gebhart/patrepeval huggingface dataset:
A Novel Organotellurium Compound (RT-01) as a New Antileishmanial Agent (2009)

Leishmaniasis is a neglected disease and endemic in developing countries. A lack of adequate and definitive chemotherapeutic agents to fight against this infection has led to the investigation of numerous compounds. The aim of this study was to investigate the effect of RT-01, an organotellurane compound presenting biological activities, in 2 experimental systems against Leishmania amazonensis. The in vitro system consisted of promastigotes and amastigotes forms of the parasite, and the in vivo system consisted of L. amazonensis infected BALB/c mice, an extremely susceptible mouse strain. The compound proved to be toxic against promastigotes and amastigotes. The study also showed that treatment with RT-01 produces an effect similar to that treatment with the reference antimonial drug, Glucantime, in L. amazonensis infected mice. The best results were obtained following RT-01 intralesional administration (720 microg/kg/day); mice showed significant delay in the development of cutaneous lesions and decreased numbers of parasites obtained from the lesions. Significant differences in tissue pathology consisted mainly of no expressive accumulation of inflammatory cells and well-preserved structures in the skin tissue of RT-01-treated mice compared with expressive infiltration of infected cells replacing the skin tissue in lesions of untreated mice. These findings highlight the fact that the apparent potency of organotellurane compounds, together with their relatively simple structure, may represent a new avenue for the development of novel drugs to combat parasitic diseases.
Cancer hyperthermia using magnetic nanoparticles (2011)

Magnetic-nanoparticle-mediated intracellular hyperthermia has the potential to achieve localized tumor heating without any side effects. The technique consists of targeting magnetic nanoparticles to tumor tissue followed by application of an external alternating magnetic field that induces heat through Néel relaxation loss of the magnetic nanoparticles. The temperature in tumor tissue is increased to above 43°C, which causes necrosis of cancer cells, but does not damage surrounding normal tissue. Among magnetic nanoparticles available, magnetite has been extensively studied. Recent years have seen remarkable advances in magnetite-nanoparticle-mediated hyperthermia; both functional magnetite nanoparticles and alternating-magnetic-field generators have been developed. In addition to the expected tumor cell death, hyperthermia treatment has also induced unexpected biological responses, such as tumor-specific immune responses as a result of heat-shock protein expression. These results suggest that hyperthermia is able to kill not only local tumors exposed to heat treatment, but also tumors at distant sites, including metastatic cancer cells. Currently, several research centers have begun clinical trials with promising results, suggesting that the time may have come for clinical applications. This review describes recent advances in magnetite nanoparticle-mediated hyperthermia.
Modeling of a constant Q; methodology and algorithm for an efficient and optimally inexpensive viscoelastic technique (1995)

Abstract Linear anelastic phenomena in wave propagation problems can be well modeled through a viscoelastic mechanical model consisting of standard linear solids. In this paper we present a method for modeling of constant Q as a function of frequency based on an explicit closed formula for calculation of the parameter fields. Several standard linear solids connected in parallel can be tuned through a single parameter to yield an excellent constant Q approximation. The proposed method enables substantial savings in computations and memory requirements. Experiments show that the new method also yields higher accuracy in the modeling of Q than, e.g., the Pade approximant method.
The Classification and Age Determination of Ballpoint Pen Inks in Questioned Documents (2004)

The aim of this study was to investigate questioned documents written with blue or black ballpoint pen on paper by nondestructive technique. In this work, 21 blue and 22 black ballpoint pen inks which were purchased on different brands were analyzed by using Microspectrophotometry (MSP). The reflectance spectra were obtained from these ink samples and their shapes and the wavelength of the maximum intensity were compared. In the blue and black ballpoint pen inks, the discriminating powers (DP) were 0.85 and 0.61, respectively. The changes of the reflectance intensity at their wavelength of maximum intensity and their shapes appeared according to the exposure time to sunshine in a laboratory, especially in the blue ballpoint pen inks. Therefore it is possible to distinguish ink entries on the same paper with the relative age in case of questioned letters written with blue ballpoint pen.
Real-time depth reconstruction from stereo sequences (2005)

