gebhart/patrepeval huggingface dataset:
Synthesis and Evaluation of Bifunctional Aminothiazoles as Antiretrovirals Targeting the HIV-1 Nucleocapsid Protein (2018)

Small molecule inhibitors of the HIV-1 nucleocapsid protein (NC) are considered as promising agents in the treatment of HIV/AIDS. In an effort to exploit the privileged 2-amino-4-phenylthiazole moiety in NC inhibition, here we conceived, synthesized, and tested <i>in vitro</i> 18 NC inhibitors (NCIs) bearing a double functionalization. In these NCIs, one part of the molecule is deputed to interact noncovalently with the NC hydrophobic pocket, while the second portion is designed to interact with the N-terminal domain of NC. This binding hypothesis was verified by molecular dynamics simulations, while the linkage between these two pharmacophores was found to enhance antiretroviral activity both on the wild-type virus and on HIV-1 strains with resistance to currently licensed drugs. The two most interesting compounds <b>6</b> and <b>13</b> showed no cytotoxicity, thus becoming valuable leads for further investigations.
Pathogenic role for skin macrophages in a mouse model of keratinocyte-induced psoriasis-like skin inflammation (2006)

Psoriasis is a common skin disease, the pathogenesis of which has not yet been resolved. In mice, epidermis-specific deletion of inhibitor of NF-kappaB (IkappaB) kinase 2 (IKK2) results in a skin phenotype that mimics human psoriasis in several aspects. Like psoriasis, this skin disease shows pronounced improvement when mice are treated with a TNF-neutralizing agent. We have found previously that this phenotype does not depend on the presence of alphabeta T lymphocytes. In order to evaluate contributions of other immune cell populations to the skin disease, we selectively eliminated macrophages and granulocytes from the skin of mice with epidermis-specific deletion of IKK2 (K14-Cre-IKK2fl/fl mice). Elimination of skin macrophages by subcutaneous injection of clodronate liposomes was accompanied by inhibition of granulocyte migration into the skin and resulted in a dramatic attenuation of psoriasis-like skin changes. The hyperproliferative, inflammatory skin disease in K14-Cre-IKK2fl/fl mice was a direct consequence of the presence of macrophages in the skin, as targeted deletion of CD18, which prevented accumulation of granulocytes but not macrophages, did not lead to major changes in the phenotype. Targeted deletion of the receptor for IFN-gamma revealed that the pathogenesis of the skin disease does not depend on classical IFN-gamma-mediated macrophage activation. Our results demonstrate that in mice epidermal keratinocytes can initiate a hyperproliferative, inflammatory, IFN-gamma-independent, psoriasis-like skin disease whose development requires essential contributions from skin macrophages but not from granulocytes or alphabeta T lymphocytes.
Evolutionary Implications of Three Novel Members of the Human Sarcomeric Myosin Heavy Chain Gene Family (2002)

Sarcomeric myosin heavy chain (MyHC) is the major contractile protein of striated muscle. Six tandemly linked skeletal MyHC genes on chromosome 17 and two cardiac MyHC genes on chromosome 14 have been previously described in the human genome. We report the identification of three novel human sarcomeric MyHC genes on chromosomes 3, 7, and 20, which are notable for their atypical size and intron-exon structure. Two of the encoded proteins are structurally most like the slow-beta MyHC, whereas the third one is closest to the adult fast IIb isoform. Data from pairwise comparisons of aligned coding sequences imply the existence of ancestral genomes with four sarcomeric genes before the emergence of a dedicated smooth muscle MyHC gene. To further address the evolutionary relationships of the distinct sarcomeric and nonsarcomeric rod sequences, we have identified and further annotated human genomic DNA sequences corresponding to 14 class-II MyHCs. An extensive analysis provides a timeline for intron gain and loss, gene contraction and expansion, and gene conversion among genes encoding class-II myosins. One of the novel human genes is found to have introns at positions shared only with the molluscan catchin/MyHC gene, providing evidence for the structure of a pre-Cambrian ancestral gene.
ChemInform Abstract: Synthesis and Characterization of Fluorodinitroamine, FN(NO2)2. (2015)

