gebhart/patrepeval huggingface dataset:
Bacterioplankton community structure and dynamics after large-scale release of nonindigenous bacteria as revealed by low-molecular-weight-RNA analysis (1992)

A set of freshwater mesocosms (1.7 m3 each) was inoculated with large amounts of Escherichia coli, Pseudomonas putida, and their culture medium to substantially disturb the natural microbial community. To monitor microbial community dynamics, low-molecular-weight RNA (5S rRNA and tRNA) obtained directly from bacterioplankton was analyzed by using high-resolution electrophoresis. The introduced bacteria showed no significant effect on the community structure of the natural bacterial assemblage and its dynamics for 16 days. In contrast, the addition of culture medium resulted within 2 days in a reduction of community diversity due to dominance of a single 5S rRNA band from an indigenous bacterium. Partial sequencing of several 5S rRNAs demonstrated the molecular homogeneity of most of the abundant bands and enabled the identification of corresponding bacterial isolates and/or species. The dominating bacterium (around 54% of the total 5S rRNA) in the nutrient-amended mesocosms could be identified by partial sequencing as a member of the Aeromonas hydrophila complex. Another bloom of heterotrophic bacteria belonging to the Cytophaga johnsonae complex was detected in the nutrient-amended mesocosms after 13 days. The dominance of this C. johnsonae-like bacterium could even be seen in the environmental tRNAs of the bacterioplankton, where its specific tRNAs prevailed from day 13 onward. This event was also independent of the introduced nonindigenous bacteria because it occurred at the same time in all nutrient-amended mesocosms. By contrast, in the unamended experiments, a different small 5S rRNA could by observed from day 10 onward with less pronounced dominance.(ABSTRACT TRUNCATED AT 250 WORDS)
A functional assessment of insulin/insulin-like growth factor-I hybrid receptors (1995)

Insulin/insulin-like growth factor-I (IGF-I) hybrid receptors are composed of an alpha beta-heterodimer from an insulin receptor and an alpha beta-heterodimer from an IGF-I receptor. In this study, we evaluate the effect of insulin receptor overexpression on hybrid formation. The more human insulin receptors expressed in rodent fibroblasts, the greater the percentage of endogenous rat IGF-I receptors that form hybrid receptors. The IGF-I receptor in rodent fibroblasts has two receptor isoforms, one with a 95-kilodalton (kDa) beta-subunit and one with an 105 kDa beta-subunit. A truncated mutant insulin receptor was used to demonstrate that only activated IGF-I receptors with the 105-kDa beta-subunit form hybrid receptors with the insulin receptor. Insulin/IGF-I hybrid receptors with a kinase-defective insulin heterodimer undergo trans and a small amount of cis autophosphorylation, but overall autophosphorylation is markedly decreased from that seen in hybrids with a kinase-competent insulin receptor. The kinase-defective insulin receptor heterodimer functions as a dominant-negative, inhibiting phosphorylation by the kinase-competent IGF-I receptor heterodimer. The kinase-defective hybrid receptors are, however, able to undergo internalization. Despite an increasing percentage of insulin/IGF-I hybrid receptors in the three cell lines studied, the rates of IGF-I internalization and degradation remain similar to those mediated by the IGF-I receptor and distinct from those of insulin receptor heterotetramers. In conclusion, IGF-I-stimulated insulin/IGF-I hybrid receptors function like IGF-I receptors, rather than like insulin receptors.
A Self-Adaptive System for Vehicle Information Security Applications (2015)

To provide complete vehicle information protection mechanism, this work proposes a self-adaptive system for vehicle information security applications (SAV). Different from the conventional software-based information access method, in the SAV, the access control policies are designed by the protection matrices and implemented as reconfigurable hardware modules. The information access method becomes specific and not generic, so the risks of illegal access of vehicle information can be reduced. To not only meet real-time requirements but also enhance hardware resource utilization, the cryptographic functions in the SAV are also implemented as reconfigurable hardware modules. Thus, the SAV can adapt its access control policies and cryptographic functions at runtime to different system requirements. Our experiments have also demonstrated the SAV can accelerate by up to 3.78x the processing time required by using the software-based design. Compared to the conventional embedded system design, the SAV can also reduce 27.1% of slice registers and 26.5% of slice LUTs in the Xilinx Virtex-5 XC5VLX110T FPGA.
Multi-Carrier Ultra-Wideband Multiple-Access with Good Resilience against Multiuser Interference (2003)