We propose a fast depth reconstruction algorithm for stereo sequences using camera geometry and disparity estimation. In disparity estimation process, we calculate dense background disparity fields in an initialization step so that only disparities of moving object regions are updated in the main process using real-time segmentation and hierarchical disparity estimation techniques. The estimated dense disparity fields are converted into depth information by camera geometry. Experimental results show that the proposed algorithm provides accurate depth information with an average processing speed of 15 frames/sec for 320x240 stereo sequences on a common PC. We also verified the performance of the proposed algorithm by applying it to real applications.
Hereditary spherocytosis in zebrafish<i>riesling</i>illustrates evolution of erythroid β-spectrin structure, and function in red cell morphogenesis and membrane stability (2000)

Spectrins are key cytoskeleton proteins with roles in membrane integrity, cell morphology, organelle transport and cell polarity of varied cell types during development. Defects in erythroid spectrins in humans result in congenital hemolytic anemias with altered red cell morphology. Although well characterized in mammals and invertebrates, analysis of the structure and function of non-mammalian vertebrate spectrins has been lacking. The zebrafish riesling (ris) suffers from profound anemia, where the developing red cells fail to assume terminally differentiated erythroid morphology. Using comparative genomics, erythroid beta-spectrin (sptb) was identified as the gene mutated in ris. Zebrafish Sptb shares 62.3% overall identity with the human ortholog and phylogenetic comparisons suggest intragenic duplication and divergence during evolution. Unlike the human and murine orthologs, the pleckstrin homology domain of zebrafish Sptb is not removed in red cells by alternative splicing. In addition, apoptosis and abnormal microtubule marginal band aggregation contribute to hemolysis of mutant erythrocytes, which are features not present in mammalian red cells with sptb defects. This study presents the first genetic characterization of a non-mammalian vertebrate sptb and demonstrates novel features of red cell hemolysis in non-mammalian red cells. Further, we propose that the distinct mammalian erythroid morphology may have evolved from specific modifications of Sptb structure and function.
Dynamic temperature selection for parallel tempering in Markov chain Monte Carlo simulations (2015)

Modern problems in astronomical Bayesian inference require efficient methods for sampling from complex, high-dimensional, often multimodal probability distributions. Most popular methods, such as MCMC sampling, perform poorly on strongly multimodal probability distributions, rarely jumping between modes or settling on just one mode without finding others. Parallel tempering addresses this problem by sampling simultaneously with separate Markov chains from tempered versions of the target distribution with reduced contrast levels. Gaps between modes can be traversed at higher temperatures, while individual modes can be efficiently explored at lower temperatures. In this paper, we investigate how one might choose the ladder of temperatures to achieve more efficient sampling, as measured by the autocorrelation time of the sampler. In particular, we present a simple, easily implemented algorithm for dynamically adapting the temperature configuration of a sampler while sampling. This algorithm dynamically adjusts the temperature spacing to achieve a uniform rate of exchanges between chains at neighbouring temperatures. We compare the algorithm to conventional geometric temperature configurations on a number of test distributions and on an astrophysical inference problem, reporting efficiency gains by a factor of 1.2–2.5 over a well-chosen geometric temperature configuration and by a factor of 1.5–5 over a poorly chosen configuration. On all of these problems, a sampler using the dynamical adaptations to achieve uniform acceptance ratios between neighbouring chains outperforms one that does not.
Red blood cell transfusion need at diagnosis adversely affects survival in primary myelofibrosis—increased serum ferritin or transfusion load does not (2009)

Serum ferritin level at diagnosis was available in 185 patients with primary myelofibrosis (PMF); twenty-two (12%) patients had serum ferritin >1,000 ng/mL and 32 (17%) were red blood cell (RBC) transfusion-dependent. As expected, RBC transfusion need and increased serum ferritin displayed strong correlation (P < 0.0001); in addition, the latter but not the former correlated with advanced age (P < 0.0001). During median follow-up of 28 months (range 0.5-231), peak serum ferritin levels exceeded 1,000 ng/mL in 41 (22%) patients. On multivariable analysis that included age as a covariate, RBC transfusion need at diagnosis (P < 0.0001), but not increased serum ferritin or transfusion load, predicted shortened survival. The prognostic relevance of RBC transfusion need was independent of the International Prognostic Scoring System and was also illustrated for leukemia-free survival (P = 0.003). In PMF, the presence of a more severe erythropoietic defect, and not iron overload, has additional adverse prognostic value.
Isolation of the progenitor cells of the sympathoadrenal lineage from embryonic sympathetic ganglia with the SA monoclonal antibodies (1991)

