride. Identification, suppression and possible uses of N-cyanomethyl by-products (1982)

Reductive methylation of protein amino groups with formaldehyde and sodium cyanoborohydride is shown to give up to 25% yield of N-cyanomethyl (-CH2CN) product; on work up of the reaction this is hydrolysed back to starting amine, lowering the methylation yield. Addition of metal ions such as Ni2+, which complex with free cyanide ion, improve reductive methylation yields by suppressing by-product formation. The N-cyanomethyl group itself, produced in good yield when cyanide ion replaces cyanoborohydride, may have some value as a reversible modifier of amino groups in proteins.
Heterogenous glycosylation of ICAM‐3 and lack of interaction with Mac‐1 and p150,95 (1995)

Intercellular adhesion molecule (ICAM)-1, ICAM-2, and ICAM-3 have been identified as counter-receptors for the leukocyte integrin lymphocyte function-associated antigen 1 (LFA-1). The other leukocyte integrins, Mac-1 and p150,95, also interact with ICAM-1. ICAM-1 and ICAM-3 are highly homologous, and an undefined ligand for Mac-1 is present on neutrophils where ICAM-3 is well expressed. In addition, glycosylation has been shown to affect the interaction of ICAM-1 with Mac-1. We therefore sought to characterize ICAM-3 heterogeneity and determine whether ICAM-3 was a ligand for either Mac-1 or p150,95. Despite extensive differences in N-linked glycosylation, ICAM-3 purified from lymphoid cells and from neutrophils supports adhesion of LFA-1-bearing cells equally well; however, neither supports adhesion of Mac-1 or p150,95-expressing chinese hamster ovary cell transfectants. Similarly, purified Mac-1 does not support adhesion of ICAM-2 or ICAM-3-expressing L cell transfectants. ICAM-3 on neutrophils does not participate in Mac-1-dependent homotypic aggregation. Thus, ICAM-3 is not a counter-receptor for either Mac-1 or p150,95.
Computational identification of the selenocysteine tRNA (tRNASec) in genomes (2017)

Selenocysteine (Sec) is known as the 21st amino acid, a cysteine analogue with selenium replacing sulphur. Sec is inserted co-translationally in a small fraction of proteins called selenoproteins. In selenoprotein genes, the Sec specific tRNA (tRNASec) drives the recoding of highly specific UGA codons from stop signals to Sec. Although found in organisms from the three domains of life, Sec is not universal. Many species are completely devoid of selenoprotein genes and lack the ability to synthesize Sec. Since tRNASec is a key component in selenoprotein biosynthesis, its efficient identification in genomes is instrumental to characterize the utilization of Sec across lineages. Available tRNA prediction methods fail to accurately predict tRNASec, due to its unusual structural fold. Here, we present Secmarker, a method based on manually curated covariance models capturing the specific tRNASec structure in archaea, bacteria and eukaryotes. We exploited the non-universality of Sec to build a proper benchmark set for tRNASec predictions, which is not possible for the predictions of other tRNAs. We show that Secmarker greatly improves the accuracy of previously existing methods constituting a valuable tool to identify tRNASec genes, and to efficiently determine whether a genome contains selenoproteins. We used Secmarker to analyze a large set of fully sequenced genomes, and the results revealed new insights in the biology of tRNASec, led to the discovery of a novel bacterial selenoprotein family, and shed additional light on the phylogenetic distribution of selenoprotein containing genomes. Secmarker is freely accessible for download, or online analysis through a web server at http://secmarker.crg.cat.
<title>Optical proximity correction on attenuated phase-shifting photo mask for dense contact array</title> (1995)

The application of attenuated PSM to dense contact array is restricted by intense optical interference of sidelobe peaks around hole pattern which is called proximity effect. In order to reduce the effect of proximity, it is necessary to optimize the transmittance of mask field and the exposing energy which cause mask bias. The vast of data are required for doing above job. Using simulation, however, by sidelobe, E- D curves can not be used directly to find the depth of focus. The criterion for sidelobe was defined to find process window from E-D curve. To reduce sidelobe in dense contact hole array, the auxiliary patterns were placed between holes. By simulations and experiments, attenuated PSM with auxiliary pattern could be applied effectively to the dense contact hole of 64MDRAM.
Biological and immunological properties of Sugi basic protein-pullulan conjugate. II. Is the reduced ability to elicit the Arthus reaction based on the poor activation of complement by immune complex consisting of anti-Sugi basic protein and Sugi basic protein-pullulan? (1990)

