gebhart/patrepeval huggingface dataset:
Optimized tuning of TALEN specificity using non-conventional RVDs (2015)

A key feature when designing DNA targeting tools and especially nucleases is specificity. The ability to control and tune this important parameter represents an invaluable advance to the development of such molecular scissors. Here, we identified and characterized new non-conventional RVDs (ncRVDs) that possess novel intrinsic targeting specificity features. We further report a strategy to control TALEN targeting based on the exclusion capacities of ncRVDs (discrimination between different nucleotides). By implementing such ncRVDs, we demonstrated in living cells the possibility to efficiently promote TALEN-mediated processing of a target in the HBB locus and alleviate undesired off-site cleavage. We anticipate that this method can greatly benefit to designer nucleases, especially for therapeutic applications and synthetic biology.
Recurrent 14q32 translocations determine the prognosis of multiple myeloma, especially in patients receiving intensive chemotherapy (2002)

Recently, we have described the biological correlations associated with the main translocations involving the 14q32 chromosomal region, that is, t(14q32), in patients with multiple myeloma (MM). We have now extended the analysis to the prognostic value of these chromosomal rearrangements in 168 consecutive patients with newly diagnosed MM receiving intensive chemotherapy within clinical trials of the Intergroupe Francophone du Myelome (IFM). Patients with t(4;14) displayed a poor outcome (short event-free survival and short overall survival), whereas those with t(11;14) displayed long survival. On the other hand, patients with neither t(4;14) nor t(11;14) presented an intermediate outcome. Importantly, chromosome 13 abnormalities (C13As) significantly influence the prognosis of this latter group. In contrast, C13As affected the outcome of the other patients to a much lesser extent, either because of an almost constant association (in the t(4;14) group) or because of a lack of any significant prognostic impact (in the t(11;14) group; only one event occurred in the 10 patients with t(11;14) and C13As). Considering that t(4;14) and t(11;14) (1) are the only (so far recognized) true, recurrent t(14q32)'s, (2) are linked to specific immunoglobulin isotypes, and (3) display specific outcomes, they represent distinct entities corresponding to a specific oncogenesis and prognosis. These data emphasized the interest in analyzing these two translocations by fluorescence in situ hybridization in prospective therapeutic trials in order to consider these translocations as distinct entities.
Narrow Band Gap Lead Sulfide Hole Transport Layers for Quantum Dot Photovoltaics (2016)

The band structure of colloidal quantum dot (CQD) bilayer heterojunction solar cells is optimized using a combination of ligand modification and QD band gap control. Solar cells with power conversion efficiencies of up to 9.33 ± 0.50% are demonstrated by aligning the absorber and hole transport layers (HTL). Key to achieving high efficiencies is optimizing the relative position of both the valence band and Fermi energy at the CQD bilayer interface. By comparing different band gap CQDs with different ligands, we find that a smaller band gap CQD HTL in combination with a more p-type-inducing CQD ligand is found to enhance hole extraction and hence device performance. We postulate that the efficiency improvements observed are largely due to the synergistic effects of narrower band gap QDs, causing an upshift of valence band position due to 1,2-ethanedithiol (EDT) ligands and a lowering of the Fermi level due to oxidation.
(P(C6H5)3)CpRu+-Catalyzed Deprotection of Allyl Carboxylic Esters (2002)

A new and efficient catalytic method for deprotection of allyl carboxylic esters using a transition metal complex is reported. The reaction proceeds with a high substrate/catalyst ratio and without use of additional nucleophiles, giving the deprotected carboxylic acid in a quantitative yield. A variety of substrates, including the multifunctional amino acids and peptides, are also usable. The new method is more efficient, safe, and operationally simple in comparison to the conventional palladium-catalyzed method.
Incentive Mechanism Considering Variety of User Cost in P2P Content Sharing (2008)

