gebhart/patrepeval huggingface dataset:
Improved determination of biplane imaging geometry from two projection images and its application to three‐dimensional reconstruction of coronary arterial trees (1997)

A technique has been developed for accurate estimation of three-dimensional (3D) biplane imaging geometry and reconstruction of 3D objects based on two perspective projections acquired at arbitrary orientations, without the need of calibration. The required prior information (i.e., the intrinsic parameters of each single-plane imaging system) for determination of biplane imaging geometry includes (a) the distance between each focal spot and its image plane, SID (the focal-spot to imaging-plane distance); (b) the pixel size, psize (e.g., 0.3 mm/pixel); (c) the distance between the two focal spots ff' or the known 3D distance between two points in the projection images; and (d) for each view, an approximation of the magnification factor, MF (e.g., 1.2), which is the ratio of the SID and the approximate distance of the object to the focal spot. Item (d) is optional but may provide a more accurate estimation if it is available. Given five or more corresponding object points in both views, a constrained nonlinear optimization algorithm is applied to obtain an optimal estimate of the biplane imaging geometry in the form of a rotation matrix R and a translation vector t that characterize the position and orientation of one imaging system relative to the other. With the calculated biplane imaging geometry, 3D spatial information concerning the object can then be reconstructed. The accuracy of this method was evaluated by using a computer-simulated coronary arterial tree and a cube phantom object. Our simulation study showed that a computer-simulated coronary tree can be reconstructed from two views with less than 2 and 8.4 mm root-mean-square (rms) configuration (or relative-position) error and absolute-position error, respectively, even if the input errors in the corresponding 2D points are fairly large (more than two pixels = 0.6 mm). In contrast, input image error of more than one pixel (= 0.3 mm) can yield 3D position errors of 10 cm or more when other existing methods based on linear approaches are employed. For the cube phantom images acquired from a routine biplane system, rms errors in the 3D configuration of the cube and the 3D absolute position were 0.6-0.9 mm and 3.9-5.0 mm, respectively.
Congestion management for non-blocking clos networks (2007)

We propose a distributed congestion management scheme for non-blocking, 3-stage Clos networks, comprising plain buffered crossbar switches. VOQ requests are routed using multipath routing to the switching elements of the 3rd-stage, and grants travel back to the linecards the other way around. The fabric elements contain independent single-resource schedulers, that serve requests and grants in a pipeline. As any other network with limited capacity, this scheduling network may suffer from oversubscribed links, hotspot contention, etc., which we identify and tackle. We also reduce the cost of internal buffers, by reducing the data RTT, and by allowing sub-RTT crosspoint buffers. Performance simulations demonstrate that, with almost all outputs congested, packets destined to non-congested outputs experience very low delays ( ow isolation). For applications requiring very low communication delays, we propose a second, parallel operation mode, wherein linecards can forward a few packets eagerly, each, bypassing the request-grant latency overhead.
Solution-processed flexible transparent conductors composed of silver nanowire networks embedded in indium tin oxide nanoparticle matrices (2012)

Although silver nanowire meshes have already demonstrated sheet resistance and optical transmittance comparable to those of sputter-deposited indium tin oxide thin films, other critical issues including surface morphology, mechanical adhesion and flexibility have to be addressed before widely employing silver nanowire networks as transparent conductors in optoelectronic devices. Here, we demonstrate the efficacy of low temperature solution-processed flexible metal nanowire networks embedded in a conductive metal oxide nanoparticle matrix as transparent conductors, and investigate their microstructural, optoelectronic, and mechanical properties in attempting to resolve nearly all of the technological issues imposed on silver nanowire networks. Surrounding silver nanowires by conductive indium tin oxide nanoparticles offers low wire to wire junction resistance, smooth surface morphology, and excellent mechanical adhesion and flexibility while maintaining the high transmittance and the low sheet resistance. In addition, we discuss the relationship between sheet resistance and transmittance in the silver nanowire composite transparent conductors and their maximum achievable transmittance. Although we have selected silver nanowires and indium tin oxide nanoparticle matrix as demonstration materials, we anticipate that various metal nanowire meshes embedded in various conductive metal oxide nanoparticle matrices can effectively serve as transparent conductors for a wide variety of optoelectronic devices owing to their superior performance, simple, cost-effective, and gentle processing.
Neuronal nitric oxide synthase (NOS1) and its adaptor, NOS1AP, as a genetic risk factors for psychiatric disorders (2015)

