gebhart/patrepeval huggingface dataset:
Efficient Synthesis of O-Linked Glycopeptide by a Transglycosylation Using Endo α-N-Acetylgalactosaminidase from Streptomyces sp. (2001)

Gal beta-(1-->3)-GalNAc-linked hexapeptide was synthesized by a transglycosylation using Gal beta-(1-->3)-GalNAc beta-pNP as a donor and a serine-containing hexapeptide as an acceptor using endo GalNAc-ase from Streptomyces sp.. The Gal beta-(1-->3)-GalNAc residue was transferred to the hydroxyl group of the serine residue of the peptide. The total yield of the glycopeptide via this process was better than that of the chemoenzymatic method. This process was confirmed to be a versatile method for the synthesis of O-linked glycopeptides.
The new vascular disrupting agent combretastatin-A1-disodium-phosphate (OXi4503) enhances tumour response to mild hyperthermia and thermoradiosensitization (2007)

OXi4503 is a highly potent VDA, which is capable of significantly enhancing the anti-cancer effect of mild hyperthermia. Mild temperature thermoradiosensitization was also enhanced.
Individualized HRTFs from few measurements: a statistical learning approach (2006)

Virtual auditory space (VAS) refers to the synthesis and simulation of spatial hearing using earphones and/or a speaker system. High-fidelity VAS requires the use of individualized head-related transfer functions (HRTFs) which describe the acoustic filtering properties of the listener's external auditory periphery. HRTFs serve the increasingly dominant role of implementation 3-D audio systems, which have been realized in some commercial applications. However, the cost of a 3-D audio system cannot be brought down because the efficiency of computation, the size of memory, and the synthesis of unmeasured HRTFs remain to be made better. Because HRTFs are unique for each user depending on his morphology, the economically realist synthesis of individualized HRTFs has to rely on some measurements. This paper presents a way to reduce the cost of a 3-D audio system using a statistical modeling which allows to use only few measurements for each user.
Postsynthetic Modifications of Iron-Carboxylate Nanoscale Metal−Organic Frameworks for Imaging and Drug Delivery (2009)

Fe(III)-carboxylate nanoscale metal-organic frameworks (NMOFs) with the MIL-101 structure were synthesized using a solvothermal technique with microwave heating. The approximately 200 nm particles were characterized using a variety of methods, including SEM, PXRD, nitrogen adsorption measurements, TGA, and EDX. By replacing a percentage of the bridging ligand (terephthalic acid) with 2-amino terephthalic acid, amine groups were incorporated into the framework to provide sites for covalent attachment of biologically relevant cargoes while still maintaining the MIL-101 structure. In proof-of-concept experiments, an optical contrast agent (a BODIPY dye) and an ethoxysuccinato-cisplatin anticancer prodrug were successfully incorporated into the Fe(III)-carboxylate NMOFs via postsynthetic modifications of the as-synthesized particles. These cargoes are released upon the degradation of the NMOF frameworks, and the rate of cargo release was controlled by coating the NMOF particles with a silica shell. Potential utility of the new NMOF-based nanodelivery vehicles for optical imaging and anticancer therapy was demonstrated in vitro using HT-29 human colon adenocarcinoma cells.
Transmission de la clause compromissoire : accessoires en cascade.. (2008)

International audience
Up-regulation of cochlear aquaporin-3 mRNA expression after intra-endolymphatic sac application of dexamethasone (2003)

The final aim of the present study is to see if the endolymphatic sac is really available as a drug delivery system to have effect on the inner ear organs. In the present study, we examined effects of a single insertion of dexamethasone into the rat unilateral endolymphatic sac on mRNA expression of the inner ear aquaporin (AQP) family, transmembrane water transporters and putative endolymphatic fluid modulators, by means of real-time quantitative PCR. Only AQP-3 mRNA expression in the ipsilateral cochlea was significantly up-regulated in comparison with controls and the up-regulation was demonstrated both in dose-dependent and time-dependent manners. These findings suggest that the intra-endolymphatic sac steroids could make regulatory effects on the inner ear AQP-3 expression via vestibular aqueduct and modulate the homeostasis of endolymphatic fluids, encouraging the possibility that the endolymphatic sac could be a therapeutic window for the inner ear disease.
Synthesis of L‐glutamine‐S‐14C, L‐glutamic acid‐5‐14C, and L‐ornithine‐5‐14C (1970)

