gebhart/patrepeval huggingface dataset:
AzureBlast (2010)

Cloud computing has emerged as a new approach to large scale computing and is attracting a lot of attention from the scientific and research computing communities. Despite its growing popularity, it is still unclear just how well the cloud model of computation will serve scientific applications. In this paper we analyze the applicability of cloud to the sciences by investigating an implementation of a well known and computationally intensive algorithm called BLAST. BLAST is a very popular life sciences algorithm used commonly in bioinformatics research. The BLAST algorithm makes an excellent case study because it is both crucial to many life science applications and its characteristics are representative of many applications important to data intensive scientific research. In our paper we introduce a methodology that we use to study the applicability of cloud platforms to scientific computing and analyze the results from our study. In particular we examine the best practices of handling the large scale parallelism and large volumes of data. While we carry out our performance evaluation on Microsoft's Windows Azure the results readily generalize to other cloud platforms.
Metabolism of docetaxel by human cytochromes P450: interactions with paclitaxel and other antineoplastic drugs. (1996)

The metabolism of docetaxel by human liver microsomes was investigated in vitro and compared with that of paclitaxel. A main docetaxel metabolite was generated by human liver microsomes in the presence of NADPH: retention time in high pressure liquid chromatography and its ion fragmentation in mass spectrometry were identical to those of the authentic derivative hydroxylated at the butyl group of the C13 side chain. Kinetic measurements and chemical and immunological inhibitions demonstrated that CYP3A was implicated in the hydroxylation of docetaxel: Km (2 microM) and Vm values of docetaxel for human liver microsomes were comparable to those calculated for the formation of metabolite p-hydroxy-phenyl C3' paclitaxel (M4). Docetaxel hydroxylation correlated only with the CYP3A content of microsomes and with CYP3A-dependent 6 beta-hydroxylation of testosterone and 16-hydroxylation of dehydroepiandrosterone. The formation of hydroxydocetaxel was strongly reduced by CYP3A inhibitors such as ketoconazole, midazolam, erythromycin, testosterone, orphenadrine, and troleandomycin, whereas quinidine (CYP2D6), hexobarbital, tolbutamide, and mephenytoin (CYP2C) had no or little effect. The hydroxylation of docetaxel exhibited a highly positive correlation with the formation of metabolite M4 of paclitaxel (r = 0.929, P < 0.0001, n = 12), but not with its 6-hydroxylation (r = 0.48, P > 0.15). Docetaxel abolished the hydroxylation of paclitaxel metabolite M4, but was totally inactive on its 6 alpha-hydroxylation. Conversely, paclitaxel reduced significantly the hydroxylation of docetaxel. We examined in vitro the possible interaction among docetaxel, paclitaxel, and drugs which could be associated during chemotherapy. Cisplatin, verapamil, doxorubicin, vinblastine, and vincristine at concentrations usually recommended did not markedly modify taxoid metabolism. Ranitidine and diphenylhydramine had no effect, but 100 microM cimetidine partially inhibited the formation of 6 alpha-hydroxypaclitaxel. Pretreatment of patients with barbiturates strikingly stimulated docetaxel hydroxylation, whereas no acceleration of docetaxel hydroxylation was noticed in a patient receiving steroids.
On the used of EMIR® method to realize 3D characterization of radio wave fields (2020)

Since the pioneering works of Iizuka
Activity of Cyclic‐AMP Phosphodiesterase in Permeabilised Cells of Bakers' Yeast (1982)

Yeast cyclic-AMP phosphodiesterases were assayed in situ, using cells permeabilised with cytochrome c, to get information about the kinetics of these enzymes at the high concentrations of macromolecules occurring in vivo. Protamine treatment was not suitable, because it perturbed the intracellular localisations of both the (Mg-dependent) low-Km enzyme and the (EDTA-insensitive) high-Km enzyme. The pH-dependence of Km and V for EDTA-insensitive activity in situ agreed well with the behaviour of pure high-Km enzyme, except that near pH 8 Hofstee plots were bent slightly upwards both for activity in situ and with crude broken-cell preparations. Hofstee plots of Mg-dependent activity in situ were distinctly concave, and could be resolved mathematically into two activities, one (accounting for about 30% of the Mg-dependent V) with a Km close to the value in vitro of 0.2 microM, and the other with an apparent Km of 3 microM. The 3 microM Km activity probably represents a fraction of the low-Km enzyme that is particle-bound at the high protein concentrations occurring in situ.
[The Netherton syndrome: clinical characteristics, differential diagnosis and new ways of therapy]. (1984)

