gebhart/patrepeval huggingface dataset:
Enhancement of microfluidic particle separation using cross-flow filters with hydrodynamic focusing (2016)

A microfluidic chip is proposed to separate microparticles using cross-flow filtration enhanced with hydrodynamic focusing. By exploiting a buffer flow from the side, the microparticles in the sample flow are pushed on one side of the microchannels, lining up to pass through the filters. Meanwhile a larger pressure gradient in the filters is obtained to enhance separation efficiency. Compared with the traditional cross-flow filtration, our proposed mechanism has the buffer flow to create a moving virtual boundary for the sample flow to actively push all the particles to reach the filters for separation. It further allows higher flow rates. The device only requires soft lithograph fabrication to create microchannels and a novel pressurized bonding technique to make high-aspect-ratio filtration structures. A mixture of polystyrene microparticles with 2.7 μm and 10.6 μm diameters are successfully separated. 96.2 ± 2.8% of the large particle are recovered with a purity of 97.9 ± 0.5%, while 97.5 ± 0.4% of the small particle are depleted with a purity of 99.2 ± 0.4% at a sample throughput of 10 μl/min. The experiment is also conducted to show the feasibility of this mechanism to separate biological cells with the sample solutions of spiked PC3 cells in whole blood. By virtue of its high separation efficiency, our device offers a label-free separation technique and potential integration with other components, thereby serving as a promising tool for continuous cell filtration and analysis applications.
An interpersonal multimedia visualization system (1991)

Media View, a system that can be used to produce an electronic document containing mathematics, data sets, and associated visualizations, is discussed. Animations and other substructures persist through electronic mailing and can be awakened by the recipient. The features of Media View documents are described. Analysis and visualization with Media View are examined, including linking to Mathematica, producing locally derived animations, visualizing remotely produced data sets, and viewing video sequences. The architectural details of Media View are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Efficient similarity search in digital libraries (2002)

Digital libraries are a core information technology. When the stored data is complex, e.g. high-resolution images or molecular protein structures, simple query types such as exact match query are hardly applicable. In such environments similarity queries, particularly range queries and k-nearest neighbor queries, are important query types. Numerous approaches have been proposed for the processing of similarity queries which mainly concentrate on highly dynamic data sets where insertion, update, and deletion operations occur. However, only little effort has been devoted to the case of rather static data sets-frequently, occurring in digital libraries. In this paper we introduce a novel technique for efficient similarity search on top of static or rarely changing data sets. In particularly we propose a special sorting order on the data objects which can be effectively exploited to substantially reduce the total query time of similarity queries. An extensive experimental evaluation with real-world data sets emphasizes the practical impact of our technique.
Increase in AdultClostridium difficile–related Hospitalizations and Case-Fatality Rate, United States, 2000–2005 (2008)

Virulence of and deaths from Clostridium difficile-associated disease (CDAD) are on the rise in the United States. The incidence of adult CDAD hospitalizations doubled from 5.5 cases per 10,000 population in 2000 to 11.2 in 2005, and the CDAD-related age-adjusted case-fatality rate rose from 1.2% in 2000 to 2.2% in 2004.
Original Research: A Patented Strain ofBacillus coagulansIncreased Immune Response to Viral Challenge (2009)

The patented GanedenBC30 probiotic may be a safe and effective therapeutic option for enhancing T-cell response to certain viral respiratory tract infections.
A scalable and high performance software iSCSI implementation (2005)

