gebhart/patrepeval huggingface dataset:
A Potential Role of Collagens Expression in Distinguishing Between Premalignant and Malignant Lesions in Stomach (2009)

Lack of clinical biomarkers for early gastric cancer without specific early symptoms leads to delayed diagnosis, which contributes to high mortality of gastric cancer. Here, we used oligonucleotide microarray to systematically examine differential gene expression among 33 samples from normal, premalignant, and malignant lesions in stomach. A focal adhesion pathway mainly composed of collagen genes was found to have a significantly different expression profile in gastric cancers compared to premalignant lesions. A subset of collagen genes efficiently separated malignant from premalignant tissues, and two representative genes COL11A1 and COL1A1 were validated in 42 tissue samples with quantitative reverse transcription-PCR and in situ hybridization. The data above suggest that focal adhesion pathway may have a role in the pathogenesis of gastric cancer, and the expression profile of collagen genes may be a potential biomarker to distinguish malignant from premalignant lesions in stomach.
Therapy of ulcerative colitis: state of the art (2008)

Purpose of reviewAdvances in conventional therapy, novel targets and therapeutic goals are the highlights of treatment for ulcerative colitis in the last year. There have also been disappointments. This review summarizes the highs and lows, with an emphasis on strategy as opposed to seeking the newe
Distributed scheduling of tasks with deadlines and resource requirements (1989)

A set of four heuristic algorithms is presented to schedule tasks that have headlines and resource requirements in a distributed system. When a task arrives at a node, the local scheduler at that node attempts to guarantee that the task will complete execution on that node before its deadline. If the attempt fails, the scheduling components on individual nodes cooperate to determine which other node in the system has sufficient resource surplus to guarantee the task. Simulation studies are performed to compare the performance of these algorithms with respect to each other as well to two baselines. The first baseline is the noncooperative algorithm where a task that cannot be guaranteed locally is not sent to any other node. The second is an (ideal) algorithm that behaves exactly like the bidding algorithm but incurs no communication overheads. The simulation studies examine how communication delay, task laxity, load differences on the nodes, and task computation times affect the performance of the algorithms. The results show that distributed scheduling is effective even in a hard real-time environment and that the relative performance of these algorithms is a function of the system state.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Techniques for measuring arrival times of pulsar signals 1: DSN observations from 1968 to 1980 (1980)

Techniques used in the ground based observations of pulsars are described, many of them applicable in a navigation scheme. The arrival times of the pulses intercepting Earth are measured at time intervals from a few days to a few months. Low noise, wide band receivers, amplify signals intercepted by 26 m, 34, and 64 m antennas. Digital recordings of total received signal power versus time are cross correlated with the appropriate pulse template.
Cloning of glycoprotein D cDNA, which encodes the major subunit of the Duffy blood group system and the receptor for the Plasmodium vivax malaria parasite. (1993)

