gebhart/patrepeval huggingface dataset:
Marked Epitope- and Allele-Specific Differences in Rates of Mutation in Human Immunodeficiency Type 1 (HIV-1) Gag, Pol, and Nef Cytotoxic T-Lymphocyte Epitopes in Acute/Early HIV-1 Infection (2008)

During acute human immunodeficiency virus type 1 (HIV-1) infection, early host cellular immune responses drive viral evolution. The rates and extent of these mutations, however, remain incompletely characterized. In a cohort of 98 individuals newly infected with HIV-1 subtype B, we longitudinally characterized the rates and extent of HLA-mediated escape and reversion in Gag, Pol, and Nef using a rational definition of HLA-attributable mutation based on the analysis of a large independent subtype B data set. We demonstrate rapid and dramatic HIV evolution in response to immune pressures that in general reflect established cytotoxic T-lymphocyte (CTL) response hierarchies in early infection. On a population level, HLA-driven evolution was observed in approximately 80% of published CTL epitopes. Five of the 10 most rapidly evolving epitopes were restricted by protective HLA alleles (HLA-B*13/B*51/B*57/B*5801; P = 0.01), supporting the importance of a strong early CTL response in HIV control. Consistent with known fitness costs of escape, B*57-associated mutations in Gag were among the most rapidly reverting positions upon transmission to non-B*57-expressing individuals, whereas many other HLA-associated polymorphisms displayed slow or negligible reversion. Overall, an estimated minimum of 30% of observed substitutions in Gag/Pol and 60% in Nef were attributable to HLA-associated escape and reversion events. Results underscore the dominant role of immune pressures in driving early within-host HIV evolution. Dramatic differences in escape and reversion rates across codons, genes, and HLA restrictions are observed, highlighting the complexity of viral adaptation to the host immune response.
Augmenting Dialogue Response Generation With Unstructured Textual Knowledge (2019)

The dialogue response generation is a challenging task in chatbot applications. Recently neural-network-based dialogue models, including the sequence-to-sequence model and the RNN language models, are able to generate fluent and grammatically compliant responses, while there is a major limitation that most of the responses generated by these models are of chit-chat style instead of being informative. After investigating the currently used models, we found that one primary challenge is to model and generate informative words, such as named entities, especially when the entities have sparsely existed in training corpus. To address this problem, we propose to augment neural network-based generative architecture with knowledge embedding and knowledge attentive reader to incorporate external textual knowledge into the dialogue model to facilitate the dialogue modeling and generation. We evaluate the model with the Ubuntu dataset through automatic evaluation metrics and human evaluation. The experimental study has shown our methods outperform strong baselines in multiple metrics. We also visualize how the attention works in the dialogue context to verify the effectiveness of knowledge attentive reader mechanism.
A rhesus macaque model of Asian-lineage Zika virus infection (2016)

Infection with Asian-lineage Zika virus (ZIKV) has been associated with Guillain-Barré syndrome and fetal abnormalities, but the underlying mechanisms remain poorly understood. Animal models of infection are thus urgently needed. Here we show that rhesus macaques are susceptible to infection by an Asian-lineage ZIKV closely related to strains currently circulating in the Americas. Following subcutaneous inoculation, ZIKV RNA is detected in plasma 1 day post infection (d.p.i.) in all animals (N=8, including 2 pregnant animals), and is also present in saliva, urine and cerebrospinal fluid. Non-pregnant and pregnant animals remain viremic for 21 days and for up to at least 57 days, respectively. Neutralizing antibodies are detected by 21 d.p.i. Rechallenge 10 weeks after the initial challenge results in no detectable virus replication, indicating protective immunity against homologous strains. Therefore, Asian-lineage ZIKV infection of rhesus macaques provides a relevant animal model for studying pathogenesis and evaluating potential interventions against human infection, including during pregnancy.
A flow cytometric technique to accurately measure post‐filtration white blood cell counts (1989)

