gebhart/patrepeval huggingface dataset:
Role of human immunodeficiency virus type 1-specific protease in core protein maturation and viral infectivity (1989)

It is generally believed that the gag gene product of human immunodeficiency virus type 1 (HIV-1) is processed into several core proteins by a virus-specific protease. We used deletion mutation analysis to study the role of HIV-specific protease in the processing of core proteins and its requirement for viral infectivity. Several mutant genomes with deletions in the protease gene were constructed. A mammalian cell line, COS-M6, transfected with the wild-type viral genome was shown to produce virions containing processed core proteins, while COS-M6 cells transfected with two mutated genomes could express only the core protein precursor, Pr56gag. The wild-type transfectant produced infectious virus; both transfectants expressing the mutated genomes also produced virions, and one of them still retained reverse transcriptase activity. However, the mutant viral particles were devoid of infectivity. Virions with a distinct central core and an electron-dense nucleoid budded out from the plasma membrane of COS-M6 cells transfected with the wild-type genome. In contrast, noninfectious virions that budded either into cytoplasmic vacuoles or out from the plasma membrane of COS-M6 cells transfected with mutant genomes contained ring-shaped nucleoids. These results indicate that the HIV-1 protease plays a role not only in the maturation of the core proteins but also in the assembly of the virus and thus is required for viral infectivity.
Vaginal Estrogen Preparations: A Review of Safety and Efficacy for Vaginal Atrophy (2002)

All preparations are effective in decreasing signs and symptoms of vaginal atrophy, but they differ slightly in their adverse event profiles. Long-term safety of the preparations is best established for estradiol tablets (1 year), but is lacking for all preparations.
Antimicrobial Postexposure Prophylaxis for Anthrax: Adverse Events and Adherence (2002)

We collected data during postexposure antimicrobial prophylaxis campaigns and from a prophylaxis program evaluation 60 days after start of antimicrobial prophylaxis involving persons from six U.S. sites where Bacillus anthracis exposures occurred. Adverse events associated with antimicrobial prophylaxis to prevent anthrax were commonly reported, but hospitalizations and serious adverse events as defined by Food and Drug Administration criteria were rare. Overall adherence during 60 days of antimicrobial prophylaxis was poor (44%), ranging from 21% of persons exposed in the Morgan postal facility in New York City to 64% of persons exposed at the Brentwood postal facility in Washington, D.C. Adherence was highest among participants in an investigational new drug protocol to receive additional antibiotics with or without anthrax vaccine--a likely surrogate for anthrax risk perception. Adherence of <60 days was not consistently associated with adverse events.
The activation of the alternative pathway C3 convertase by human plasma kallikrein. (1982)

Human plasma kallikrein can replace factor D for the activation of the alternative pathway C3 convertase of human complement. The factor B cleavage patterns by factor D and kallikrein are indistinguishable. The ability of kallikrein to cleave factor B is influenced by the magnesium ion concentration and the C3b concentration. Factor D is about ten-fold more effective on a molar basis, for the alternative pathway C3 convertase activation than is kallikrein. The physiological role of the action of kallikrein on the alternative pathway C3 convertase is discussed.
Rational Strategies for Efficient Perovskite Solar Cells (2016)

