gebhart/patrepeval huggingface dataset:
Toward a Benchmarking Data Set Able to Evaluate Ligand- and Structure-based Virtual Screening Using Public HTS Data (2015)

Virtual screening has the potential to accelerate and reduce costs of probe development and drug discovery. To develop and benchmark virtual screening methods, validation data sets are commonly used. Over the years, such data sets have been constructed to overcome the problems of analogue bias and artificial enrichment. With the rapid growth of public domain databases containing high-throughput screening data, such as the PubChem BioAssay database, there is an increased possibility to use such data for validation. In this study, we identify PubChem data sets suitable for validation of both structure- and ligand-based virtual screening methods. To achieve this, high-throughput screening data for which a crystal structure of the bioassay target was available in the PDB were identified. Thereafter, the data sets were inspected to identify structures and data suitable for use in validation studies. In this work, we present seven data sets (MMP13, DUSP3, PTPN22, EPHX2, CTDSP1, MAPK10, and CDK5) compiled using this method. In the seven data sets, the number of active compounds varies between 19 and 369 and the number of inactive compounds between 59 405 and 337 634. This gives a higher ratio of the number of inactive to active compounds than what is found in most benchmark data sets. We have also evaluated the screening performance using docking and 3D shape similarity with default settings. To characterize the data sets, we used physicochemical similarity and 2D fingerprint searches. We envision that these data sets can be a useful complement to current data sets used for method evaluation.
Epidermal growth factor receptor expression correlates with poor prognosis in non-small cell lung cancer patients with p53 overexpression. (2000)

To determine whether cancer patients with tumor suppressor gene abnormality survive for a shorter time when their growth was stimulated by growth factors, we examined 290 non-small cell lung cancer (NSCLC) specimens for p53 and epidermal growth factor receptor (EGFR) protein expressions using immunohistochemical staining. The distribution of cases by pathological stage of tumor was 155 cases of stage I, 30 cases of stage II, 96 cases of stage III and 9 cases of stage IV. Pathological types were 142 adenocarcinomas, 127 squamous cell carcinomas, 17 large cell carcinomas and 4 other types of malignancy. Immunohistochemical staining was performed on the formalin fixed, paraffin-embedded materials with monoclonal antibodies DO-7 and clone EGFR.133. positive staining for EGFR was seen in 124 (42.8%) cases. More EGFR positive cases were found in squamous cell carcinomas than in non-squamous cell carcinomas (p=0.0121). Staining for p53 protein was observed in 147 (50.7%) specimens. Multivariate proportional hazard model analyses revealed EGFR protein expression as a risk factor in the patients with NSCLC (p=0.0240). Patients negative for both EGFR and p53 survived for a longer period of time (p=0.0427).
Gene Expression Atlas at the European Bioinformatics Institute (2009)

The Gene Expression Atlas (http://www.ebi.ac.uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive of Functional Genomics Data. A simple interface allows the user to query for differential gene expression either (i) by gene names or attributes such as Gene Ontology terms, or (ii) by biological conditions, e.g. diseases, organism parts or cell types. The gene queries return the conditions where expression has been reported, while condition queries return which genes are reported to be expressed in these conditions. A combination of both query types is possible. The query results are ranked using various statistical measures and by how many independent studies in the database show the particular gene-condition association. Currently, the database contains information about more than 200,000 genes from nine species and almost 4500 biological conditions studied in over 30,000 assays from over 1000 independent studies.
Satem: Trusted Service Code Execution across Transactions (2006)

Web services and service oriented architectures are becoming the de facto standard for Internet computing. A main problem faced by users of such services is how to ensure that the service code is trusted. While methods that guarantee trusted service code execution before starting a client-service transaction exist, there is no solution for extending this assurance to the entire lifetime of the transaction. This paper presents Satem, a Service-aware trusted execution monitor that guarantees the trustworthiness of the service code across a whole transaction. The Satem architecture consists of an execution monitor residing in the operating system kernel on the service provider platform, a trust evaluator on the client platform, and a service commitment protocol. During this protocol, executed before every transaction, the client requests and verifies against its local policy a commitment from the service platform that promises trusted code execution. Subsequently, the monitor enforces this commitment for the duration of the transaction. To initialize the trust on the monitor, we use the Trusted Platform Module specified by the Trusted Computing Group. We implemented Satem under the Linux 2.6.12 kernel and tested it for a Web service and DNS. The experimental results demonstrate that Satem does not incur significant overhead to the protected services and does not impact the unprotected services
Word-Based Alignment, Phrase-Based Translation: What's the Link? (2006)