Abstract On alkylation of K 14 CN with the methyl ester of L‐α‐benzyl‐oxycarbonylamino‐γ‐bromobutyric acid, the methyl ester of L‐α‐benzyloxycarbonylamino‐γ‐cyano‐ 14 C‐butyric acid (II) was obtained The latter was submitted to mild alkaline hydrolysis to yield the free nitrilo acid III which on treatment with hydrogen bromide solution in acetic acid gave L‐glutamine‐5‐ 14 C in one reaction step. L‐Ornithine‐5‐ 14 C was prepared by catalytic hydrogenation of the nitrilo ester II, and L‐glutamic‐5‐ 14 C acid was obtained on acid hydrolysis of the same compound (II). The activated ester (2, 4, 5‐trichlorophenyl ester) of acid III may serve as a suitable intermediate for the preparation of glutamine or ornithine peptides. All prepared substances were optically active L‐forms.
Receptor-directed contrast agents for MR imaging: preclinical evaluation with affinity assays. (1992)

In this study, the target-specific behavior of magnetic resonance (MR) imaging contrast agents directed at human hepatic asialoglycoprotein (ASG) receptors was evaluated in vitro with use of two novel assays: relaxation time measurements of incubated human cell membrane solutions and iron staining of biopsy samples. Specific uptake of ASG receptor-directed agents was demonstrated in human samples of normal liver tissue, areas of hepatitis, regenerating nodules, areas of focal nodular hyperplasia, and hepatic adenomas. A conventional iron oxide preparation not directed at ASG receptors failed to demonstrate specific uptake in these tissues. Attachment of the ASG receptor-directed agents was competitively blocked with a receptor agonist (D(+)-galactose) in these tissues. No attachment of conventional or receptor agents was seen in areas of hepatocellular carcinoma, cholangiocarcinoma, or liver metastases. The studies indicate that in vitro receptor assays are useful in predicting the affinity of new receptor-directed MR imaging contrast agents in human tissue prior to clinical trials.
Dataflow analysis of branch mispredictions and its application to early resolution of branch outcomes (1998)

The goal of this study is twofold: to analyze in detail the nature of conditional branch mispredictions in correlation based branch predictors, and, based on this analysis, to reduce the impact of branch mispredictions on processor performance by decreasing the branch resolution delay instead of improving the branch prediction accuracy. We classify conditional branches with the highest number of mispredictions according to the nature of their branch condition analytical expression. Based on these expressions, we can analyze and even precisely explain the origin of mispredictions in many cases. Moreover we find that many such branches belong to small sets of blocks inside loops, and within such sets we find that some of the branch expressions have regularity properties. We show how to exploit this regularity property by anticipating the branch outcome, where anticipation is a combination of value prediction and normal dataflow execution. We investigate a hardware mechanism to implement the concept of branch outcome anticipation. This mechanism relies on the separate execution of the normal program flow and a branch flow, which is a subset of the program flow corresponding to copies of the instructions needed to compute branch outcomes. The branch flow uses the regularity properties of branch condition expressions to get ahead of the normal program flow whenever possible. Currently, the mechanism can only target a subset of the conditional branches, but with these branches we experimentally show that the anticipation mechanism successfully reduces the average branch misprediction latency by 60%.
Limitations on Mass Separation by the Weakly Ionized Plasma Centrifuge (1980)

bstract A In weakly ionized argon and xenon rotating plasmas the rotational velocity and the temperature and pressure distribution have been measured. The stationary discharge is generated by two opposed cathode-anode configurations. The arc current of 100 A is drawn across an axial magnetic field up to 0.26 T. The filling pressure ijs varied between 1 and 10 torr. The rotational velocity is found to be proportional to the discharge current and the magnetic field and inversely proportional to the viscosity of the neutral gas. The rotational kinetic energies of the particles in the argon and xenon discharge are about equal. Because the temperature of the argon discharge is lower than that of the xenon discharge, the pressure rise in radial direction due to centrifugal forces is steeper for the former. A theoretical analysis taking into account viscous dissipation as the only heating mechanism yields a heavy particle temperature T which imposes an upper limit to the ratio X =½m υ θ 2 /kT of order unity. The maximum attainable separation factor α is therefore limited in these types of centrifuges. Experimentally, in the parameter region studied, X is found not to exceed a value 0.4 in argon discharges and 0.2 in xenon discharges. A rough estimate shows that besides viscous dissipation other heating mechanisms are also important. Ohmic heating, for instance, is at least a factor 6 larger than the viscous dissipation.
Efficient Updates for Web-Scale Indexes over the Cloud (2012)