Nitric oxide (NO) is a gaseous transmitter produced by nitric oxide synthases (NOSs). The neuronal isoform (NOS-I, encoded by NOS1) is the main source of NO in the central nervous system (CNS). Animal studies suggest that nitrinergic dysregulation may lead to behavioral abnormalities. Unfortunately, the large number of animal studies is not adequately reflected by publications concerning humans. These include post-mortem studies, determination of biomarkers, and genetic association studies. Here, we review the evidence for the role of NO in psychiatric disorders by focusing on the human NOS1 gene as well as biomarker studies. Owing to the complex regulation of NOS1 and the varying function of NOS-I in different brain regions, no simple, unidirectional association is expected. Rather, the 'where, when and how much' of NO formation is decisive. Present data, although still preliminary and partially conflicting, suggest that genetically driven reduced NO signaling in the prefrontal cortex is associated with schizophrenia and cognition. Both NOS1 and its interaction partner NOS1AP have a role therein. Also, reduced NOS1 expression in the striatum determined by a length polymorphism in a NOS1 promoter (NOS1 ex1f-VNTR) goes along with a variety of impulsive behaviors. An association of NOS1 with mood disorders, suggested by animal models, is less clear on the genetic level; however, NO metabolites in blood may serve as biomarkers for major depression and bipolar disorder. As the nitrinergic system comprises a relevant target for pharmacological interventions, further studies are warranted not only to elucidate the pathophysiology of mental disorders, but also to evaluate NO function as a biomarker.
Prevention of hepatic tumor metastases in rats with herpes viral vaccines and gamma-interferon. (1997)

Previous studies showed that gammaIFN decreases metastatic hepatic tumor growth by stimulating Kupffer cells (KC). The present studies examine whether lymphocyte stimulation via cells engineered to secrete GM-CSF or IL-2 decreases hepatic tumor growth, and whether stimulation of both macrophages and lymphocytes is more effective than either individually. Rats were immunized with irradiated hepatoma cells transduced by herpes viral amplicon vectors containing the genes for GM-CSF, IL-2 or LacZ. On day 18, half of each group was treated with 5 x 10(4) U gammaIFN, or saline intraperitoneally for 3 d. On day 21, all rats received 5 x 10(5) hepatoma cells intrasplenically. On day 41, rats were killed and tumor nodules were counted. Separate rats underwent splenocyte and KC harvest for assessment of lymphocyte- and macrophage-mediated tumor cell kill in vitro. GM-CSF or IL-2 vaccines or gammaIFN decreased tumor nodules significantly (GM-CSF 13+/-4, IL-2 14+/-6 vs. control 75+/-24, P < 0.001). Combination therapy was more effective, and completely eliminated tumor in 4 of 12 IFN-GM-CSF and 8 of 11 IFN-IL-2 animals. Additional rats underwent partial hepatectomy, an immunosuppressive procedure known to accelerate the growth of hepatic tumor, following tumor challenge. Therapy was equally effective in this immunosuppressive setting. Vaccination is associated with enhancement of splenocyte-mediated tumoricidal activity, whereas the effect of gammaIFN is mediated by KC. GM-CSF and IL-2 vaccine therapy and pretreatment with gammaIFN represent effective strategies in reducing hepatic tumor. Combination therapy targets both lymphocytes and macrophages, and is more effective in reducing tumor than either therapy alone.
PROTOFIBRILS, PORES, FIBRILS, AND NEURODEGENERATION: Separating the Responsible Protein Aggregates from The Innocent Bystanders (2003)