State-of-the-art statistical machine translation is based on alignments between phrases – sequences of words in the source and target sentences. The learning step in these systems often relies on alignments between words. It is often assumed that the quality of this word alignment is critical for translation. However, recent results suggest that the relationship between alignment quality and translation quality is weaker than previously thought. We investigate this question directly, comparing the impact of highquality alignments with a carefully constructed set of degraded alignments. In order to tease apart various interactions, we report experiments investigating the impact of alignments on different aspects of the system. Our results confirm a weak correlation, but they also illustrate that more data and better feature engineering may be more beneficial than better alignment. 1
Inhibition of human hepatocarcinoma cell proliferation by mammalian and fish gonadotropin-releasing hormones (1995)

This study provides the first demonstration that human hepatocarcinoma-derived cell line HepG2 contains GnRH receptors and responds to various molecular forms of GnRH in terms of inhibition of proliferation in a time- and dose-related manner. In addition, GnRH peptides also significantly inhibited the uptake of [3H]thymidine by these cells. The effect of GnRH was specific because GnRH antagonists reversed the GnRH-mediated inhibition, and non-GnRH peptides had no effect on HepG2 cell proliferation. An important finding is that certain fish GnRH molecules such as lamprey GnRH, which has little gonadotropin (LH) release activity in mammals, suppress hepatocarcinoma cell proliferation with similar potency to a superactive mammalian GnRH analog, [D-Lys6]GnRH. These findings may have profound implications in the development of an effective chemotherapy for treatment of human liver cancer. An added advantage is that fish GnRH forms will likely exert little side effect in terms of human pituitary gonadotropin release, gonadal steroidogenesis, and reproductive functions in general.
A Peptide from Heat Shock Protein 60 Is the Dominant Peptide Bound To Qa-1 in the Absence of the MHC Class Ia Leader Sequence Peptide Qdm (2003)

The MHC class Ib molecule Qa-1 binds specifically and predominantly to a single 9-aa peptide (AMAPRTLLL) derived from the leader sequence of many MHC class Ia proteins. This peptide is referred to as Qdm. In this study, we report the isolation and sequencing of a heat shock protein 60-derived peptide (GMKFDRGYI) from Qa-1. This peptide is the dominant peptide bound to Qa-1 in the absence of Qdm. A Qa-1-restricted CTL clone recognizes this heat shock protein 60 peptide, further verifying that it binds to Qa-1 and a peptide from the homologous Salmonella typhimurium protein GroEL (GMQFDRGYL). These observations have implications for how Qa-1 can influence NK cell and T cell effector function via the TCR and CD94/NKG2 family members, and how this effect can change under conditions that cause the peptides bound to Qa-1 to change.
Elevated Intrasynaptic Dopamine Release in Tourette’s Syndrome Measured by PET (2002)

Greater putamen dopamine release was seen in adults with Tourette's syndrome than in comparison subjects after a pharmacologic challenge with amphetamine. These results suggest that the underlying pathobiology in Tourette's syndrome is a phasic dysfunction of dopamine transmission.
Analysis of mRNA populations by cDNA·mRNA hybrid-mediated inhibition of cell-free protein synthesis (1978)