We propose a multi-carrier based multiple-access scheme for ultra-wideband (UWB) communications that is capable of deterministic re- moval of multiuser interference, irrespective of the users' multipath channels, in asynchronous mode. The receivers for dieren t users have the same struc- ture, except for a dieren t mixer front-end. The maximum-likelihood receiver can be matched-lter based, with only the desired user's channel state in- formation, and hence without the need for multiuser detection. Performance simulation shows signican t improvement as compared with existing time-hopping
Multisite oligonucleotide-mediated mutagenesis: application to the conversion of a mitochondrial gene to universal genetic code. (1995)

Using multisite oligonucleotide-mediated mutagenesis in conjunction with a mutagenesis selection procedure and rapid screening by allele-specific oligonucleotide hybridization has allowed us to develop a reliable protocol that enables a large number of base changes to be introduced rapidly into a piece of DNA, with the minimum number of manipulations. We have applied this protocol to generate synthetic versions of four mouse mitochondrial genes capable of being expressed in the nucleus/cytosol.
Change-point detection in dynamical systems using auto-associative neural networks (2012)

In this research work, auto-associative neural networks have been used for changepoint detection.This is a nonlinear technique that employs the use of artificial neural networks as inspired among other by Frank Rosenblatt's linear perceptron algorithm for classification.An auto-associative neural network was used successfully to detect change-points for various types of time series data.Its performance was compared to that of singular spectrum analysis developed by Moskvina and Zhigljavsky.Fraction of Explained Variance (FEV) was also used to compare the performance of the two methods.FEV indicators are similar to the eigenvalues of the covariance matrix in principal component analysis.Two types of time series data were used for change-point detection: Gaussian data series and nonlinear reaction data series.The Gaussian data had four series with different types of change-points, namely a change in the mean value of the time series (T1), a change in the variance of the time series (T2), a change in the autocorrelation of the time series (T3), and a change in the crosscorrelation of two time series (T4).Both linear and nonlinear methods were able to detect the changes for T1, T2 and T4.None of them could detect the changes in T3.With the Gaussian data series, linear singular spectrum analysis (LSSA) performed as well as the NLSSA for the change point detection.This is because the time series was linearand the nonlinearity of the NLSSA was therefore not important.LSSA did even better than NLSSA when comparing FEV values, since it is not subject to suboptimal solutions as could sometimes be the case with autoassociative neural networks.The nonlinear data consisted of the Belousov-Zhabotinsky (BZ) reactions, autocatalytic reaction time series data and data representing a predator-prey system.With the NLSSA methods, change points could be detected accurately in all three systems, while LSSA only managed to detect the change-point on the BZ reactions and the predator-prey system.The NLSSA method also fared better than the LSSA method when comparing FEV values for the BZ reactions.The LSSA method was able to model the autocatalytic reactions fairly accurately, being able to explain 99% of the variance in the data with one component only.NLSSA with two nodes on the bottleneck attained an FEV of 87%.The performance of both NLSSA and LSSA were comparable for the predator-prey system, both systems, where both could
<title>Automatic Fingerprint Identification</title> (1979)