A long-standing dream in the large scale application of solar energy conversion is the fabrication of solar cells with high-efficiency and long-term stability at low cost. The realization of such practical goals depends on the architecture, process and key materials because solar cells are typically constructed from multilayer heterostructures of light harvesters, with electron and hole transporting layers as a major component. Recently, inorganic-organic hybrid lead halide perovskites have attracted significant attention as light absorbers for the fabrication of low-cost and high-efficiency solar cells via a solution process. This mainly stems from long-range ambipolar charge transport properties, low exciton binding energies, and suitable band gap tuning by managing the chemical composition. In our pioneering work, a new photovoltaic platform for efficient perovskite solar cells (PSCs) was proposed, which yielded a high power conversion efficiency (PCE) of 12%. The platform consisted of a pillared architecture of a three-dimensional nanocomposite of perovskites fully infiltrating mesoporous TiO2, resulting in the formation of continuous phases and perovskite domains overlaid with a polymeric hole conductor. Since then, the PCE of our PSCs has been rapidly increased from 3% to over 20% certified efficiency. The unprecedented increase in the PCE can be attributed to the effective integration of the advantageous attributes of the refined bicontinuous architecture, deposition process, and composition of perovskite materials. Specifically, the bicontinuous architectures used in the high efficiency comprise a layer of perovskite sandwiched between mesoporous metal-oxide layer, which is a very thinner than that of used in conventional dye-sensitized solar cells, and hole-conducting contact materials with a metal back contact. The mesoporous scaffold can affect the hysteresis under different scan direction in measurements of PSCs. The hysteresis also greatly depends on the cell architecture and perovskite composition. In this Account, we will describe what we do with major aspects including (1) the film morphology through the development of intermediate chemistry retarding the rapid reaction between methylammonium or formamidinium iodide and lead halide (PbI2) for improved perovskite film formation; (2) the phase stability and band gap tuning of the perovskite layer through the materials engineering; (3) the development of electron and hole transporting materials for carrier-selective contacting layers; and (4) the adoption of p-i-n and n-i-p architectures depending on the position of the electron or hole conducting layer in front of incident light. Finally, we will summarize the recent incredible achievements in PSCs, and finally provide challenges facing the future development and commercialization of PSCs.
Highly Aligned Scalable Platinum-Decorated Single-Wall Carbon Nanotube Arrays for Nanoscale Electrical Interconnects (2009)

We present the fabrication and characterization of nanoscale electrical interconnect test structures constructed from aligned single-wall carbon nanotubes using a template-based fluidic assembly process. This CMOS-friendly process enables the formation of highly aligned parallel nanotube interconnect structures on SiO(2)/Si substrates of widths and lengths that are limited only by lithographical limits and, hence, can be easily integrated onto existing Si-based platforms. These structures can withstand current densities of approximately 10(7) A.cm(-2), comparable or better than copper at similar dimensions. Both the nanotube alignment and failure current density improve with decreasing structure width. In addition, we present a novel Pt nanocluster decoration method that drastically decreases the resistivity of the test structures. Ab initio density functional theory calculations indicate that the increase in conductivity of the nanotubes is caused by an increase in conduction channels close to their Fermi levels due to the platinum nanocluster decoration, with a possible conversion of the semiconducting single-wall carbon nanotubes into metallic ones. These results reflect a huge step toward the proposed replacement of copper-based interconnects with carbon nanotubes at gigascale integration levels.
Calculation of the elasto-dynamic Green's function in layered media by means of a modified propagator matrix method (1983)

The calculation of the two-dimensional elasto-dynamic Green's function for a stratified medium is investigated. The solution is represented in the form of an inverse Fourier integral which is to be integrated along a properly chosen path in the complex wavenumber plane. The integrand is computed using a modified propagator matrix method.
Systemic administration of a bispecific antibody targeting EGFRvIII successfully treats intracerebral glioma (2012)

Bispecific antibodies (bscAbs), particularly those of the bispecific T-cell engager (BiTE) subclass, have been shown to effectively redirect T cells against cancer. Previous efforts to target antigens expressed in both tumors and normal tissues have produced significant toxicity, however. Moreover, like other large molecules, bscAbs may be restricted from entry into the "immunologically privileged" CNS. A tumor-specific mutation of the epidermal growth factor receptor, EGFRvIII, is a constitutively activated tyrosine kinase not found in normal tissues but frequently expressed in glioblastomas and many other neoplasms. Because it is localized solely to tumor tissue, EGFRvIII presents an ideal target for immunotherapy. Here we report the preclinical evaluation of an EGFRvIII-targeted BiTE, bscEGFRvIIIxCD3. Our results show that bscEGFRvIIIxCD3 activates T cells to mediate potent and antigen-specific lysis of EGFRvIII-expressing gliomas in vitro (P < 0.001) at exceedingly low concentrations (10 ng/mL) and effector-to-target ratios (2.5:1). Treatment with i.v. bscEGFRvIIIxCD3 yielded extended survival in mice with well-established intracerebral tumors (P < 0.05) and achieved durable complete cure at rates up to 75%. Antitumor efficacy was significantly abrogated on blockade of EGFRvIII binding, demonstrating the need for target antigen specificity both in vitro and in vivo. These results demonstrate that BiTEs can be used to elicit functional antitumor immunity in the CNS, and that peptide blockade of BiTE-mediated activity may greatly enhance the safety profile for antibody-redirected T-cell therapies. Finally, bscEGFRvIIIxCD3 represents a unique advancement in BiTE technology given its exquisite tumor specificity, which enables precise elimination of cancer without the risk of autoimmune toxicity.
On atypical database transactions: identification of probable frauds using machine learning for user profiling (2002)