Leukocyte-depleted blood products are being used with increasing frequency in hopes of preventing or delaying platelet alloimmunization. However, accurately monitoring the efficiency of leukocyte (WBC) removal is a difficult problem because electronic cell counters are not accurate at very low WBC numbers and hemocytometer counts are tedious and time consuming. A simple flow cytometric technique was developed which accurately and rapidly measures extremely low WBC counts. Using a propidium iodide solution which causes DNA to fluoresce, the residual WBC count was measured in 42 units of blood products after leukocyte depletion using a commercial filter. There was a significant correlation with simultaneous hemocytometer counts, r = 0.672, but residual WBC could be identified in every unit using the flow cytometer, whereas in 19% of the units no WBC were seen using the hemocytometer. Extremely low counts, as low as a single WBC/4 microliters could be reproducibly obtained. In addition, serial dilution studies yielded a correlation coefficient of 0.997. Because most clinical laboratories now have access to flow cytometers, this technique can be widely used.
Induction and preliminary characterization of intracellular Î²-glucosidases from a cellulolytic<i>Streptomyces</i>strain (1995)

The cellulolytic actinomycete Streptomyces sp. QM-B814 possess an intracellular beta-glucosidase system which is induced by cellobiose and carboxymethylcellulose. Maximal beta-glucosidase activity was attained 8-10 h after inducer addition to exponential phase growing cultures. The induction is depressed in the presence of glucose. The system is composed of two electrophoretically different beta-glucosidases forms showing relative molecular masses of about 60 and 35 kDa, and pI values in the range 4.2-4.5. Both beta-glucosidases are synthesized de novo. The enzymes share substrate preference and are both inhibited by delta-gluconolactone and p-chloromercuribenzoate. The induction pattern and glucose inhibition are similar for both enzymes.
Time lapse gravity gradiometry (1999)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1999Time lapse gravity gradiometryAuthors: Manik TalwaniMel SchweitzerWalter FeldmanDan DiFrancescoWilliam KonigManik TalwaniRice University, Mel SchweitzerLockheed Martin Undersea Systems, Walter FeldmanLockheed Martin Undersea Systems, Dan DiFrancescoLockheed Martin Undersea Systems, and William KonigLockheed Martin Undersea Systemshttps://doi.org/10.1190/1.1821033 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1821033FiguresReferencesRelatedDetailsCited ByFeasibility of time-lapse gravity and gravity gradiometry monitoring for steam-assisted gravity drainage reservoirsAnya Reitz, Richard Krahenbuhl, and Yaoguo Li9 March 2015 | GEOPHYSICS, Vol. 80, No. 2Feasibility of time-lapse gravity gradiometry for SAGD monitoringAnya Reitz, Richard Krahenbuhl, and Yaoguo Li19 August 2013Feasibility analysis of time-lapse gravity gradiometry for reservoir monitoringAnya Reitz, Richard A. Krahenbuhl, Yaoguo Li, and Dan DiFrancesco25 October 2012Finding the shape of a local heterogeneity by means of a structural inversion with constraints23 November 2002 | Geophysical Prospecting, Vol. 50, No. 2 SEG Technical Program Expanded Abstracts 1999ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1999 Pages: 2061 publication data© 1999 Copyright © 1999 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 04 Jan 2005 CITATION INFORMATION Manik Talwani, Mel Schweitzer, Walter Feldman, Dan DiFrancesco, and William Konig, (1999), "Time lapse gravity gradiometry," SEG Technical Program Expanded Abstracts : 397-397. https://doi.org/10.1190/1.1821033 Plain-Language Summary PDF DownloadLoading ...
Use of imiquimod 5% cream (Aldara™) in cats with multicentric squamous cell carcinoma <i>in situ</i>: 12 cases (2002–2005)* (2008)