cDNA clones encoding the major subunit of the Duffy blood group were isolated from a human bone marrow cDNA library using a PCR-amplified DNA fragment encoding an internal peptide sequence of glycoprotein D (gpD) protein. The open reading frame of the 1267-bp cDNA clone indicated that gpD protein was composed of 338 amino acids, predicting a M(r) of 35,733, which was the same as a deglycosylated gpD protein. Portions of the predicted amino acid sequence, matched with six CNBr/pepsin peptides obtained from affinity-purified gpD protein. In ELISA analysis, an anti-Duffy murine monoclonal antibody reacted with a synthetic peptide deduced from the cDNA clone. Hydropathy analysis suggested the presence of 9 membrane-spanning alpha-helices. In bone marrow RNA blot analysis, the gpD cDNA detected a 1.27-kb mRNA in Duffy-positive but not in Duffy-negative individuals. It also identified the same size mRNA in adult kidney, adult spleen, and fetal liver; in brain, it detected a prominent 8.5-kb and a minor 2.2-kb mRNA. In Southern blot analysis, gpD cDNA identified a single gene in Duffy-positive and -negative individuals. Duffy-negative individuals, therefore, have the gpD gene, but it is not expressed in bone marrow. The same or a similar gene is active in adult kidney, adult spleen, and fetal liver of Duffy-positive individuals. Whether this is true in Duffy-negative individuals remains to be demonstrated. A GenBank sequence search yielded a significant protein sequence homology to human and rabbit interleukin-8 receptors.
Polymerization of Dicyclopentadiene:  A Tale of Two Mechanisms (1996)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTPolymerization of Dicyclopentadiene: A Tale of Two MechanismsT. A. Davidson, K. B. Wagener, and D. B. PriddyView Author Information Department of Chemistry and Center for Macromolecular Science and Engineering, University of Florida, Gainesville, Florida 32611Cite this: Macromolecules 1996, 29, 2, 786–788Publication Date (Web):January 15, 1996Publication History Received16 June 1995Revised13 October 1995Published online15 January 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ma950852xhttps://doi.org/10.1021/ma950852xbrief-reportACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views3669Altmetric-Citations93LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Catalysts,Hydrocarbons,Metathesis,Metathesis polymerization,Polymers Get e-Alerts
Long-term outcome and psychiatric comorbidity of adolescent-onset anorexia nervosa (2019)

Sixty-six percent of adolescents who completed the assessment achieved remission of their AN. Comorbidity was more common in the current ED group. The variable that best predicted complete remission was the number of years without treatment, showing the importance of detection and early intervention.
ChemInform Abstract: Synthesis of Oxypropanolamine Derivatives of 3,4‐Dihydro‐2H‐1,4‐benzoxazine, β‐Adrenergic Affinity, Inotropic, Chronotropic and Coronary Vasodilating Activities. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Topical TrustRank (2006)

Web spam is behavior that attempts to deceive search engine ranking algorithms. TrustRank is a recent algorithm that can combat web spam. However, TrustRank is vulnerable in the sense that the seed set used by TrustRank may not be sufficiently representative to cover well the different topics on the Web. Also, for a given seed set, TrustRank has a bias towards larger communities. We propose the use of topical information to partition the seed set and calculate trust scores for each topic separately to address the above issues. A combination of these trust scores for a page is used to determine its ranking. Experimental results on two large datasets show that our Topical TrustRank has a better performance than TrustRank in demoting spam sites or pages. Compared to TrustRank, our best technique can decrease spam from the top ranked sites by as much as 43.1%.
Capacity of human large granular lymphocytes (LGL) to produce multiple lymphokines: interleukin 2, interferon, and colony stimulating factor. (1983)

Human large granular lymphocytes (LGL), which are known to be responsible for natural killer (NK) cell activity, also produced a variety of lymphokines including interleukin 2 (IL 2), colony stimulating factor (CSF), and interferon (IFN) in response to phytohemagglutinin (PHA) or concanavalin A (Con A). Human peripheral blood LGL, which were purified by removal of monocytes adhering to plastic flasks and nylon columns, followed by separation on a discontinuous Percoll gradient, and additional treatment with anti-OKT3 and Leu-M1 plus complement, were more potent producers of these lymphokines than unseparated mononuclear cells (MNC), nylon column-eluted cells, or purified T lymphocytes. Moreover, IL 2 production by LGL could be further distinguished in that it was not enhanced by the addition of macrophages or macrophage-derived factor, i.e., IL 1, whereas addition of macrophages did potentiate IL 2 production by T lymphocytes. Further analysis of cells in the LGL population using various monoclonal antibodies revealed that removal of cells with OKT11 or AF-10, a monoclonal antibody against human HLA-DR antigen, decreased IL 2 production, whereas removal of OKT8+, OKM1+, Leu-M1+, or Leu-7+ cells led to enhanced IL 2 production. The LGL population is therefore heterogeneous and includes at least three functionally and phenotypically distinct subsets. An atypical T cell subset (OKT3-, Leu-1-, OKT11+) rather than the myeloid subset of LGL (Leu-M1+ or OKMI+) was the source of LGL-derived IL 2, whereas the latter subset and/or another subset of OKT8+ cells appear to regulate this IL 2 production. In addition to performing NK activity, LGL on a per cell basis seem to be more effective than T lymphocytes in producing lymphokines, namely, IL2, CSF, and IFN.
Lc, a member of the maize R gene family responsible for tissue-specific anthocyanin production, encodes a protein similar to transcriptional activators and contains the myc-homology region. (1989)

