gebhart/patrepeval huggingface dataset:
Immunobiology of Inhibitor Development in Hemophilia A (2003)

After treatment with factor (F) VIII concentrate a significant number of patients with hemophilia A develop inhibitory antibodies that neutralize FVIII. Epitope mapping revealed that antibodies bind to selected regions within the A2, A3, and C2 domains of FVIII. Anti-A2 and anti-A3 antibodies interfere with assembly of FVIIIa with FIXa, whereas anti-C2 antibodies impede the interaction of FVIII with phospholipids. The immunologic mechanisms underlying inhibitor development in hemophilia A have not been fully elucidated. FVIII is recognized by the immune system as a foreign antigenic substance that evokes the T cell-dependent formation of high-affinity antibodies. Clonal analysis of B cell responses in hemophilia A patients has given further insight into the epitope specificity and molecular characteristics of FVIII inhibitors. Costimulatory blockade of FVIII-reactive T cells in a mouse model for hemophilia A has suggested new approaches for treatment of inhibitor patients. In this article, recent studies on the immunobiology of FVIII inhibitors are summarized and discussed with reference to their potential impact on treatment and prevention of immune responses in patients with hemophilia.
Application of picosecond light pulses generated from an AlGaInP visible diode laser for photoluminescence decay measurement of GaAs/AlGaAs quantum wells (1988)

The photoluminescence decay of GaAs/AlGaAs quantum wells was successfully measured at room temperature by using 660-nm picosecond light pulses from an AlGaInP diode laser driven by short pulse current. Our experimental results reveal that picosecond light pulses from visible diode lasers may be widely applicable, in place of mode-locked gas, solid-state, or dye lasers, for studying the fast carrier recombination properties of many kinds of materials including GaAs and AlGaAs in the wavelength region of deep red to infrared.
Network anomaly detection using autonomous system flow aggregates (2014)

Detecting malicious traffic streams in modern computer networks is a challenging task due to the growing traffic volume that must be analyzed. Traditional anomaly detection systems based on packet inspection face a scalability problem in terms of computational and storage capacity. One solution to this scalability problem is to analyze traffic based on IP flow aggregates. However, IP aggregates can still result in prohibitively large datasets for networks with heavy traffic loads. In this paper, we investigate whether anomaly detection is still possible when traffic is aggregated at a coarser scale. We propose a volumetric analysis methodology that aggregates traffic at the Autonomous System (AS) level. We show that our methodology reduces the number of flows to be analyzed by several orders of magnitude compared with IP flow level analysis, while still detecting traffic anomalies.
Predicting Gene Regulatory Elements in Silico on a Genomic Scale (1998)

We performed a systematic analysis of gene upstream regions in the yeast genome for occurrences of regular expression-type patterns with the goal of identifying potential regulatory elements. To achieve this goal, we have developed a new sequence pattern discovery algorithm that searches exhaustively for a priori unknown regular expression-type patterns that are over-represented in a given set of sequences. We applied the algorithm in two cases, (1) discovery of patterns in the complete set of >6000 sequences taken upstream of the putative yeast genes and (2) discovery of patterns in the regions upstream of the genes with similar expression profiles. In the first case, we looked for patterns that occur more frequently in the gene upstream regions than in the genome overall. In the second case, first we clustered the upstream regions of all the genes by similarity of their expression profiles on the basis of publicly available gene expression data and then looked for sequence patterns that are over-represented in each cluster. In both cases we considered each pattern that occurred at least in some minimum number of sequences, and rated them on the basis of their over-representation. Among the highest rating patterns, most have matches to substrings in known yeast transcription factor-binding sites. Moreover, several of them are known to be relevant to the expression of the genes from the respective clusters. Experiments on simulated data show that the majority of the discovered patterns are not expected to occur by chance.
Realizing Molecular Pixel System for Full-Color Fluorescence Reproduction: RGB-Emitting Molecular Mixture Free from Energy Transfer Crosstalk (2013)