Multicentric squamous cell carcinoma in situ (MSCCIS) is a variant of squamous cell carcinoma in cats, commonly referred to as Bowen's-like disease. Imiquimod 5% cream (Aldara) is a novel immune response modifier (IRM) that has been reported as a successful treatment for Bowen's disease in humans. The purpose of this study was to describe clinical findings, treatment protocols and survival in cats with MSCCIS treated with imiquimod 5% cream and to examine the effects of imiquimod 5% cream in cats with MSCCIS. The expression of papillomavirus group-specific antigen in the study population was also determined. From review of medical records, 12 cats were identified with a histologic diagnosis of MSCCIS and treatment with imiquimod 5% cream. Initial lesions responded to imiquimod 5% cream in all cats. Most cats (75%) developed new lesions. New lesions also responded to imiquimod 5% cream in all cats treated. Five cats (41%) had side effects suspected to be associated with the use of imiquimod 5% cream, including local erythema (25%), increased liver enzymes and neutropenia (8%), and partial anorexia and vomiting (8%). Kaplan-Meier median treatment duration and median survival time probabilities for cats in this study were 1189 days, respectively. A time to failure model was generated as many cats were censored from analysis well before the aforementioned projected median. This model resulted in a shorter median survival time of 243 days. No patient-related, tumour-related or treatment-related prognostic variables were identified. No expression for papilloma group-specific antigen was found. Imiquimod 5% cream appears to be well tolerated in the majority of cats, and further studies are warranted to further examine its usefulness in cats with this disease.
Nanostructured cobalt on porous silicon substrate: Structure and magnetic behaviour (2007)

Abstract During an anodization process, porous silicon (PS) consisting of pores with a diameter of about 40 nm and a depth from 5 µm to 40 µm has been produced. To achieve oriented channels in this mesoporous range, a p + ‐type Si wafer was electrochemically etched in an aqueous electrolyte of HF. We report the formation, after the anodization step, of a cobalt nanostructure in a porous silicon matrix. Co nanocrystals on and in a porous silicon layer have been prepared by the UHV evaporation technique and characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS). This technique was performed to show the chemical element distribution within the channels. It is found that the deposition condition is an important factor for obtaining nano‐structures. Initial deposition leads to Co particle penetration in silicon pores whereas subsequent deposition results only in an increase of the thickness at the surface with no further penetration. Additional experiments were carried out by using the magneto‐optical Kerr effect to obtain information about the magnetic properties. The first results show that the magnetic response for layers <5 nm presents an important perpendicular component of magnetization whereas for thicker deposited layers (8 nm < t < 20 nm) the magnetic response seems to act as that of a thin film in which the squareness of the hysteresis loop decreases with increasing film thickness. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Vom <i>o</i>‐Terphenylen‐quecksilber zum 1‐Phenyl‐tribenzo‐cycloheptatrienyl‐Radikal (1962)

Abstract Die Bildung von Phenylen‐quecksilber (1) aus o ‐Dibrombenzol und Alkalimetallamalgam in Äther wird in Solventien größerer Polarität zugunsten der von o ‐Terphenylen‐quecksilber (III) zurückgedrängt; ein Phänomen, das diskutiert wird. Aus III ließ sich über die Stufenfolge VIII, IX das Bis‐[1‐phenyl‐tribenzo‐cycloheptatriehnyl] (X) synthetisieren, das aus den hier erörterten Gründen sehr viel schwieriger als das ebenfalls präparierte Bis‐[1‐phenyl‐dibenzo‐cycloheptatrienyl] (XIII) eine Radikaldissoziation eingeht und mit Chinon den zugehörigen Hydrochinonäther liefert.
The Acylation of Methyl Ketones with Aliphatic Esters by Means of Sodium Amide. Synthesis of β-Diketones of the Type RCOCH<sub>2</sub>COR<sup>1</sup> (1944)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Acylation of Methyl Ketones with Aliphatic Esters by Means of Sodium Amide. Synthesis of β-Diketones of the Type RCOCH2COR1Joe T. Adams and Charles R. HauserCite this: J. Am. Chem. Soc. 1944, 66, 7, 1220–1222Publication Date (Print):July 1, 1944Publication History Published online1 May 2002Published inissue 1 July 1944https://pubs.acs.org/doi/10.1021/ja01235a045https://doi.org/10.1021/ja01235a045research-articleACS PublicationsRequest reuse permissionsArticle Views1102Altmetric-Citations116LEARN 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
Early Revascularization in Acute Myocardial Infarction Complicated by Cardiogenic Shock (1999)