Many neurodegenerative diseases, including Alzheimer's and Parkinson's and the transmissible spongiform encephalopathies (prion diseases), are characterized at autopsy by neuronal loss and protein aggregates that are typically fibrillar. A convergence of evidence strongly suggests that protein aggregation is neurotoxic and not a product of cell death. However, the identity of the neurotoxic aggregate and the mechanism by which it disables and eventually kills a neuron are unknown. Both biophysical studies aimed at elucidating the precise mechanism of in vitro aggregation and animal modeling studies support the emerging notion that an ordered prefibrillar oligomer, or protofibril, may be responsible for cell death and that the fibrillar form that is typically observed at autopsy may actually be neuroprotective. A subpopulation of protofibrils may function as pathogenic amyloid pores. An analogous mechanism may explain the neurotoxicity of the prion protein; recent data demonstrates that the disease-associated, infectious form of the prion protein differs from the neurotoxic species. This review focuses on recent experimental studies aimed at identification and characterization of the neurotoxic protein aggregates.
Patterns of Transcription of Human Cytomegalovirus in Permissively Infected Cells (1980)

The rate of accumulation of cytomegalovirus transcripts in permissively infected human embryonic lung (HEL) cells was analyzed at various times after infection by hybridization of infected cell RNA to undigested or restriction endonuclease-digested cytomegalovirus DNA fixed to nitrocellulose filters. Differences in patterns of transcript accumulation were determined by measuring the abundance levels of RNA which hybridized to different HindIII-, XbaI-, or EcoRI-generated fragments of cytomegalovirus DNA. The results showed that a small but significant amount of cytomegalovirus RNA was detectable within the first 3 h after infection and that the rate of accumulation of these transcripts was static during the first 24 h, but increased thereafter. In general, the viral transcripts accumulating in infected cells could be divided into three classes. Immediate-early RNA (synthesized in the absence of protein synthesis in infected cells) hybridizes predominantly to a very restricted part of the genome and can be identified during the first 2 to 4 h postinfection. Early RNA (synthesized up to about 24 h after infection) originates from most regions of the genome but is characterized by the presence of transcripts which hybridize in great abundance to certain fragments. Late RNA (synthesized after 24 h, i.e., after the onset of viral DNA synthesis) hybridizes in approximately equal abundance to most regions of the viral genome. These results showed that a block in the transition from immediate-early to early RNA did not account for the extended period of time that elapses between the time of infection and the initiation of viral DNA synthesis. Interestingly, despite rapid adsorption and penetration and a static level of accumulation of transcripts in the cultures during the first 24 h, the number of cells that synthesized detectable amounts of viral antigens increased steadily during this time.
TRACER: In-vehicle, GPS-based, Wireless Technology for Traffic Surveillance and Management (2003)

The fundamental principle of intelligent transportation systems is to match the complexity of travel demands with advanced supply-side analysis, evaluation, management, and control strategies. A fundamental limitation is the lack of basic knowledge of travel demands at the network level. Modeling and sensor technology is primarily limited to aggregrate parameters or micro-simluations based on aggregate distributions of behavior. Global Positioning Systems (GPS) are one of several available technologies which allow individual vehicle trajectories to be recorded and analyzed. Potential applications of GPS which are relevant to the ATMS Testbed are implemented in probe vehicles to deliver real-time performance data to complement loop and other sensor data and implementation in vehicles from sampled households to record route choice behavior. An Extensible GPS-based in-vehicle Data Collection Unit (EDCU)has been designed, tested, and applied in selected field tests. Each unit incorporates GPS, data logging capabilities, two-way wireless communications, and a user interface in an extensible system which eliminates driver interaction. Together with supporting software, this system is referred to as TRACER. The design and initial implementation tests Testbed are presented herein. This research is a continuation of PATH MOU 3006; selected portions of the interim report for that MOU are repeated here to provide a complete overview of the research effort
Anaerotruncus colihominis gen. nov., sp. nov., from human faeces (2004)

Phenotypic and phylogenetic studies were performed on two isolates of an unidentified Gram-positive, anaerobic, non-spore-forming, rod-shaped bacterium that was isolated from human faeces. The organisms were catalase-negative, produced acetic and butyric acids as end products of metabolism and possessed a DNA G+C content of approximately 54 mol%. Comparative 16S rRNA gene sequencing demonstrated that the two isolates were related closely to each other and formed a hitherto unknown sublineage within the Clostridium leptum rRNA cluster of organisms. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium should be classified in a novel genus as Anaerotruncus colihominis gen. nov., sp. nov. The type strain of Anaerotruncus colihominis is WAL 14565(T)=CCUG 45055(T)=CIP 107754(T).
2-Sulfonyl-4-chloroanilino Moiety:  A Potent Pharmacophore for the Anti-Human Immunodeficiency Virus Type 1 Activity of Pyrrolyl Aryl Sulfones (1996)