Our previous articles in this series described the production of five monoclonal antibodies (SA1-5) that bind to adrenal chromaffin cells and to cells in embryonic sympathetic ganglia and adrenal primordia (Carnahan and Patterson, 1991), and the downregulation of the sympathoadrenal (SA) antigens in vivo as neuronal markers begin to be expressed (Anderson et al., 1991). These results support the hypothesis that sympathetic neurons and adrenal chromaffin cells are derived from a common embryonic progenitor that displays both neuron- and chromaffin cell-specific markers. We have taken advantage of the fact that at least some of the SA antigens are expressed on the cell surface to isolate SA+ cells from embryonic day 14.5 rat superior cervical, sympathetic ganglia by fluorescence-activated cell sorting. This population of cells is significantly enriched in the expression of markers (tyrosine hydroxylase and neurofilament) found in the putative progenitors in situ. Growth in glucocorticoid maintains the expression of the SA antigens in the sorted cells and induces the chromaffin cell marker enzyme phenylethanolamine N-methyl transferase. In contrast, growth of the sorted cells in basic fibroblast growth factor, NGF, and insulin results in the rapid loss of SA 1 expression and the outgrowth of neurites. The ability to manipulate the fate of the SA+ cells in vitro confirms the suggestion from the in vivo observations that the SA+ cells in the ganglia are at least bipotential progenitors, capable of differentiating along the chromaffin or neuronal pathways.
Iron-Aluminium Alloys with Strengthening Carbides and Intermetallic Phases for High-Temperature Applications (2003)

An overview of materials developments of iron aluminium alloys with strengthening precipitate phases is given. The discussion is focussed on recent studies on Fe-Al-based alloys with strengthening precipitates, such as K-phase Fe 3 AlC x , MC-carbide and Laves phase. Alloys of the following alloy systems were investigated: Fe-Al-C, Fe-Al-Ta, Fe-Al-Ni, Fe-Al-Ti-Nb, and Fe-Al-M-C (M = Ti, V, Nb, Ta). The investigations were centred on microstructure, constitution, and mechanical properties of such Fe-Al-based alloys with Al contents ranging from 10 to 30 at. %. Mechanisms and problems are discussed and perspectives are outlined.
Enabling Trustworthy Service Evaluation in Service-Oriented Mobile Social Networks (2014)

In this paper, we propose a Trustworthy Service Evaluation (TSE) system to enable users to share service reviews in service-oriented mobile social networks (S-MSNs). Each service provider independently maintains a TSE for itself, which collects and stores users' reviews about its services without requiring any third trusted authority. The service reviews can then be made available to interested users in making wise service selection decisions. We identify three unique service review attacks, i.e., linkability, rejection, and modification attacks, and develop sophisticated security mechanisms for the TSE to deal with these attacks. Specifically, the basic TSE (bTSE) enables users to distributedly and cooperatively submit their reviews in an integrated chain form by using hierarchical and aggregate signature techniques. It restricts the service providers to reject, modify, or delete the reviews. Thus, the integrity and authenticity of reviews are improved. Further, we extend the bTSE to a Sybil-resisted TSE (SrTSE) to enable the detection of two typical sybil attacks. In the SrTSE, if a user generates multiple reviews toward a vendor in a predefined time slot with different pseudonyms, the real identity of that user will be revealed. Through security analysis and numerical results, we show that the bTSE and the SrTSE effectively resist the service review attacks and the SrTSE additionally detects the sybil attacks in an efficient manner. Through performance evaluation, we show that the bTSE achieves better performance in terms of submission rate and delay than a service review system that does not adopt user cooperation.
Application of the stochastic mixing model to hyperspectral resolution enhancement (2004)

