gebhart/patrepeval huggingface dataset:
Response of Simian Immunodeficiency Virus to the Novel Nucleoside Reverse Transcriptase Inhibitor 4′-Ethynyl-2-Fluoro-2′-Deoxyadenosine In Vitro and In Vivo (2012)

Nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) are essential components in first-line therapy for human immunodeficiency virus (HIV) infection. However, long-term treatment with existing NRTIs can be associated with significant toxic side effects and the emergence of drug-resistant strains. The identification of new NRTIs for the continued management of HIV-infected people therefore is paramount. In this report, we describe the response of a primary isolate of simian immunodeficiency virus (SIV) to 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) both in vitro and in vivo. EFdA was 3 orders of magnitude better than tenofovir (TFV), zidovudine (AZT), and emtricitabine (FTC) in blocking replication of SIV in monkey peripheral blood mononuclear cells (PBMCs) in vitro, and in a preliminary study using two SIV-infected macaques with advanced AIDS, it was highly effective at treating SIV infection and AIDS symptoms in vivo. Both animals had 3- to 4-log decreases in plasma virus burden within 1 week of EFdA therapy (0.4 mg/kg of body weight, delivered subcutaneously twice a day) that eventually became undetectable. Clinical signs of disease (diarrhea, weight loss, and poor activity) also resolved within the first month of treatment. No detectable clinical or pathological signs of drug toxicity were observed within 6 months of continuous therapy. Virus suppression was sustained until drug treatment was discontinued, at which time virus levels rebounded. Although the rebound virus contained the M184V/I mutation in the viral reverse transcriptase, EFdA was fully effective in maintaining suppression of mutant virus throughout the drug treatment period. These results suggest that expanded studies with EFdA are warranted.
Ordering of cosmid clones covering the Herpes Simplex virus type I (HSV-I) genome: a test case for fingerprinting by hybridisation (1990)

To allow the efficient construction of ordered clone libraries, we have been investigating the use of 'oligonucleotide fingerprinting' as an approach to identify overlapping clones, and ultimately restore the linear order of the clone set. To test the effectiveness of the procedure, we have constructed a cosmid library from the genome of the human DNA virus HSV-I and used hybridisation to multiple oligonucleotides selected from the nucleotide sequence to reconstruct the order of clones and oligonucleotides on the genome.
Stabilization of metallic glass by isochronal and isothermal annealing treatments (2007)

The internal friction (IF) of a Zr–Ti–Cu–Ni–Be metallic glass was measured using an inverted torsion pendulum with the free decay method. A single-roller melt-spinning apparatus was used for preparing the specimens. In the isochronal annealing experiment, specimens in different states were prepared by annealing, and the temperature dependence of the IF was measured from room temperature up to the crystallization temperature Tx. The glass attained a stabilized state under a long-time annealing near and below the glass transition temperature Tg. IF peaks always appeared near and below Tx, while an anomaly was observed clearly near Tg only in the stabilized state. A differential scanning calorimetry experiment was carried out for the same specimens, and the results showed the same characteristics. The isothermal annealing experiment revealed that the stabilization was a relaxation process, and how long a time was required for reaching the stabilized state. The essential features of glass-forming materials could be clearly observed when the specimens were in the stabilized state.
Anthropometric Reference Data for Children and Adults: United States, 2003-2006 (2008)

Objective-This report presents national anthropometric reference data for all ages of the U.S. population in 2007-2010, adding to results published previously from the years 1960-2006. Methods-Data are from the National Health and Nutrition Examination Survey (NHANES), a complex, stratified, and multistage probability sample of the civilian noninstitutionalized U.S. population. Anthropometry measurements were obtained from 20,015 survey participants. The anthropometric measures included weight, height, recumbent length, circumferences, limb lengths, and skinfold thickness measurements. Results-The tables in this report include weighted population means, standard errors of the means, and selected percentiles of body measurement values. Because measurements varied by sex and age (as well as race and ethnicity in adults), results are reported by these subgroups. Conclusions-These latest NHANES data add to the knowledge about trends in child growth and development and trends in the distribution of body measurements, such as weight and height, in the U.S. population.
Potential role for focal adhesion kinase in migrating and proliferating keratinocytes near epidermal wounds and in culture. (1994)