In patients with cardiogenic shock, emergency revascularization did not significantly reduce overall mortality at 30 days. However, after six months there was a significant survival benefit. Early revascularization should be strongly considered for patients with acute myocardial infarction complicated by cardiogenic shock.
Comparative Functional Genomics of Lactobacillus spp. Reveals Possible Mechanisms for Specialization of Vaginal Lactobacilli to Their Environment (2014)

Lactobacilli are found in a wide variety of habitats. Four species, Lactobacillus crispatus, L. gasseri, L. iners, and L. jensenii, are common and abundant in the human vagina and absent from other habitats. These may be adapted to the vagina and possess characteristics enabling them to thrive in that environment. Furthermore, stable codominance of multiple Lactobacillus species in a single community is infrequently observed. Thus, it is possible that individual vaginal Lactobacillus species possess unique characteristics that confer to them host-specific competitive advantages. We performed comparative functional genomic analyses of representatives of 25 species of Lactobacillus, searching for habitat-specific traits in the genomes of the vaginal lactobacilli. We found that the genomes of the vaginal species were significantly smaller and had significantly lower GC content than those of the nonvaginal species. No protein families were found to be specific to the vaginal species analyzed, but some were either over- or underrepresented relative to nonvaginal species. We also found that within the vaginal species, each genome coded for species-specific protein families. Our results suggest that even though the vaginal species show no general signatures of adaptation to the vaginal environment, each species has specific and perhaps unique ways of interacting with its environment, be it the host or other microbes in the community. These findings will serve as a foundation for further exploring the role of lactobacilli in the ecological dynamics of vaginal microbial communities and their ultimate impact on host health.
Principles and Procedures of Statistics: A Biometrical Approach (1980)

Observations probability sampling from a normal distribution comparisons involving two sample means principles of experimental design analysis of variance I - the one-way classification mutiple comparisons analysis of variance II - multiway classification linear regression linear correlation matrix notation linear regression in matrix notation multiple and partial regression and correlation analysis of variance III - factorial experiments analysis of variance analysis of covariance IV analysis of covariance analysis of variance V - unequal subclass numbers some uses of chi-square enumeration data I - one-way classifications enumeration data II - contingency tables categorical models some discrete distributions nonparametric statistics sampling finite populations.
A 14-&#956;A 3-ppm/&#176;C CMOS Bandgap Voltage Reference (2006)

The work presented in this paper improves on a high order curvature-compensated CMOS band-gap reference circuit design. A cascoded current mirror is utilized in order to increase the bandgap voltage's power supply rejection ratio (PSRR) and decrease the mismatch current. A source follower is inserted in series with the capacitor to guarantee the system stable. Simulated in the standard 0.18/spl mu/m CMOS technology, the proposed voltage reference can operate down to 1.5V supply and consumes supply current of 14/spl mu/A. A temperature coefficient of 3-ppm//spl deg/C is achieved through the temperature-dependent resistor ratio.
Articulated hands: Force control and kinematic issues (1981)

Kinematic and control issues are discussed in the context of an articulated, multifinger mechanical hand. Hand designs with particular mobility properties are illustrated, and a definition of accuracy points within manipulator workspace is given. Optimization of tlte physical dimensions of the Stanford-JPL hand is described. Several architectures for position and force control of this multiloop mechanism are described, including a way of dealing with the internal forces inherent in such systems. Preliminary results are shown for the joint torque subsystem used in the hand controller.
Molecular Mechanisms of Fenretinide‐Induced Apoptosis of Neuroblastoma Cells (2004)