Ability of Sugi basic protein (SBP)-pullulan conjugate to elicit the Arthus reaction was found to be markedly reduced, about 100 times lower than that of native SBP. To analyze this reduced ability, activation of complement by immune complex consisting of SBP-pullulan and anti-SBP antibodies was studied. Tests for complement consumption, C3 conversion and cleavage of factor B revealed that immune complex formed with SBP-pullulan is incapable of supporting efficient activation of the complement system. Previously, we have shown data suggesting that SBP-pullulan conjugate would be a good candidate for desensitization therapy against cedar pollinosis. The results presented in this paper provide additional support for the suggestion.
A Multicenter Evaluation of Variables Affecting the Predictability of Creatinine Clearance (1982)

Data from 722 urine collections (627 patients) from 14 medical facilities were used to compare measured creatinine clearance values with clearance estimates calculated using three "urine-free' mathematical formulas. The influence of two patient weight variables (actual weight, lean body weight) and the level of renal function on clearance prediction was assessed. In addition, site parameters (region, facility), time parameters (month, day, day of the week), and patient parameters (age, sex, height, weight, diagnoses) were evaluated for their statistical influence on the relationship between measured clearance and estimates calculated with one of the methods. Strong, statistically significant correlations were observed between clearance values estimated with each prediction method and measured clearances. Although statistical differences were noticed between mean values predicted with each method, these differences were clinically insignificant. Use of lean body weight for calculation of creatinine excretion produced clearance estimates that were significantly lower than those obtained with actual weight and substantially closer to measured clearance values. Among patient variables, age and two specific diagnoses (congestive heart failure and pregnancy), were statistically associated with variability in the relationship between measured and predicted clearance. Interregional and interfacility differences in the measured-predicted clearance relationship, variability associated with the day of the week of collection, and tendency of the urine-free formulas to over-predict clearance support potential inaccuracy of measured clearance determination. The results suggest that inaccuracies in clearance determination, rather than inadequacies of urine-free prediction methods, account for the majority of the observed variability in the relationship.
Uranium Reoxidation in Previously Bioreduced Sediment by Dissolved Oxygen and Nitrate (2007)

Flow-through sediment column experiments examined the reoxidation of microbially reduced uranium with either oxygen or nitrate supplied as the oxidant. The uranium was reduced and immobilized via long-term (70 days) acetate biostimulation resulting in 62-92% removal efficiency of the 20 microM influent uranium concentration. Uranium reduction occurred simultaneously with iron reduction as the dominant electron accepting process. The columns were reoxidized by discontinuing the supply of acetate and either replacing the anaerobic gas used to purge the influent media with a gas mixture containing 20% oxygen (resulting in a dissolved oxygen concentration of 0.27 mM) or adding 1.6 mM nitrate to the influent media. Both oxygen and nitrate resolubilized the majority (88 and 97%, respectively) of the uranium precipitated during bioreduction within 54 days. Although oxygen is more thermodynamically favorable an oxidant than nitrate, nitrate-dependent uranium oxidation occurred significantly faster than oxygen-dependent uranium oxidation at the beginning of our experiment due, in part, to oxygen reacting more strongly with other reduced compounds. Nitrate breakthrough at the effluent of the column occurred within 12 h, which was significantly earlier than when oxygen was detected at the effluent (26 days). Although, over time, the majority of uranium was reoxidized by either oxidant, these results indicate that the type of oxidant and its reactivity with other reduced compounds will influence the fate of reduced uranium during a short-term oxidation event that may occur during a uranium bioremediation scenario.
Neutrophil Elastase and Acute Pulmonary Damage in Neonates With Severe Respiratory Distress Syndrome (1993)