The synthesis and the evaluation of cytotoxicity and anti-HIV-1 activity of new aryl pyrrolyl (8) and aryl indolyl (9) sulfones are reported. Preparation of above sulfones was achieved by reacting arylsulfonyl chlorides with substituted pyrroles and indoles or by condensing sulfonamides with 2,5-dimethoxytetrahydrofuran in glacial acetic acid according to the Clauson-Kaas method. Chemical requisites relevant to the anti-HIV-1 activity of these compounds are both a 2-sulfonyl-4-chloroanilino moiety and an alkoxycarbonyl group at position 2 of the pyrrole ring. The best activity and selectivity were obtained with ethoxycarbonyl and isopropoxycarbonyl substituents. Substitutions at the amino group of the pharmacophore moiety led to inactive products (alkylation) or weakened (acylation) anti-HIV-1 activity. Among test derivatives, 16 compounds showed EC50 values ranging between 10 and 1 microM, and five (8b',d',f',h'j') showed EC50S in the sub-micromolar range. The compounds were active against HIV-1, both wild type and AZT-resistant strains, but not against HIV-2. Moreover, in enzyme assays they potently inhibited the HIV-1 recombinant reverse transcriptase, were 10 times less active against enzymes from nevirapine- and TIBO-resistant strains, and were totally inactive against the HIV-2 recombinant enzyme. Interestingly, some compounds (8r'-y') were inactive against the recombinant reverse transcriptase while being active in tissue culture.
The Staphylococcus aureus allelic genetic loci for serotype 5 and 8 capsule expression contain the type-specific genes flanked by common genes (1997)

The nucleotide sequences of two gene clusters, cap5 and cap8, involved in the synthesis of Staphylococcus aureus type 5 and type 8 capsular polysaccharides (CPs), respectively were determined. Each gene cluster contained 16 ORFs, which were named cap5A through cap5P for type 5 CP and cap8A through cap8P for type 8 CP. The cap5 and cap8 loci were allelic and were mapped to the SmaI-G fragment in the standard SmaI map of Staph. aureus strain NCTC 8325. The predicted gene products of cap5A through cap5G and cap5L through cap5P are essentially identical to those of cap8A through cap8G and cap8L through cap8P, respectively, with very few amino acid substitutions. Four ORFs located in the central region of each locus are type-specific. A comparison of the predicted amino acid sequences of cap5 and cap8 with sequences found in the databases allowed tentative assignment of functions to 15 of the 16 ORFs. The majority of the capsule genes are likely to be involved in amino sugar synthesis; the remainder are likely to be involved in sugar transfer, capsule chain-length regulation, polymerization and transport.
Cleavage of trehalose‐phosphate in Bacillus subtilis is catalysed by a Phospho‐α‐(1–1)‐glucosidase encoded by the treA gene (1995)

A 2.5 kb DNA fragment contain a gene encoding a phospho-alpha-(1-1)-glucosidase (phosphotrehalase), designated treA, was isolated from a Bacillus subtilis chromosomal library by complementation of the tre-12 mutation. The major TreA activity was found in the cytoplasm. TreA exhibits high sequence similarity to thermostable oligo 1,6 beta-glucosidases of several species and the trehalose-6-phosphate hydrolase TreC of Escherichia coli. TreA activity is induced by trehalose and repressed by glucose, fructose or mannitol. Induction by trehalose and repression by glucose are concentration dependent. The highest activity of TreA occurs 90 min before the end of the exponential growth phase in crude cell extracts. The enzyme is able to cleave para-nitrophenyl-glucopyranoside and trehalose-6-phosphate but not trehalose. These results indicate that treA encodes a specific phospho-alpha-(1-1)-glucosidase which cleaves trehalose-6-phosphate in the cytoplasm after transport and phosphorylation of trehalose. The 5' flanking region of treA contains an open reading frame which was partially sequenced, whose product shows about 40% identity to sucrose Enzyme II of the phosphotransferase transport system from several organisms.
YddG fromEscherichia colipromotes export of aromatic amino acids (2007)