Users in peer-to-peer (P2P) content sharing can share their content by contributing their own resources to one another. However, since there is no incentive for contributing contents or resources to others, users may attempt to obtain content without any contribution. To motivate users to contribute their resources to the service, incentive-rewarding mechanisms have been proposed. On the other hand, emerging wireless technologies, such as IEEE 802.11 wireless local area networks, beyond third generation (B3G) cellular networks and mobile WiMAX, provide high-speed Internet access for wireless users. Using these high-speed wireless access, wireless users can use P2P services and share their content with other wireless users and with fixed users. However, this diversification of access networks makes it difficult to appropriately assign rewards to each user according to their contributions. This is because the cost necessary for contribution is different in different access networks. In this paper, we propose a novel incentive-rewarding mechanism called EMOTIVER that can assign rewards to users appropriately. The proposed mechanism uses an external evaluator and interactive learning agents. We also investigate a way of appropriately controlling rewards based on the system service's quality and managing policy.
P-258 (2012)

Swiss Tropical and Public Health Institute (Swiss TPH), Switzerland Swiss Tropical and Public Health Institute (Swiss TPH), Switzerland Swiss Tropical and Public Health Institute (Swiss TPH), Switzerland, [email protected]
Enhanced Delivery and Antitumor Effect of Doxorubicin Encapsulated in Long-Circulating Liposomes (1994)

Long-circulating liposomes containing amphipathic polyethyleneglycol (PEG) or ganglioside GM1 (GM1) have been tested for their utility as enhanced delivery system of doxorubicin (DXR) in vivo. DXR was entrapped into liposomes by pH gradient method.The long-circulating LUV (200 nm in size) composed of DSPC/CH (1:1, m/m) and either 6 mol% of DSPE-PEG1000 or GM1 entrapped DXR with >95% in trapping efficiency. DXR-long-circulating LUVs were administered to leukemic (LI210) mice via the tail vein at a dose of 5mg DXR/kg. The high blood concentration was kept for long time, and significantly increased survival time was observed as compared with free DXR and DXR-LUV. The data indicated that DXR was slowly released from long-circulating LUV during that stayed in bloodstream for long time. Administration of DXR-long-circulating SUV (100 nm) to the colon 26 bearing mice produced the increased DXR level in tumor compared with bear SUV or free drug did, respectively, and resulted in effective tumor growth retardation and increased survival time. DXR was delivered to tumor by accumulation of SUVs themselves.Long-circulating thermosensitive liposomes (TSL) were prepared from DPPC /DSPC (9:1, m/m) and 3-6 mol% of PEG1000 or GM1. DXR was entrapped with >95% in trapping efficiency. Accumulation of DXR into tumor tissue by local hyperthermia after injection of DXR-long-circulating TSL to colon 26 bearing mice was significantly higher man that of DXR-bare TSL or free DXR, and resulted in effective tumor growth retardation and increased survival time. It was suggested that the entrapped DXR was efficiently released from long-circulating TSL by hyperthermia at the tumor site and entered the tumor tissue by simple diffusion.
Predicting concrete properties using neural networks (NN) with principal component analysis (PCA) technique (2012)

This paper discusses the combined application of two different techniques, Neural Networks (NN) and Principal Component Analysis (PCA), for improved prediction of concrete properties. The combination of these approaches allowed the development of six neural networks models for predicting slump and compressive strength of concrete with mineral additives such as blast furnace slag, fly ash and silica fume. The Back-Propagation Multi-Layer Perceptron (BPMLP) with Bayesian regularization was used in all these models. They are produced to implement the complex nonlinear relationship between the inputs and the output of the network. They are also established through the incorporation of a huge experimental database on concrete organized in the form Mix-Property. Thus, the data comprising the concrete mixtures are much correlated to each others. The PCA is proposed for the compression and the elimination of the correlation between these data. After applying the PCA, the uncorrelated data were used to train the six models. The predictive results of these models were compared with the actual experimental trials. The results showed that the elimination of the correlation between the input parameters using PCA improved the predictive generalisation performance models with smaller architectures and dimensionality reduction. This study showed also that using the developed models for numerical investigations on the parameters affecting the properties of concrete is promising.
CLEAVAGE OF DEHYDROALANINE‐CONTAINING PEPTIDES WITH MERCURIC ACETATE (1981)