The Netherton-syndrome is a rare disease which is probably inherited through an autosomal recessive trait. It is defined by a triad of symptoms: congenital ichthyosiform erythrodermia , trichorrhexis invaginata et nodosa ("bamboo hair") and atopy. Additional disorders affect the immune system, the metabolism of amino acids and the physical development. On the basis of a new case, the cellular immune defect and the genetic background of the disease are more clearly defined. A new form of treatment--a combination of photochemotherapy (PUVA) and systematic application of aromatic retinoid--has so far proved to be successful. In order to establish an accurate diagnosis--a prerequisite for this promising therapeutic approach--diseases with similar symptoms are discussed for comparison.
Immunologic monitoring (2003)

The development of reliable in vitro assays that could allow the quantitation and characterization of anti-donor alloimmune responses has always been a goal in clinical transplantation, both to predict presensitization to the transplanted tissue and to be able to identify rejection without resorting to more invasive tests. With recent development in our understanding of transplantation biology and therapeutics, there is a real expectation that these tests may be used to identify tolerance as much as to predict rejection. The traditional limiting dilution assays still have a contribution to make and are being complemented by an array of tools, such as ELISpot, flow cytometry-based techniques, and microarray analysis. The assays that have been informative, to date, are discussed in this review. This information will lead, at least, to a better understanding of how and when the rejection process occurs. More interestingly, the objective is to apply this information to evaluate tolerance-inducing strategies or to identify patients that have become tolerant to their graft and can be weaned of immunosuppression. Of course sensitive, accurate and specific immunologic monitoring has applications well beyond the field of transplantation.
8B.06 (2015)

Objective: Previous reports have indicated that blood pressure (BP) reductions imparted by baroreflex activation therapy (BAT) in patients with resistant hypertension (rHTN) are maintained for at least 5 years. Because such reports have focused only on patients who remain active, it is possible that selection bias could overstate the impact of BAT. The purpose of this investigation is to comprehensively describe long-term BP reductions in rHTN patients receiving BAT using all data currently available. Design and method: Following collection of the pre-specified 12-month endpoints, patients were followed every 6 months. BP data were collected at each follow-up using a protocol-defined technique to minimize bias. Results: Original trial enrollment consisted of 322 patients. Of those, 182 presently remain active while 140 are inactive due to withdrawal from the study (112) or death (28). Consistent with earlier reports, BP reductions were > 30/15 mmHg for at least 6 years. Long-term therapy safety was excellent with low rates of stroke, myocardial infarction and hypertensive urgency.Conclusions: BAT-induced BP reductions in rHTN patients were remarkably consistent over time, maintaining high levels of clinical and statistical significance. Previous reports of only active patients faithfully represent the true course of BP response to BAT in a large rHTN cohort.
Viscous Friction in Foams and Concentrated Emulsions under Steady Shear (2008)

We present a model for the viscous friction in foams and concentrated emulsions, subject to steady shear flow. First, we calculate the energy dissipated due to viscous friction inside the films between two neighboring bubbles or drops, which slide along each other in the flow. Next, from this energy we calculate the macroscopic viscous stress of the sheared foam or emulsion. The model predictions agree well with experimental results obtained with foams and emulsions.
Interactions of Molecular Species with Graphene and Graphene Sensing (2019)

This chapter contains sections titled: Introduction CVD Synthesis of Pristine and Doped Graphene Interaction of Pure and Doped Graphene with Adsorbed Molecules Graphene-Enhanced Raman Scattering Effect Concluding Remarks
Single Crystal Nanowire Vertical Surround-Gate Field-Effect Transistor (2004)