A full-color molecular pixel system is realized for the first time using simple mixtures composed of RGB-emitting excited-state intramolecular proton transfer (ESIPT) dyes, each of which has delicately tailored Stokes shift and independent emission capability completely free from energy transfer crosstalk between them. It is demonstrated that the whole range of emission colors enclosed within the RGB color triangle on the CIE 1931 diagram is predictable and conveniently reproducible from the RGB molecular pixels not only in the solution but also in the polymer film. It must be noted that mixing ratios to reproduce the desired color coordinates can be precisely calculated on the basis of additive color theory according to their molecular pixel behavior.
Surrogate markers and clinical indices, alone or combined, as indicators for endoscopic remission in anti-TNF-treated luminal Crohn's disease (2012)

Clinical scores commonly used in the assessment of disease activity are unreliable at differentiating endoscopic remission from active CD. Despite this, a score based on a combination of fecal calprotectin and the HBI is a new promising tool for identifying endoscopic remission.
An integrated electronic telephone circuit (1983)

An integrated electronic telephone circuit (ETC) providing all the necessary elements of a telephone station apparatus is described. The ETC includes a speech network, tone ringer, dual-tone multifrequency (DTMF) dialer and DC line interface circuit. A microprocessor port facilitates automatic dialing features under control of a separate microprocessor. The speech network and dialer circuits operate with instantaneous input voltage as low as 1.4 V. The DTMF generator incorporates a high-precision frequency synthesis technique. Because of the reduction of frequency errors, an inexpensive ceramic resonator can be used as the frequency reference for the dialer. A linear/I/SUP 2/L process with two-layer metal interconnects is used to fabricate the 125/spl times/146 mil ETC die.
What Makes Good Antioxidants in Lipid-Based Systems? The Next Theories Beyond the Polar Paradox (2013)

The polar paradox states that polar antioxidants are more active in bulk lipids than their nonpolar counterparts, whereas nonpolar antioxidants are more effective in oil-in-water emulsion than their polar homologs. However, recent results, showing that not all antioxidants behave in a manner proposed by this hypothesis in oil and emulsion, lead us to revisit the polar paradox and to put forward new concepts, hypotheses, and theories. In bulk oil, new evidences have been brought to demonstrate that the crucial site of oxidation is not the air-oil interface, as postulated by the polar paradox, but association colloids formed with traces of water and surface active molecules such as phospholipids. The role of these association colloids on lipid oxidation and its inhibition by antioxidant is also addressed as well as the complex influence of the hydrophobicity on the ability of antioxidants to protect lipids from oxidation. In oil-in water emulsion, we have covered the recently discovered non linear (or cut-off) influence of the hydrophobicity on antioxidant capacity. For the first time, different mechanisms of action are formulated in details to try to account for this nonlinear effect. As suggested by the great amount of biological studies showing a cut-off effect, this phenomenon could be widespread in dispersed lipid systems including emulsions and liposomes as well as in living systems such as cultured cells. Works on the cut-off effect paves the way for the determination of the critical chain length which corresponds to the threshold beyond which antioxidant capacity suddenly collapses. The systematic search for this new physico-chemical parameter will allow designing novel phenolipids and other amphiphilic antioxidants in a rational fashion. Finally, in both bulk oils and emulsions, we feel that it is now time for a paradigm shift from the polar paradox to the next theories.
Helenalin triggers a CD95 death receptor-independent apoptosis that is not affected by overexpression of Bcl-x(L) or Bcl-2. (2001)

