gebhart/patrepeval huggingface dataset:
PepX: a structural database of non-redundant protein–peptide complexes (2009)

Although protein-peptide interactions are estimated to constitute up to 40% of all protein interactions, relatively little information is available for the structural details of these interactions. Peptide-mediated interactions are a prime target for drug design because they are predominantly present in signaling and regulatory networks. A reliable data set of nonredundant protein-peptide complexes is indispensable as a basis for modeling and design, but current data sets for protein-peptide interactions are often biased towards specific types of interactions or are limited to interactions with small ligands. In PepX (http://pepx.switchlab.org), we have designed an unbiased and exhaustive data set of all protein-peptide complexes available in the Protein Data Bank with peptide lengths up to 35 residues. In addition, these complexes have been clustered based on their binding interfaces rather than sequence homology, providing a set of structurally diverse protein-peptide interactions. The final data set contains 505 unique protein-peptide interface clusters from 1431 complexes. Thorough annotation of each complex with both biological and structural information facilitates searching for and browsing through individual complexes and clusters. Moreover, we provide an additional source of data for peptide design by annotating peptides with naturally occurring backbone variations using fragment clusters from the BriX database.
Unsafe and potentially safe herbal therapies (1999)

Unsafe and potentially safe herbal therapies are discussed. The use of herbal therapies is on the rise in the United States, but most pharmacists are not adequately prepared educationally to meet patients' requests for information on herbal products. Pharmacists must also cope with an environment in which there is relatively little regulation of herbal therapies by FDA. Many herbs have been identified as unsafe, including borage, calamus, coltsfoot, comfrey, life root, sassafras, chaparral, germander, licorice, and ma huang. Potentially safe herbs include feverfew, garlic, ginkgo, Asian ginseng, saw palmetto, St. John's wort, and valerian. Clinical trials have been used to evaluate feverfew for migraine prevention and rheumatoid arthritis; garlic for hypertension, hyperlipidemia, and infections; ginkgo for circulatory disturbances and dementia; ginseng for fatigue and cancer prevention; and saw palmetto for benign prostatic hyperplasia. Also studied in formal trials have been St. John's wort for depression and valerian for insomnia. The clinical trial results are suggestive of efficacy of some herbal therapies for some conditions. German Commission E, a regulatory body that evaluates the safety and efficacy of herbs on the basis of clinical trials, cases, and other scientific literature, has established indications and dosage recommendations for many herbal therapies. Pharmacists have a responsibility to educate themselves about herbal therapies in order to help patients discern the facts from the fiction, avoid harm, and gain what benefits may be available.
Circuits and trees in oriented linear graphs (1951)

In this $ we state the problem which gave rise to our investigations about graphs. The further contents of the paper are independent of this $ 1.
MCM-41-Supported Co-Mo Catalysts for Deep Hydrodesulfurization of Light Cycle Oil-Based Real Feedstock (2002)

Introduction The increasing stringency of sulfur specifications has motivated intensive research in the hydrodesulfurization (HDS) of liquid hydrocarbon transportation fuels such as gasoline, diesel, and jet fuel. Most studies have, however, focused on mixtures of model compounds to simulate real feedstocks [1-5]. The few studies that have used real feedstocks to evaluate HDS catalysts have relied on hydrotreated [6-12] or low sulfur content feedstocks [13-15]. Previous work from our laboratory has established the superiority of MCM-41-supported catalysts for the HDS of a model compound [16] and a real feedstock [17]. This paper reports on further studies on HDS of real feedstocks; specifically a blend of light cycle oil (LCO) and refined chemical oil (RCO).
The Anchors of Partisanship: A Comparative Analysis of Voting Behavior in Four Southern European Democracies (2000)

The four Southern European democracies reveal greatly differing patterns of electoral volatility: the Spanish party system underwent a profound restructuring as a result of the &quot;electoral earthquake &quot; of 1982, but has become outstandingly stable since then; the Italian party system had been impressively stable from the 1950s until 1992, but then underwent a complete transformation. But despite the extremely high levels of &quot;total volatility &quot; exhibited by these two party systems, very few voters crossed over the divide separating parties of the left from the right. In contrast, both the Greek and Portuguese party systems have frequently exhibited high levels of &quot;inter-bloc &quot; volatility. What explains these differing patterns? A cursory examination of the varying degrees of organizational development and social penetration of parties, as well as of their linkages to other secondary associations, suggests that these patterns of stability and volatility cannot be attributed to the organizational bases of partisanship. Neither can these patterns be explained by cross-national differences in the extent to which voters identify with parties. A more powerful explanation of these varying and evolving patterns of party-system stabilization and volatility can be found in the extent of
Clinical trial of<i>Rhodiola rosea</i>L. extract SHR-5 in the treatment of mild to moderate depression (2007)