Previous studies have suggested that the R locus of maize is responsible for determining the temporal and spatial pattern of anthocyanin pigmentation in the plant. In this report we demonstrate that three members of the R gene family, P, S, and Lc, encode homologous transcripts 2.5 kilobases in length. The structure of one R gene, Lc, was determined by sequencing cDNA and genomic clones. The putative Lc protein, deduced from the cDNA sequence, is composed of 610 amino acids and has homology to the helix-loop-helix DNA-binding/dimerization motif found in the L-myc gene product and other regulatory proteins. It also contains a large acidic domain that may be involved in transcriptional activation. Consistent with its proposed role as a transcriptional activator is our finding that a functional R gene is required for the accumulation of transcripts of at least two genes in the anthocyanin biosynthetic pathway. We discuss the possibility that the diverse patterns of anthocyanin pigmentation conditioned by different R genes reflect differences in the R gene promoters rather than their gene products.
Interaction effects in spin-valve structures (2007)

Most applications in electronics are based on manipulation of the electron charge. Currently, there is also a lot of research into the possibility to make use of the electron spin, for example in magnetoelectronics. This field of research studies hybrid systems consisting of ferromagnetic metals, paramagnetic metals and insulators. In this thesis we present a theoretical description of a number of physical structures whose operation is based on the spin-valve principle. A spin valve consists of two ferromagnetic elements with a non-magnetic material in between. The electrical resistance of a spin valve can be varied by changing the angle between the magnetization directions of the two ferromagnets. We are especially interested in effects of the interaction between electrons on electronic transport in spin-valve structures. As the experimentally studied structures are getting smaller, interactions play an increasingly important role.
Duodenal levodopa infusion in Parkinson's disease - long-term experience (2001)

Motor fluctuations in parkinsonian patients can be reduced by intraduodenal infusion of levodopa. Between 1991 and 1998 continuous daytime administration of levodopa through a transabdominal port has been used in 28 very advanced patients over a total period of 1045 months. A stable suspension of levodopa and carbidopa (Duodopa) has been developed. Patients were characterized by early onset, long history of disease and levodopa therapy. The reason for infusion was in all cases related to on-off fluctuations. All patients experienced a general improvement after the introduction of continuous treatment. There have been no severe complications. Six patients have taken the decision to curtail their treatment. The mean daily levodopa consumption has been slightly reduced on infusion as compared to oral therapy. Nine of the first group of patients participating in the new therapy have been regularly evaluated by means of rating scales and movement analyses. Short-term results have already been published and a follow-up showing continued positive effect after 4-7 years of continuous duodenal infusion is presented.
Plakoglobin, or an 83-kD homologue distinct from beta-catenin, interacts with E-cadherin and N-cadherin. (1992)

E- and N-cadherin are members of a family of calcium-dependent, cell surface glycoproteins involved in cell-cell adhesion. Extracellularly, the transmembrane cadherins self-associate, while, intracellularly, they interact with the actin-based cytoskeleton. Several intracellular proteins, collectively termed catenins, have been noted to co-immunoprecipitate with E- and N-cadherin and are thought to be involved in linking the cadherins to the cytoskeleton. Two catenins have been identified recently: a 102-kD vinculin-like protein (alpha-catenin) and a 92-kD Drosophila armadillo/plakoglobin-like protein (beta-catenin). Here, we show that plakoglobin, or an 83-kD plakoglobin-like protein, co-immunoprecipitates and colocalizes with both E- and N-cadherin. The 83-kD protein is immunologically distinct from the 92-kD beta-catenin and, because of its molecular mass, likely represents the cadherin-associated protein called gamma-catenin. Thus, two different members of a plakoglobin family associate with N- and E-cadherin and, together with the 102-kD alpha-catenin, appear to participate in linking the cadherins to the actin-based cytoskeleton.
Engagement in Reading and Hobbies and Risk of Incident Dementia: The MoVIES Project (2010)