In normal, differentiating skin, hemidesmosomes make the stable attachment of basal epidermal keratinocytes to the dermis by linking the cytoplasmic keratin intermediate filaments to components of the basal lamina. In contrast, laterally migrating and proliferating basal keratinocytes in culture and presumably in repairing wounds use focal adhesions to form dynamic attachments to the dermis by linking actin microfilaments to the extracellular matrix. Focal adhesion kinase (FAK), a non-receptor protein tyrosine kinase concentrated along with phosphotyrosine-containing proteins in the focal adhesions of some cultured cells, is activated in vitro when cells attach, form focal adhesions, and spread. This report finds that FAK is activated, as determined from its increased phosphotyrosine content and from its increased labeling with [gamma-32P]ATP, in immunoprecipitates from human cultured keratinocytes attached and spreading on fibronectin compared to those attached but not spreading on polylysine. Furthermore, immunofluorescence shows that both FAK and phosphotyrosine are concentrated in the focal adhesions of cultured keratinocytes attached and spreading on extracellular matrix components known to facilitate cellular migration (fibronectin, collagens I or IV, and epiligrin). Finally, immunohistochemistry localizes FAK to the epidermal-dermal junction in repairing partial thickness burn wounds. FAK is found at the epidermal-dermal junction at sites and times which coincide with actively migrating or rapidly proliferating basal keratinocytes, suggesting that this distribution represents FAK concentrated and activated in adhesions analogous to the focal adhesions seen in cultured cells. Hence, FAK appears to have an important in vivo role in the reepithelialization of human wounds.
Security issues surrounding programming languages for mobile code (1998)

JAVA is claimed to be a system programming language having a number of advantages over traditional programming languages. These advantages stem from the fact that it is a platform - independent language, thus promising truly network oriented computing as long as a nearly universal system for distributing applications. On the other hand, although being an interpreted, much simpler, scripting language, Safe-Tcl was proposed as an executable contents type of MIME and thus as the standard language for executable contents within email. Consequently, both languages claim to be suitable for transmitting executable content over the Internet, in other words manipulating mobile code. However, the ability to download, integrate, and execute code from a remote computer raises serious concerns about JAVA's as well as Safe-Tcl's effect on network security. In this paper, the potential security risks of mobile code are discussed, a brief introduction to both programming languages is given, and the details of each of the proposed security mechanisms are presented. Finally a comparison of the two security models is given, centered upon the efficiency and flexibility of current implementations as well as upcoming extensions.
Depth-resolved birefringence and differential optical axis orientation measurements with fiber-based polarization-sensitive optical coherence tomography (2004)

Conventional polarization-sensitive optical coherence tomography (PS-OCT) can provide depth-resolved Stokes parameter measurements of light reflected from turbid media. A new algorithm that takes into account changes in the optical axis is introduced to provide depth-resolved birefringence and differential optical axis orientation images by use of fiber-based PS-OCT. Quaternion, a convenient mathematical tool, is used to represent an optical element and simplify the algorithm. Experimental results with beef tendon and rabbit tendon and muscle show that this technique has promising potential for imaging the birefringent structure of multiple-layer samples with varying optical axes.
Subwavelength resolution Fourier ptychography with hemispherical digital condensers (2018)

Fourier ptychography (FP) is a promising computational imaging technique that overcomes the physical space-bandwidth product (SBP) limit of a conventional microscope by applying angular-varied illuminations. However, to date, the effective imaging numerical aperture (NA) achievable with a commercial LED board is still limited to the range of 0.3-0.7 with a 4 × /0.1NA objective due to the geometric constraint with the declined illumination intensities and attenuated signal-to-noise ratio (SNR). Thus the highest achievable half-pitch resolution is usually constrained between 500-1000 nm, which cannot meet the requirements of high-resolution biomedical imaging applications. Although it is possible to improve the resolution by using a high-NA objective lens, the FP approach is less appealing as the decrease of field-of-view (FOV) will far exceed the improvement of spatial resolution in this case. In this paper, we initially present a subwavelength resolution Fourier ptychography (SRFP) platform with a hemispherical digital condenser to provide high-angle programmable plane-wave illuminations of 0.95NA, attaining a 4 × /0.1NA objective with the final effective imaging performance of 1.05NA at a half-pitch resolution of 244 nm with the incident wavelength of 465 nm across a wide FOV of 14.60 mm<sup>2</sup>, corresponding to a SBP of 245 megapixels. Our work provides an essential step of FP towards high-throughput imaging applications.
Fish oils and plasma lipid and lipoprotein metabolism in humans: a critical review. (1989)