The objective of this study was to assess the efficacy and safety of standardized extract SHR-5 of rhizomes of Rhodiola rosea L. in patients suffering from a current episode of mild/moderate depression. The phase III clinical trial was carried out as a randomized double-blind placebo-controlled study with parallel groups over 6 weeks. Participants, males and females aged 18-70 years, were selected according to DSM-IV diagnostic criteria for depression, the severity of which was determined by scores gained in Beck Depression Inventory and Hamilton Rating Scale for Depression (HAMD) questionnaires. Patients with initial HAMD scores between 21 and 31 were randomized into three groups, one of which (group A: 31 patients) received two tablets daily of SHR-5 (340 mg/day), a second (group B: 29 patients) received two tablets twice per day of SHR-5 (680 mg/day), and a third (group C: 29 patients) received two placebo tablets daily. The efficacy of SHR-5 extract with respect to depressive complaints was assessed on days 0 and 42 of the study period from total and specific subgroup HAMD scores. For individuals in groups A and B, overall depression, together with insomnia, emotional instability and somatization, but not self-esteem, improved significantly following medication, whilst the placebo group did not show such improvements. No serious side-effects were reported in any of the groups A-C. It is concluded that the standardized extract SHR-5 shows anti-depressive potency in patients with mild to moderate depression when administered in dosages of either 340 or 680 mg/day over a 6-week period.
Detection of antibodies to respiratory syncytial virus attachment and nucleocapsid proteins with recombinant baculovirus-expressed antigens (1997)

The ability to measure antibodies against individual respiratory syncytial virus (RSV) proteins is important in the analysis of immune responses to RSV. We expressed the nucleocapsid (N) protein and the group A and B RSV attachment (G) proteins from recombinant baculoviruses. The three recombinant RSV proteins were used individually in an enzyme-linked immunosorbent assay (ELISA; bac-ELISA for results from assays of all three proteins). The bac-ELISA results were compared to the results obtained by a whole-virus ELISA (RS-ELISA for results from assays of both group A and B viruses). Antibody samples from 113 children were tested. The determination of seronegative or seropositive status by the bac-ELISA was compared to the same determination by the RS-ELISA; the sensitivity of bac-ELISA was 87% (95% confidence interval [CI], 78 to 93%), the specificity was 82% (CI, 59 to 94%), and the positive and negative predictive values were 95% (CI, 86 to 98%) and 60% (CI, 41 to 77%), respectively. The group specificity of the G-protein ELISA was confirmed by testing antibodies from experimentally immunized animals. Thus, the bac-ELISA was shown to be comparable to the whole-virus ELISA in detecting antibody responses to RSV, while it offered the advantage of measuring specific antibody responses to individual RSV proteins.
An Effective Transform Unit Size Decision Method for High Efficiency Video Coding (2014)

High efficiency video coding (HEVC) is the latest video coding standard. HEVC can achieve higher compression performance than previous standards, such as MPEG‐4, H.263, and H.264/AVC. However, HEVC requires enormous computational complexity in encoding process due to quadtree structure. In order to reduce the computational burden of HEVC encoder, an early transform unit (TU) decision algorithm (ETDA) is adopted to pruning the residual quadtree (RQT) at early stage based on the number of nonzero DCT coefficients (called NNZ‐EDTA) to accelerate the encoding process. However, the NNZ‐ETDA cannot effectively reduce the computational load for sequences with active motion or rich texture. Therefore, in order to further improve the performance of NNZ‐ETDA, we propose an adaptive RQT‐depth decision for NNZ‐ETDA (called ARD‐NNZ‐ETDA) by exploiting the characteristics of high temporal‐spatial correlation that exist in nature video sequences. Simulation results show that the proposed method can achieve time improving ratio (TIR) about 61.26%~81.48% when compared to the HEVC test model 8.1 (HM 8.1) with insignificant loss of image quality. Compared with the NNZ‐ETDA, the proposed method can further achieve an average TIR about 8.29%~17.92%.
Quantum Dot Infrared Photodetectors: Photoresponse Enhancement Due to Potential Barriers (2010)

Potential barriers around quantum dots (QDs) play a key role in kinetics of photoelectrons. These barriers are always created, when electrons from dopants outside QDs fill the dots. Potential barriers suppress the capture processes of photoelectrons and increase the photoresponse. To directly investigate the effect of potential barriers on photoelectron kinetics, we fabricated several QD structures with different positions of dopants and various levels of doping. The potential barriers as a function of doping and dopant positions have been determined using nextnano(3) software. We experimentally investigated the photoresponse to IR radiation as a function of the radiation frequency and voltage bias. We also measured the dark current in these QD structures. Our investigations show that the photoresponse increases ~30 times as the height of potential barriers changes from 30 to 130 meV.
Inhibition of Biological Activities of the Aerobactin Receptor Protein in Rough Strains of Escherichia coli by Polyclonal Antiserum Raised against Native Protein (1989)

