gebhart/patrepeval huggingface dataset:
Cloned Genomic DNA of Type 2 Porcine Circovirus Is Infectious When Injected Directly into the Liver and Lymph Nodes of Pigs: Characterization of Clinical Disease, Virus Distribution, and Pathologic Lesions (2002)

Infection of animals with a molecular viral clone is critical to study the genetic determinants of viral replication and virulence in the host. Type 2 porcine circovirus (PCV2) has been incriminated as the cause of postweaning multisystemic wasting syndrome (PMWS), an emerging disease in pigs. We report here for the first time the construction and use of an infectious molecular DNA clone of PCV2 to characterize the disease and pathologic lesions associated with PCV2 infection by direct in vivo transfection of pigs with the molecular clone. The PCV2 molecular clone was generated by ligating two copies of the complete PCV2 genome in tandem into the pBluescript SK (pSK) vector and was shown to be infectious in vitro when transfected into PK-15 cells. Forty specific-pathogen-free pigs at 4 weeks of age were randomly assigned to four groups of 10 each. Group 1 pigs served as uninoculated controls. Pigs in group 2 were each inoculated intranasally with about 1.9 x 10(5) 50% tissue culture infective doses of a homogeneous PCV2 live virus stock derived from the molecular clone. Pigs in group 3 were each injected intrahepatically with 200 microg of the cloned PCV2 plasmid DNA, and pigs in group 4 were each injected into the superficial iliac lymph nodes with 200 microg of the cloned PCV2 plasmid DNA. Animals injected with the cloned PCV2 plasmid DNA developed infection resembling that induced by intranasal inoculation with PCV2 live virus stock. Seroconversion to PCV2-specific antibody was detected in the majority of pigs from the three inoculated groups at 35 days postinoculation (DPI). Viremia, beginning at 14 DPI and lasting 2 to 4 weeks, was detected in the majority of the pigs from all three inoculated groups. There were no remarkable clinical signs of PMWS in control or any of the inoculated pigs. Gross lesions in pigs of the three inoculated groups were similar and were characterized by systemically enlarged, tan lymph nodes and lungs that failed to collapse. Histopathological lesions and PCV2-specific antigen were detected in numerous tissues and organs, including brain, lung, heart, kidney, tonsil, lymph nodes, spleen, ileum, and liver of infected pigs. This study more definitively characterizes the clinical course and pathologic lesions exclusively attributable to PCV2 infection. The data from this study indicate that the cloned PCV2 genomic DNA may replace infectious virus for future PCV2 pathogenesis and immunization studies. The data also suggest that PCV2, although essential for development of PMWS, may require other factors or agents to induce the full spectrum of clinical signs and lesions associated with advanced cases of PMWS.
A Novel Method For Spatial Measurement Of Holes (1987)

Accurately locating the three dimensional position of a hole is critical for many manufacturing applications of machine vision. A novel method for locating a hole combines the use of backlighting with structured light. The centroid of the image of the backlit hole defines a line in space along which the center of the actual hole must lie. The cross of structured light is then used to determine the plane( surface ) on which the hole is located. Hence, the intersection of the line and plane defines the three dimensional position of the hole in space. The strength of the approach is the large amount of data used to obtain both the line position and the plane location. Thus, the approach is robust and has good immunity to noise, unlike many pure structured light techniques. The approach is also unaffected by changes in the orientation of the hole. It avoids the difficult problem encountered in stereo vision of having to create good images from two different viewing angles.
Porphyromonas gingivalis Type IX Secretion Substrates Are Cleaved and Modified by a Sortase-Like Mechanism (2015)