Abstract The title compound is synthesized by reaction of NF 4 SbF 6 and KN(NO 2 ) 2 using SO 2 or MeCN as solvent (vacuum, ‐196 °C followed by warming to the melting point of the solvent) and characterized by multinuclear NMR and Raman spectroscopy, and quantum chemical DFT calculations.
Management of Postinjury Coagulopathy (2005)

SUMMARY Coagulopathy is commonly seen in seriously injured patients and can make control of hemorrhage more difficult. An observed defect in blood clotting may be preexisting, due to severe injury, a result of delayed treatment, or exacerbated by resuscitation efforts. Factors that promote coagulopathy include hypothermia, acidosis, intravascular consumption and extravascular loss of coagulation factors and platelets, reduced platelet effectiveness secondary to low hematocrit, interactions of coagulation proteins and platelets with volume expanders, and the hemodilution associated with massive transfusion. Management of the hemorrhagic diathesis involves treatment of hypothermia, avoidance of excessive colloid and crystalloid volume in the resuscitation effort, damage‐control surgery, appropriate use of blood products and, in selected cases, the use of tissue sealants and recombinant factor VIIa.
Bacterial shifts associated with coral–macroalgal competition in the Caribbean Sea (2013)

Present-day coral reefs are impacted by frequent disturbance and increasing global stressors, which provide an environment that supports the growth of alternative dominants, such as macroalgae, sponges, and tunicates, rather than stony corals. Competitively damaging interactions arise between macroalgae and reef-building corals that can involve chemical, physical, and microbial mechanisms. Using 16S rRNA denaturing gradient gel electrophoresis (DGGE), amplicon sequencing, and multivariate analyses, we examined coral-and algae-associated bacterial assemblages along interaction gradients between the common Caribbean stony corals Montastraea faveolata and Porites astreoides and the benthic macroalgae Halimeda opuntia and Dictyota menstrualis. Benthic surveys were conducted in 3 Caribbean locations, and interactions were sampled for bacterial analyses. Both macroalgae were capable of inducing shifts in coralassociated bacteria to an assemblage that more closely resembled macroalgal-associated bacteria. Overall, M. faveolata-associated bacteria were more significantly affected by macroalgal competitors than were P. astreoides-associated bacteria at all sites. Bacteria associated with M. faveolata corals changed during > 83% of interactions, even when samples were taken 5 cm away from competing macroalgae. Detectable shifts in coral-associated bacteria at all sampling sites suggest that macroalgae play a large role in coral holobiont health. The degree to which coral species maintain stable microbial assemblages in the face of environmental fluctuations and competitive stress may indicate specific species and coral reefs that have the capacity to resist perturbations and those that may need additional protection in the future.
Wifi-reports (2009)

Wi-Fi clients can obtain much better performance at some commercial hotspots than at others. Unfortunately, there is currently no way for users to determine which hotspot access points (APs) will be sufficient to run their applications before purchasing access. To address this problem, this paper presents Wifi-Reports, a collaborative service that provides Wi-Fi clients with historical information about AP performance and application support. The key research challenge in Wifi-Reports is to obtain accurate user-submitted reports. This is challenging because two conflicting goals must be addressed in a practical system: preserving the privacy of users' reports and limiting fraudulent reports. We introduce a practical cryptographic protocol that achieves both goals, and we address the important engineering challenges in building Wifi-Reports. Using a measurement study of commercial APs in Seattle, we show that Wifi-Reports would improve performance over previous AP selection approaches in 30%-60% of locations.
Influence of polymer characteristics and melt‐spinning conditions on the production of fine denier poly(ethylene terephtalate) fibers. Part I. Rheological characterization of PET polymer melt (1992)

Abstract The rheological characterization of four poly(ethylene terephtalate) (PET) polymers, with viscosity average molecular weight ranging from 2.7 × 10 4 to 7.1 × 10 4 , has been performed in the Instron capillary rheometer. The apparent elongational viscosity was obtained from the shear flow and entrance pressure data, following the methods proposed by Cogswell and Binding in contraction flow experiments. The PET polymers showed a tension thinning behavior in the deformation rate range of 300–3000 s −1 employed in this study. These results were explained on the basis of the network model. Polymers with similar behavior in shear may be distinct in elongational and may lead to distinct polymer processability. Polymers with lower apparent elongational viscosity level were shown to allow spinning of finer denier fibers, which is determined by the polymer spinnability.
Analytic solutions to compartmental models of the HIV/AIDS epidemic (2000)