The aerobactin iron-uptake system of plasmid ColV-K30, genetically isolated from other plasmid determinants by molecular cloning, was sufficient to restore full virulence in a mouse peritonitis model to a clinical Escherichia coli isolate, D551 (O78:H-), whose resident aerobactin-encoding ColV plasmid had been lost by curing. Antiserum was raised in rabbits against live E. coli K12 cells expressing the outer-membrane aerobactin receptor protein and absorbed with an isogenic strain lacking the receptor. This antiserum inhibited binding of aerobactin, cloacin DF13 and bacteriophage B74K to the native protein in whole E. coli K12 bacteria expressing the receptor, or in membranes prepared from such organisms. However, it did not react with the native receptor protein in several wild strains unless lipopolysaccharide was first removed by treatment with trichloroacetic acid, nor did it protect mice in experimental infections with strain D551. Antisera raised in rabbits against partially or fully denatured forms of the aerobactin receptor reacted only in assays involving denatured protein; they showed no inhibition of the biological activities of the native receptor.
Siloxane Coupling Agents (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSiloxane Coupling AgentsLeanne G. Britcher, David C. Kehoe, Janis G. Matisons, and A. Geoffrey SwincerCite this: Macromolecules 1995, 28, 9, 3110–3118Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://pubs.acs.org/doi/10.1021/ma00113a013https://doi.org/10.1021/ma00113a013research-articleACS PublicationsRequest reuse permissionsArticle Views1131Altmetric-Citations85LEARN 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
Prediction and early detection of preterm labor (2003)

Studies of cervical sonography, fetal fibronectin, and uterine contraction monitoring during pregnancy have improved our understanding of how preterm labor occurs, but their use in practice remains uncertain. This article reviews the use of these tests to improve the accuracy of diagnosis of preterm labor and to estimate the likelihood of preterm birth in women with historical risk factors. Because the clinical criteria for a diagnosis of preterm labor are inaccurate until labor is well established, over-diagnosis is common. A cervical length measurement of more than 30 mm or a negative fibronectin obtained from a patient with possible preterm labor can avoid over-diagnosis and unnecessary treatment. There is no role for routine use of either cervical sonography or fibronectin to screen pregnant women for preterm birth risk, but women thought to be at increased risk may be reassured by negative test results. Uterine contraction monitoring has low sensitivity for detecting women at risk of preterm birth. Current use of cervical length and fetal fibronectin in pregnancy is limited to situations where a negative result can avoid unnecessary interventions.
Gene Therapy with Helper-Dependent Adenoviral Vectors: Current Advances and Future Perspectives (2010)

Recombinant Adenoviral vectors represent one of the best gene transfer platforms due to their ability to efficiently transduce a wide range of quiescent and proliferating cell types from various tissues and species. The activation of an adaptive immune response against the transduced cells is one of the major drawbacks of first generation Adenovirus vectors and has been overcome by the latest generation of recombinant Adenovirus, the Helper-Dependent Adenoviral (HDAd) vectors. HDAds have innovative features including the complete absence of viral coding sequences and the ability to mediate high level transgene expression with negligible chronic toxicity. This review summarizes the many aspects of HDAd biology and structure with a major focus on in vivo gene therapy application and with an emphasis on the unsolved issues that these vectors still presents toward clinical application.
Vapor−Liquid Equilibria for the Systems Difluoromethane + Chlorodifluoromethane, Difluoromethane + Dichlorodifluoromethane, and Difluoromethane + Chloromethane at 10.0 °C (1996)

Isothermal vapor−liquid equilibria for the three binary systems (difluoromethane + chlorodifluoromethane, difluoromethane + dichlorodifluoromethane, and difluoromethane + chloromethane) have been measured at 10.0 °C. The experimental data for the binary systems are correlated with the Wilson equation and the relevant parameters are presented. The difluoromethane + dichlorodifluoromethane system forms a minimum boiling azeotrope, but the others do not.
Room temperature ferromagnetism of Cu doped ZnO nanowire arrays (2009)

We report the room temperature ferromagnetism of Cu doped ZnO nanowire arrays embedded in anodic aluminum oxide template. The nanowires about 100 nm in diameter were fabricated by electrodepositing Zn2+ and Cu2+ into the template and postoxidation annealing in air atmosphere. Magnetization measurements indicated that the Zn1−xCuxO (x=0.05 and 0.07) nanowires exhibit room temperature ferromagnetism and the Zn0.93Cu0.07O nanowires annealed in vacuum reveals an enhancement of the ferromagnetism. X-ray diffraction pattern, x-ray photoelectron spectroscopy, and Raman spectra measurements showed that all the samples possess a typical wurtzite structure and no other impurity phases were observed.
EXPLOSIVE INJURY DUE TO SOLID CARBON DIOXIDE (1943)