The type IX secretion system (T9SS) of Porphyromonas gingivalis secretes proteins possessing a conserved C-terminal domain (CTD) to the cell surface. The C-terminal signal is essential for these proteins to translocate across the outer membrane via the T9SS. On the surface the CTD of these proteins is cleaved prior to extensive glycosylation. It is believed that the modification on these CTD proteins is anionic lipopolysaccharide (A-LPS), which enables the attachment of CTD proteins to the cell surface. However, the exact site of modification and the mechanism of attachment of CTD proteins to the cell surface are unknown. In this study we characterized two wbaP (PG1964) mutants that did not synthesise A-LPS and accumulated CTD proteins in the clarified culture fluid (CCF). The CTDs of the CTD proteins in the CCF were cleaved suggesting normal secretion, however, the CTD proteins were not glycosylated. Mass spectrometric analysis of CTD proteins purified from the CCF of the wbaP mutants revealed the presence of various peptide/amino acid modifications from the growth medium at the C-terminus of the mature CTD proteins. This suggested that modification occurs at the C-terminus of T9SS substrates in the wild type P. gingivalis. This was confirmed by analysis of CTD proteins from wild type, where a 648 Da linker was identified to be attached at the C-terminus of mature CTD proteins. Importantly, treatment with proteinase K released the 648 Da linker from the CTD proteins demonstrating a peptide bond between the C-terminus and the modification. Together, this is suggestive of a mechanism similar to sortase A for the cleavage and modification/attachment of CTD proteins in P. gingivalis. PG0026 has been recognized as the CTD signal peptidase and is now proposed to be the sortase-like protein in P. gingivalis. To our knowledge, this is the first biochemical evidence suggesting a sortase-like mechanism in Gram-negative bacteria.
A comparison of probabilistic classifiers for sleep stage classification (2018)

The results suggest that CRFt is not only better at learning and predicting more complex and irregular sleep architectures, but that it also performs reasonably well in five-class classification-the standard for sleep scoring used in clinical PSG. Additionally, and albeit with a decrease in performance when compared with healthy participants, sleep stage classification in OSA patients using cardiorespiratory features and CRFt seems feasible with reasonable accuracy.
Propane/Propylene Separation by Simulated Moving Bed II. Measurement and Prediction of Binary Adsorption Equilibria of Propane, Propylene, Isobutane, and 1-Butene on 13X Zeolite (2009)

Abstract The design of a simulated moving bed (SMB) process relies on valid thermodynamic predictions of multicomponent adsorption built up from accurate binary adsorption equilibrium data. Experimental adsorption equilibria of binary mixtures constituted by propane, propylene, isobutane and 1-butene on 13X zeolite were determined using breakthrough experiments at 373 K and 150 kPa. In addition, these binary adsorption experiments allow to confirm the choice of isobutane as an interesting desorbent for the separation of propane-propylene by SMB, since it has an intermediate selectivity between the two species to separate. Various prediction models are available in the literature but only a few of them have both physical and thermodynamical consistency. The ideal adsorbed solution theory (IAST), the thermodynamically consistent extended Toth model (TCET), and the physically-consistent extended Toth isotherm (PCET) were used to predict binary adsorption equilibria from pure component adsorption isotherms parameters. The PCET model was found suitable for representing the adsorption equilibrium of the different hydrocarbon mixtures with a reasonably good accuracy.
Optical Absorption of Silver in Photochromic Glasses: Optically Induced Dichroism (1980)

The absorption spectrum of silver halide‐based photochromic glasses darkened by uv light is shown to vary with glass composition and photochromic heat treatment. The nature of the absorption is explained in terms of the anisotropic geometry of the photolytically produced silver specks. A correlation is established between the uv‐induced spectrum and the dichroic behavior that can be induced by bleaching with polarized light. A specific model is proposed for the silver‐speck geometry and calculations show goad agreement with experimental data.
Semisynthetic Artemisinin, the Chemical Path to Industrial Production (2014)

A new commercial-scale alternative manufacturing process to produce a complementary source of artemisinin to supplement the plant-derived supply is described by conversion of biosynthetic artemisinic acid into semisynthetic artemisinin using diastereoselective hydrogenation and photooxidation as pivotal steps. This process was accepted by Prequalification of Medicines Programme (PQP) in 2013 as a first source of nonplant-derived-artemisinin in industrial scale from Sanofi production facility in Garessio, Italy.
Full-diversity full-rate complex-field space-time coding (2003)