In this paper we present two novel techniques for improving the performance of the Internet Small Computer Systems Interface (iSCSI) protocol, which is the basis for IP-based networked block storage today. We demonstrate that by making a few modifications to an existing iSCSI implementation, it is possible to increase the iSCSI protocol processing throughput from 1.4 Gbps to 3.6 Gbps. Our solution scales with the CPU clock speed and can be easily implemented in software using any general purpose processor without requiring specialized iSCSI protocol processing hardware.To gain an in-depth understanding of the processing costs associated with an iSCSI protocol implementation, we built an iSCSI fast path in a user-level sandbox environment. We discovered that the generation of Cyclic Redundancy Codes (CRCs) which is required for data integrity, and the data copy operations which are required for the interaction between iSCSI and TCP represent the main bottlenecks in iSCSI protocol processing. We propose two optimizations to iSCSI implementations to address these bottlenecks. Our first optimization is on the way CRCs are being calculated. We replace the industry standard algorithm proposed by Prof. Dilip Sarwate with 'Slicing-by-8' (SB8), a new algorithm capable of ideally reading arbitrarily large amounts of data at a time while keeping its memory requirement at reasonable level. Our second optimization is on the way iSCSI interacts with the TCP layer. We interleave the compute-intensive data integrity checks with the memory access-intensive data copy operations to benefit from cache effects and hardware pipeline parallelism.
Pro- and anti-inflammatory responses are regulated simultaneously from the first moments of septic shock (2011)

The relationships between cytokine responses in septic shock are currently poorly understood. Some studies have pointed to a biphasic model, with an initial proinflammatory phase, followed by a reactive, anti-inflammatory response to explain the pathogenesis of the most severe form of sepsis. However, evidence for the coexistence of both responses has been found. In this study, the plasma levels of 17 cytokines and chemokines, in 20 patients with septic shock, 11 patients with systemic inflammatory response syndrome (SIRS), during the first 24 hours following diagnosis, and 10 healthy controls, were analyzed and compared. Patients with septic shock showed increased levels of IL-6, IL-8, MCP-1, MIP-1β, IFN-γ, GM-CSF and IL-10 compared to healthy controls. Patients with SIRS showed higher levels of IL-6, IL-8, MCP-1, MIP-1β, G-CSF and IL-10 than controls. Patients with septic shock showed higher levels of IL-8, GM-CSF, MIP-1β than those with SIRS. The Spearman test demonstrated a positive association between the pro-inflammatory mediators IL-6, IL-8, MCP-1, MIP-1β, IFN-γ, GM-CSF and the immunomodulatory cytokine IL-10 in septic shock. Consequently, correlation studies supported the notion that secretion of pro- and anti-inflammatory mediators in septic shock occurs as a simultaneous immune response program initiated early in the course of the disease, revealing that both types of cytokine play a role from the very beginning of this life-threatening condition.
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes (2010)

Supplementary data are available at Bioinformatics online.
Subjective MSE Measures (1986)

The question of using the mean squared error (MSE) measure as a quality criterion in image processing is addressed. The MSE was evaluated as a measure of perceived similarity between an original and processed picture by comparing computed MSE values with similarity judgements. In addition, several other measures that weighted the error in accordance with assumed properties of the visual system were studied. The results obtained indicated that MSE is not very valid as a quality criterion for pictures reproduced for human viewing and the improved measures could be derived by weighting the error in accordance with assumed properties of the visual system. However, none of the tested measures were valid for all kinds of pictures. Thus picture properties also had to be incorporated in subjective error measures.
Dose escalation study of nab-paclitaxel followed by carboplatin as first line therapy in advanced non-small cell lung cancer (NSCLC) (2006)