Carbon dioxide is of increasing importance commercially. Many of its uses rely on its rapid expansion when released from a compressed state.<sup>1</sup>That this expansile force of solid carbon dioxide, the familiar "dry ice," is tremendous can perhaps best be appreciated by the realization that a rifle is now being manufactured using crushed "dry ice" as the propelling force. One loading is sufficient to "fire" 1,800 bullets of 0.22 caliber.<sup>2</sup>It was surprising, therefore, that reports of explosive injuries due to solid carbon dioxide are not to be found in the literature. Indeed, reports of all types of injuries are meager, though Stout<sup>3</sup>and Som and Neffson<sup>4</sup>have each drawn attention to the danger of aspiration. That the continued availability of "dry ice" to enterprising children remains a danger is illustrated by the case reported here: <h3>REPORT OF CASE</h3> K. L., a school boy aged 14,
Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element. (1997)

RNA transcripts corresponding to the 250-nt 3' untranslated region of the R2 non-LTR retrotransposable element are recognized by the R2 reverse transcriptase and are sufficient to serve as templates in the target DNA-primed reverse transcription (TPRT) reaction. The R2 protein encoded by the Bombyx mori R2 can recognize this region from both the B. mori and Drosophila melanogaster R2 elements even though these regions show little nucleotide sequence identity. A model for the RNA secondary structure of the 3' untranslated region of the D. melanogaster R2 retrotransposon was developed by sequence comparison of 10 species aided by free energy minimization. Chemical modification experiments are consistent with this prediction. A secondary structure model for the 3' untranslated region of R2 RNA from the R2 element from B. mori was obtained by a combination of chemical modification data and free energy minimization. These two secondary structure models, found independently, share several common sites. This study shows the utility of combining free energy minimization, sequence comparison, and chemical modification to model an RNA secondary structure.
Gene and protein expressions induced by 17beta-estradiol and parathion in cultured breast epithelial cells. (2007)

Cancer of the breast is the most common form of malignant disease occurring among women of the western world and environmental substances seem to be involved in the etiology of this disease. Many studies have found an association between human cancer and exposure to agricultural pesticides and among them parathion, the organophosphorous pesticide used in agriculture to control mosquito plagues. The association between breast cancer and prolonged exposure to estrogens suggests that this hormone also may have a role in such process. However, the causative factors for breast carcinogenesis remain an enigma. The objective of this study was to determine the effects of 17beta-estradiol (E2) and parathion on cell transformation of human breast epithelial cells in vitro. The results of this study showed that parathion alone and in combination with E2 induced malignant transformation of an immortalized human breast epithelial cell line, MCF-10F, and the malignant feature was confirmed by anchorage independency and invasive capabilities. Parathion alone efficiently elevated the expression of EGFR, c-Kit, Trio, Rac 3, Rho-A, and mutant p53 proteins. Analysis of gene expression using commercially available human cell cycle array revealed transcriptional alterations in 22 out of a total of 96 genes. Among them, nine genes involved in the regulation of cell cycle were altered. These included cyclins (A1, A2, C, G1, G2, and H), cyclin-dependent kinases (CDKs), and minichromosome maintenance deficient (MCM). Results suggest that parathion has the potency to cause malignant transformation of breast epithelial cells through modulation of expression of cell cycle regulated genes.
People counting system using existing surveillance video camera (2011)

The Casa da Música Foundation, responsible for the management of Casa da Música do Porto building, has the need to obtain statistical data related to the number of building’s visitors. This information is a valuable tool for the elaboration of periodical reports concerning the success of this cultural institution. For this reason it was necessary to develop a system capable of returning the number of visitors for a requested period of time. This represents a complex task due to the building’s unique architectural design, characterized by very large doors and halls, and the sudden large number of people that pass through them in moments preceding and proceeding the different activities occurring in the building. To achieve the technical solution for this challenge, several image processing methods, for people detection with still cameras, were first studied. The next step was the development of a real time algorithm, using OpenCV libraries and computer vision concepts,to count individuals with the desired accuracy. This algorithm includes the scientific and technical knowledge acquired in the study of the previous methods. The themes developed in this thesis comprise the fields of background maintenance, shadow and highlight detection, and blob detection and tracking. A graphical interface was also built, to help on the development, test and tunning of the proposed system, as a complement to the work. Furthermore, tests to the system were also performed, to certify the proposed techniques against a set of limited circumstances. The results obtained revealed that the algorithm was successfully applied to count the number of people in complex environments with reliable accuracy.