In this paper, we present a distributed system which enables fast and frequent updates on web-scale Inverted Indexes. The proposed update technique allows incremental processing of new or modified data and minimizes the changes required to the index, significantly reducing the update time which is now independent of the existing index size. By utilizing Hadoop MapReduce, for parallelizing the update operations, and HBase, for distributing the Inverted Index, we create a high-performance, fully distributed index creation and update system. To the best of our knowledge, this is the first open source system that creates, updates and serves large-scale indexes in a distributed fashion. Experiments with over 23 million Wikipedia documents demonstrate the speed and robustness of our implementation: It scales linearly with the size of the updates and the degree of change in the documents and demonstrates a constant update time regardless of the size of the underlying index. Moreover, our approach significantly increases its performance as more computational resources are acquired: It incorporates a 15.4GB update batch to a 64.2GB indexed dataset in about 21 minutes using just 12 commodity nodes, 3.3 times faster compared to using two nodes.
On Code Parameters and Coding Vector Representation for Practical RLNC (2011)

Random Linear Network Coding (RLNC) provides a theoretically efficient method for coding. The drawbacks associated with it are the complexity of the decoding and the overhead resulting from the encoding vector. Increasing the field size and generation length presents a fundamental trade-off between packet-based throughput and operational overhead. On the one hand, decreasing the probability of redundant packets' being transmitted is beneficial for throughput and, consequently, reduces transmission energy. On the other hand, the decoding complexity and amount of header overhead increase with field size and generation length, leading to higher energy consumption. The main findings of this work are bounds for the transmission overhead due to linearly dependent packets. The optimal trade-off is system and topology dependent, as it depends on the cost in energy of performing coding operations versus transmitting data. We show that moderate field sizes are the correct choice when trade-offs are considered. The results show that sparse binary codes perform the best, unless the generation size is very low.
Isolation of Components from the Low-Sulphur Proteins of Wool by Fractional Precipitation (1974)

Abstract The two major components of the low-sulphur S-carboxymethylkerateine fraction from wool (components 7 and 8) have been isolated by methods involving fractional precipitation from n-propanol/water and from 4 M LiBr. The materials obtained in this way are similar in amino acid composition and in gel electrophoresis properties to fractions obtained by column chromatographic techniques and are of at least equal purity. The procedures are relatively quick and can be scaled up.
Evaluation of Location-Specific Predictions by a Detailed Simulation Model of Aedes aegypti Populations (2011)

This model can provide a faithful description of Ae. aegypti populations, through a process of location-specific customization that is contingent on the amount of data available from field collections. We discuss limitations presented by some specific components of the model such as the description of food dynamics and challenges that these limitations bring to model evaluation.
Addressing the Numbers Problem in Directed Evolution (2008)

Our previous contribution to increasing the efficiency of directed evolution is iterative saturation mutagenesis (ISM) as a systematic means of generating focused libraries for the control of substrate acceptance, enantioselectivity, or thermostability of enzymes. We have now introduced a crucial element to knowledge-guided targeted mutagenesis in general that helps to solve the numbers problem in directed evolution. We show that the choice of the amino acid (aa) alphabet, as specified by the utilized codon degeneracy, provides the experimenter with a powerful tool in designing "smarter" randomized libraries that require considerably less screening effort. A systematic comparison of two different codon degeneracies was made by examining the relative quality of the identically sized enzyme libraries in relation to the degree of oversampling required in the screening process. The specific example in our case study concerns the conventional NNK codon degeneracy (32 codons/20 aa) versus NDT (12 codons/12 aa). The model reaction is the hydrolytic kinetic resolution of a chiral trans-disubstituted epoxide, catalyzed by the epoxide hydrolase from Aspergillus niger. The NDT library proves to be of much higher quality, as measured by the dramatically higher frequency of positive variants and by the magnitude of catalyst improvement (enhanced rate and enantioselectivity). We provide a statistical analysis that constitutes a useful guide for the optimal design and generation of "smarter" focused libraries. This type of approach accelerates the process of laboratory evolution considerably and can be expected to be broadly applicable when engineering functional proteins in general.
Ghost: a human body part labeling system using silhouettes (2002)