7132 Background: Paclitaxel for injection formulated in Cremophor® and ethanol (Taxol®, Cremophor paclitaxel) 225 mg/m 2 and carboplatin area under the curve of 6 mg/min·ml (C6) administered every 3 weeks (q3w) has produced an overall response rate (ORR) of 17% in first line patients (pts) with NSCLC with a 1-year survival of 34% [Schiller et al., NEJM, 2002;346:92]. The aim of this phase II study is to obtain clinical experience with a 130-nanometer albumin-bound form of paclitaxel (Abraxane®, ABI-007, nab™ paclitaxel) followed by C6 in NSCLC to determine a dose that approximates the toxicity of Cremophor paclitaxel/C6. Methods: Pts with previously untreated, stage IIIB or IV NSCLC with measurable disease and a life expectancy of over 12 weeks were recruited. In a dose escalation schedule, 4 cohorts (n = 25 each) of successive pts received nab paclitaxel at doses of 225, 260, 300, or 340 mg/m 2 as 30-minute IV infusions followed by C6 q3w. The primary endpoints were the ORR (pts with an objective, confirmed complete or partial response) and toxicity. The primary efficacy analysis was based on all pts who received at least 1 dose of nab-paclitaxel and C6. Stable disease (SD) at ≥16 weeks was also assessed. Results: One hundred pts (100% white; 78% male; median age, 63; performance status score: 0 [11%], 1 [89%] were enrolled from 15 March–28 June of 2005. Accrual was completed in each cohort and serious adverse events reviewed prior to accrual at the next dose level. The results for ORR and SD at ≥16 weeks currently available are shown in the Table . The most common toxicities (any grade) were neutropenia, 43%; fatigue, 37%; sensory neuropathy, 37%; nausea, 35%; thrombocytopenia, 33%; anemia, 24%; alopecia, 24%; and vomiting, 21%. Conclusions: The combination demonstrated antitumor activity and was reasonably well tolerated. Mature data will be presented. [Table: see text] [Table: see text]
Assembly of Herpes Simplex virus Type 1 Capsids Using a Panel of Recombinant Baculoviruses (1994)

Immature or B capsids of herpes simplex virus type 1 (HSV-1) are composed of seven proteins encoded by six viral genes. The proteins encoded by UL18 (VP23), UL19 (VP5), UL35 (VP26) and UL38 (VP19C) are components of the outer capsid shell whereas those specified by UL26 (VP21 and VP24) and UL26.5 (VP22a), are involved in scaffold formation. We have used a panel of recombinant baculoviruses, each expressing one of the capsid protein genes, to examine the requirements for capsid assembly. Coexpression of the six genes in insect cells resulted in the formation of capsids that were indistinguishable in appearance and protein composition from those made during HSV-1 infection of mammalian cells. This demonstrates that the proteins encoded by the known capsid genes contain all the structural information necessary for capsid assembly and that other virus-encoded proteins are not required for this process. Omission of single recombinant baculoviruses from this system allowed the role of individual HSV-1 proteins in capsid assembly to be determined. Thus, capsid assembly did not take place in the absence of VP23, VP5 or VP19C, whereas lack of VP26 had no discernible effect on capsid formation. Capsids assembled in the absence of the UL26 gene products had a large-cored phenotype resembling that previously described for the HSV-1 mutant ts1201 which has a lesion in this gene. Some apparently intact capsid shells were also made in the absence of the major scaffolding protein, VP22a, whereas the omission of both UL26 and UL26.5 resulted in the appearance of large numbers of partial and deformed capsid shells.
Scattering and Absorption of Light by Nonspherical Dielectric Grains (1973)

A method is described for calculating approximate extinction, absorption, and scattering cross-sections for dielectric grains of arbitrary shape, with dimensions comparable to or smaller than the wavel&amp;ngth of the incident radiation. The grain is modeled by an array of N polarizable elements in vacuum. The elements are located on a simple cubic lattice, and N is of order of magnitude 100. The polarizability of an element is such that an unbounded array would exhibit, according to the Clausius-Mossotti relation, the bulk dielectric constant of the grain material. The complex vector amplitude of each oscillator in the array, which is driven by the field of the incident wave and the fields of all the other oscillators, is determined by an iterative procedure. From the N amplitudes all the cross-sections, including differential cross-sections, are obtained. The method was tested by comparing the cross-sections computed for "spherical" clusters of oscillators with exact Mie theory values for the corresponding dielectric spheres. Computed cross-sections a-c presented for five different grain shapes and three different complex refractive indices. Subject headings: interstellar matter - opacities polarization
Low-Temperature Stability and High-Temperature Reactivity of Iron-Based Core−Shell Nanoparticles (2004)