Harnessing the potential of single crystal inorganic nanowires for practical advanced nanoscale applications requires not only reproducible synthesis of highly regular one-dimensional (1D) nanowire arrays directly on device platforms but also elegant device integration which retains structural integrity of the nanowires while significantly reducing or eliminating complex critical processing steps. Here we demonstrate a unique, direct, and bottom-up integration of a semiconductor 1D nanowire, using zinc oxide (ZnO) as an example, to obtain a vertical surround-gate field-effect transistor (VSG-FET). The vertical device structure and bottom-up integration reduce process complexity, compared to conventional top-down approaches. More significantly, scaling of the vertical channel length is lithographically independent and decoupled from the device packing density. A bottom electrical contact to the nanowire is uniquely provided by a heavily doped underlying lattice-match substrate. Based on the nanowire-integrated platform, both n- and p-channel VSG-FETs are fabricated. The vertical device architecture has the potential for use in tera-level ultrahigh-density nanoscale memory and logic devices.
3D Printed Polyurethane Scaffolds for the Repair of Bone Defects (2020)

Critical-size bone defects are those that will not heal without intervention and can arise secondary to trauma, infection, and surgical resection of tumors. Treatment options are currently limited to filling the defect with autologous bone, of which there is not always an abundant supply, or ceramic pastes that only allow for limited osteo-inductive and -conductive capacity. In this study we investigate the repair of bone defects using a 3D printed LayFomm scaffold. LayFomm is a polymer blend of polyvinyl alcohol (PVA) and polyurethane (PU). It can be printed using the most common method of 3D printing, fused deposition modeling, before being washed in water-based solutions to remove the PVA. This leaves a more compliant, micro-porous PU elastomer. <i>In vitro</i> analysis of dental pulp stem cells seeded onto macro-porous scaffolds showed their ability to adhere, proliferate and form mineralized matrix on the scaffold in the presence of osteogenic media. Subcutaneous implantation of LayFomm in a rat model showed the formation of a vascularized fibrous capsule, but without a chronic inflammatory response. Implantation into a mandibular defect showed significantly increased mineralized tissue production when compared to a currently approved bone putty. While their mechanical properties are insufficient for use in load-bearing defects, these findings are promising for the use of polyurethane scaffolds in craniofacial bone regeneration.
Hydrogenation of polar functionalities with Cp*Ru(PN) catalysts (2008)

Abstract This account deals with an overview of our recent progress toward the development of molecular catalysts for the reduction in polar functionalities with molecular hydrogen (H 2 ). An emphasis is placed on the newly designed Cp*Ru(PN) complexes, which have been identified as efficient catalysts for the hydrogenation of imides. The structural modification of the complex enhances the catalytic performance and allows efficient access to various chiral synthetic intermediates.
High-Throughput Screening for Extracellular Inhibitors of the FLT3 Receptor Tyrosine Kinase Reveals Chemically Diverse and Druggable Negative Allosteric Modulators (2022)

Inhibiting receptor tyrosine kinases is commonly achieved by two main strategies targeting either the intracellular kinase domain by low molecular weight compounds or the extracellular ligand-binding domain by monoclonal antibodies. Identifying small molecules able to inhibit RTKs at the extracellular level would be highly desirable to gain exquisite selectivity but is believed to be challenging owing to the size of RTK endogenous ligands (cytokines, growth factors) and the topology of RTK extracellular domains. We here report the high-throughput screening of the French Chemical Library (48K compounds) for extracellular inhibitors of the Fms-like tyrosine kinase 3 (FLT3) receptor tyrosine kinase, by a homogeneous time-resolved fluorescence competition assay. A total of 679 small molecular weight ligands (1.4%) were confirmed to strongly inhibit (>75%) the binding of the fluorescent labeled FLT3 ligand (FL cytokine) to FLT3 overexpressed in HEK-293 cells, at two different concentrations (5 and 20 μM). Concentration-response curves, obtained for 111 lead-like molecules, confirmed the unexpected tolerance of the FLT3 extracellular domain for low molecular weight druggable inhibitors exhibiting submicromolar potencies, chemical diversity, and promising pharmacokinetic properties. Further investigation of one hit confirmed inhibitory properties in dorsal root ganglia neurons and in a mouse model of neuropathic pain.
"Riches"... et "moins riches" ou la fonction de reproduction (1986)

Rich... and less rich : What about university reproduction function ? - We call rich students those who are allotted — by birth chance — the benefice of culture and stimulating familial background. The others are less rich. Is it possible to perceive this richness or poverty among university « clientele » ? The authors try to answer this question.
Simple New Mail Notification (2005)