Exciting developments in wireless multiantenna communications have led to designs aiming mainly at one of two objectives: either high-performance by enabling the diversity provided by multi-input multi-output (MIMO) channels or high-rates by capitalizing on space-time multiplexing gains to realize the high capacity of MIMO fading channels. By concatenating a linear complex-field coder (a.k.a. linear precoder) with a layered space-time mapper, we design systems capable of achieving both goals: full-diversity and full-rate (FDFR), with any number of transmit- and receive-antennas. We develop FDFR designs not only for flat-fading but for frequency-selective, or, time-selective fading MIMO channels as well. Furthermore, we establish the flexibility of our FDFR designs in striking desirable performance-rate-complexity tradeoffs. Our theoretical claims are confirmed by simulations.
Enhancing Prostate‐Cancer‐Specific MRI by Genetic Amplified Nanoparticle Tumor Homing (2019)

Precise localization and visualization of early-stage prostate cancer (PCa) is critical to improve the success of focal ablation and reduce cancer mortality. However, it remains challenging under the current imaging techniques due to the heterogeneous nature of PCa and the suboptimal sensitivity of the techniques themselves. Herein, a novel genetic amplified nanoparticle tumor-homing strategy to enhance the MRI accuracy of ultrasmall PCa lesions is reported. This strategy could specifically drive TfR expressions in PCa under PCa-specific DD3 promoter, and thus remarkably increase Tf-USPIONs concentrations in a highly accurate manner while minimizing their non-specific off-target effects on normal tissues. Consequently, this strategy can pinpoint an ultrasmall PCa lesion, which is otherwise blurred in the current MRI, and thereby addresses the unmet key need in MRI imaging for focal therapy. With this proof-of-concept experiment, the synergistic gene-nano strategy holds great promise to boost the MRI effects of a wide variety of commonly used nanoscale and molecular probes that are otherwise limited. In addition, such a strategy may also be translated and applied to MR-specific imaging of other types of cancers by using their respective tumor-specific promoters.
Position Control in Lithographic Equipment [Applications of Control] (2011)

This article describes the basic optical principles in the lithographic tool, with the resulting positioning accuracy requirements. For three generations of lithographic tools, the mechatronic architecture and control implications are discussed. Then, six degrees of freedom (DOF) stage control is described with the main focus on actuator force decoupling, allowing the use of classical single-input, single-output (SISO) controllers.
Virtual Network Embedding With Guaranteed Connectivity Under Multiple Substrate Link Failures (2019)

This paper addresses Connectivity-aware Virtual Network Embedding (CoViNE) problem, which consists in embedding a virtual network (VN) on a substrate network while ensuring VN connectivity (without any bandwidth guarantee) against multiple substrate link failures. CoViNE provides a weaker form of survivability incurring less resource overhead than traditional VN survivability models. To optimally solve CoViNE, we present an Integer Linear Program (ILP), namely CoViNE-opt. CoViNE-opt enumerates an exponential number of edge-cuts in a VN severely limiting its scalability. Therefore, we decompose CoViNE into three sub-problems: i) augmenting a VN with virtual links to provide necessary connectivity, ii) identifying the virtual links that should be embedded disjointly, and iii) computing a VN embedding while satisfying the disjointness constraints. We introduce conflicting set abstraction that allows to address sub-problems (i) and (ii) without enumerating all the edge-cuts of a VN. We propose two novel solutions to CoViNE leveraging conflicting set, namely CoViNE-ILP and CoViNE-fast. CoViNE-ILP uses a heuristic algorithm to address sub-problems (i) and (ii), while an ILP is used for sub-problem (iii). In contrast, CoViNE-fast uses heuristics for solving all three sub-problems. Through simulation, we evaluate the optimality and scalability of our solutions and demonstrate a failure restoration use-case enabled by CoViNE.
Continuous enzymatic transformation in an enzyme membrane reactor with simultaneous NAD(H) regeneration (1981)