The paper proposes a framework for deriving users' profiles of typical behaviour and detecting atypical transactions which may constitute fraudulent events or simply a change in user's behaviour. The anomaly detection problem is presented and previous attempts to address it are discussed. The proposed approach proves that individual user profiles can be constructed and provides an algorithm that derives user profiles and an algorithm to identify atypical transactions. Lower and upper bounds for the number of misclassifications are also provided. An evaluation of this approach is discussed and some issues for further research are outlined.
Criteria for the definition of Epstein-Barr virus association in Hodgkin's disease. (1992)

There is a clear association between the Epstein-Barr virus (EBV) and Hodgkin's disease (HD). EBV is not, however, detectable within the affected tissues of all cases. The proportion of positive cases varies from 15-79% depending on the assay used to detect EBV. The techniques utilised vary not only in sensitivity but in their ability to detect viral DNA, RNA, or protein and in their ability to demonstrate the cellular localisation of the virus. Thus, the biological significance of a positive result will vary depending on the method of analysis. In the present study, four different methods of detecting EBV were compared. RNA in situ hybridization was found to be the most practical method of detecting EBV in tumour cells. Using this assay EBV was detected in the Reed-Sternberg cells of 33% and 45% of the two series of HD cases examined in this study. We believe that these cases should be considered EBV-associated.
Purification and patch clamp analysis of a 40-pS channel from rat liver mitochondria (1992)

Patch clamp analysis of membranes reconstituted with a fraction isolated from detergent-solubilized mitochondrial membranes by affinity chromatography on immobilized quinine earlier indicated the presence of two classes of ion channels, of about 40- and 140-pS conductance in medium including 150 mM KCl. Now a 57-kDa constituent of the quinine-affinity column eluate has been identified as the 40-pS channel. Protein fractions derived from the quinine-affinity column eluate by preparative isoelectric focusing with a Rotofor cell have been reconstituted into phospholipid vesicle membranes by detergent dialysis, and vesicles have been enlarged for patch clamping by dehydration and rehydration. Voltage clamp analysis has been carried out on excised patches bathed symmetrically in buffered medium containing 150 mM KCl and 100 microM CaCl2. Patches of membrane incorporating the 57-kDa protein exhibit 40-pS conductance transitions. The magnitude of conductance transitions is similar when Na+ replaces K+ in the bathing medium, indicating little selectivity of the 40-pS channel for K+ relative to Na+. Another fraction derived from the quinine-affinity column eluate is found to contain the larger channel, now estimated to have an average conductance of about 130 pS. Patches of control membrane prepared in the same way but without protein exhibit no channel activity.
Ectonucleotidase NTPDase3 is abundant in pancreatic β-cells and regulates glucose-induced insulin secretion (2013)