This study evaluated possible acute effects of neutrophil elastase on neonatal pulmonary morbidity. The activity of free elastase and alpha 1-proteinase inhibitor as well as concentrations of elastase-alpha 1-proteinase inhibitor in tracheal aspirate fluid of neonates with severe respiratory distress syndrome (fraction of inspired oxygen > 0.6, mechanical ventilation) were analyzed between 6 and 36 hours after surfactant replacement therapy. One hundred forty neonates were included in this prospective study. Characteristics, disease severity, and ventilatory requirements were nearly identical in both groups. All patients were treated with natural porcine surfactant (Curosurf) at an age of 2 to 15 hours. In 42 neonates (30%) considerable activities of free elastase were detected (805 micrograms/L; 100 to 1850 [median, 25th to 75th percentile]); in 98 neonates (70%) who had protective levels of alpha 1-proteinase inhibitor, no elastase activity was detected. The average concentrations of elastase-alpha 1-proteinase inhibitor were significantly increased in patients with free elastase activity when compared with those of the nonelastase group. In logistic regression analyses, 28-day outcome data showed a pronounced increase in risk of pulmonary interstitial emphysema for patients with free elastase activity in tracheal aspirate fluid. The incidence of other pulmonary and nonpulmonary complications was very similar in both groups. It is concluded that elastolytic damage and barotrauma may both contribute to acute pulmonary injury in the early stages of respiratory distress syndrome.
Growth and transport properties of complementary germanium nanowire field-effect transistors (2004)

n- and p-type Ge nanowires were synthesized by a multistep process in which axial elongation, via vapor–liquid–solid (VLS) growth, and doping were accomplished in separate chemical vapor deposition steps. Intrinsic, single-crystal, Ge nanowires prepared by Au nanocluster-mediated VLS growth were surface-doped in situ using diborane or phosphine, and then radial growth of an epitaxial Ge shell was used to cap the dopant layer. Field-effect transistors prepared from these Ge nanowires exhibited on currents and transconductances up to 850 μA/μm and 4.9 μA/V, respectively, with device yields of &amp;gt;85%.
Monoclonal antibodies to cell surface antigens shared by chemically induced mouse bladder carcinomas. (1985)

Rats were immunized with cultured cells from chemically induced transitional cell carcinomas of the mouse urinary bladder, and their spleen cells were hybridized with NS-1 mouse myeloma cells. Following initial screening of antibodies made by hybridoma clones, the tissue distribution of antigens defined by the antibodies was established by using a peroxidase-antiperoxidase technique with frozen sections of a variety of mouse tumors, as well as normal adult and embryonic tissues. Two antibodies were identified which detected antigens with bladder carcinoma specificity. One antibody (3B12) reacted weakly with epithelial cells from several sources, including normal bladder, while the second antibody (6.10), which bound strongly to bladder carcinoma cells, was negative on bladder epithelium and bound (weakly) to only a small fraction of all epithelial cells tested except for epidermal cells and periosteum from embryos. Both antibodies should be useful to assess the immunotherapeutic and immunoprophylactic effects of monoclonal antibodies to tumor-type specific oncofetal antigens.
Silicon Torsional Scanning Mirror (1980)

Conventional batch photolithography and thin film techniques are employed to fabricate an electrostatically driven torsional scanning mirror from single-crystal silicon. This device is extremely simple to make and operate, has operational characteristics comparable to commercial magnetically driven high-frequency scanners, and has exhibited a promising reliability.
Antiproliferative effects of luteinizing hormone-releasing hormone (LHRH) agonists on human androgen-independent prostate cancer cell line DU 145: evidence for an autocrine-inhibitory LHRH loop. (1994)