The present system for identifying latent fingerprints left at the scene of a crime still depends on the skill and patience of trained fingerprint technicians because of the low quality of the latent fingerprints. An image processing &amp; feature extraction technique has been established in order to detect minutiae (ridge endings and ridge bifurcations and ridge counts useful for latent fingerprint identification. The algorithm of the latent fingerprint identification using these features has been evaluated. Each feature is detected from the gray scale image of fingerprints and described by minutiae positions, minutiae directions and interminutia ridge counts. In the latent fingerprint identification, minutiae pairs are selected according to the similarity between latent fingerprints&apos; features and registered fingerprints&apos; features in a file. The similarity between two fingerprints is obtained through the comparison of selected minutiae pairs. In our experiments, we attempted the feature extraction of 500 registered fingerprints and 200 latent fingerprints, and the matching between them. The experiments were carried out using a high speed microcomputer, a flying spot scanner, a color display, and a tablet unit, which con-nected with a general purpose computer system (NEAC 2200/200).
DNA Cloning of Plasmodium falciparum Circumsporozoite Gene: Amino Acid Sequence of Repetitive Epitope (1984)

A clone of complementary DNA encoding the circumsporozoite (CS) protein of the human malaria parasite Plasmodium falciparum has been isolated by screening an Escherichia coli complementary DNA library with a monoclonal antibody to the CS protein. The DNA sequence of the complementary DNA insert encodes a four-amino acid sequence: proline-asparagine-alanine-asparagine, tandemly repeated 23 times. The CS beta-lactamase fusion protein specifically binds monoclonal antibodies to the CS protein and inhibits the binding of these antibodies to native Plasmodium falciparum CS protein. These findings provide a basis for the development of a vaccine against Plasmodium falciparum malaria.
Inhibition of Ets-1 DNA Binding and Ternary Complex Formation between Ets-1, NF-κB, and DNA by a Designed DNA-binding Ligand (1999)

Sequence-specific pyrrole-imidazole polyamides can be designed to interfere with transcription factor binding and to regulate gene expression, both in vitro and in living cells. Polyamides bound adjacent to the recognition sites for TBP, Ets-1, and LEF-1 in the human immunodeficiency virus, type 1 (HIV-1), long terminal repeat inhibited transcription in cell-free assays and viral replication in human peripheral blood lymphocytes. The DNA binding activity of the transcription factor Ets-1 is specifically inhibited by a polyamide bound in the minor groove. Ets-1 is a member of the winged-helix-turn-helix family of transcription factors and binds DNA through a recognition helix bound in the major groove with additional phosphate contacts on either side of this major groove interaction. The inhibitory polyamide possibly interferes with phosphate contacts made by Ets-1, by occupying the adjacent minor groove. Full-length Ets-1 binds the HIV-1 enhancer through cooperative interactions with the p50 subunit of NF-kappaB, and the Ets-inhibitory polyamide also blocks formation of ternary Ets-1. NF-kappaB.DNA complexes on the HIV-1 enhancer. A polyamide bound adjacent to the recognition site for NF-kappaB also inhibits NF-kappaB binding and ternary complex formation. These results broaden the application range of minor groove-binding polyamides and demonstrate that these DNA ligands are powerful inhibitors of DNA-binding proteins that predominantly use major groove contacts and of cooperative protein-DNA ternary complexes.
ChemInform Abstract: A Versatile and Convenient Method for the Preparation of α‐Z‐1‐Alkenyl Ketones from β‐Keto Benzyl Esters. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Long-Term Depletion of Naive T Cells in Patients Treated for Hodgkin's Disease (1997)

We investigated the representation of T cells in patients who had been treated for Hodgkin's disease (HD). We found a marked depletion in both CD4 and CD8 naive T-cell counts that persists up to 30 years after completion of treatment. In contrast, CD4 and CD8 memory T-cell subsets recovered to normal or above normal levels by 5 years posttreatment. Thus, the previously-reported long-term deficit in total CD4 T-cell counts after treatment for HD is due to specific depletion of naive T cells. Similarly, total CD8 T-cell counts return to normal by 5 years only because CD8 memory T cells expand to higher than normal levels. These findings suggest that the treatment (mediastinal irradiation) results in a longterm dysregulation of T-cell subset homeostasis. The profound depletion of naive T cells may explain the altered T-cell function in treated patients, including the poor response to immunization after treatment for HD. Further, in some individuals, we identified expansions of unusual subsets expressing low levels of CD8. Eight-color fluorescence-activated cell sorting analyses showed that these cells largely express CD8alphaalpha homodimers and CD57, consistent with the phenotype of potentially extrathymically derived T cells. In addition, these cells, both CD4+ and CD4-, are probably cytotoxic lymphocytes, as they express high levels of intracellular perforin. In adults treated for HD, an increased activity of extrathymic T-cell differentiation may partially compensate for the loss of thymic-derived T cells.
Rapid mRNA Degradation Mediated by the c- fos 3′ AU-Rich Element and That Mediated by the Granulocyte-Macrophage Colony-Stimulating Factor 3′ AU-Rich Element Occur through Similar Polysome-Associated Mechanisms (1995)