Iron-based core-shell nanoparticles have been prepared that exhibit low-temperature stability and high-temperature reactivity toward oxygen in solution. The concentration of oxygen was determined from the fluorescence decay of pyrene. At low temperatures (<110 degrees C), the decays are short, indicating oxygen in solution. At higher temperatures (>110 degrees C), the decays become long and are consistent with no oxygen in solution. The change is abrupt, occurring over a narrow temperature range, and reproducible.
Structure and function in rhodopsin: High-level expression of rhodopsin with restricted and homogeneous N-glycosylation by a tetracycline-inducible N -acetylglucosaminyltransferase I-negative HEK293S stable mammalian cell line (2002)

An HEK293S cell line resistant to ricin was prepared by mutagenesis by using ethyl methanesulfonate. It was shown to lack N-acetylglucosaminyltransferase I (GnTI) activity, and consequently unable to synthesize complex N-glycans. The tetracycline-inducible opsin expression system was assembled into this GnTI(-) HEK293S cell line. Stable cell lines were isolated that gave tetracycline/sodium butyrate-inducible expression of the WT opsin gene at levels comparable with those observed in the parent tetracycline-inducible HEK293S cell line. Analysis of the N-glycan in rhodopsin expressed by the HEK293S GnTI(-) stable cell line showed it to be Man(5)GlcNAc(2). In a larger-scale expression experiment (1.1 liter) a WT opsin production level of 6 mg/liter was obtained. Further, the toxic constitutively active rhodopsin mutant, E113Q/E134Q/M257Y, previously shown to require inducible expression, has now been expressed in an HEK293S GNTI(-)-inducible cell line at levels comparable with those obtained with WT rhodopsin.
Cloning, expression, and type II collagenolytic activity of matrix metalloproteinase-13 from human osteoarthritic cartilage. (1996)

Proteolysis of triple-helical collagen is an important step in the progression toward irreversible tissue damage in osteoarthritis. Earlier work on the expression of enzymes in cartilage suggested that collagenase-1 (MMP-1) contributes to the process. Degenerate reverse transcription polymerase chain reaction experiments, Northern blot analysis, and direct immunodetection have now provided evidence that collagenase-3 (MMP-13), an enzyme recently cloned from human breast carcinoma, is expressed by chondrocytes in human osteoarthritic cartilage. Variable levels of MMP-13 and MMP-1 in cartilage was significantly induced at both the message and protein levels by interleukin-1 alpha. Recombinant MMP-13 cleaved type II collagen to give characteristic 3/4 and 1/4 fragments; however, MMP-13 turned over type II collagen at least 10 times faster than MMP-1. Experiments with intact type II collagen as well as a synthetic peptide suggested that MMP-13 cleaved type II collagen at the same bond as MMP-1, but this was then followed by a secondary cleavage that removed three amino acids from the 1/4 fragment amino terminus. The expression of MMP-13 in osteoarthritic cartilage and its activity against type II collagen suggest that the enzyme plays a significant role in cartilage collagen degradation, and must consequently form part of a complex target for proposed therapeutic interventions based on collagenase inhibition.
Histopathological follow-up study of 66 cerebral arteriovenous malformations after therapeutic embolization with polyvinyl alcohol (1992)

Embolization with polyvinyl alcohol (PVA) is an accepted method of rendering complex arteriovenous malformations (AVM's) more amenable to surgery, but its effects on human vascular tissues have not been adequately documented. The authors reviewed the histopathology of 66 intracranial AVM's resected 1 to 76 days after embolization with PVA. The mean age of the patients was 36 years, and their AVM's were located in the cerebral hemispheres (92%), the cerebellum (6%), or the corpus callosum (2%). In 79% of cases, at least one vessel contained PVA particles; in most cases, the vessel was filled with sharp, angular PVA particles in a serpiginous pattern. Polyvinyl alcohol particles indented the endothelium in 69% of cases but were rarely found subendothelially. Clotted blood and fibroblasts were present among the particles, and abundant intraluminal mononuclear and polymorphonuclear inflammatory cells were found in all vessels containing PVA particles. Foreign-body giant cells appeared 2 to 14 days after embolization in the majority of cases. Patchy mural angionecrosis and necrotizing vasculitis were found in 39% of the cases. Recanalized lumina were seen in 18% of PVA-embolized vessels. Foreign materials resembling cotton fibers and other particulate substances, which were probably contaminants of the contrast solution or the embolic material, were found in 65% of the cases. These findings suggest a specific chain of events in the interaction between PVA and vessel wall components and may explain some important sequelae of embolization therapy.
Bio-Based Industrial Products: Priorities for Research and Commercialization (2000)