The dehydroalanine containing peptides glycyldehydroalanine and t-butyloxy-carbonyl-L-alanyldehydroalanyl-beta-methyl-D, L-aspartic acid methyl ester were synthesized, respectively, from chloroacetamide and pyruvate and from t-butyloxycarbonyl-L-alanyl-S-methyl-L-cysteinyl-beta-methyl-D, L-aspartic acid methyl ester. They were reacted with mercuric acetate in water, 50% methanol and dimethylformamide at 25 degrees and at 80 degrees for various time periods. Reaction proceeded to yield an amino acid amide from the N-terminal side of the unsaturated residue and pyruvate from the C-terminal side. Yields of amino acid amides were 76% for the dipeptide and 40% for the tripeptide. The applicability of the neutral reaction conditions employed to the cleavage of glycoproteins containing both O- and N-glycosidically-linked carbohydrate chains following beta-elimination of the serine and threonine linked oligosaccharides is pointed out.
What can short-pulse pump-probe spectroscopy tell us about Franck-Condon dynamics? (1999)

We examine the signal from pump-probe spectroscopy of a model system—nonrotating I2—at short time delays and compare signals calculated without approximation (a full quantum calculation), with a semiclassical Franck-Condon approximation, and with a classical simulation of the nuclear wave packet. In order to assess the complications of simulation and interpretation when the probe window lies in the spectroscopically and dynamically important Franck-Condon region, we concentrate on a case where pump and probe resonances are at the same internuclear distance. We find that the common practice of ignoring the pump-truncation effects of pulse overlap leads to an overestimate of the signal at short times. Moreover, both classical simulations and semiclassical Franck-Condon treatments can deviate significantly in form from the actual signal even with proper treatment of pulse overlap. The sources of these deviations can be seen in the evolution of the excited-state nuclear distributions calculated classically and under the semiclassical Franck-Condon approximation. Specifically, the differences in evolution of the classical and full quantum excited-state nuclear distributions are due to differing initial momentum distributions. We introduce an efficient method for calculating the pump-probe signal that takes advantage of the brevity of ultrashort pulses and can include pulse characteristics such as chirp. This short-pulse expansion method aids in the proper treatment of pulse-overlap and nonzero pulse duration and promises to simplify the incorporation of relaxation processes.
Enhanced expression of prostate-specific membrane antigen gene in prostate cancer as revealed by in situ hybridization. (1997)

Recently, the cDNA encoding a novel candidate for prostate cancer-specific antigen, named prostate-specific membrane antigen (PSM), was cloned from the LNCaP prostate cancer cell line (R. S. Israeli, C. T. Powell, W. R. Fair, and W. D. W. Heston, Cancer Res., 53: 227-230,1993). More recently, they also identified an alternatively spliced variant of PSM in normal prostate tissues (S. L. Su, I-P. Huang, W. R. Fair, C. T. Powell, and W. D. W. Heston, Cancer Res., 55: 1441-1443, 1995). The cDNA of this variant, named PSM', lacks 266 nucleotides present in PSM cDNA, so the transcripts derived from this particular nucleotide sequence can be regarded as PSM-specific transcripts. In this study, we investigated the expression of PSM-specific transcripts in 15 specimens of prostate cancer obtained by needle biopsy using in situ hybridization with a newly developed RNA probe. PSM-specific transcripts were detected in most of the carcinoma cells in all of the specimens examined, and the level of expression was higher in carcinoma cells from hormone-refractory patients than in the cells of those who showed a good response to hormonal therapy. In addition, increased expression of PSM-specific transcripts was also associated with an increased Gleason score. In the normal prostate, on the other hand, PSM-specific transcripts were limited to the basal cells of the prostate glands. These results clearly show that expression of PSM-specific transcripts is closely associated with malignant transformation of the prostate; thus, in situ hybridization for detection of the transcripts is useful for the diagnosis of prostate cancer.
Integrating intelligent networks in general network planning (2002)

This paper addresses aspects of intelligent network (IN) service deployment, particularly its consequences for public switched telephone network (PSTN) and signalling (SS7) network planning. Dimensioning of the general network in an IN environment, IN special links and IN nodes is considered. Facilities and capacity in both the PSTN and the SS7 network are involved in IN service provisioning. If there is a lack of resources, congestion arises and the quality of service can be degraded for the new services and for already existing services. Since new IN services are supposed to be implemented with a short delay, the effects of this traffic in the network infrastructure and performances are examined for network management and short term plans.
On the use of microjets to suppress turbulence in a Mach 0.9 axisymmetric jet (2003)