For many years compartmental models have provided useful insights into the spread of epidemics. Such models are usually fairly easy to set up, but even the simpler models have the disadvantage that they are intractable to analytic solution. In this paper we examine models of the HIV/AIDS epidemic, and show that the equations may be linearized in a piecewise manner over time, thus allowing analytic solutions to be obtained. Indications of the usefulness of this approach are provided. In particular, an analytic solution gives insight into the mechanism of the epidemic, together with a clearer picture of the sensitivity of results to changes in parameter values. Further, the processes of parameter estimation and the methodology of back-calculation also benefit from the provision of functional forms for the state variables.
Antiprotozoal and Antiglycation Activities of Sesquiterpene Coumarins from Ferula narthex Exudate (2016)

The exudate of <i>Ferula narthex</i> Boiss. (Apiaceae) is widely used in the Indian subcontinent as a spice and because of its health effects. Six sesquiterpene coumarins have been isolated from this exudate: feselol, ligupersin A, asacoumarin A, 8'-<i>O</i>-acetyl-asacoumarin A, 10'<i>R</i>-karatavacinol and 10'<i>R</i>-acetyl-karatavacinol. Based on its use in infectious and diabetic conditions, the isolated constituents were evaluated for antimicrobial and antiglycation activities. Some compounds showed activity against protozoal parasites, asacoumarin A being the most active one against <i>Plasmodium falciparum</i> K1 (IC<sub>50</sub> 1.3 μM). With regard to antiglycation activity, in the BSA-glucose test, ligupersin A displayed the highest activity (IC<sub>50</sub> 0.41 mM), being more active than the positive control aminiguanidine (IC<sub>50</sub> 1.75 mM). In the BSA-MGO assay, the highest activity was shown by 8'-<i>O</i>-acetyl-asacoumarin A (IC<sub>50</sub> 1.03 mM), being less active than aminoguanidine (IC<sub>50</sub> 0.15 mM). Hence, the antiglycation activity of the isolated constituents was due to both oxidative and non-oxidative modes of inhibition.
Optimising Automatic Tool Selection for 2½D Components (2000)

Abstract An important step in planning the manufacture of a component by CNC machining is the selection of cutting tools. Although it has long been known that the choice of cutter sizes can have a dramatic effect on the overall machining time, few algorithms for optimisation have been available to the production engineer. This paper describes a method for determining a theoretical optimal combination of cutting tools for machining a given set of 3D volumes or 2D profiles. The algorithm considers residual material left behind by oversized cutters and the relative clearance rates of cutters that can access the selected machining features. The current implementation of the procedure described does not give exact results because several machining parameters are not included in the selection process such as tool path length, plunge rates, etc. However, the experimental results suggest that while these factors may make changes to the absolute values calculated, they typically make only a small difference to the relative ranking of the tools. The results presented here suggest that the correct combination of tools could reduce machining times by significant amounts. Consequently the paper concludes with a discussion of how the tool path generation routines used in commercial CAM systems could be modified to achieve this.
Texture Mapping via Optimal Mass Transport (2009)

In this paper, we present a novel method for texture mapping of closed surfaces. Our method is based on the technique of optimal mass transport (also known as the "earth-mover's metric"). This is a classical problem that concerns determining the optimal way, in the sense of minimal transportation cost, of moving a pile of soil from one site to another. In our context, the resulting mapping is area preserving and minimizes angle distortion in the optimal mass sense. Indeed, we first begin with an angle-preserving mapping (which may greatly distort area) and then correct it using the mass transport procedure derived via a certain gradient flow. In order to obtain fast convergence to the optimal mapping, we incorporate a multiresolution scheme into our flow. We also use ideas from discrete exterior calculus in our computations.
VEWS (2015)