Epidemiological studies in Greenland Eskimos led to the hypothesis that marine oils rich in n-3 fatty acids (also referred to as omega (omega)-3 fatty acids) are hypolipidemic and ultimately antiatherogenic. Metabolically controlled trials in which large amounts of fish oil were fed to normal volunteers and hyperlipidemic patients showed that these fatty acids (FAs) are effective at lowering plasma cholesterol and triglyceride levels. Although more recent trials using smaller, more practical doses of fish oil supplements have confirmed the hypotriglyceridemic effect, they have shown little effect on total cholesterol levels; hypertriglyceridemic patients have even experienced increases in low density lipoprotein cholesterol (LDL-C) levels of 10-20% while taking n-3 FA supplements. Discrepancies among fish oil studies regarding the effects of n-3 FAs on LDL-C levels may be understood by noting that, in the majority of studies reporting reductions in LDL-C levels, saturated fat intake was lowered when switching from the control diet to the fish oil diet. When fish oil is fed and saturated fat intake is constant, LDL-C levels either do not change or may increase. Levels of high density lipoprotein cholesterol have been found to increase slightly (about 5-10%) with fish oil intake. Plasma apolipoprotein levels change in concert with their associated lipoprotein cholesterol levels. Although the decrease in triglyceride levels appears to result from an inhibition in hepatic triglyceride synthesis, the mechanisms leading to the increases in LDL and HDL have not been determined. Finally, fatty fish or linolenic acid may serve as alternative sources of long-chain n-3 FAs, but further studies will be needed to document their hypolipidemic and/or antiatherogenic effects.
Vismodegib effective against basal cell nevus syndrome (2012)

The hedgehog inhibitor drug vismodegib (Erivedge, Genentech/Roche), approved in January to treat advanced and metastatic basal cell carcinoma, has demonstrated potent clinical activity when used in patients with basal cell nevus syndrome, according to a study published recently in the New England Journal of Medicine.
Long-term remission in a patient with erythroleukemia following interferon-alpha treatment. (1989)

A patient in second relapse of acute erythroleukemia (AEL) was treated with 10 MU of recombinant interferon (IFN)-alpha subcutaneously for 24 days after he had failed standard chemotherapy. Besides fever up to 38.9 degrees C and a transient raise in liver function parameters, treatment was well tolerated but had to be discontinued because of a severe decrease in white blood cell and platelet count. After termination of IFN treatment, both cell populations showed a continuous rise during the following weeks and hemoglobin increased concomitantly. Partial remission could be reached as was demonstrated by a decrease in PAS-positive erythroblasts in bone marrow biopsy. Further studies with IFN in patients with AEL refractory to cytostatic chemotherapy are recommended.
Spectroscopic Studies of Substrate Interactions with Clavaminate Synthase 2, a Multifunctional α-KG-Dependent Non-Heme Iron Enzyme:  Correlation with Mechanisms and Reactivities (2001)

Using a single ferrous active site, clavaminate synthase 2 (CS2) activates O(2) and catalyzes the hydroxylation of deoxyguanidinoproclavaminic acid (DGPC), the oxidative ring closure of proclavaminic acid (PC), and the desaturation of dihydroclavaminic acid (and a substrate analogue, deoxyproclavaminic acid (DPC)), each coupled to the oxidative decarboxylation of cosubstrate, alpha-ketoglutarate (alpha-KG). CS2 can also catalyze an uncoupled decarboxylation of alpha-KG both in the absence and in the presence of substrate, which results in enzyme deactivation. Resting CS2/Fe(II) has a six-coordinate Fe(II) site, and alpha-KG binds to the iron in a bidentate mode. The active site becomes five-coordinate only when both substrate and alpha-KG are bound, the latter still in a bidentate mode. Absorption, CD, MCD, and VTVH MCD studies of the interaction of CS2 with DGPC, PC, and DPC provide significant molecular level insight into the structure/function correlations of this multifunctional enzyme. There are varying amounts of six-coordinate ferrous species in the substrate complexes, which correlate to the uncoupled reaction. Five-coordinate ferrous species with similar geometric and electronic structures are present for all three substrate/alpha-KG complexes. Coordinative unsaturation of the Fe(II) in the presence of both cosubstrate and substrate appears to be critical for the coupling of the oxidative decarboxylation of alpha-KG to the different substrate oxidation reactions. In addition to the substrate orientation relative to the open coordination position on the iron site, it is hypothesized that the enzyme can affect the nature of the reactivity by further regulating the binding energy of the water to the ferrous species in the enzyme/succinate/product complex.
Structure−Activity Relationships for Antiplasmodial Activity among 7-Substituted 4-Aminoquinolines (1998)