Engaging in hobbies for 1 or more hours every day might be protective against dementia in late life.
Mechanistic analysis of Xenopus EXO1's function in 5'-strand resection at DNA double-strand breaks (2011)

The processing of DNA double-strand breaks (DSBs) into 3' single-stranded tails is the first step of homology-dependent DSB repair. A key player in this process is the highly conserved eukaryotic exonuclease 1 (EXO1), yet its precise mechanism of action has not been rigorously determined. To address this issue, we reconstituted 5'-strand resection in cytosol derived from unfertilized interphase eggs of the frog Xenopus laevis. Xenopus EXO1 (xEXO1) was found to display strong 5'→3' dsDNA exonuclease activity but no significant ssDNA exonuclease activity. Depletion of xEXO1 caused significant inhibition of 5' strand resection. Co-depletion of xEXO1 and Xenopus DNA2 (xDNA2) showed that these two nucleases act in parallel pathways and by distinct mechanisms. While xDNA2 acts on ssDNA unwound mainly by the Xenopus Werner syndrome protein (xWRN), xEXO1 acts directly on dsDNA. Furthermore, xEXO1 and xWRN are required for both the initiation stage and the extension stage of resection. These results reveal important novel information on the mechanism of 5'-strand resection in eukaryotes.
Negative charge and charging dynamics in Al2O3 films on Si characterized by second-harmonic generation (2008)

Thin films of Al2O3 synthesized by atomic layer deposition provide an excellent level of interface passivation of crystalline silicon (c-Si) after a postdeposition anneal. The Al2O3 passivation mechanism has been elucidated by contactless characterization of c-Si/Al2O3 interfaces by optical second-harmonic generation (SHG). SHG has revealed a negative fixed charge density in as-deposited Al2O3 on the order of 1011 cm−2 that increased to 1012–1013 cm−2 upon anneal, causing effective field-effect passivation. In addition, multiple photon induced charge trapping dynamics suggest a reduction in recombination channels after anneal and indicate a c-Si/Al2O3 conduction band offset of 2.02±0.04 eV.
Spinal Cord Intramedullary Pressure (1994)

The results indicated that the intramedullary pressure of the cervical spinal cord increases when the neck is flexed. This phenomenon might play an important role in syrinx growth.
Tunstall adaptive coding and miscoding (1996)

In the first part of this paper, we tackle the case where a variable length-to-block Tunstall code is used to encode the wrong source (miscoding). It turns out that, exactly as happens in the case with Huffman coding, the asymptotic excess rate is given by the informational divergence between the probability distribution ruling the source and the probability distribution for which the Tunstall code had been devised. We also prove asymptotic equality between the individual rate of a codeword and the corresponding self-information. This allows us to bound the maximal and the minimal length in a Tunstall tree. In the second part of the paper we study the case where the probability distribution of the source changes in time. If this happens, it is necessary to frequently update the current code, to ensure that the optimality conditions concerning its rate are met. This coding procedure is known as adaptive coding. We propose some schemes for adaptive Tunstall coding, based on the structure of the coding tree, on the "ordering property", analogous to Gallager's (1978) sibling property of the Huffman code, and on the "Tunstall regions", analogous to the attraction regions due to Longo and Galasso (1982).
Temporal Compression Of Speech: An Evaluation (2008)