Abstract Multienzyme reaction systems with simultaneous coenzyme regeneration have been investigated in a continuously operated membrane reactor at bench scale. NAD(H) covalently bound to polyethylene glycol with a molecular weight of 10 4 [PEG‐10,000‐NAD(H)] was used as coenzyme. It could be retained in the membrane reactor together with the enzymes. L ‐leucine dehydrogenase (LEUDH) was used as catalyze for the reductive amination of α‐ketoisocaproate (2‐oxo‐4‐methylpentanoic acid) to L ‐leucine. Format dehydrogenease (FDH) was used for the regeneration of NADH. Kinetic experiments were carried out to obtain data which could be used in a kinetic model in order to predict the performance of an enzyme membrane reactor for the continuous production of L ‐leucine. The kinetic constants V max and K m of enzymes are all in the same range regardless of whether native NAD(H) or PEG‐10,000‐NAD(H) is used as coenzyme. L ‐leucine was produced continuously out of α‐ketoisocaproate for 48 days; a maximal conversion of 99.7% was reached. The space‐time yield was 324 mmol/L day (or 42.5 g/L day).
New consistency theorem of motion contaminated projection data and applications in motion artifacts correction (2012)

In recent years, iterative image reconstruction algorithms have received much interest in x-ray CT imaging. Images reconstructed by the conventional filtered backprojection algorithm are often used as seed images to start the iterations. This paper presents a new consistency property of the measured CT projection data and the forward projected data from a motion contaminated image reconstructed using an analytical image reconstruction algorithm. It is theoretically proven and numerically validated that, when the measured projection data is not redundant, the measured projection data is consistent with the forward projected data of a reconstructed image using analytical image reconstruction algorithms, no matter whether motion artifacts are present in the image or not. However, when there is redundancy in the measured projection data, the consistency depends on the choice of weighting function used for the redundant data. The forward projected data is always consistent with those measured projections with the weight 1.0, no matter what weighting schemes are used. For the measured projection data with a weight smaller than 1.0, the forward projected data is consistent with the weighted sum of redundantly measured projection data. With this new property, some potential issues of directly using FBP images as seed images for iterative algorithms are discussed.
Enzymatic Production of<i>trans</i>-4-Hydroxy-<scp>L</scp>-proline by Regio- and Stereospecific Hydroxylation of<scp>L</scp>-Proline (2000)

A proline 4-hydroxylase gene, which was cloned from Dactylosporangium sp. RH1, was overexpressed in Escherichia coli W1485 on a plasmid under a tryptophan tandem promoter after the codon usage of the 5' end of the gene was optimized. The proline 4-hydroxylase activity was l600-fold higher than that in Dactylosporangium sp. RH1. trans-4-Hydroxy-L-proline(Hyp) was produced and accumulated to 41 g/L (87% yield from L-proline) in 100 h when the recombinant E. coli was cultivated in a medium containing L-proline and glucose. 2-Oxoglutarate, which is necessary for the hydroxylation of L-proline by proline 4-hydroxylase, was apparently supplied from glucose through the cellular metabolic pathway. The putA mutant of W1485, which is not able to degrade L-proline, has allowed the quantitative conversion of L-proline to Hyp. The formation of other isomers of hydroxyproline was not observed. Productivity of Hyp was almost the same in a larger-scale culture. The method of manufacturing Hyp from L-proline was established.
Functional activity of antibodies to the group B polysaccharide of group B streptococci elicited by a polysaccharide-protein conjugate vaccine (1994)