Apoptosis is required for proper tissue homeostasis. Defects in apoptosis signaling pathways, thus, contribute to carcinogenesis and chemoresistance. A major goal in chemotherapy is, therefore, to find cytotoxic agents that restore the ability of tumor cells to undergo apoptosis. We show here that the sesquiterpene lactone helenalin (10-50 microM) induces apoptosis in leukemia Jurkat T cells even if they lack the CD95 death receptor or overexpress the antiapoptotic proteins Bcl-x(L) or Bcl-2. Activated peripheral blood mononuclear cells, however, are not affected (10-50 microM helenalin). Helenalin led to a time-dependent (0-24 h) cleavage of the specific caspase-3-like substrate Asp-Glu-Val-Asp-7-amino-4-trifluoromethylcoumarin as well as to the proteolytic processing of procaspase-3 and -8. Caspase activation was a necessary requirement for apoptosis because the broad-spectrum caspase inhibitor benzyloxycarbonyl-Val-Ala-Asp(OMe)-fluoromethylketone (zVAD-fmk, 50 microM) completely abrogated helenalin-induced DNA fragmentation as well as phosphatidylserin translocation. Although the initiator caspase-8 was activated, the helenalin-induced signaling pathway did not require the CD95 death receptor as shown using cells without or with an antibody (ZB4)-blocked CD95 receptor. Helenalin also did not induce CD95 or CD95-ligand expression. On the other hand, helenalin was found to induce the release of cytochrome c from mitochondria that was not inhibited by the caspase inhibitor zVAD-fmk, which indicated that cytochrome c release precedes caspase activation. Cytochrome c release was accompanied by dissipation of the mitochondrial transmembrane potential (DeltaPsi(m)), which was partly inhibited by zVAD-fmk, which suggests that caspases are involved in loss of DeltaPsi(m). Most importantly, overexpression of the mitochondria protecting proteins Bcl-x(L) or Bcl-2 failed to confer resistance to helenalin-induced apoptosis, although the data presented here suggest that helenalin induces a mitochondria-dependent pathway. Thus, helenalin is a promising experimental cytotoxic agent that possibly points to new strategies to overcome apoptosis resistance attributable to overexpression of antiapoptotic Bcl-2 proteins.
Branched-Chain Amino Acid Metabolism in<i>Arabidopsis thaliana</i> (2010)

Valine, leucine and isoleucine form the small group of branched-chain amino acids (BCAAs) classified by their small branched hydrocarbon residues. Unlike animals, plants are able to de novo synthesize these amino acids from pyruvate, 2-oxobutanoate and acetyl-CoA. In plants, biosynthesis follows the typical reaction pathways established for the formation of these amino acids in microorganisms. Val and Ile are synthesized in two parallel pathways using a single set of enzymes. The pathway to Leu branches of from the final intermediate of Val biosynthesis. The formation of this amino acid requires a three-step pathway generating a 2-oxoacid elongated by a methylene group. In Arabidopsis thaliana and other Brassicaceae, a homologous three-step pathway is also involved in Met chain elongation required for the biosynthesis of aliphatic glucosinolates, an important class of specialized metabolites in Brassicaceae. This is a prime example for the evolutionary relationship of pathways from primary and specialized metabolism. Similar to animals, plants also have the ability to degrade BCAAs. The importance of BCAA turnover has long been unclear, but now it seems apparent that the breakdown process might by relevant under certain environmental conditions. In this review, I summarize the current knowledge about BCAA metabolism, its regulation and its particular features in Arabidopsis thaliana.
Personal Web Space (2003)

This paper describes the functional requirement and architecture of a software system called Personal Web Space (PWS). A PWS is a system to manage the information from the WWW, for either leisure or work related use. Similar to bookmarks, a PWS stores a set of URL addresses but, in addition, it caches on a proxy server pages of high interest. PWS is developed through an evolutionary process that is outlined in the paper. First, a method is prescribed to rank a page (or an URL address) based on the degree of importance to a person as determined by search engine responses and user input. Second, the information stored in a PWS must be refreshed periodically to keep up with the new state of information available on network; therefore a technique is proposed for determining and monitoring freshness. Thirdly, a PWS evolves through enlargement to include more information domains, or refinement to concentrate on smaller sub-domains. The paper describes how enlargement and refinement operations are mapped on to the stored PWS data dictionary. Finally, key-word queries can be issued against a PWS to get interesting information quickly. In this sense, a PWS uses a combination of information caching, information retrieval and bookmark technique to enhance significantly user performance on the Web.
Influence of sorghum wax, glycerin, and sorbitol on physical properties of soy protein isolate films (2003)

Abstract Sorghum wax, sorbitol, glycerin, and soy protein isolate (SPI) composite films were prepared. Effects of sorghum wax, sorbitol, and glycerin concentrations on various films were evaluated using response surface methodology. All independent variables significantly ( P <0.05) affected film water vapor permeability (WVP), tensile strength (TS), elongation at break (E), total color difference, and total soluble matter (TSM). Increasing the sorghum wax concentration decreased WVP and E. As sorbitol content increased in the composite films, WVP and TS increased. Sorbitol had a critical point of 2–5 g/5 g SPI for low values of TSM. The addition of sorbitol contributed more to the properties of the film than did glycerin.
<title>WeatherDigest: an experiment in media conversion</title> (1996)