We study the problem of detecting vandals on Wikipedia before any human or known vandalism detection system reports flagging potential vandals so that such users can be presented early to Wikipedia administrators. We leverage multiple classical ML approaches, but develop 3 novel sets of features. Our Wikipedia Vandal Behavior (WVB) approach uses a novel set of user editing patterns as features to classify some users as vandals. Our Wikipedia Transition Probability Matrix (WTPM) approach uses a set of features derived from a transition probability matrix and then reduces it via a neural net auto-encoder to classify some users as vandals. The VEWS approach merges the previous two approaches. Without using any information (e.g. reverts) provided by other users, these algorithms each have over 85% classification accuracy. Moreover, when temporal recency is considered, accuracy goes to almost 90%. We carry out detailed experiments on a new data set we have created consisting of about 33K Wikipedia users (including both a black list and a white list of editors) and containing 770K edits. We describe specific behaviors that distinguish between vandals and non-vandals. We show that VEWS beats ClueBot NG and STiki, the best known algorithms today for vandalism detection. Moreover, VEWS detects far more vandals than ClueBot NG and on average, detects them 2.39 edits before ClueBot NG when both detect the vandal. However, we show that the combination of VEWS and ClueBot NG can give a fully automated vandal early warning system with even higher accuracy.
Incidence of Immune Recovery Vitritis in Cytomegalovirus Retinitis Patients following Institution of Successful Highly Active Antiretroviral Therapy (1999)

This study was conducted to determine the likelihood of the development of a new ocular inflammatory syndrome (immune recovery vitritis, IRV), which causes vision loss in AIDS patients with cytomegalovirus (CMV) retinitis, who respond to highly active antiretroviral therapy (HAART). We followed 30 HAART-responders with CD4 cell counts of >/=60 cells/mm3. Patients were diagnosed with IRV if they developed symptomatic vitritis of >/=1+ severity associated with inactive CMV retinitis. Symptomatic IRV developed in 19 (63%) of 30 patients and in 26 (59%) of 44 eyes over a median follow-up from HAART response of 13.5 months. The annual incidence of IRV was 83/100 person-years. Excluding patients with previous cidofovir therapy did not significantly alter the time course of IRV (P=.79). These data suggest that IRV develops in a significant number of HAART-responders with CMV retinitis and is unrelated to previous cidofovir therapy.
New High Efficiency Deep UV Raman Spectrometer for Standoff Detection (2021)

UV resonance Raman spectroscopy is uniquely suitable for standoff measurements due to its high sensitivity and selectivity. When excitation wavelength falls within an electronic transition of a molecule, Raman band intensities associated with the chromophore vibrations are significantly enhanced. This resonance Raman Effect, as well as negligible fluorescence interference in the deep UV, enable the detection and investigation of enhanced species at trace concentrations at a distance. We developed a state-of-the-art, high-efficiency standoff deep UV Raman spectrometer. This spectrometer is based on a custom deep UV F/8 Cassegrain telescope with a 200 mm primary mirror. This telescope is equipped with an electric secondary focus operating from infinity to 3 m distance. The UV Raman spectrograph utilizes high-efficiency deep UV transmission grating and custom Rayleigh rejection filter. As an excitation source for Raman measurements, we utilized a recently developed 228 nm compact solid state deep UV laser. The 228 nm resonance excitation enhances the Raman intensities of vibrations of NOx groups, peptide bonds, aromatic amino acid side chains, and DNA/RNA nucleotides. We used this novel spectrometer for detection of NOx-based explosive materials at trace concentrations at a stand-off distance.
Late irradiation‐induced lesions of the lumbosacral plexus (1983)

Lumbosacral plexus lesions developed in two women 8 and 14 years, respectively, after operation and irradiation for carcinoma of the uterus. In both patients, a left femoral nerve lesion was the presenting sign. The irradiation dose was about 5,000 rad on both sides in patient 1 and 8,400 rad on the affected side in patient 2. Both patients had low-frequency periodic discharges in the EMG.
Mechanism of catheter thrombosis: comparison of the antithrombotic activities of fondaparinux, enoxaparin, and heparin in vitro and in vivo (2011)