The therapeutic options for the treatment of androgen-independent prostatic cancers are rather limited; this is mainly because our understanding of the local mechanisms involved in the control of androgen-independent proliferation of the tumor is still very poor. The present experiments have been performed to verify whether luteinizing hormone-releasing hormone (LHRH) agonists may possess a direct effect on the growth of the human androgen-independent prostate cancer cells DU 145 and whether a LHRH growth regulatory system may be present in these cells. The data have shown that two potent LHRH agonists (Zoladex and Buserelin) exert a significant and dose-dependent antiproliferative action on DU 145 cells, after 4 days of treatment. The inhibitory action of Zoladex and Buserelin is completely counteracted by the simultaneous treatment of the cells with a potent LHRH antagonist, suggesting that the action of the LHRH agonists may be mediated by specific receptors. This hypothesis has been confirmed by the demonstration that low-affinity binding sites for 125I-Buserelin are present on DU 145 cell membranes, particularly when cells are cultured in serum-free conditions. By using the reverse transcription-polymerase chain reaction technique, in the presence of a pair of specific oligonucleotide primers complementary to the human LHRH complementary DNA, it has been demonstrated that a mRNA for LHRH is expressed in DU 145 cells. Taken together, these data seem to indicate that an autocrine/paracrine LHRH (or LHRH-like) loop is present in androgen-independent prostate cancer cells, and may participate in the regulation of tumor cell growth. To verify this hypothesis, DU 145 cells have been cultured in serum-free conditions, and treated with a LHRH antagonist for 4 days. The treatment resulted in a significant increase of cell proliferation, suggesting an inhibitory role for the LHRH system in the local regulation of cell growth. In conclusion, these data demonstrate that: (a) LHRH agonists exert a specific antiproliferative action on the human androgen-independent DU 145 cells; (b) an autocrine/paracrine LHRH (or LHRH-like) loop, which seems to be inhibitory on cell proliferation, is expressed in DU 145 cells.
Detecting F-formations as dominant sets (2011)

The first step towards analysing social interactive behaviour in crowded environments is to identify who is interacting with whom. This paper presents a new method for detecting focused encounters or F-formations in a crowded, real-life social environment. An F-formation is a specific instance of a group of people who are congregated together with the intent of conversing and exchanging information with each other. We propose a new method of estimating F-formations using a graph clustering algorithm by formulating the problem in terms of identifying dominant sets. A dominant set is a form of maximal clique which occurs in edge weighted graphs. As well as using the proximity between people, body orientation information is used; we propose a socially motivated estimate of focus orientation (SMEFO), which is calculated with location information only. Our experiments show significant improvements in performance over the existing modularity cut algorithm and indicates the effectiveness of using a local social context for detecting F-formations.
Survey of resistance of Pseudomonas aeruginosa from UK patients with cystic fibrosis to six commonly prescribed antimicrobial agents (2003)

The level of resistance to front line antipseudomonal agents, with the exception of colistin, is disturbingly high. The prudent use of antimicrobial drugs and closer monitoring of accumulation of resistant strain populations should be actively considered.
CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter (2016)

DNA hypermethylation at the promoter of tumour-suppressor genes is tightly correlated with their transcriptional repression and recognized as the hallmark of majority of cancers. Epigenetic silencing of tumour suppressor genes impairs their cellular functions and activates a cascade of events driving cell transformation and cancer progression. Here, we examine site-specific and spatiotemporal alteration in DNA methylation at a target region in BRCA1 gene promoter, a model tumour suppressor gene. We have developed a programmable CRISPR-Cas9 based demethylase tool containing the deactivated Cas9 (dCas9) fused to the catalytic domain (CD) of Ten-Eleven Translocation (TET) dioxygenase1 (TET1CD). The fusion protein selectively demethylates targeted regions within BRCA1 promoter as directed by the designed single-guide RNAs (sgRNA), leading to the transcriptional up-regulation of the gene. We also noticed the increment in 5-hydroxymethylation content (5-hmC) at the target DNA site undergoing the most profound demethylation. It confirms the catalytic activity of TET1 in TET1-dCas9 fusion proteins-mediated demethylation at these target sequences. The modular design of the fusion constructs presented here allows for the selective substitution of other chromatin or DNA modifying enzymes and for loci-specific targeting to uncover epigenetic regulatory pathways at gene promoters and other selected genomic regions.
Characterization of Herpes Simplex Virus Strains Differing in their Effects on Social Behaviour of Infected Cells (1968)

Summary Established (laboratory) strains and fresh isolates of herpes simplex virus from patients with skin and genital lesions were classified into four groups depending on their effects on the social interaction among infected hep-2 cells. The groups comprised strains causing (1) rounding of cells but no adhesion or fusion, (2) loose aggregation of rounded cells, (3) tight adhesion of rounded cells, and (4) fusion of cells into polykaryocytes. Protype strains from each group were found to differ with respect to immunologic specificity, buoyant density in CsCl solutions and stability at 4°.