A maximum a posteriori (MAP) estimation method is described for enhancing the spatial resolution of a hyperspectral image using a higher resolution coincident panchromatic image. The approach makes use of a stochastic mixing model (SMM) of the underlying spectral scene content to develop a cost function that simultaneously optimizes the estimated hyperspectral scene relative to the observed hyperspectral and panchromatic imagery, as well as the local statistics of the spectral mixing model. The incorporation of the stochastic mixing model is found to be the key ingredient for reconstructing subpixel spectral information in that it provides the necessary constraints that lead to a well-conditioned linear system of equations for the high-resolution hyperspectral image estimate. Here, the mathematical formulation of the proposed MAP method is described. Also, enhancement results using various hyperspectral image datasets are provided. In general, it is found that the MAP/SMM method is able to reconstruct subpixel information in several principal components of the high-resolution hyperspectral image estimate, while the enhancement for conventional methods, like those based on least squares estimation, is limited primarily to the first principal component (i.e., the intensity component).
ATP-binding sites in the membrane components of histidine permease, a periplasmic transport system. (1984)

Two components of the histidine permease in Salmonella typhimurium, the membrane-bound P and M proteins, react with the photoaffinity labeling reagent 8-azido-ATP in isolated membranes. The extent of labeling is decreased by the addition of ATP and somewhat less by addition of GTP, CTP, UTP, and ADP. Cyclic AMP, NAD, FAD, and S-adenosylmethionine have little effect. We propose that one or both of these proteins have a site capable of binding an adenine nucleotide and that, therefore, they may be involved in the energy-coupling step in active transport.
<i>Prx1</i> and <i>Prx2</i> in skeletogenesis: roles in the craniofacial region, inner ear and limbs (1998)

Prx1 and Prx2 are closely related paired-class homeobox genes that are expressed in very similar patterns predominantly in mesenchyme. Prx1 loss-of-function mutants show skeletal defects in skull, limbs and vertebral column (Martin, J. F., Bradley, A. and Olson, E. N. (1995) Genes Dev. 9, 1237-1249). We report here that mice in which Prx2 is inactivated by a lacZ insertion had no skeletal defects, whereas Prx1/Prx2 double mutants showed many novel abnormalities in addition to an aggravation of the Prx1 single mutant phenotype. We found defects in external, middle and inner ear, reduction or loss of skull bones, a reduced and sometimes cleft mandible, and limb abnormalities including postaxial polydactyly and bent zeugopods. A single, or no incisor was present in the lower jaw, and ectopic expression of Fgf8 and Pax9 was found medially in the mandibular arch. A novel method to detect &bgr ;-galactosidase activity in hydroxyethylmethacrylate sections allowed detailed analysis of Prx2 expression in affected structures. Our results suggest a role for Prx genes in mediating epitheliomesenchymal interactions in inner ear and lower jaw. In addition, Prx1 and Prx2 are involved in interactions between perichondrium and chondrocytes that regulate their proliferation or differentiation in the bones of the zeugopods.
Cloning and Functional Analysis of a cDNA Encoding Ginkgo biloba Farnesyl Diphosphate Synthase (2004)

Farnesyl diphosphate synthase (FPS; EC2.5.1.1/EC2. 5.1.10) catalyzes the synthesis of farnesyl diphosphate, and provides precursor for biosynthesis of sesquiterpene and isoprenoids containing more than 15 isoprene units in Ginkgo biloba. Here we report the cloning, characterization and functional analysis of a new cDNA encoding FPS from G. biloba. The full-length cDNA (designated GbFPS) had 1731 bp with an open reading frame of 1170 bp encoding a polypeptide of 390 amino acids. The deduced GbFPS was similar to other known FPSs and contained all the conserved regions of trans-prenyl chain-elongating enzymes. Structural modeling showed that GbFPS had the typical structure of FPS, the most prominent feature of which is the arrangement of 13 core helices around a large central cavity. Southern blot analysis revealed a small FPS gene family in G. biloba. Expression analysis indicated that GbFPS expression was high in roots and leaves, and low in stems. Functional complementation of GbFPS in an FPS-deficient strain confirmed that GbFPS mediates farnesyl diphosphate biosynthesis.
Patia: adaptive distributed Webserver (A position paper) (2003)