Efficient browsing of speech recordings is problematic. The linear nature of speech, coupled with the lack of abstraction that the medium affords, means that listeners have to listen to long segments of a recording to locate points of interest. We explore temporal compression algorithms that attempt to reduce the amount of time users require to listen to speech recordings, while retaining the important content. This paper implements two main approaches to temporal compression: artificial speech rate alteration (speed-up) and unimportant segment removal (excision). We evaluate the effectiveness of these approaches by having listeners rate comprehension and listening effort for different types of temporal compression. For different compression levels, we compare performance of various implementations of speed-up and excision as well as techniques based on semantic features and acoustic features. Our results indicate that listeners prefer low compression levels, excision over speed-up, and algorithms based on semantic rather than acoustic features. Finally, listeners were negative about hybrid algorithms that used speed-up to indicate missing regions in an excised recording.
Binding Modes of Peptidomimetics Designed to Inhibit STAT3 (2012)

STAT3 is a transcription factor that has been found to be constitutively activated in a number of human cancers. Dimerization of STAT3 via its SH2 domain and the subsequent translocation of the dimer to the nucleus leads to transcription of anti-apoptotic genes. Prevention of the dimerization is thus an attractive strategy for inhibiting the activity of STAT3. Phosphotyrosine-based peptidomimetic inhibitors, which mimic pTyr-Xaa-Yaa-Gln motif and have strong to weak binding affinities, have been previously investigated. It is well-known that structures of protein-inhibitor complexes are important for understanding the binding interactions and designing stronger inhibitors. Experimental structures of inhibitors bound to the SH2 domain of STAT3 are, however, unavailable. In this paper we describe a computational study that combined molecular docking and molecular dynamics to model structures of 12 peptidomimetic inhibitors bound to the SH2 domain of STAT3. A detailed analysis of the modeled structures was performed to evaluate the characteristics of the binding interactions. We also estimated the binding affinities of the inhibitors by combining MMPB/GBSA-based energies and entropic cost of binding. The estimated affinities correlate strongly with the experimentally obtained affinities. Modeling results show binding modes that are consistent with limited previous modeling studies on binding interactions involving the SH2 domain and phosphotyrosine(pTyr)-based inhibitors. We also discovered a stable novel binding mode that involves deformation of two loops of the SH2 domain that subsequently bury the C-terminal end of one of the stronger inhibitors. The novel binding mode could prove useful for developing more potent inhibitors aimed at preventing dimerization of cancer target protein STAT3.
Synthesis of a thioanalogue of neamine. The reaction of nitrosochloroadducts of glycals with thiols (1979)

The reaction of the dimeric 4-O-acetyl-6-azido-2,3,6-trideoxy-2-nitroso-α-D-ribo-hexopyranosyl chloride 2 with cyclohexanethiol and 2-propanethiol is stereospecific and produces the corresponding 2-hydroxyimino-1-thio-α-D-erythro-hexopyranosides 3a and 3c in high yields. Acetylation of the oxime 3a followed by reduction with borane, then by reduction with sodium borohydride and acetylation gave cyclohexyl 2,6-diacetamido-4-O-acetyl-2,3,6-trideoxy-l-thio-α-D-ribo-hexopyranoside (4b). By a similar sequence of reactions, the oxime 3c was converted to isopropyl 2,6-dibenzamido-4-O-benzoyl-2,3,6-trideoxy-l-thio-α-D-ribo-hexopyranoside (4c).Condensation of the nitrosochloro adduct 2 with (1S,2S,4R,5R)-2,4-diethoxycarbonylamino-5-hydroxycyclohexanethiol (5c) gave the α-D-thioglycoside 6c which, after acetylation followed by reduction and removal of the protective groups, yielded (1S,2S,4R,5R)-2,4-diamino-5-hydroxycyclohexyl 2,6-diamino-2,3,6-trideoxy-l-thio-α-D-ribo-hexopyranoside (7c), a thioanalogue of neamine.
De novo characterization of a whitefly transcriptome and analysis of its gene expression during development (2010)

Our data provides the most comprehensive sequence resource available for whitefly study and demonstrates that the Illumina sequencing allows de novo transcriptome assembly and gene expression analysis in a species lacking genome information. We anticipate that next generation sequencing technologies hold great potential for the study of the transcriptome in other non-model organisms.