We have experimentally studied the effect of microjets on the flow field of a Mach 0.9 round jet. Planar and three-dimensional velocity field measurements using particle image velocimetry show a significant reduction in the near-field turbulent intensities with the activation of microjets. The axial and normal turbulence intensities are reduced by about 15% and 20%, respectively, and an even larger effect is found on the peak values of the turbulent shear stress with a reduction of up to 40%. The required mass flow rate of the microjets was about 1% of the primary jet mass flux. It appears that the microjets influence the mean velocity profiles such that the peak normalized vorticity in the shear layer is significantly reduced, thus inducing an overall stabilizing effect. Therefore, we seem to have exploited the fact that an alteration in the instability characteristics of the initial shear-layer can influence the whole jet exhaust including its noise field. We have found a reduction of about 2 dB in the near-field overall sound pressure level in the lateral direction with the use of microjets. This observation is qualitatively consistent with the measured reduced turbulence intensities.
Prenatal diagnosis of congenital adrenal hyperplasia by direct detection of mutations in the steroid 21‐hydroxylase gene (1993)

First trimester prenatal diagnosis of steroid 21-hydroxylase deficiency was achieved in three pregnancies with a strategy based on direct detection of gene mutations.
Practical memory leak detection using guarded value-flow analysis (2007)

This paper presents a practical inter-procedural analysis algorithm for detecting memory leaks in C programs. Our algorithm tracks the flow of values from allocation points to deallocation points using a sparse representation of the program consisting of a value flow graph that captures def-use relations and value flows via program assignments. Edges in the graph are annotated with guards that describe branch conditions in the program. The memory leak analysis is reduced to a reachability problem over the guarded value flowgraph. Our implemented tool has been effective at detecting more than 60 memory leaks in the SPEC2000 benchmarks and in two open-source applications, bash and sshd, while keeping the false positive rate below 20%. The sparse program representation makes the tool efficient in practice, and allows it to report concise error messages.
Diagnostic Tests: The diagnosis of recurrent deep venous thrombosis (2007)

Duplex ultrasound is the preferred investigation for the diagnosis of initial and recurrent deep venous thrombosis. The contralateral leg should be scanned when thrombosis is diagnosed as it is bilateral in 30% of cases. At the completion of anticoagulant therapy a venous duplex scan should be performed to establish a new baseline. Recurrent deep venous thrombosis can subsequently be diagnosed if there is a 5 cm increase in the extent of residual thrombus or an increase in the compressed thrombus diameter of more than 2 mm. If there is any doubt about the presence of a recurrent thrombosis serial ultrasound should be used.
Dendritic Cell Survival and Maturation Are Regulated by Different Signaling Pathways (1998)

Although dendritic cell (DC) activation is a critical event for the induction of immune responses, the signaling pathways involved in this process have not been characterized. In this report, we show that DC activation induced by lipopolysaccharide (LPS) can be separated into two distinct processes: first, maturation, leading to upregulation of MHC and costimulatory molecules, and second, rescue from immediate apoptosis after withdrawal of growth factors (survival). Using a DC culture system that allowed us to propagate immature growth factor-dependent DCs, we have investigated the signaling pathways activated by LPS. We found that LPS induced nuclear translocation of the nuclear factor (NF)-kappaB transcription factor. Inhibition of NF-kappaB activation blocked maturation of DCs in terms of upregulation of major histocompatibility complex and costimulatory molecules. In addition, we found that LPS activated the extracellular signal-regulated kinase (ERK), and that specific inhibition of MEK1, the kinase which activates ERK, abrogated the ability of LPS to prevent apoptosis but did not inhibit DC maturation or NF-kappaB nuclear translocation. These results indicate that ERK and NF-kappaB regulate different aspects of LPS-induced DC activation: ERK regulates DC survival whereas NF-kappaB is responsible for DC maturation.
Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions (2002)