Ghost is a real time system for estimating human body posture and detecting body parts in monochromatic imagery. It constructs a silhouette based body model to determine the location of the body parts while people are in generic postures. It combines hierarchical body pose estimation, a convex hull analysis of the silhouette, and a partial mapping from the body parts to the silhouette segments using a distance transform method that does not violate the topology of the human body. Experimental results demonstrate robustness and real-time performance of the proposed algorithm.
Tunable Linear Thermal Expansion Coefficient of Amorphous Zirconium Tungstate (2006)

Zirconium tungstate (α‐ZrW 2 O 8 ) exhibits isotropic negative thermal expansion over a wide range of temperatures. Under high pressure it transforms to a metastable amorphous phase with positive thermal expansion coefficient. α‐ZrW 2 O 8 can be fully recovered by annealing the amorphous phase at temperatures slightly above 600°C, at room pressure. In this work, we describe the dependency of the linear thermal expansion coefficient of amorphous ZrW 2 O 8 with the annealing temperature, showing that it can be continuously tuned, in two stages, from about 7.5° to −9°C −1 . These two stages are related to the relaxation of the amorphous phase and the onset of recrystallization, respectively.
An In Vivo Mobile Robot for Surgical Vision and Task Assistance (2006)

Current laparoscopic surgical robots are expensive, bulky, and fundamentally constrained by the small entry incisions. A potential new approach to minimally invasive surgery is to place the robot completely within the patient. We have developed several such miniature mobile robots and conducted tests during animal surgeries. These robots can provide vision and task assistance to the surgeon without being constrained by the entry port. We used a mobile biopsy and camera robot to sample hepatic tissue from an anesthetized porcine animal model. This successful test demonstrated the capability of performing a single port laparoscopic biopsy procedure. In the future, a family of such robots could be remotely controlled and used to perform surgical procedures without the need for conventional laparoscopic tools.
Lenvatinib versus Placebo in Radioiodine-Refractory Thyroid Cancer (2015)

Lenvatinib, as compared with placebo, was associated with significant improvements in progression-free survival and the response rate among patients with iodine-131-refractory thyroid cancer. Patients who received lenvatinib had more adverse effects. (Funded by Eisai; SELECT ClinicalTrials.gov number, NCT01321554.).
A genetic transformation system for Streptococcus pyogenes. (1991)

An efficient protoplast transformation system for Streptococcus pyogenes has been developed. Efficiencies of up to 7.1 x 10(6) transformants/micrograms DNA were achieved, with transformants recovered on selective media in 24-48 h. The system was characterized as to optimal protoplasting conditions, effective facilitators, dependency on concentration of transforming DNA, plasmid copy number in transformants and stability of transformants. Three isolates of S. pyogenes were used as recipients, and four plasmids were used as the transforming DNA. Growth of S. pyogenes in glycine followed by lysozyme treatment was necessary for optimal protoplast formation. The exact concentrations of these protoplasting agents which were used varied with each isolate tested. Both polyethylene glycol and dextran sulphate were efficient facilitators of transformation, at final concentrations of 10%. An inverse relationship between DNA concentration and efficiency of transformation was shown. The copy number of the AC-1 plasmid in the transformants was shown to be equivalent to that of the wild type S. pyogenes (AC-1) (one or two copies per chromosomal equivalent). Approximately 50% of the AC-1 transformants were stable after one passage on non-selective media, and 100% of those that retained the plasmid were stable for an additional twenty generations. Erythromycin resistance encoded on the AC-1 plasmid was inducible, and transformants with a constitutive mutant of the AC-1 plasmid were detected by growth on selective media. This plasmid may prove useful as a vector as it is readily transformed, expressed, and contains at least three unique restriction sites which could serve as insertion points for cloned DNA.
DNA Methyltransferase-1 Inhibitors as Epigenetic Therapy for Cancer (2013)