Petroleum-based industrial products have gradually replaced products derived from biological materials. However, biologically based products are making a comeback--because of a threefold increase in farm productivity and new technologies. Biobased Industrial Products envisions a biobased industrial future, where starch will be used to make biopolymers and vegetable oils will become a routine component in lubricants and detergents. Biobased Industrial Products overviews the U.S. land resources available for agricultural production, summarizes plant materials currently produced, and describes prospects for increasing varieties and yields. The committee discusses the concept of the biorefinery and outlines proven and potential thermal, mechanical, and chemical technologies for conversion of natural resources to industrial applications. The committee also illustrates the developmental dynamics of biobasedproducts through existing examples, as well as products still on the drawing board, and itidentifies priorities for research and development. Authors: Committee on Biobased Industrial Products, National Research Council
Correction of scoliosis using segmental pedicle screw instrumentation versus hybrid constructs with hooks and screws. (2006)

Eighteen consecutive patients with scoliosis surgically treated by posterior correction and fusion were recruited. The major coronal curve averaged 65.8 degrees (range 51 degrees -87 degrees ). Eight patients were treated by hybrid constructs and four of them had anterior release before posterior surgery. Ten patients were treated by posterior correction and fusion alone with pedicle screw instrumentation. Flexibility was assessed by radiographs using the active bending and the fulcrum bending techniques. Two correction indices were not statistically different between the two groups. However, there was a tendency towards better correction in the screw group: mean surgical correction was 62.6+/-11.8% in the hook group and 71.6+/-12.3% in the screw group (p=0.07). Comparable pre- and post-operative radiographic results may indicate the advantages of posterior-only segmental pedicle screw instrumentation over hybrid constructs.
Cyclic RGD peptide inhibits alpha 4 beta 1 interaction with connecting segment 1 and vascular cell adhesion molecule (1994)

The integrin supergene family includes receptors for a variety of extracellular matrix as well as cell surface proteins. Integrin alpha 4 has been shown to play an important role in leukocyte adhesion and extravasation during immune and inflammatory reactions. One recognition sequence known to interact with alpha 4 is the Leu-Asp-Val (LDV) site contained in the connecting segment 1 region of fibronectin. Here we present evidence that shows that a conformationally restricted RGD-containing peptide is a potent inhibitor of cell adhesion mediated by alpha 4 beta 1, a receptor not convincingly documented to interact with RGD peptides. This peptide, 1-adamantaneacetyl-Cys-Gly-Arg-Gly-Asp-Ser-Pro-Cys (disulfide bridge between residues 1-8), blocks Jurkat cell adhesion to connecting segment 1-containing peptides as well as cell adhesion to cytokine-activated endothelial cells. Adhesion of Jurkat cells to either vascular cell adhesion molecule-expressing cells or recombinant vascular cell adhesion molecule-coated plates was likewise inhibited by this peptide. Furthermore, alpha 4 beta 1 can bind directly to a cyclic RGD peptide immobilized to Sepharose. Integrins, alpha 5 beta 1, alpha v beta 3, alpha IIb/beta IIIa, alpha 2 beta 1, alpha v beta 1, alpha v beta 5, alpha v beta 6, and alpha 3 beta 1, have been shown to recognize the Arg-Gly-Asp (RGD) sequence present in a variety of extracellular matrix proteins, and our data support the addition of alpha 4 beta 1 to this group. Further studies using molecular modeling of such cyclic RGD peptides could help in the design of more potent peptides or nonpeptide mimetics that could effectively block alpha 4-mediated activity and have potential application in a number of inflammatory diseases.