Basidiomycetous yeasts in the Urediniomycetes and Hymenomycetes were examined by sequence analysis in two ribosomal DNA regions: the D1/D2 variable domains at the 5' end of the large subunit rRNA gene (D1/D2) and the internal transcribed spacers (ITS) 1 and 2. Four major lineages were recognized in each class: Microbotryum, Sporidiobolus, Erythrobasidium and Agaricostilbum in the Urediniomycetes; Tremellales, Trichosporonales, Filobasidiales and Cystofilobasidiales in the Hymenomycetes. Bootstrap support for many of the clades within those lineages is weak; however, phylogenetic analysis provides a focal point for in-depth study of biological relationships. Combined sequence analysis of the D1/D2 and ITS regions is recommended for species identification, while species definition requires classical biological information such as life cycles and phenotypic characterization.
Growth of Aluminum Nitride Films on Silicon by Electron-Cyclotron-Resonance-Assisted Molecular Beam Epitaxy (1992)

Aluminum nitride thin films have been prepared on silicon substrates by electron-cyclotron-resonance plasma-assisted molecular beam epitaxy (ECR-MBE). Epitaxial AlN films have been obtained by Al evaporation and 250 eV nitrogen ion irradiation on a clean Si surface at 700°C. AlN films with two kinds of crystal orientations were grown epitaxially on Si(111). The dominant one is AlN (0001)//Si(111); AlN[011̄0]//Si[112̄] and the another one is AlN(011̄0)//Si(111); AlN[0001]//Si[112̄].
In Vivo Immune Evasion Mediated by the Herpes Simplex Virus Type 1 Immunoglobulin G Fc Receptor (1998)

Herpes simplex virus (HSV) glycoproteins gE and gI form an immunoglobulin G (IgG) Fc receptor (FcgammaR) that binds the Fc domain of human anti-HSV IgG and inhibits Fc-mediated immune functions in vitro. gE or gI deletion mutant viruses are avirulent, probably because gE and gI are also involved in cell-to-cell spread. In an effort to modify FcgammaR activity without affecting other gE functions, we constructed a mutant virus, NS-gE339, that has four amino acids inserted into gE within the domain homologous to mammalian IgG FcgammaRs. NS-gE339 expresses gE and gI, is FcgammaR-, and does not participate in antibody bipolar bridging since it does not block activities mediated by the Fc domain of anti-HSV IgG. In vivo studies were performed with mice because the HSV-1 FcgammaR does not bind murine IgG; therefore, the absence of an FcgammaR should not affect virulence in mice. NS-gE339 causes disease at the skin inoculation site comparably to wild-type and rescued viruses, indicating that the FcgammaR- mutant virus is pathogenic in animals. Mice were passively immunized with human anti-HSV IgG and then infected with mutant or wild-type virus. We postulated that the HSV-1 FcgammaR should protect wild-type virus from antibody attack. Human anti-HSV IgG greatly reduced viral titers and disease severity in NS-gE339-infected animals while having little effect on wild-type or rescued virus. We conclude that the HSV-1 FcgammaR enables the virus to evade antibody attack in vivo, which likely explains why antibodies are relatively ineffective against HSV infection.
An Antigen Detected Frequently in Human Sera With Elevated Levels of Alanine Aminotransferase: A Potential Marker For Non-A, Non-B Hepatitis (1980)

SUMMARY In a search for additional antigens associated with virus-induced human liver disease a radioimmunoassay (RIA) was developed using IgG from sera of a multiply transfused person. Polystyrene beads coated with IgG F(ab)′2 fragments, dinitrophenylated F(ab)′2 fragments and 125I-labelled anti-2,4-dinitrophenyl antibodies (Neurath &amp; Strick, 1979) were used in the RIA. An apparently new antigen or the corresponding antibodies were detected in 155 serum specimens from 35/37 (94%) individuals who developed non-A, non-B hepatitis. The antigen was also present in hepatitis B surface antigen-negative sera of blood donors with normal (13.2%) and elevated levels of alanine aminotransferase (34%). The antigen has an approximate mol. wt. of 45000, a buoyant density of 1.23 g/ml and an isoelectric point of 7.