Hybridization of mRNA to its corresponding cDNA was found to specifically inhibit translation of the mRNA in vitro. Using hybridization of globin cDNA to globin mRNA as a model system, we found that equivalent amounts of cDNA were required both for the saturation of the mRNA hybridization and for complete inhibition of globin synthesis. Also, the rate of inactivation of translation was identical to the rate of hybridization and followed the predicted kinetic form. This assay has been applied to the analysis of a set of abundant mRNAs in mouse liver. Hybridization of liver mRNA with total liver cDNA in slight excess to a low C(0)t value specifically inhibited translation of several major polypeptides. Melting of the hybrids prior to translation restored synthesis of these polypeptides. Moreover, we found that different liver mRNAs are inactivated with different kinetics; the results suggest that the mRNAs for the major urinary polypeptide and for albumin are the most abundant and second most abundant, respectively, in mouse liver. The general applications of this technique are discussed.
The Sortase-Dependent Fimbriome of the Genus Bifidobacterium: Extracellular Structures with Potential To Modulate Microbe-Host Dialogue (2017)

Bifidobacteria are important gut commensals of mammals, including humans, of any age. However, the molecular mechanisms by which these microorganisms establish themselves in the mammalian gut and persist in this environment are largely unknown. Here, we analyzed the genetic diversity of the predicted arsenal of sortase-dependent pili of known and sequenced members of the <i>Bifidobacterium</i> genus and constructed a bifidobacterial sortase-dependent fimbriome database. Our analyses revealed considerable genetic variability of the sortase-dependent fimbriome among bifidobacterial (sub)species, which appears to have been due to horizontal gene transfer events and for which we were able to perform evolutionary mapping. Functional assessment by transcriptome analysis and binding assays involving different substrates demonstrates how bifidobacterial pili are pivotal in promoting various abilities for adhesion to glycans and extracellular matrix proteins, thereby supporting the ecological success of bifidobacteria in the mammalian gut.<b>IMPORTANCE</b> Adhesion of bifidobacterial cells to the mucosa of the large intestine is considered a hallmark for the persistence and colonization of these bacteria in the human gut. In this context, we analyzed the genetic diversity of the predicted arsenal of sortase-dependent pili of known and sequenced members of the <i>Bifidobacterium</i> genus, and constructed a bifidobacterial sortase-dependent fimbriome database. Our analyses revealed considerable genetic variability of the sortase-dependent fimbriome among bifidobacterial (sub)species, which appears to have been due to horizontal gene transfer events. In addition, functional assessment by transcriptome analysis and binding assays involving different substrates demonstrates how bifidobacterial pili are crucial in promoting various abilities for adhesion to glycans and extracellular matrix proteins, thereby supporting the ecological success of bifidobacteria in the mammalian gut. This study represents a complete genomic study regarding the presence of fimbriae in the genus <i>Bifidobacterium</i>.
A single domestication for maize shown by multilocus microsatellite genotyping (2002)

There exists extraordinary morphological and genetic diversity among the maize landraces that have been developed by pre-Columbian cultivators. To explain this high level of diversity in maize, several authors have proposed that maize landraces were the products of multiple independent domestications from their wild relative (teosinte). We present phylogenetic analyses based on 264 individual plants, each genotyped at 99 microsatellites, that challenge the multiple-origins hypothesis. Instead, our results indicate that all maize arose from a single domestication in southern Mexico about 9,000 years ago. Our analyses also indicate that the oldest surviving maize types are those of the Mexican highlands with maize spreading from this region over the Americas along two major paths. Our phylogenetic work is consistent with a model based on the archaeological record suggesting that maize diversified in the highlands of Mexico before spreading to the lowlands. We also found only modest evidence for postdomestication gene flow from teosinte into maize.
A randomized, controlled, feasibility study of RD-X19 in patients with mild-to-moderate COVID-19 in the outpatient setting (2021)