Extracellular ATP released from pancreatic β-cells acts as a potent insulinotropic agent through activation of P2 purinergic receptors. Ectonucleotidases, a family of membrane-bound nucleotide-metabolizing enzymes, regulate extracellular ATP levels by degrading ATP and related nucleotides. Ectonucleotidase activity affects the relative proportion of ATP and its metabolites, which in turn will impact the level of purinergic receptor stimulation exerted by extracellular ATP. Therefore, we investigated the expression and role of ectonucleotidases in pancreatic β-cells. Of the ectonucleotidases studied, only ENTPD3 (gene encoding the NTPDase3 enzyme) mRNA was detected at fairly abundant levels in human and mouse pancreatic islets as well as in insulin-secreting MIN6 cells. ARL67156, a selective ectonucleotidase inhibitor, blocked degradation of extracellular ATP that was added to MIN6 cells. The compound also decreased degradation of endogenous ATP released from cells. Measurements of insulin secretion in MIN6 cells as well as in mouse and human pancreatic islets demonstrated that ARL67156 potentiated glucose-dependent insulin secretion. Downregulation of NTPDase3 expression in MIN6 cells with the specific siRNA replicated the effects of ARL67156 on extracellular ATP hydrolysis and insulin secretion. Our results demonstrate that NTPDase3 is the major ectonucleotidase in pancreatic β-cells in multiple species and that it modulates insulin secretion by controlling activation of purinergic receptors.
In VivoImaging of Zebrafish Reveals Differences in the Spinal Networks for Escape and Swimming Movements (2001)

Most studies of spinal interneurons in vertebrate motor circuits have focused on the activity of interneurons in a single motor behavior. As a result, relatively little is known about the extent to which particular classes of spinal interneurons participate in different behaviors. Similarities between the morphology and connections of interneurons activated in swimming and escape movements in different fish and amphibians led to the hypothesis that spinal interneurons might be shared by these behaviors. To test this hypothesis, we took advantage of the optical transparency of zebrafish larvae and developed a new preparation in which we could use confocal calcium imaging to monitor the activity of individual identified interneurons noninvasively, while we simultaneously filmed the movements of the fish with a high-speed digital camera. With this approach, we could directly examine the involvement of individual interneurons in different motor behaviors. Our work revealed unexpected differences in the interneurons activated in swimming and escape behaviors. The observations lead to predictions of different behavioral roles for particular classes of spinal interneurons that can eventually be tested directly in zebrafish by using laser ablations or mutant lines with interneuronal deficits.
Influence of Cornual Insemination on Conception in Dairy Cattle (1988)

The objective of this study was to compare conception to artificial insemination (AI) services in dairy cattle when semen was deposited into the uterine body or into both uterine horns (cornual insemination). Nine herdsman inseminators (HI) in four commercial dairy herds in Washington constituted the experimental units. Herds ranged in size from 393 cows to 964 cows. The duration of the experiment was 12 mo in three herds and 18 mo in the fourth herd. At the beginning of the experiment all inseminators were trained to deposit semen in the body of the uterus. Inseminators were instructed to use this method for 6 mo. Following employment of body deposition, the same inseminators were retrained to deposit one-half of the semen into the right uterine horn and one-half into the left uterine horn. Cornual inseminations were performed for 6 mo. A total of 4,178 services constituted the data set. Milk samples were collected from cows on the day of insemination and later were assayed for progesterone (P4). There was variation (P less than .01) in conception associated with month of insemination and insemination method (P less than .001). The monthly variation was not associated with season of the year. Least squares means for conception when semen was deposited in the uterine body was 44.7%, compared with 64.6% when cornual insemination was employed. The insemination treatment X inseminator interaction was not significant. Results suggest that cornual insemination provides an alternative to deposition of semen in the uterine body.
MSCs: Delivery Routes and Engraftment, Cell-Targeting Strategies, and Immune Modulation (2013)

Mesenchymal stem cells (MSCs) are currently being widely investigated both in the lab and in clinical trials for multiple disease states. The differentiation, trophic, and immunomodulatory characteristics of MSCs contribute to their therapeutic effects. Another often overlooked factor related to efficacy is the degree of engraftment. When reported, engraftment is generally low and transient in nature. MSC delivery methods should be tailored to the lesion being treated, which may be local or systemic, and customized to the mechanism of action of the MSCs, which can also be local or systemic. Engraftment efficiency is enhanced by using intra-arterial delivery instead of intravenous delivery, thus avoiding the “first-pass” accumulation of MSCs in the lung. Several methodologies to target MSCs to specific organs are being developed. These cell targeting methodologies focus on the modification of cell surface molecules through chemical, genetic, and coating techniques to promote selective adherence to particular organs or tissues. Future improvements in targeting and delivery methodologies to improve engraftment are expected to improve therapeutic results, extend the duration of efficacy, and reduce the effective (MSC) therapeutic dose.
Characterization of DNA binding and retinoic acid binding properties of retinoic acid receptor. (1991)