This paper describes an experimental system (WeatherDigest) for automatic conversion of TV weather forecasts to HTML documents. This application is presented as an example of a larger system dealing with media understanding, representation and dissemination. An object model for media representation and processing is described and WeatherDigest is presented in terms of this object model. The concepts explored in WeatherDigest are then generalized to a repository of multimedia information (media server). This server can handle requests from clients with different requirements allowing to retrieve the same information in multiple formats.
Advancing Towards a Tissue-engineered Tympanic Membrane: Silk Fibroin as a Substratum for Growing Human Eardrum Keratinocytes (2009)

Human tympanic membrane cells (hTMCs), harvested from tympanic membrane (TM) explants, were grown in culture and then seeded on membranes prepared from silkworm (Bombyx mori) silk fibroin (BMSF) and on tissue-culture plastic membranes (PET). Fibroin was isolated from silk cast into membranes with a thickness of 10-15 microm. The hTMCs were cultured on both materials for 15 days in a serum-containing culture medium. The cells grown on both substrata were subjected to nuclear staining (DAPI) and counted. Further, the cultures were immunostained for a number of protein markers related to the epithelial/keratinocyte phenotype and cell adhesion complexes. The BMSF membranes supported levels of hTMC growth higher than that observed on the PET membranes. The immunofluorochemical analysis indicated unequivocally that BMSF is a more suitable substratum than PET with respect to the growth patterns, proliferation, and cell-cell contact and adhesion. BMSF appear as a promising substratum in the tissue-engineered constructs for the replacement of TM in case of nonhealing perforations.
Effects of Terminal Nonhomology and Homeology on Double-Strand-Break-Induced Gene Conversion Tract Directionality (1996)

Double-strand breaks (DSBs) greatly enhance gene conversion in the yeast Saccharomyces cerevisiae. In prior plasmid x chromosome crosses, conversion tracts were often short ( < 53 bp) and usually extended in only one direction from a DSB in an HO recognition sequence inserted into ura3. To allow fine-structure analysis of short and unidirectional tracts, phenotypically silent markers were introduced at 3- and 6-bp intervals flanking the HO site. These markers, which created a 70-bp homeologous region (71% homology), greatly increased the proportion of bidirectional tracts. Among products with short or unidirectional tracts, 85% were highly directional, converting markers on only one side (the nearest marker being 6 bp from the HO site). A DSB in an HO site insertion creates terminal nonhomologies. The high degree of directionality is a likely consequence of the precise cleavage at homology/nonhomology borders in hybrid DNA by Rad1/10 endonuclease. In contrast, terminal homeology alone yielded mostly unidirectional tracts. Thus, nonhomology flanked by homeology yields primarily bidirectional tracts, but terminal homeology or nonhomology alone yields primarily unidirectional tracts. These results are inconsistent with uni- and bidirectional tracts arising from one- and two-ended invasion mechanisms, respectively, as reduced homology would be expected to favor one-ended events. Tract spectra with terminal homeology alone with similar in RAD1 and rad1 cells, indicating that the high proportion of bidirectional tracts seen with homeology flanking nonhomology is not a consequence of Rad1/10 cleavage at homology/homeology boundaries. Instead, tract directionality appears to reflect the influence of the degree of broken-end homology on mismatch repair.
<i>Form‐Geitleria</i> (2015)

Geit.ler' i.a . M.L. fem. n. Geitleria Geitler, named after L. Geitler, Austrian botanist and specialist in cyanobacteria, 1899–1990. Cyanobacteria / Subsection V / Incertae Sedis / Form‐Geitleria Branching is pseudodichotomous, dichotomous, and lateral (Figure 1). The sheath becomes heavily calcified, and only cells near the tips of trichomes are able to give rise to a lateral branch or, when an apical cell undergoes an oblique division followed by further divisions of both cells, to a false dichotomy (Friedmann, 1955). The ultrastructure of decalcified specimens, including pore channels (i.e. “pit connections”), has been studied by Couté (1982, 1985) (Figure 1). No cultures of this genus have been established.
Identifying QTLs for thermo--tolerance of amylose content and gel consistency in rice (2006)