ABSTRACT These studies aimed to further understand the antiviral effects of safe, visible light and demonstrate a therapeutic effect of an investigational treatment device for outpatients with mild to moderate COVID-19. RD-X19 is a handheld medical device precisely engineered to emit blue light through the oral cavity to target the oropharynx and surrounding tissues. At doses that are well-tolerated in an in vitro human epithelial tissue model, the monochromatic visible light delivered by RD-X19 results in light-initiated expression of IL-1α and IL-1β cytokines with corresponding inhibition of SARS-CoV-2 replication. A randomized, double-blind, sham-controlled early feasibility study using the investigational device enrolled 31 subjects with a positive SARS-CoV-2 antigen test and possessing at least two moderate COVID-19 signs and symptoms. Subjects were randomized 2:1 (RD-X19 to sham), treated twice daily for four days, and evaluated over one week. Prespecified outcome measures included assessments of SARS-CoV-2 viral load and clinical assessments of COVID-19. There were no local application site reactions and no device-related adverse events. The time-weighted average change in log viral load throughout the study demonstrated a favorable reduction for RD-X19 compared to sham and at the end of study the mean change in log 10 viral load was -3.29 for RD-X19 and -1.81 for sham at Day 8, demonstrating a treatment benefit of -1.48 [95% confidence internal (CI), -2.88 to -0.071]. Among the clinical outcome measures, differences between RD-X19 and sham were also observed, with a 57-hour reduction of median time to sustained resolution of COVID-19 signs and symptoms.
Oral Tolerance: Immunologic Mechanisms and Treatment of Animal and Human Organ-Specific Autoimmune Diseases by Oral Administration of Autoantigens (1994)

Oral tolerance is a long recognized method to induce peripheral immune tolerance. The primary mechanisms by which orally administered antigen induces tolerance are via the generation of active suppression or clonal anergy. Low doses of orally administered antigen favor active suppression whereas higher doses favor clonal anergy. The regulatory cells that mediate active suppression act via the secretion of suppressive cytokines such as TGF beta and IL-4 after being triggered by the oral tolerogen. Furthermore, antigen that stimulates the gut-associated lymphoid tissue preferentially generates a Th2 type response. Because the regulatory cells generated following oral tolerization are triggered in an antigen-specific fashion but suppress in an antigen nonspecific fashion, they mediate "bystander suppression" when they encounter the fed autoantigen at the target organ. Thus it may not be necessary to identify the target autoantigen to suppress an organ-specific autoimmune disease via oral tolerance; it is necessary only to administer orally a protein capable of inducing regulatory cells that secrete suppressive cytokines. Orally administered autoantigens suppress several experimental autoimmune models in a disease- and antigen-specific fashion; the diseases include experimental autoimmune encephalomyelitis (EAE), uveitis, and myasthenia, collagen- and adjuvant-induced arthritis, and diabetes in the NOD mouse. In addition, orally administered alloantigen suppresses alloreactivity and prolongs graft survival. Initial clinical trials of oral tolerance in multiple sclerosis, rheumatoid arthritis, and uveitis have demonstrated positive clinical effects with no apparent toxicity and decreases in T cell autoreactivity.
Extended survival in advanced and refractory multiple myeloma after single-agent thalidomide: identification of prognostic factors in a phase 2 study of 169 patients (2001)

This report of a phase 2 trial of thalidomide (THAL) (200 mg/d; 200 mg increment every 2 weeks to 800 mg) for 169 patients with advanced myeloma (MM) (abnormal cytogenetics (CG), 67%; prior autotransplant, 76%) extends earlier results in 84 patients. A 25% myeloma protein reduction was obtained in 37% of patients (50% reduction in 30% of patients; near-complete or complete remission in 14%) and was more frequent with low plasma cell labeling index (PCLI) (below 0.5%) and normal CG. Two-year event-free and overall survival rates were 20% +/- 6% and 48% +/- 6%, respectively, and these were superior with normal CG, PCLI of less than 0.5%, and beta(2)-microglobulin of 3 mg/L. Response rates were higher and survival was longer especially in high-risk patients given more than 42 g THAL in 3 months (median cumulative dose) (landmark analysis); this supports a THAL dose-response effect in advanced MM.
Two alternative mRNAs coding for the angiogenic factor, placenta growth factor (PlGF), are transcribed from a single gene of chromosome 14. (1993)

We have previously reported on the identification of a cDNA (placenta growth factor, PlGF) coding for a novel angiogenic factor expressed in placental tissue that is similar to vascular permeability factor/vascular endothelial growth factor (VPF/VEGF). Biochemical and functional characterization of PlGF derived from transfected COS-1 cells revealed that it is a glycosylated dimeric secreted protein able to stimulate endothelial cell growth in vitro. Here, we report the isolation and characterization of the PlGF gene located on chromosome 14. At least two different mRNAs are produced from this single-copy gene in different cell lines and tissues. Sequence comparison of the polypeptides encoded by the two different isolated cDNAs indicates that they are identical except for the insertion of a highly basic 21 amino acid stretch at the carboxyl end of the protein. RNA expression analysis of several tissues, tumors and cell lines indicates differential distribution of the two PlGF mRNAs. Finally, preliminary results indicate that the PIGF gene has been conserved in evolution, since the human PlGF cDNA hybridizes to sequences present in the genomic DNA of Drosophila, Xenopus, chicken and mouse.
The effect of two-week L-carnitine supplementation on exercise -induced oxidative stress and muscle damage. (2014)

These results suggest that two-week daily oral supplementation of L-carnitine has alleviating effects on lipid peroxidation and muscle damage markers following an acute bout of exercise in active healthy young men.
Isolation, primary structure, and synthesis of human hypothalamic somatocrinin: growth hormone-releasing factor. (1984)

The hypophysiotropic peptide, growth hormone-releasing factor (GRF), was isolated from human hypothalamic-hypophysial tissues by means of acid extraction, immunoaffinity chromatography, gel filtration, and two steps of reverse-phase high-performance liquid chromatography. Amino acid sequence determination using a gas-phase sequencer and reverse-phase liquid chromatography of the native peptide and its synthetic replicates showed its primary structure to be as follows: H-Tyr-Ala-Asp-Ala-Ile-Phe-Thr-Asn-Ser-Tyr-Arg-Lys-Val-Leu-Gly-Gln -Leu-Ser-Ala-Arg-Lys-Leu-Leu-Gln-Asp-Ile-Met-Ser-Arg-Gln-Gln-Gly-Glu-Ser -Asn-Gln-Glu-Arg-Gly-Ala-Arg-Ala-Arg-Leu-NH2, which is identical to that of the GRF recently isolated and characterized from a human pancreatic tumor that had caused acromegaly. Human hypothalamic GRF shows major homologies (93%, 89%, and 86%, respectively) when its primary structure is compared to that of the hypothalamic GRF from the porcine, bovine, caprine, and ovine species.
Petroleum production systems (1994)

1. The Role of Petroleum Production Engineering. 2. Production from Undersaturated Oil Reservoirs. 3. Production from Two-Phase Reservoirs. 4. Production from Natural Gas Reservoirs. 5. The Near-Wellbore Condition and Damage Characterization Skin Effects. 6. Gravel Pack Completions. 7. Wellbore Flow Performance. 8. Well Deliverability. 9. Forecast of Well Production. 10. Wellhead and Surface Gathering Systems. 11. Modern Well Test Analysis. 12. Well Test Design and Data Acquisition. 13. Production Logging Measurements and Analysis. 14. Well Diagnosis with Production Logging. 15. Pressure Transient Testing with Measured Sandface Flow Rates. 16. Gas Well Testing. 17. Matrix Simulation-Chemistry of Acid Rock Reactions. 18. Sandstone Acidizing Design. 19. Carbonate Acidizing Design. 20. Hydraulic Fracturing for Well Simulation. 21. Design of Hydraulic Fracture Treatments. 22. The Performance of Hydraulically-Fractured and Long-Flowing Wells. 23. Gas Lift. 24. Pump-Assisted Lift. 25. Petroleum System Analysis. 26. Environmental Issues in Petroleum Production. Appendix.
MONOMOLECULAR FILMS OF FATTY ACIDS ON GLASS (1934)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMONOMOLECULAR FILMS OF FATTY ACIDS ON GLASSKatharine B. BlodgettCite this: J. Am. Chem. Soc. 1934, 56, 2, 495Publication Date (Print):February 1, 1934Publication History Published online1 May 2002Published inissue 1 February 1934https://pubs.acs.org/doi/10.1021/ja01317a513https://doi.org/10.1021/ja01317a513research-articleACS PublicationsRequest reuse permissionsArticle Views1507Altmetric-Citations390LEARN 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 Get e-Alerts