High-level expression of the full-length human retinoic acid receptor (RAR) alpha and the DNA binding domain of the RAR in Escherichia coli was achieved by using a T7 RNA polymerase-directed expression system. After induction, full-length RAR protein was produced at an estimated level of 20% of the total bacterial proteins. Both intact RAR molecules and the DNA binding domain bind to the cognate DNA response element with high specificity in the absence of retinoic acid. However, this binding is enhanced to a great extent upon the addition of eukaryotic cell extracts. The factor responsible for this enhancement is heat-sensitive and forms a complex with RAR that binds to DNA and exhibits a distinct migration pattern in the gel-mobility-shift assay. The interaction site of the factor with RAR is localized in the 70-amino acid DNA binding region of RAR. The hormone binding ability of the RAR alpha protein was assayed by a charcoal absorption assay and the RAR protein was found to bind to retinoic acid with a Kd of 2.1 x 10(-10) M.
Platelets inhibit fibrinolysis in vitro by both plasminogen activator inhibitor-1-dependent and -independent mechanisms (1994)

Abstract Platelet-rich thrombi are resistant to lysis by tissue-type plasminogen activator (t-PA). Although platelet alpha-granules contain plasminogen activator inhibitor-1 (PAI-1), a fast-acting inhibitor of t-PA, the contribution of PAI-1 to the antifibrinolytic effect of platelets has remained a subject of controversy. We recently reported a patient with a homozygous mutation within the PAI-1 gene that results in complete loss of PAI-1 expression. Platelets from this individual constitute a unique reagent with which to probe the role of platelet PAI-1 in the regulation of fibrinolysis. The effects of PAI-1-deficient platelets were compared with those of normal platelets in an in vitro clot lysis assay. Although the incorporation of PAI-1-deficient platelets into clots resulted in a moderate inhibition of t-PA-mediated fibrinolysis, normal platelets markedly inhibited clot lysis under the same conditions. However, no difference between PAI-1-deficient platelets and platelets with normal PAI-1 content was observed when streptokinase or a PAI-1-resistant t-PA mutant were used to initiate fibrinolysis. In addition, PAI-1-resistant t-PA was significantly more efficient in lysing clots containing normal platelets than wild-type t-PA. We conclude that platelets inhibit t-PA-mediated fibrinolysis by both PAI- 1-dependent and PAI-1-independent mechanisms. These results have important implications for the role of PAI-1 in the resistance of platelet-rich thrombi to lysis in vivo.
Prognostic Value of Preoperative Serum Cell-Free Circulating DNA in Men with Prostate Cancer Undergoing Radical Prostatectomy (2007)

Our study suggests that preoperative serum cell-free DNA concentration may be a useful prognostic biomarker for men with clinically localized prostate cancer treated with radical prostatectomy.
Total Synthesis of Epothilone A: The Macrolactonization Approach (1997)

This highly convergent and practical total synthesis of the antitumor agent epothilone A uses a macrolactonization (see below) as the key step. The strategy may provide access to a variety of epothilones desirable for biological screening.
De la lutte armée à la nation palestinienne : Vers une relecture des rapports entre l'OLP et les réfugiés (2003)

Résumé La question des réfugiés palestiniens se trouve au cœur du conflit israélo-arabe depuis plus de cinquante ans. Les guerres qui ont déchiré le Moyen-Orient dans la seconde moitié du xx e siècle, puis la lutte armée développée par la Résistance palestinienne à la fin des années soixante ont exercé une influence déterminante sur la structuration du mouvement national palestinien, et entraîné une redéfinition profonde de la société palestinienne. Face à la persistance du conflit, les camps de réfugiés deviennent des espaces mémoires, supports symboliques de la Palestine perdue. En 1969, l’Organisation de libération de la Palestine prend en main les camps de réfugiés du Liban. La figure des fedayin se substitue alors progressivement à celle des réfugiés tributaires de l’assistance internationale, et tente, à travers son emprise croissante sur les camps, de formuler un projet de société fondé sur la prise en main par les Palestiniens de leur destin.