A mapping population of 98 backcross inbred lines （BILs） derived from a backcross, Nipponbare/Kasalath// Nipponbare, was used to identify the quantitative trait loci（QTL） conferring the thermo tolerance of amylose content and gel consistency in rice by mixed linear model approaches. A total of nine QTLs including three QTLs for thermo-tolerance of amylose content and six QTLs for thermo-tolerance of gel consistency were detected in Nanchang and Nanjing, respectively. Three QTLs for these two traits were common in the two experimental locations. The same region as Wx locus on chromosome 6 and interval of G1073-R727 on chromosome 8 were important regions for the thermo-tolerance of amylose content and gel consistency respectively.
Sorption of As (V) from waters by use of novel amine-containing sorbents prior to HGAAS and ICP-MS determination (2008)

A novel sorption method utilizing several amine-containing sorbents was developed for arsenic determination in waters by hydride generation atomic absorption spectrometry (HGAAS) and inductively coupled plasma mass spectrometry (ICP-MS).Chitosan, chitosan-immobilized sodium silicate, chitosan-modified macroporous silicate, and aminopropyl triethoxysilane-treated macroporous silicate were among the sorbents investigated for As(V) sorption.Sorption parameters were optimized for As(V) using chitosan and chitosanimmobilized sodium silicate and were then applied in all sorption studies. These parameters, namely, sorption pH, amount of sorbent, reaction temperature, and shaking time were 3.0, 50.0 mg, 25 .C, and 30 min, respectively. The sorption for chitosan under the optimized conditions was 89% (±1) while that for As(III) was lower than 10% at all pHs. In addition, chitosan-modified and amine-modified macroporous silicate demonstrated 88% (±3) and 68% (±12) sorption, respectively. After the sorption, the release of arsenate from chitosan and chitosan-immobilized sodium silicate was realized using two eluents; namely, 2.0% (v/v) acetic acid which dissolved chitosan, and 1.0% (w/v) L-cysteine solution having a pH of 3.0 adjusted with HCl which eluted arsenate by reducing to arsenite. Their respective desorption percentages were 90% (±1) and 100% (±4) for chitosan, and 67% (±2) and 100% (±1) for chitosan-immobilized sodium silicate.The preconcentration study performed using an absolute amount of 150.0 ng As(V) in bottled drinking water at the enrichment factors of 1, 2, and 10 has given 98% (±3), 95% (±2), and 78% (±4) recoveries, respectively. The accuracy of the proposed methodology with chitosan was verified with spike recovery tests for various water types at a concentration of 10.0 .g/L As(V). With matrix-matched calibration, the percentage spike recovery values were determined to be 114 (±4), 112 (±2), 43 (±4), and 0 (±1), for ultrapure, bottled, tap and sea water, respectively. These results have shown the strong suppression effect of the tap and the sea water matrixes.
Patterns of Azathioprine Metabolites in Neutrophils, Lymphocytes, Reticulocytes, and Erythrocytes (1997)

Monitoring of azathioprine (AZA) therapy by the measurement of 6-thioguanine nucleotides (6-TGN) concentrations in red blood cells (RBC) may improve safety and ensure optimal immunosuppressive effects of AZA in organ transplantation. The authors explored the rationale for such monitoring by measuring thiopurine metabolites in peripheral blood cell types that are more relevant to the effects and kinetics of AZA and its active metabolites. Neutrophil granulocytes were isolated by density gradient centrifugation, and CD4+ lymphocytes and reticulocytes by using specific immunomagnetic beads. In neutrophils, 6-TGN concentrations had median measurements 31 times higher than in RBCs. In contrast to the high methylated mercaptopurine (me-MP) concentrations in RBCs, these metabolites were not detected in the neutrophils. Thiopurine metabolite levels were lower than the analytic limit of detection in all the CD4+ samples. The concentrations of 6-TGN and me-MPs were lower in reticulocytes than in RBCs in general, indicating that thiopurine metabolites are taken up by RBCs in the circulation. This study's findings, that 6-TGN concentrations are very high in neutrophils, whereas me-MPs are undetectable, many explain the specific neutropenic adverse effect of AZA. The results also add support to monitoring AZA through measurements of 6-TGN and me-MPs in RBCs.