In patients undergoing percutaneous coronary intervention, catheter thrombosis is more frequent with fondaparinux than heparin. This study was undertaken to identify the responsible mechanism and to develop strategies for its prevention. Percutaneous coronary intervention catheter segments shortened plasma clotting times from 971 ± 92 to 352 ± 22 seconds. This activity is factor XII (fXII) dependent because it was attenuated with corn trypsin inhibitor and was abolished in fXII-deficient plasma. Heparin and enoxaparin blocked catheter-induced clotting at 0.5 and 2 anti-Xa U/mL, respectively, whereas fondaparinux had no effect. Addition of fondaparinux to bivalirudin or low-dose heparin attenuated catheter-induced clotting more than either agent alone. In a rabbit model of catheter thrombosis, a 70 anti-Xa U/kg intravenous bolus of heparin or enoxaparin prolonged the time to catheter occlusion by 4.6- and 2.5-fold, respectively, compared with saline, whereas the same dose of fondaparinux had no effect. Although 15 anti-Xa U/kg heparin had no effect on its own, when given in conjunction with 70 anti-Xa U/kg fondaparinux, the time to catheter occlusion was prolonged 2.9-fold. These findings indicate that (1) catheters are prothrombotic because they trigger fXII activation, and (2) fondaparinux does not prevent catheter-induced clotting unless supplemented with low-dose heparin or bivalirudin.
Efficient Models for Reverberation and Distance Rendering in Computer Music and Virtual Audio Reality (1997)

This paper discusses efficient digital signal processing algorithms for real-time synthesis of dynamically controllable, natural-sounding artificial reverberation. A general modular framework is proposed for configuring a spatial sound processing and mixing system according to the reproduction format or setup and the listening conditions, over loudspeakers or headphones. In conclusion, the implementation and applications of a spatial sound processing software are described, and approaches to control interface design and effective distance effects are reviewed. 1 Introduction Immersive real-time audio requires synthesizing and dynamically controlling directional panning and room reverberation effects over headphones or loudspeakers. Artificial reverberation is necessary to ensure a convincing degree of realism of the virtual sound scene and provide control over the perceived distance of virtual sound sources. Applications of spatial sound processing and artificial reverberation techniq...
The relationship between aerobic fitness level and metabolic profiles in healthy adults (2013)

This study demonstrates a relationship between fitness level and the amino acid profile. Moreover, the metabolite changes show that a reduced excretion of amino acids in adults is associated with increased fitness levels and an increased fat oxidation rate during exercise. Interestingly, higher levels of branched chain amino acids were associated with lower fitness levels and higher insulin resistance.
Etude de l'effet de transfert de Spin dans des jonctions tunnel magnétiques en géométrie nanoring (2013)

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Cisplatin combined with prostaglandin E1 chemotherapy in rat peritoneal carcinomatosis (2000)

Cisplatin intraperitoneal (i.p.) chemotherapy is frequently performed for patients with peritoneal carcinomatosis. However, cisplatin penetrates only the surface of the peritoneal tumor and has serious side effects on renal cells. Thus, cisplatin i.p. chemotherapy had been limited to use for these patients. Prostaglandin E1 (PGE1) has been used for reducing the toxic effects of anticancer drugs because of its cytoprotective effects and has been reported to enhance tumoricidal activity of anticancer drugs. In our study, the effects of PGE1 on the rat peritoneal carcinomatosis model treated with cisplatin i.p. chemotherapy were evaluated. Cisplatin (5 mg/kg) was given in an i.p. administration to 70 tumor-free rats. PGE1 was administered to 35 rats through the tail vein at an infusion rate of 0.1 microg/kg/min (1 ml/hr), and the remaining 35 rats were injected with physiological saline. Forty rats were given an i.p. injection of 1 x 10(7) AH100B cells. Ten days after injection, cisplatin (5 mg/kg) was administered with PGE1 to 20 and the remaining 20 were injected with physiological saline. The accumulation of platinum in the tissues and apoptotic renal cells were analyzed. The maximum concentrations of platinum in the kidneys of PGE1 untreated rats (tumor-free: 10.11 microg/g; tumor-bearing: 11.45 microg/g) did not differ from those of platinum in the kidneys of PGE1-treated rats (tumor-free: 10.28 microg/g; tumor-bearing: 13.28 microg/g). The number of apoptotic renal cells was significantly reduced by PGE1 administration in both tumor-free and tumor-bearing rats. Moreover, PGE1 increased the maximum platinum concentration in tumor masses (5.31 microg/g) of the treated group compared with that in tumor mass of the control group (2.72 microg/g, p = 0.009). These results indicate that PGE1 may increase the anticancer effect of cisplatin by increasing tumor platinum concentration and may reduce the chance of cisplatin-induced renal failure. Intraperitoneal cisplatin chemotherapy combined with PGE1 treatment may have a therapeutic benefit for patients with peritoneal carcinomatosis.