Aminoquinolines (AQs) with diaminoalkane side chains (-HNRNEt2) shorter or longer than the isopentyl side chain [-HNCHMe(CH2)3NEt2] of chloroquine are active against both chloroquine-susceptible and -resistant Plasmodium falciparum. (De, D.; et al. Am. J. Trop. Med. Hyg. 1996, 55, 579-583). In the studies reported here, we examined structure-activity relationships (SARs) among AQs with different N, N-diethyldiaminoalkane side chains and different substituents at the 7-position occupied by Cl in chloroquine. 7-Iodo- and 7-bromo-AQs with diaminoalkane side chains [-HN(CH2)2NEt2, -HN(CH2)3NEt2, or -HNCHMeCH2NEt2] were as active as the corresponding 7-chloro-AQs against both chloroquine-susceptible and -resistant P. falciparum (IC50s of 3-12 nM). In contrast, with one exception, 7-fluoro-AQs and 7-trifluoromethyl-AQs were less active against chloroquine-susceptible P. falciparum (IC50s of 15-50 nM) and substantially less active against chloroquine-resistant P. falciparum (IC50s of 18-500 nM). Furthermore, most 7-OMe-AQs were inactive against both chloroquine-susceptible (IC50s of 17-150 nM) and -resistant P. falciparum (IC50s of 90-3000 nM).
[Survivin antisense RNA enhances taxol-induced apoptosis in leukemia cell line HL-60]. (2003)

Survivin antisense RNA could enhance taxol-induced apoptosis in leukemia cell line HL-60. This may lay an experimental foundation for further research of gene therapy in leukemia.
Analyses of DNA content of living spermatozoa using flow cytometry techniques (1993)

A two-dimensional fluorescence analysis of spermatozoa stained with Hoechst 33342 was carried out using an Epics V flow cytometer. This analysis involved the measurement of fluorescence both in the conventional manner at 90 degrees and at a narrow forward angle (nominally 0 degree) to the direction of the interrogating laser beam. The arrangement provided an optical means of distinguishing the orientation of flattened particles passing through the interrogation system and enabled the verification and reinterpretation of one-dimensional (90 degree) fluorescence histogram data obtained previously. We now consider that the distinction between live and dead spermatozoa was over simplified and that the observed differences are due partly to an artefact of orientation. It has been confirmed that our earlier use of the low fluorescence peak, consisting of (bull, rabbit, sheep and pig) spermatozoa passing through the interrogation point obliquely to both detectors, as criterion for sorting X- from Y-bearing spermatozoa, is more practical than the use of a very much smaller subpopulation, based on limits imposed by selecting only spermatozoa accurately orientated with their narrow edges to one detector, while measurement of total fluorescence (DNA content) was made simultaneously from a broad face by the other detector. We report marked differences in the rate of staining and in attainment of a staining equilibrium between spermatozoa from different animals or from different ejaculates collected on the same or different days from the same animal. This variation introduces an element of subjectivity into the use of flow cytometry for sorting X- and Y-spermatozoa.(ABSTRACT TRUNCATED AT 250 WORDS)
Isolate- and Group-Specific Immune Responses to the Envelope Protein of Human Immunodeficiency Virus Induced by a Live Recombinant Vaccinia Virus in Macaques (1989)

The immune responses produced by four macaques inoculated intradermally with a recombinant vaccinia virus that expresses the envelope gene of human immunodeficiency virus (HIV) were analyzed. Antibody capable of immunoprecipitating the glycosylated envelope protein precursor gp160 was detected in all animals within 3 weeks after the primary intradermal vaccination. The level of antibody was increased following a booster inoculation, and the sera from three of the four animals were then capable of immunoprecipitating gp120. Sera from two of the macaques with anti-gp120 antibody were able to prevent syncytium formation mediated by the parent HIV but not that induced by an unrelated HIV isolate. The fusion-inhibiting antibody was directed toward the highly variable central portion of the gp120 molecule since the effect was abrogated by incubation with PB1. The latter is a recombinant protein produced in Escherichia coli containing amino acids 295-474, a major neutralizing epitope. Sera from the three macaques with anti-gp120 neutralized HIV infectivity in an isolate-specific manner. The serum with highest neutralizing activity was also best at inhibiting syncytium formation. In contrast to the isolate-specific nature of the neutralizing antibody, T lymphocytes from immunized animals proliferated in response to divergent HIV isolates as well as to purified gp120. These studies provide baseline immunologic information for further development of recombinant vaccinia virus vectors.
Dynamics of .alpha.-CH Deprotonation and .alpha.-Desilylation Reactions of Tertiary Amine Cation Radicals (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDynamics of .alpha.-CH Deprotonation and .alpha.-Desilylation Reactions of Tertiary Amine Cation RadicalsXiaoming Zhang, Syun-Ru Yeh, Seok Hong, Mauro Freccero, Angelo Albini, Daniel E. Falvey, and Patrick S. MarianoCite this: J. Am. Chem. Soc. 1994, 116, 10, 4211–4220Publication Date (Print):May 1, 1994Publication History Published online1 May 2002Published inissue 1 May 1994https://pubs.acs.org/doi/10.1021/ja00089a010https://doi.org/10.1021/ja00089a010research-articleACS PublicationsRequest reuse permissionsArticle Views1967Altmetric-Citations186LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts