gebhart/patrepeval huggingface dataset:
Multi-robot exploration of an unknown environment, efficiently reducing the odometry error (1997)

This paper deals with the intelligent exploration of an unknown environment by autonomous robots. In particular, we present an algorithm and associated analysis for collaborative exploration using two mobile robots. Our approach is based on robots with range sensors limited by distance. By appropriate behavioural strategies, we show that odometry (motion) errors that would normally present problems for mapping can be severely reduced. Our analysis includes polynomial complexity bounds and a discussion of possible heuristics. 1 1 Introduction The problem of exploring an unknown environment and constructing a map is central to mobile robotics. The ability to build an internal representation of the environment is also critical to most intelligent organisms. Existing approaches that have been proposed for this problem range from idealized solutions involving perfect virtual robots to practical solutions of indeterminate complexity with real robots. The range of environment and terrain ty...
Effects of vitamin B6deficiency and repletion on the uptake of steroid hormones into uterus slices and isolated liver cells of rats (1989)

1. In vitro, pyridoxal phosphate extracts steroid-hormone receptors from tight nuclear binding (Cidlowski & Thanassi, 1981); in vitamin B6-deficient rats there is increased and prolonged nuclear accumulation of oestradiol in the uterus and testosterone in the prostate, associated with enhanced biological responsiveness of these target tissues to steroid hormone action (Symes et al. 1984; Bowden et al. 1986). 2. Slices of uterus from vitamin B6-deficient rats accumulated more [3H]oestradiol than did tissue from repleted animals. Acute repletion with vitamin B6 (0.5-1 h before killing) further increased the uptake of the steroid. 3. Isolated hepatocytes from vitamin B6-deficient rats accumulated more [3H]dexamethasone than did cells from repleted animals. Pre-incubation of the hepatocytes with pyridoxal phosphate resulted in a further increase in the uptake of the steroid. 4. The results suggest that in addition to the putative role of pyridoxal phosphate in releasing steroid-hormone-receptor complexes from tight nuclear binding (Cidlowski & Thanassi, 1981), vitamin B6 deficiency may also increase the concentration of steroid-hormone receptors or enzymes and other steroid-binding proteins in target tissues.
CHEMOAFFINITY IN THE ORDERLY GROWTH OF NERVE FIBER PATTERNS AND CONNECTIONS (1963)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
PRODUCTION OF TRANSGENIC CITRUS PLANTS EXPRESSING THE CITRUS TRISTEZA VIRUS COAT PROTEIN GENE (1993)

Citrus tristeza virus (CTV) is the most devastating citrus virus world-wide. Studies in a number of laboratories have shown that protection against a virus may be achieved by the introduction of the cloned viral coat protein (CP) into transgenic plants. The CTV CP has been isolated and sequenced [Sekiya et al., J. Gen. Virol. (1991) 72:1013-1020] and cloned into a custom engineered plant expression vector [Slightom JL, Gene (1991) 100:251-255]. We have also developed a protocol for the Agrobacterium -mediated transformation of internodal stem sections of Citrus seedlings [Moore et al., Plant Cell Rep. (1992) 11:238-242]. Transgenic plants of Carrizo citrange [ C. sinensis (L.) Osb. × Poncirus trifoliata (L.) Raf.] and sour orange ( C. aurantium L.) expressing the CTV CP gene have been identified based on β-glucuronidase expression, PCR and Southern analyses, and immunoblot analysis with antibody to the CP. Transgenic sour orange plants are being propagated to generate sufficient material to test whether the plants are resistant to challenge by CTV.
The Penn Treebank (1994)

The Penn Treebank has recently implemented a new syntactic annotation scheme, designed to highlight aspects of predicate-argument structure. This paper discusses the implementation of crucial aspects of this new annotation scheme. It incorporates a more consistent treatment of a wide range of grammatical phenomena, provides a set of coindexed null elements in what can be thought of as "underlying" position for phenomena such as wh-movement, passive, and the subjects of infinitival constructions, provides some non-context free annotational mechanism to allow the structure of discontinuous constituents to be easily recovered, and allows for a clear, concise tagging system for some semantic roles.
CD4 T Cell Tolerance to Human C-reactive Protein, an Inducible Serum Protein, Is Mediated by Medullary Thymic Epithelium (1998)

Inducible serum proteins whose concentrations oscillate between nontolerogenic and tolerogenic levels pose a particular challenge to the maintenance of self-tolerance. Temporal restrictions of intrathymic antigen supply should prevent continuous central tolerization of T cells, in analogy to the spatial limitation imposed by tissue-restricted antigen expression. Major acute-phase proteins such as human C-reactive protein (hCRP) are typical examples for such inducible self-antigens. The circulating concentration of hCRP, which is secreted by hepatocytes, is induced up to 1,000-fold during an acute-phase reaction. We have analyzed tolerance to hCRP expressed in transgenic mice under its autologous regulatory regions. Physiological regulation of basal levels (<10(-9) M) and inducibility (>500-fold) are preserved in female transgenics, whereas male transgenics constitutively display induced levels. Surprisingly, crossing of hCRP transgenic mice to two lines of T cell receptor transgenic mice (specific for either a dominant or a subdominant epitope) showed that tolerance is mediated by intrathymic deletion of immature thymocytes, irrespective of widely differing serum levels. In the absence of induction, hCRP expressed by thymic medullary epithelial cells rather than liver-derived hCRP is necessary and sufficient to induce tolerance. Importantly, medullary epithelial cells also express two homologous mouse acute-phase proteins. These results support a physiological role of "ectopic" thymic expression in tolerance induction to acute-phase proteins and possibly other inducible self-antigens and have implications for delineating the relative contributions of central versus peripheral tolerance.
CLINICAL NEPHROTOXINS: renal injury from drugs and chemicals (1998)

CLINICAL NEPHROTOXINS: renal injury from drugs and chemicals , CLINICAL NEPHROTOXINS: renal injury from drugs and chemicals , کتابخانه مرکزی دانشگاه علوم پزشکی ایران
Towards Elucidating Carnosic Acid Biosynthesis in Lamiaceae: Functional Characterization of the Three First Steps of the Pathway in Salvia fruticosa and Rosmarinus officinalis (2015)

Carnosic acid (CA) is a phenolic diterpene with anti-tumour, anti-diabetic, antibacterial and neuroprotective properties that is produced by a number of species from several genera of the Lamiaceae family, including Salvia fruticosa (Cretan sage) and Rosmarinus officinalis (Rosemary). To elucidate CA biosynthesis, glandular trichome transcriptome data of S. fruticosa were mined for terpene synthase genes. Two putative diterpene synthase genes, namely SfCPS and SfKSL, showing similarities to copalyl diphosphate synthase and kaurene synthase-like genes, respectively, were isolated and functionally characterized. Recombinant expression in Escherichia coli followed by in vitro enzyme activity assays confirmed that SfCPS is a copalyl diphosphate synthase. Coupling of SfCPS with SfKSL, both in vitro and in yeast, resulted in the synthesis miltiradiene, as confirmed by 1D and 2D NMR analyses (1H, 13C, DEPT, COSY H-H, HMQC and HMBC). Coupled transient in vivo assays of SfCPS and SfKSL in Nicotiana benthamiana further confirmed production of miltiradiene in planta. To elucidate the subsequent biosynthetic step, RNA-Seq data of S. fruticosa and R. officinalis were searched for cytochrome P450 (CYP) encoding genes potentially involved in the synthesis of the first phenolic compound in the CA pathway, ferruginol. Three candidate genes were selected, SfFS, RoFS1 and RoFS2. Using yeast and N. benthamiana expression systems, all three where confirmed to be coding for ferruginol synthases, thus revealing the enzymatic activities responsible for the first three steps leading to CA in two Lamiaceae genera.
A map of human genome variation from population-scale sequencing (2010)

The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother-father-child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10(-8) per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research.
Coding in 2D: Using Intentional Dispersity to Enhance the Information Capacity of Sequence‐Coded Polymer Barcodes (2016)

A 2D approach was studied for the design of polymer-based molecular barcodes. Uniform oligo(alkoxyamine amide)s, containing a monomer-coded binary message, were synthesized by orthogonal solid-phase chemistry. Sets of oligomers with different chain-lengths were prepared. The physical mixture of these uniform oligomers leads to an intentional dispersity (1st dimension fingerprint), which is measured by electrospray mass spectrometry. Furthermore, the monomer sequence of each component of the mass distribution can be analyzed by tandem mass spectrometry (2nd dimension sequencing). By summing the sequence information of all components, a binary message can be read. A 4-bytes extended ASCII-coded message was written on a set of six uniform oligomers. Alternatively, a 3-bytes sequence was written on a set of five oligomers. In both cases, the coded binary information was recovered.
Evolutionary genomics of Staphylococcus aureus : Insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic (2001)

An emerging theme in medical microbiology is that extensive variation exists in gene content among strains of many pathogenic bacterial species. However, this topic has not been investigated on a genome scale with strains recovered from patients with well-defined clinical conditions. Staphylococcus aureus is a major human pathogen and also causes economically important infections in cows and sheep. A DNA microarray representing >90% of the S. aureus genome was used to characterize genomic diversity, evolutionary relationships, and virulence gene distribution among 36 strains of divergent clonal lineages, including methicillin-resistant strains and organisms causing toxic shock syndrome. Genetic variation in S. aureus is very extensive, with approximately 22% of the genome comprised of dispensable genetic material. Eighteen large regions of difference were identified, and 10 of these regions have genes that encode putative virulence factors or proteins mediating antibiotic resistance. We find that lateral gene transfer has played a fundamental role in the evolution of S. aureus. The mec gene has been horizontally transferred into distinct S. aureus chromosomal backgrounds at least five times, demonstrating that methicillin-resistant strains have evolved multiple independent times, rather than from a single ancestral strain. This finding resolves a long-standing controversy in S. aureus research. The epidemic of toxic shock syndrome that occurred in the 1970s was caused by a change in the host environment, rather than rapid geographic dissemination of a new hypervirulent strain. DNA microarray analysis of large samples of clinically characterized strains provides broad insights into evolution, pathogenesis, and disease emergence.
Activation of Interferon Response Through Toll-Like Receptor 3 Impacts Viral Pathogenesis and Pulmonary Toll-Like Receptor Expression During Respiratory Syncytial Virus and Influenza Infections in the Cotton Rat Sigmodon hispidus Model (2009)

Interferon (IFN) therapy in humans often causes flu-like symptoms by an unknown mechanism. Poly ICLC is a synthetic dsRNA and a Toll-like receptor 3 (TLR3) agonist with a strong IFN-inducing ability. In this work, we analyzed the effect of poly ICLC on pulmonary responses to influenza and respiratory syncytial virus (RSV) infections in the cotton rat (Sigmodon hispidus) model. Viral replication, pulmonary inflammation, and expression of IFN, TLR, and chemokines were monitored and compared. Antiviral effect of poly ICLC against influenza virus and RSV was best achieved at high poly ICLC concentrations that, in the absence of virus infection, induced a strong IFN response. The antiviral doses of poly ICLC, however, also increased lung inflammation, an unexpected finding because of the reported poly ICLC safety in BALB/c mice. Similarly, in contrast to murine model, pathology of RSV infection was increased in cotton rats treated with poly ICLC. Augmented lung inflammation was accompanied by an earlier induction of IFN and TLR responses and a stronger chemokine expression. Overall, these findings indicate significant association between antiviral IFN action and pulmonary inflammation and highlight important animal model-specific variations in the potential of IFN to cause pathology.
Real-time, scalable route planning using a stream-processing infrastructure (2010)

A key transportation service is traffic-dependent route planning, i.e., finding a path from a source to a destination on a road network that incurs the minimum travel time delay and that considers current and future traffic conditions on all road links. This kind of route planning requires dynamic time-dependent shortest path computations, since the cost of each link is different at different intervals of time, and these time-dependent costs get updated as new traffic information is obtained. In this paper, we describe a stream-processing infrastructure that can perform scalable, real-time, time-dependent shortest path computations with high throughput and low latency on large road networks. In our performance experiments, we show that it can perform hundreds of such shortest path computations per second, with an average delay of less than 1 second on a road network with tens of thousands of nodes and links. Our experiments were carried out on the Stockholm road network, and the traffic data for purposes of getting the travel time delay on each link was derived from a real GPS data-set obtained from vehicles on this network. In this paper, we also highlight the benefits of performing dynamic, time-dependent shortest path computations. For example, our data from Stockholm suggests that computing traffic-dependent shortest paths can help decrease travel time by up to 62% compared to using a less dynamic method based on fixed road speed limits. Also the shortest path for various origin-destination pairs changes frequently during the course of a day. These findings motivate the need for highly scalable, real-time time-dependent shortest-path computations, as performed by our stream processing infrastructure.
Single Rapid Real-Time Monitored Isothermal RNA Amplification Assay for Quantification of Human Immunodeficiency Virus Type 1 Isolates from Groups M, N, and O (2001)

Because human immunodeficiency virus type 1 (HIV-1) subtypes and circulating recombinant forms (CRFs) are spreading rapidly worldwide and are becoming less confined to a geographical area, RNA assays that can detect and quantify all HIV-1 isolates reliably are in demand. We have developed a fast, real-time monitored RNA assay based on an isothermal nucleic acid sequence-based amplification technology that amplifies a part of the long terminal repeat region of the HIV-1 genome. Real-time detection was possible due to the addition of molecular beacons to the amplification reaction that was monitored in a fluorimeter with a thermostat. The lower level of detection of the assay was 10 HIV-1 RNA molecules per reaction, and the lower level of quantification was 100 copies of HIV-1 RNA with a dynamic range of linear quantification between 10(2) and 10(7) RNA molecules. All HIV-1 groups, subtypes, and CRFs could be detected and quantified with equal efficiency, including the group N isolate YBF30 and the group O isolate ANT70. To test the clinical utility of the assay, a series of 62 serum samples containing viruses that encompassed subtypes A through G and CRFs AE and AG of HIV-1 group M were analyzed, and these results were compared to the results of a commercially available assay. This comparison showed that the quantification results correlated highly (R(2) = 0.735) for those subtypes that could be well quantified by both assays (subtypes B, C, D, and F), whereas improved quantification was obtained for subtypes A and G and CRFs AE and AG. A retrospective study with six individuals infected with either a subtype A, B, C, or D or an AG isolate of HIV-1 group M, who were treated with highly active antiretroviral therapy, revealed that the assay was well suited to the monitoring of therapy effects. In conclusion, the newly developed real-time monitored HIV-1 assay is a fast and sensitive assay with a large dynamic range of quantification and is suitable for quantification of most if not all subtypes and groups of HIV-1.
CLOUD SHREDDER: Removing the Laptop On-road Data Disclosure Threat in the Cloud Computing Era (2011)

Data Disclosure due to laptop loss, especially in travel, is a top threat to businesses, governments, and non- profit organizations. An effective protection against this threat should guarantee the data confidentiality, even if the adversary has physically possessed the laptop. Current technology does not satisfy this requirement. This paper proposes a novel approach to remove the threat under the emerging condition of ubiquitous internet access and cloud computing. We name this approach "Cloud Shredder", implying that the confidential files are shredded and hidden in the semi-trusted cloud storage service. Cloud Shredder is a generic and transparent security service that allows legitimate user access the files in exactly the same way as with commodity file systems, whereas the attackers only get meaningless junk even if they have obtained every byte on the hard drive. Rather than the traditional encryption-based protection, Cloud Shredder limits the attacker's opportunity in a short time window. We implemented a prototype that is compatible with the typical cloud storage service, Amazon S3, and supports two popular document applications, Acrobat Reader and Open Office. Our experiments show that the influence on file access performance is reasonable and should not ruin the user experience. Cloud Shredder is also applicable to smart phone, netbook and other computing devices with internet connection.
Role and regulation of expression of 92‐kDa type‐IV collagenase (MMP‐9) in 2 invasive squamous‐cell‐carcinoma cell lines of the oral cavity (1993)

The present study was undertaken to determine the role of the metalloproteinase MMP-9 in the invasive phenotype of squamous-cell carcinoma of the oral cavity and the regulation of its expression. Zymographic analysis of conditioned medium from 2 highly invasive squamous-cell-carcinoma cell lines indicated large amounts of an enzyme which was indistinguishable, in size (92 kDa) from the MMP-9 pro-enzyme. Conversion of the 92-kDa gelatinase into a lower-molecular-weight species (84 kDa), identical in size to the activated gelatinase, was evident when both cell lines, which are avid secretors of urokinase, were cultured in the presence of plasminogen. Penetration of an extracellular-matrix-coated filter was dramatically reduced in the presence of the collagenase inhibitor, tissue inhibitor of metalloproteinase-2, suggesting a critical role for MMP-9 in the invasive process. Immunohistochemical studies demonstrating the presence of MMP-9 in tumor cells of resected squamous-cell cancers suggested that secretion of this collagenase by cells in vitro was reflective of the in vivo setting. Since several phorbol-ester response elements are present in the MMP-9 promoter, we determined the role of protein-kinase-C pathways in the regulation of MMP-9 expression in cultured SCC. Treatment of cells with PMA resulted in a more-than-20-fold increase in the level of protein and mRNA. Conversely, culturing of cells in the presence of the protein-kinase-C inhibitor, calphostin-C, led to a dose-dependent decrease in the amount of MMP-9 mRNA and protein, suggesting that the constitutive expression of this collagenase reflects activation of this signal transduction pathway. In summary, our data suggest that, for a sub-population of squamous-cell carcinomas, secreted MMP-9 is an important determinant of the invasive phenotype, and that the expression of this metalloproteinase is regulated by protein-kinase-C pathways.
Motor Skills Training Enhances Lesion-Induced Structural Plasticity in the Motor Cortex of Adult Rats (1999)

To assess behavioral experience effects on synaptic plasticity after brain damage, the present study examined the effects of complex motor skills training (the acrobatic task) on synaptic changes in layer V of the motor cortex opposite unilateral damage to the forelimb sensorimotor cortex (FLsmc). Adult male rats were given lesions or sham operations followed by 28 d of training on the acrobatic task [acrobat condition (AC)]. As a motor activity control [motor control (MC)], lesion and sham animals were given simple repetitive exercise. Previously, FLsmc lesions and acrobatic training have independently been found to result in increases in synapse to neuron ratios in the intact motor cortex relative to controls, and both of these effects were replicated in the present study. In addition, acrobat training after lesions significantly increased layer V synapses per neuron relative to sham-AC and lesion-MC rats. Thus, the combination of acrobatic training and lesions resulted in an enhanced synaptogenic response. Synapse subtypes were also differentially affected by the conditions. Lesion-MC and sham-AC primarily had increases in the number of synapses per neuron formed by multiple synaptic boutons in comparison to sham-MC. In contrast, lesion-AC had increases in both multiple and single synapses. Multiple synaptic spines and perforated synapses were also differentially affected by training versus lesions. On tests of coordinated forelimb use, lesion-AC rats performed better than lesion-MC rats. In addition to supporting a link between behavioral experience and structural plasticity after brain damage, these findings suggest that adaptive neural plasticity may be enhanced using behavioral manipulations as "therapy."