This memo documents a long-standing technique, supported by a large
number of mail servers, which allows users to be notified of new mail.
In addition to server support, there are a number of clients that
support this, ranging from full email clients to specialized clients
whose only purpose is to receive new mail notifications and alert a
mail client. In brief, the server sends the string nm_notifyuser
CRLF to the finger port on the IP address (either configured or last
used) of the user who has received new mail. This memo provides
information for the Internet community.
FDTD analysis of a pulsed microwave confocal system for breast cancer detection (2002)

A novel focused active microwave system is investigated for detecting breast cancer. In contrast to x-ray and ultrasound modalities, the method reviewed here exploits the breast-tissue physical properties unique to the microwave spectrum, namely, the translucent nature of normal breast tissues and the high dielectric contrast between malignant and normal breast tissues. The system uses a confocal technique and time-gating to enhance the detection of malignant tumors while suppressing the effects of tissue heterogeneity and absorption. Using published data for the dielectric properties of normal and malignant breast tissues, we have conducted a preliminary 2-D finite-difference time-domain (FDTD) computational electromagnetics analysis of the system. We considered two types of inhomogeneities of normal tissue: a statistically random variation of the dielectric parameters throughout the breast in a /spl plusmn/10% range, and a spatially coherent inhomogeneity representing a vein. The modeled excitation was a pulsed 6-GHz waveform. The FDTD simulations showed that malignant tumors as small as 2 mm in diameter could be robustly detected in the presence of the background clutter generated by the heterogeneity of the surrounding normal tissue. Spatial resolution of the tumor location was found to be in the order of 1 cm.
A New Application of Charged Aerosol Detection in Liquid Chromatography for the Simultaneous Determination of Polar and Less Polar Ginsenosides in Ginseng Products (2013)

Concentrations of 14 ginsenosides were determined simultaneously in one homemade red ginseng and 13 commercial ginseng products of different types (liquid and solid samples), and results showed that ginsenoside content varied significantly among the samples tested. The method developed could serve as a useful analytical tool for the quality control of ginseng products.
The immunomodulatory effect of protein S in pulmonary fibrosis (2013)

Background: Protein S (PS) is a K-dependent plasma glycoprotein with an important role in blood coagulation. PS itself may directly regulate inflammatory responses. Pulmonary fibrosis is the end stage of interstitial lung diseases that leads to a progressive loss of pulmonary function. Objective: This study evaluated the role of PS in pulmonary fibrosis. Method: Lung fibrosis was induced in wild type (WT/BLM) C57BL/6 and PS transgenic mice (PS/BLM) by bleomycin (BLM). Control groups were treated with saline (WT/SAL &amp; PS/SAL). Result: WT/BLM group presented increased lung infiltration of immune cells compared to control groups and PS/BLM group. Lung collagen, hydroxyproline and plasma IL-10 levels were also significantly increased in WT/BLM compared to control and PS/BLM groups. The lung weight was significantly lower in PS/BLM group than in the WT/BLM group. The expression of the apoptosis-related markers, Casp-3 and APAF-1, was increased in the lungs of WT/BLM group compared to control and PS/BLM groups. Conclusion: This study showed that pulmonary fibrosis and inflammation are ameliorated in PS transgenic mice. Immunomodulatory effect of protein S may explain this protective role.
Periprosthetic osteolysis: Characterizing the innate immune response to titanium wear‐particles (2010)

Osteolysis of bone following total hip replacement is a major clinical problem. Examination of the areas surrounding failed implants has indicated an increase in the bone-resorption-inducing cytokine, interleukin 1β (IL-1β). NALP3, a NOD-like receptor protein located in the cytosol of macrophages, signals the cleavage of pro-IL-1β into its mature, secreted form, IL-1β. Here we showed that titanium particles stimulate the NALP3 inflammasome. We demonstrated that titanium induces IL-1β secretion from macrophages. This response depended on the expression of components of the NALP3 inflammasome, including NALP3, ASC, and Caspase-1. We also showed that titanium particles trigger the recruitment of neutrophils and that this acute inflammatory response depends on the expression of the IL-1 receptor and IL-1α/β. Moreover, administration of the IL-1 receptor antagonist (IL-1Ra) diminished neutrophil recruitment in response to titanium particles. Together, these results suggest that titanium particle-induced acute inflammation is due to activation of the NALP3 inflammasome, which leads to increased IL-1β secretion and IL-1-associated signaling, including neutrophil recruitment. Efficacy of IL-1Ra treatment introduces the potential for antagonist-based therapies for implant osteolysis.
Development of a Nanobody-Based Lateral Flow Immunoassay for Detection of Human Norovirus (2016)