DNA methylation is an epigenetic modification involved in gene expression regulation. In cancer, the DNA methylation pattern becomes aberrant, causing an array of tumor suppressor genes to undergo promoter hypermethylation and become transcriptionally silent. Reexpression of methylation silenced tumor suppressor genes by inhibiting the DNA methyltransferases (DNMT1, DNMT3A, and DNMT3B) has emerged as an effective strategy against cancer. The expression of DNA methyltransferase 1 (DNMT1) being high in S-phase of cell cycle makes it a specific target for methylation inhibition in rapidly dividing cells as in cancer. This review discusses nucleoside analogues (azacytidine, decitabine, zebularine, SGI-110, CP-4200), non-nucleoside ihibitors both synthetic (hydralazine, RG108, procaine, procainamide, IM25, disulfiram) and natural compounds (curcumin, genistein, EGCG, resveratrol, equol, parthenolide) which act through different mechanisms to inhibit DNMTs. The issues of bioavailability, toxicity, side effects, hypomethylation resistance and combinatorial therapies have also been highlighted.
Hybrid vigor, fetal overgrowth, and viability of mice derived by nuclear cloning and tetraploid embryo complementation (2001)

To assess whether heterozygosity of the donor cell genome was a general parameter crucial for long-term survival of cloned animals, we tested the ability of embryonic stem (ES) cells with either an inbred or F(1) genetic background to generate cloned mice by nuclear transfer. Most clones derived from five F(1) ES cell lines survived to adulthood. In contrast, clones from three inbred ES cell lines invariably died shortly after birth due to respiratory failure. Comparison of mice derived from nuclear cloning, in which a complete blastocyst is derived from a single ES cell, and tetraploid blastocyst complementation, in which only the inner cell mass is formed from a few injected ES cells, allows us to determine which phenotypes depend on the technique or on the characteristics of the ES cell line. Neonatal lethality also has been reported in mice entirely derived from inbred ES cells that had been injected into tetraploid blastocysts (ES cell-tetraploids). Like inbred clones, ES cell-tetraploid pups derived from inbred ES cell lines died shortly after delivery with signs of respiratory distress. In contrast, most ES cell-tetraploid neonates, derived from six F(1) ES cell lines, developed into fertile adults. Cloned pups obtained from both inbred and F(1) ES cell nuclei frequently displayed increased placental and birth weights whereas ES cell-tetraploid pups were of normal weight. The potency of F(1) ES cells to generate live, fertile adults was not lost after either long-term in vitro culture or serial gene targeting events. We conclude that genetic heterozygosity is a crucial parameter for postnatal survival of mice that are entirely derived from ES cells by either nuclear cloning or tetraploid embryo complementation. In addition, our results demonstrate that tetraploid embryo complementation using F(1) ES cells represents a simple, efficient procedure for deriving animals with complex genetic alterations without the need for a chimeric intermediate.
Depletion of Regulatory T Cells Induces High Numbers of Dendritic Cells and Unmasks a Subset of Anti-Tumour CD8+CD11c+ PD-1lo Effector T Cells (2016)

Natural regulatory T (Treg) cells interfere with multiple functions, which are crucial for the development of strong anti-tumour responses. In a model of 4T1 mammary carcinoma, depletion of CD25+Tregs results in tumour regression in Balb/c mice, but the mechanisms underlying this process are not fully understood. Here, we show that partial Treg depletion leads to the generation of a particular effector CD8 T cell subset expressing CD11c and low level of PD-1 in tumour draining lymph nodes. These cells have the capacity to migrate into the tumour, to kill DCs, and to locally regulate the anti-tumour response. These events are concordant with a substantial increase in CD11b+ resident dendritic cells (DCs) subsets in draining lymph nodes followed by CD8+ DCs. These results indicate that Treg depletion leads to tumour regression by unmasking an increase of DC subsets as a part of a program that optimizes the microenvironment by orchestrating the activation, amplification, and migration of high numbers of fully differentiated CD8+CD11c+PD1lo effector T cells to the tumour sites. They also indicate that a critical pattern of DC subsets correlates with the evolution of the anti-tumour response and provide a template for Treg depletion and DC-based therapy.