Group B streptococci (GBS) are a major cause of sepsis and meningitis in infants. While antibodies directed to the type-specific GBS capsule have been shown to be protective, it is less clear whether antibodies to the group B polysaccharide, a noncapsular, cell wall-associated antigen, may play a role in immunity. To investigate the functional activity of group B polysaccharide-specific antibodies, we tested sera from rabbits vaccinated with group B polysaccharide coupled to tetanus toxoid (B-TT). Anti-B-TT was weakly opsonic in vitro for a highly encapsulated type III strain, while antiserum elicited by vaccination with type III capsular polysaccharide linked to tetanus toxoid (III-TT) was a very effective opsonin. In contrast to anti-III-TT, anti-B-TT given before or after bacterial challenge was only marginally effective in protecting newborn mice against lethal infection with type III GBS. The number of C3 molecules bound to type III GBS was augmented by anti-III-TT but not by high antibody concentrations of anti-B-TT. These results suggest that the difference in opsonic activity between anti-B-TT and anti-III-TT may be due to a difference in their ability to deposit C3. In addition, the maximum number of antibody molecules bound to the bacterial surface was greater for anti-III-TT than for anti-B-TT. That anti-B-TT binds to fewer sites than anti-III-TT may explain the differences in complement activation and in opsonic and protective efficacy of antibodies to group B polysaccharide compared with antibodies to the type-specific capsular polysaccharide.
Circulating miRNAs as Surrogate Markers for Circulating Tumor Cells and Prognostic Markers in Metastatic Breast Cancer (2012)

This is the first study to document the capacity of circulating miRNAs to indicate CTC status and their potential as prognostic markers in patients with MBC.
Photodynamic therapy for malignant pleural mesothelioma: the future of treatment? (2011)

Malignant pleural mesothelioma is a deadly incurable cancer, with a median survival of approximately 9 months. The best available chemotherapy, arguably the standard of care, only yields a 40% response rate and an 11-week extension in median survival. Surgery, the modality most likely to be associated with prolonged remission, remains investigational and must always be combined with other modalities in an effort to treat the microscopic disease that will remain even after the most aggressive operations. One such modality, photodynamic therapy, is a light-based cancer treatment that has features making it particularly well suited as a component of a surgery-based multimodal treatment plan. Utilizing intraoperative photodynamic therapy has enabled development of a less drastic surgical procedure that is also yielding some encouraging survival results. A unique aspect of photodynamic therapy is its stimulation of a tumor-directed immune response, a feature that offers promise for designing future treatments.
ChemInform Abstract: A Practical Synthesis of Azetidine. (1988)

Abstract A method for the large scale synthesis of azetidine (V) is described and compared with other syntheses of (V).
A Porcine Model for Adipose Tissue-Derived Endothelial Cell Transplantation (1992)

The transplantation of endothelial cells represents a technology which has been suggested for applications ranging from improvement in function of implanted vascular devices to genetic therapy. The use of microvascular endothelial cell transplantation has seen increased use both in animal studies as well as clinical use. This report describes our techniques for the isolation and establishment of initial cultures of microvascular endothelial cells derived from porcine fat. A variety of anatomic sites within the pig were evaluated to determine the appropriateness of different sources of fat for endothelial cell isolation. The properitoneal fat was determined to be optimal due to the predominance of endothelium in this tissue and the ease of isolation of microvascular endothelium following collagenase digestion. The study of endothelial cell transplantation in the porcine model is now possible using the methods described for adipose tissue-derived microvessel endothelial cell isolation.
Data Prefetching for Large Tiered Storage Systems (2017)

In multi-tier storage systems with large amounts of data, most of the data is stored on inexpensive slower tiers such as cloud or tape to achieve cost savings. This also implies that retrieving the data from the slower storage tiers incurs high latency. Therefore, it would be beneficial to proactively prefetch data from slower tiers to faster tiers by predicting future data accesses. State-of-the-art access prediction methods typically record access history of individual files, data objects, or data segments. However, in systems with large amounts of infrequently accessed (or cold) data, file-level access history is often unavailable for much of the data due to the low frequency of access. In this paper, we extract information from file metadata to predict file accesses in a storage system. The proposed method relies on the hypothesis that users and applications access data stored in the system in a given context and that the context and, therefore, the set of files that are likely to be accessed can be identified by detecting access patterns in file metadata. As an application, we consider the LOFAR radio telescope's long term archive, where the access patterns are learned based on a rich set of metadata, and these patterns are then used to make predictions as to likely future accesses by the astronomers.