Human noroviruses are the dominant cause of outbreaks of acute gastroenteritis. These viruses are usually detected by molecular methods, including reverse transcriptase PCR (RT-PCR) and enzyme-linked immunosorbent assay (ELISA). Human noroviruses are genetically and antigenically diverse, with two main genogroups that are further subdivided into over 40 different genotypes. During the past decade, genogroup 2 genotype 4 (GII.4) has dominated in most countries, but recently, viruses belonging to GII.17 have increased in prevalence in a number of countries. A number of commercially available ELISAs and lateral flow immunoassays were found to have lower sensitivities to the GII.17 viruses, indicating that the antibodies used in these methods may not have a high level of cross-reactivity. In this study, we developed a rapid Nanobody-based lateral flow immunoassay (Nano-immunochromatography [Nano-IC]) for the detection of human norovirus in clinical specimens. The Nano-IC assay detected virions from two GII.4 norovirus clusters, which included the current dominant strain and a novel variant strain. The Nano-IC method had a sensitivity of 80% and specificity of 86% for outbreak specimens. Norovirus virus-like particles (VLPs) representing four genotypes (GII.4, GII.10, GII.12, and GII.17) could be detected by this method, demonstrating the potential in clinical screening. However, further modifications to the Nano-IC method are needed in order to improve this sensitivity, which may be achieved by the addition of other broadly reactive Nanobodies to the system. <b>IMPORTANCE</b> We previously identified a Nanobody (termed Nano-85) that bound to a highly conserved region on the norovirus capsid. In this study, the Nanobody was biotinylated and gold conjugated for a lateral flow immunoassay (termed Nano-IC). We showed that the Nano-IC assay was capable of detecting at least four antigenically distinct GII genotypes, including the newly emerging GII.17. In the clinical setting, the Nano-IC assay had sensitivities equivalent to other commercially available lateral flow systems. The Nano-IC method was capable of producing results in ~5 min, which makes this method useful in settings that require rapid diagnosis, such as cruise ship outbreaks and elder care facilities. The Nano-IC assay has several advantages over antibody-based IC methods: for example, Nanobodies can be readily produced in large quantities, they are generally more stable than conventional antibodies, and the Nanobody binding sites can be easily obtained by X-ray crystallography.
Molecular cloning and overexpression of DGA1, an acyl-CoA-dependent diacylglycerol acyltransferase, in the oleaginous yeast Rhodosporidiobolus fluvialis DMKU-RK253 (2017)

Triacylglycerol (TAG) is a major component of lipid storage in yeast. The acyl CoA: diacylgycerol acyltransferase (DGAT) that catalyzes the final and rate-limiting step in the production of TAG is rather interesting. Consequently, cloning and analysis of the gene-encoding TAG synthase, diacylglycerol acyltransferase gene (DGA1), of the oleaginous yeast Rhodosporidiobolus fluvialis DMKU-RK253 were undertaken. Analysis of the deduced amino acid sequence of DGA1 from R. fluvialis DMKU-RK253 (RfDGA1) showed similarity with the acyl-CoA:diacylglycerol acyltransferase 2 (DGAT2) from other organisms. The cDNA of RfDGA1 was cloned into the yeast expression vector pYES2 and heterologously overexpressed in Saccharomyces cerevisiae. One of the transformants showed a 1.6-fold increase in lipid content compared with the wild-type strain harbouring the pYES2 empty vector. Furthermore, DGA1 overexpression in R. fluvialis DMKU-RK253 resulted in a 2.5-fold increase in lipid content when compared with the wild-type strain, and no significant differences in fatty acid composition were observed between RfDGA1-overexpressed and wild-type strains. Taken together, our results supported our hypothesis that the RfDGA1 is a genetic factor that can be used for the development of a strain with improved lipid accumulation capabilities.