The different 3' noncoding AU-rich elements (ARE) that mediate the degradation of many short-lived mRNAs may function through distinct decay pathways; translation-dependent and -independent mechanisms have been proposed. To investigate the cotranslational model, we designed an expression system that exploits the properties of the ferritin iron-responsive element to shuttle chimeric mRNAs from ribonucleoproteins to polyribosomes. The iron-responsive element was introduced in the 5' untranslated regions of alpha-globin mRNAs that harbored in their 3' untranslated regions either the c-fos ARE or the granulocyte-macrophage colony-stimulating factor ARE as prototypes of the different ARE subsets. The cytoplasmic location of the transcripts was controlled by intracellular iron availability and monitored by polysomal profile analysis. We report that these two mRNA subsets behaved identically in this system. Iron deprivation by desferrioxamine treatment stabilized both transcripts by sequestering them away from polyribosomes. Sequential treatments with desferrioxamine, followed by hemin to concentrate the mRNAs in the ribonucleoprotein pool prior to translation, showed that rapid degradation occurred only upon redistribution of the transcripts to polyribosomes. Deletion of a critical cytosine in the iron-responsive element abolished targeted sequestration and restored high-level constitutive mRNA instability. These observations demonstrate that the c-fos and granulocyte-macrophage colony-stimulating factor ARE subsets mediate selective mRNA degradation through similar polysome-associated mechanisms coupled with ongoing translation.
Synthesis and Biological Evaluation of Novel Pyrazoles and Indazoles as Activators of the Nitric Oxide Receptor, Soluble Guanylate Cyclase (2000)

Database searching and compound screening identified 1-benzyl-3-(3-dimethylaminopropyloxy)indazole (benzydamine, 3) as a potent activator of the nitric oxide receptor, soluble guanylate cyclase. A comprehensive structure-activity relationship study surrounding 3 clearly showed that the indazole C-3 dimethylaminopropyloxy substituent was critical for enzyme activity. However replacement of the indazole ring of 3 by appropriately substituted pyrazoles maintained enzyme activity. Compounds were evaluated for inhibition of platelet aggregation and showed a general lipophilicity requirement. Aryl-substituted pyrazoles 32, 34, and 43 demonstrated potent activation of soluble guanylate cyclase and potent inhibition of platelet aggregation. Pharmacokinetic studies in rats showed that compound 32 exhibits modest oral bioavailability (12%). Furthermore 32 has an excellent selectivity profile notably showing no significant inhibition of phosphodiesterases or nitric oxide synthases.
AML1/ETO-expressing nonleukemic stem cells in acute myelogenous leukemia with 8;21 chromosomal translocation (2000)

Leukemia-specific AML1/ETO transcripts are detectable in most patients with t(8;21) acute myelogenous leukemia (AML) in long-term remission. To understand the inconsistency between the clinical cure and the presence of "residual disease" at a molecular level, we separated and identified the cells expressing AML1/ETO by phenotype and function. Here we demonstrate that AML1/ETO transcripts are present in a fraction of stem cells, monocytes, and B cells in remission marrow, and in a fraction of B cells in leukemic marrow, but not in T cells. AML1/ETO transcripts also were demonstrated in a fraction of colony-forming cells of erythroid, granulocyte-macrophage, and/or megakaryocyte lineages in both leukemic and remission marrow. These data strongly suggest that the acquisition of the t(8;21) occurs at the level of stem cells capable of differentiating into B cells as well as all myeloid lineages, and that a fraction of the AML1/ETO-expressing stem cells undergo additional oncogenic event(s) that ultimately leads to transformation into AML.
An embedded sensor validation system for adaptive condition monitoring of a wind farms (2007)