This paper introduces the Patia adaptive Web server architecture, which is distributed and consists of semi-autonomous agents called flys. The fly carries with it the set of rules and adaptivity policies required to deliver the data to the requesting client. Where a change in the fly's external environment could affect performance, it is the fly's responsibility to change the method of delivery (or the actual object being delivered). It is our conjecture that the success of today's multimedia Web sites in terms of dependability and performance lies in the architecture of the underlying servers and their ability to adapt to changes in demand, resource availability, as well as their ability to scale. We believe that the distributed and autonomous nature of this system is the key factor in achieving this.
Role of the carboxy-terminus of polypeptide D1 in the assembly of a functional water-oxidizing manganese cluster in photosystem II of the cyanobacterium Synechocystis sp. PCC 6803:assembly requires a free carboxyl group at C-terminal position 344 (1992)

The D1 polypeptide of the photosystem II (PSII) reaction center is synthesized as a precursor polypeptide which is posttranslationally processed at the carboxy terminus. It has been shown in spinach that such processing removes nine amino acids, leaving Ala344 as the C-terminal residue [Takahashi, M., Shiraishi, T., & Asada, K. (1988) FEBS Lett. 240, 6-8; Takahashi, Y., Nakane, H., Kojima, H., & Satoh, K. (1990) Plant Cell Physiol. 31, 273-280]. We show here that processing on the carboxy side of Ala344 also occurs in the cyanobacterium Synechocystis 6803, resulting in the removal of 16 amino acids. By constructing a deletion strain of Synechocystis 6803 that lacks the three copies of the psbA gene encoding D1, we have developed a system for generating psbA mutants. Using this system, we have constructed mutants of Synechocystis 6803 that are modified in the region of the C-terminus of the D1 polypeptide. Characterization of these mutants has revealed that (1) processing of the D1 polypeptide is blocked when the residue after the cleavage site is changed from serine to proline (mutant Ser345Pro) with the result that the manganese cluster is unable to assemble correctly; (2) the C-terminal extension of 16 amino acid residues can be deleted with little consequence either for insertion of D1 into the thylakoid membrane or for assembly of D1 into a fully active PSII complex; (3) removal of only one more residue (mutant Ala344stop) results in a loss of assembly of the manganese cluster; and (4) the ability of detergent-solubilized PSII core complexes (lacking the manganese cluster) to bind and oxidize exogenous Mn2+ by the secondary donor, Z+, is largely unaffected in the processing mutants (the Ser345Pro mutant of Synechocystis 6803 and the LF-1 mutant of Scenedesmus obliquus) and the truncation mutant Ala344stop. Our results are consistent with a role for processing in regulating the assembly of the photosynthetic manganese cluster and a role for the free carboxy terminus of the mature D1 polypeptide in the ligation of one or more manganese ions of the cluster.
Identification and analysis of a glutaryl‐CoA dehydrogenase‐encoding gene and its cognate transcriptional regulator from <i>Azoarcus</i> sp. CIB (2007)

Summary In this work, the gcdH gene from the denitrifying β‐proteobacterium Azoarcus sp. CIB was shown to encode a glutaryl‐CoA dehydrogenase, which is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The primary structure of the GcdH protein is highly conserved in many organisms. The divergently transcribed gcdR gene, encoding a LysR‐type transcriptional regulator, accounts for the glutaconate/glutarate‐specific activation of the Pg promoter driving expression of gcdH . The Azoarcus sp. CIBd gcdH mutant strain harbouring a disrupted gcdH gene was used as host to identify heterologous gcdH genes, such as that from Pseudomonas putida KT2440. Moreover, the expression of gcdH from P. putida can be efficiently controlled by the GcdR activator in Azoarcus sp. CIB, demonstrating the existence of cross‐talk between GcdR regulators and gcdH promoters from members of different phylogenetic subgroups of proteobacteria.