The inner membrane protein YddG of Escherichia coli is a homologue of the known amino acid exporters RhtA and YdeD. It was found that the yddG gene overexpression conferred resistance upon E. coli cells to the inhibiting concentrations of l-phenylalanine and aromatic amino acid analogues, dl-p-fluorophenylalanine, dl-o-fluorophenylalanine and dl-5-fluorotryptophan. In addition, yddG overexpression enhanced the production of l-phenylalanine, l-tyrosine or l-tryptophan by the respective E. coli-producing strains. On the other hand, the inactivation of yddG decreased the aromatic amino acid accumulation by these strains. The cells of the E. colil-phenylalanine-producing strain containing overexpressed yddG accumulated less l-phenylalanine inside and exported the amino acid at a higher rate than the cells of the isogenic strain containing wild-type yddG. Taken together, these results indicate that YddG functions as an aromatic amino acid exporter.
Contact Stiffness and Damping Estimation for Robotic Systems (2003)

In this paper, we review and compare four algorithms for the identification of contact stiffness and damping during robot constrained motion. The intended application is dynamics modeling and simulation of robotic assembly operations in space. Accurate simulation of these tasks requires contact dynamics models, which in turn use contact stiffness and damping to calculate contact forces. Hence, our primary interest in identifying contact parameters stems from their use as inputs to simulation software with contact dynamics capability. Estimates of environmental stiffness and damping are also valuable for force tracking and stability of impedance controllers. The algorithms considered in this work include: a signal processing method, an indirect adaptive controller with modifications to identify environment damping, a model reference adaptive controller and a recursive least-squares estimation technique. The last three methods have been proposed for real-time implementation in impedance and force-tracking controllers. The signal processing scheme uses a frequency estimate calculated with fast Fourier transform of the force signal and is an off-line method. The algorithms are first evaluated using numerical simulation of a benchmark test. Experiments conducted with a robotic arm contacting a flexible wall provide a further demonstration of their performance. Our results indicate that the indirect adaptive controller has the best combination of performance and ease of use. In addition, the effect of persistently exciting signals is discussed.
Aminoglycoside-Induced Reduction in Nucleotide Mobility at the Ribosomal RNA A-Site as a Potentially Key Determinant of Antibacterial Activity (2006)

Steady-state and time-resolved fluorescence techniques have been used to characterize the energetics and dynamics associated with the interaction of an E. coli 16 S rRNA A-site model oligonucleotide and four aminoglycoside antibiotics that exhibit a broad range of antibacterial activity. The results of these characterizations suggest that aminoglycoside-induced reduction in the mobility of an adenine residue at position 1492 of the rRNA A-site is a more important determinant of antibacterial activity than drug affinity for the A-site. This observation is consistent with a recently proposed model for the mechanism of protein synthesis inhibition by aminoglycosides that invokes a drug-induced alteration in the conformational equilibrium of the rRNA A-site (centered around the conserved adenine residues at positions 1492 and 1493), which, in turn, promotes an enhanced interaction between the rRNA and the minihelix formed by the tRNA anticodon and the mRNA codon, even when the anticodon is noncognate. Regarded as a whole, the results reported here indicate that the rational design of antibiotics that target the 16 S rRNA A-site requires consideration of not only the structure and energetics of the drug-RNA complex but also the dynamics associated with that complex.
The Plasticity of Dendritic Cell Responses to Pathogens and Their Components (2001)

Dendritic cells are involved in the initiation of both innate and adaptive immunity. To systematically explore how dendritic cells modulate the immune system in response to different pathogens, we used oligonucleotide microarrays to measure gene expression profiles of dendritic cells in response to Escherichia coli, Candida albicans, and influenza virus as well as to their molecular components. Both a shared core response and pathogen-specific programs of gene expression were observed upon exposure to each of these pathogens. These results reveal that dendritic cells sense diverse pathogens and elicit tailored pathogen-specific immune responses.