Sensor validation plays a key role in automatic control and online monitoring of complex systems, ensuring high performance and guaranteeing safety. Even in cases of safe industrial processes, the unreliability of sensor measurements may lead to a degraded performance and a reduced system yield. It is therefore both economical and essential to validate the credibility of sensor measurements. Timely detection and accurate diagnosis of actual, or even impending, sensor failures enable appropriate remedial actions to be taken, such as rescheduling of maintenance, reconfiguration of corrupted control loops or initialization of emergency shutdown. This paper presents a sensor validation coprocessing element, which is being developed in a FPGA- based processing node. The goal of the processing node is to provide adaptive conditioning monitoring, for a sensor network operating within a wind farm.
Pomalidomide (CC4047) Plus Low-Dose Dexamethasone As Therapy for Relapsed Multiple Myeloma (2009)

The combination of pomalidomide and low-dose dexamethasone is extremely active in the treatment of relapsed multiple myeloma, including high response rates in patients refractory to other novel agents.
The Human Oral Microbiome (2010)

The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible (www.homd.org). The HOMD includes 619 taxa in 13 phyla, as follows: Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Euryarchaeota, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, SR1, Synergistetes, Tenericutes, and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.
Localization of factor VIIIC: antigen in guinea‐pig tissues and isolated liver cell fractions (1984)

Factor VIIIC:antigen (VIII:CAg) was estimated in guinea-pig tissues by an immunoradiometric assay using a human inhibitor antibody. In homogenized guinea-pig tissues, VIII:CAg was shown to be stable and to be predominantly located in the liver (9 +/- 1.2 units; mean +/- SEM, n = 8). Lesser amounts were detected in spleen (1.3 +/- 0.02 units), lung (0.6 +/- 0.07) and kidney (0.4 +/- 0.06). In isolated liver cell fractions separated by centrifugal elutriation VIII:CAg was mainly detected in the hepatocyte fraction (0.3 +/- 0.07 units/10(8) cells;mean +/- SEM, n = 5) and in lesser amounts in the endothelial (0.02 +/- 0.01 units/10(8) cells) and the Kupffer cell fractions (0.05 +/- 0.02 units/10(8) cells). The liver concentration of VIII:CAg was (0.17 +/- 0.02 units/g) which was 20% of the plasma concentration (0.96 +/- 0.01 units/ml, n = 8) suggesting that VIII:CAg may not be stored in the liver but is rapidly exported following synthesis.
Multi-DoF probe trajectory reconstruction with local sensors for 2D-to-3D ultrasound (2010)

Handheld 2D ultrasound is very useful for intra-operative imaging, but requires some reconstruction effort in order to create 3D US volumes, unless one is using large and expensive 3D US probes. Unlike common probe tracking approaches involving either global or local tracking algorithms (suffering from jitter and complexity or from drift), we propose to use a combination of local sensors to reconstruct the probe trajectory with multiple degrees of freedom. The presented sensors are very low-cost- optical mice and a Wii Remote - yet enable flexible 3D US acquisition with no global tracking overhead. The resulting trajectories are then used as input for a dynamically expanding, pixel-nearest-neighbor 3D US volume reconstruction.
New Domain Motif: the Structure of Pectate Lyase C, a Secreted Plant Virulence Factor (1993)

Pectate lyases are secreted by pathogens and initiate soft-rot diseases in plants by cleaving polygalacturonate, a major component of the plant cell wall. The three-dimensional structure of pectate lyase C from Erwinia chrysanthemi has been solved and refined to a resolution of 2.2 angstroms. The enzyme folds into a unique motif of parallel beta strands coiled into a large helix. Within the core, the amino acids form linear stacks and include a novel asparagine ladder. The sequence similarities that pectate lyases share with pectin lyases, pollen and style proteins, and tubulins suggest that the parallel beta helix motif may occur in a broad spectrum of proteins.