Synthetic retinoids such as fenretinide [N-(4-hydroxyphenyl)retinamide] induce apoptosis of neuroblastoma cells, act synergistically with chemotherapeutic drugs, and may provide opportunities for novel approaches to neuroblastoma therapy. Fenretinide-induced cell death of neuroblastoma cells is caspase dependent and results in the release of cytochrome c from mitochondria independently of changes in permeability transition. This is mediated by a signaling pathway characterized by the generation of reactive oxygen species (ROS) via 12-lipoxygenase (12-LOX), and an oxidative-stress-dependent induction of the transcription factor, GADD153 and the BCL2-related protein BAK. Upstream events of fenretinide-induced signaling involve increased levels of ceramide as a result of increased sphingomyelinase activity, and the subsequent metabolism of ceramide to gangliosides via glucosylceramide synthase and GD3 synthase. These gangliosides may be involved in the regulation of 12-LOX leading to oxidative stress and apoptosis via the induction of GADD153 and BAK. The targeting of sphingomyelinases or downstream effectors such as 12-LOX or GADD153 may present novel approaches for the development of more effective and selective drugs for neuroblastoma therapy.
Actin Filaments Modulate Both Stomatal Opening and Inward K+-Channel Activities in Guard Cells of Vicia faba L (1997)

Actin antagonists have previously been shown to alter responses of Commelina communis stomata to physiological stimuli, implicating actin filaments in the control of guard cell volume changes (M. Kim, P.K. Hepler, S.-O. Eun, K.S. Ha, Y. Lee [1995] Plant Physiol 109: 1077-1084). Since K+ channels in the guard cell play an important role in stomatal movements, we examined the possible regulation of K+-channel activities by the state of actin polymerization. Agents affecting actin polymerization altered light-induced stomatal opening and inward K+-channel activities measured by patch clamping in Vicia faba. Cytochalasin D, which induces depolymerization of actin filaments, promoted light-induced stomatal opening and potentiated the inward K+ current in guard cell protoplasts. Phalloidin, a stabilizer of filamentous actin, inhibited both light-induced stomatal opening and inward K+ current. Inward K+-channel activities in outside-out membrane patches showed responses to these agents that support results at the whole-cell current level, suggesting that cytochalasin D facilitates and phalloidin inhibits K+ influx in intact guard cells, thus resulting in enhancement and inhibition of stomatal opening, respectively. To our knowledge, this is the first report that provides evidence that actin filaments may regulate an important physiological process by modulating the activities of ion channels in plant cells.
Endometriosis-associated dyspareunia: the impact on women's lives (2007)

The experience of dyspareunia is a significant factor in the quality of life and relationships for women living with endometriosis. For most of the women in the study it was very severe and resulted in their reducing or curtailing sexual activity. Qualitative research can produce salient data that highlight the impact of dyspareunia on self-esteem and sexual relationships.
Protein accumulation in cerebrospinal fluid during -90 degrees head-down tilt in rabbit (1994)

Plasma proteins are only somewhat larger than the intercellular spaces of the cerebral microvessels that constitute the blood-brain barrier or of the choroid plexus villi that elaborate cerebrospinal fluid (CSF). We hypothesized that the integrity of these barriers in anesthetized rabbits might be compromised during head-down tilt (HDT). Plasma protein and osmolality, hematocrit, and CSF protein concentration were compared in rabbits exposed to 1 h of HDT (n = 20) and prone rabbits (n = 10). In addition, the concentration of trypan blue dye, injected intravenously at the end of HDT or the prone position, was measured in brain homogenate. Finally, arterial blood pressure was measured via a catheterized carotid artery. HDT disrupted the barrier between blood and CSF, as indicated by a significantly (P < 0.01) greater brain trypan blue concentration in the HDT rabbits [172.2 +/- 14.4 (SD) micrograms/g dry wt] than in the prone rabbits (29.8 +/- 4.4 micrograms/g dry wt). Moreover CSF protein 5 min after HDT onset was significantly increased compared with control in HDT rabbits (54.6 +/- 1.9 vs. 81.4 +/- 5.2 mg/dl; n = 8) but not in prone rabbits (55.6 +/- 2.7 vs. 57.2 +/- 5.0 mg/dl; n = 6). Changes in the plasma protein-to-hematocrit ratio in the HDT animals, but not in the prone animals, were also compatible with a loss of fluid from the vascular compartment.(ABSTRACT TRUNCATED AT 250 WORDS)