gebhart/patrepeval huggingface dataset:
Spatially Controlled Chemistry Using Remotely Guided Nanoliter Scale Containers (2006)

In this communication we describe a new chemical encapsulation and release platform using 3D microfabricated nanoliter scale containers with controlled porosity. The containers can be fabricated of magnetic materials that allow them to be remotely guided using magnetic fields. The favorable attributes of the containers that include a versatile highly parallel fabrication process, precisely engineered porosity, isotropic/anisotropic chemical release profiles, and remote magnetic guiding provide an attractive platform for engineering spatially controlled chemical reactions in microfluidic systems.
Detection and Characterization of Verocytotoxin-Producing Escherichia coli by Automated 5′ Nuclease PCR Assay (2003)

In recent years increased attention has been focused on infections caused by isolates of verocytotoxin-producing Escherichia coli (VTEC) serotypes other than O157. These non-O157 VTEC isolates are commonly present in food and food production animals. Easy detection, isolation, and characterization of non-O157 VTEC isolates are essential for improving our knowledge of these organisms. In the present study, we detected VTEC isolates in bovine fecal samples by a duplex 5' nuclease PCR assay (real-time PCR) that targets vtx1 and vtx2. VTEC isolates were obtained by colony replication by use of hydrophobic-grid membrane filters and DNA probe hybridization. Furthermore, we have developed 5' nuclease PCR assays for the detection of virulence factors typically present in VTEC isolates, including subtypes of three genes of the locus of enterocyte effacement (LEE) pathogenicity island. The 22 assays included assays for the detection of verocytotoxin genes (vtx1, vtx2), pO157-associated genes (ehxA, katP, espP, and etpD), a recently identified adhesin (saa), intimin (eae, all variants), seven subtypes of eae, four subtypes of tir, and three subtypes of espD. A number of reference strains (VTEC and enteropathogenic E. coli strains) and VTEC strains isolated from calves were tested to validate the PCR assays. The expected virulence profiles were detected for all reference strains. In addition, new information on the subtypes of LEE genes was obtained. For reference strains as well as bovine isolates, a consistent relationship between subtypes of the LEE genes was found, so that a total of seven different combinations of these were recognized (corresponding to the seven subtypes of eae). Isolates with 15 different serogroup-virulence profiles were isolated from 16 calves. Among these, 53% harbored LEE and 73% harbored factors carried by the large virulence plasmid. One LEE-negative isolate had the gene for the adhesin Saa. The most common virulence profile among the bovine isolates was vtx1, eae-zeta, tir-alpha, ehxA, and espP. This panel of assays offers an easy method for the extensive characterization of VTEC isolates.
Graph Databases (2013)

Discover how graph databases can help you manage and query highly connected data. With this practical book, you’ll learn how to design and implement a graph database that brings the power of graphs to bear on a broad range of problem domains. Whether you want to speed up your response to user queries or build a database that can adapt as your business evolves, this book shows you how to apply the schema-free graph model to real-world problems. Learn how different organizations are using graph databases to outperform their competitors. With this book’s data modeling, query, and code examples, you’ll quickly be able to implement your own solution.Model data with the Cypher query language and property graph model Learn best practices and common pitfalls when modeling with graphs Plan and implement a graph database solution in test-driven fashion Explore real-world examples to learn how and why organizations use a graph database Understand common patterns and components of graph database architecture Use analytical techniques and algorithms to mine graph database information
Secular Trends in the Rates of Preeclampsia, Eclampsia, and Gestational Hypertension, United States, 1987-2004 (2008)

The increase in gestational hypertension may be exaggerated because of the revised clinical guidelines published in the 1990s; these same revisions would likely have reduced diagnoses of preeclampsia. Therefore, our observation of a small but consistent increase in preeclampsia is a conservative indication of a true population-level change.
Car trajectory prediction in image processing and control manners (2016)

This paper studies car trajectory predictions desired in several active safety systems, such as automatic emergency braking (AEB) systems and lane keeping systems (LKS). In the former, the car trajectory is estimated such that objects detected within this trajectory in front of current host vehicle are taken into consideration of collision avoidance. In LKS, the trajectory predictor is utilized to evaluate a lateral displacement so as to keep the host car running within the selected lane by reducing this displacement. To accomplish the prediction task, a trajectory estimation strategy is newly proposed in a fusion manner. First, a road model - capturing road geometry characteristics and combined with a vehicle dynamics - is referred; it includes two parameters related to road curvature, which are both estimated in a nonlinear manner. An image processing mechanism is alternatively adopted as a compensating curvature estimator if the proposed observer was in transient response. After the evaluation of road curvature, the vehicle trajectory in future few seconds are estimated in a series of path positions for the car mass center. Experimental results show the proposed predictor guarantees at least 95% of estimation preciseness compared to a real path. Target sensing in AEB worked rapidly in real-world tests with the aid of the path estimator.
Efficient capture of circulating tumor cells with a novel immunocytochemical microfluidic device (2011)

Ability to perform cytogenetic interrogations on circulating tumor cells (CTCs) from the blood of cancer patients is vital for progressing toward targeted, individualized treatments. CTCs are rare compared to normal (bystander) blood cells, found in ratios as low as 1:10(9). The most successful isolation techniques have been immunocytochemical technologies that label CTCs for separation based on unique surface antigens that distinguish them from normal bystander cells. The method discussed here utilizes biotin-tagged antibodies that bind selectively to CTCs. The antibodies are introduced into a suspension of blood cells intending that only CTCs will display surface biotin molecules. Next, the cell suspension is passed through a microfluidic channel that contains about 9000 transverse, streptavidin coated posts. A CTC making contact with a post has the opportunity to engage in a biotin-streptavidin reaction that immobilizes the cell. Bystander blood cells remain in suspension and pass through the channel. The goal of the present study is to establish the technical performance of these channels as a function of antigen density and operating conditions, especially flow rate. At 18 μL/min, over 70% of cells are captured at antigen densities greater than 30 000 sites/cell while 50% of cells are captured at antigen densities greater than 10 000. It is found that lower flow rates lead to decreasing cell capture probabilities, indicating that some streamlines develop which are never close enough to a post to allow cell-post contact. Future modeling and streamline studies using computational fluid dynamics software could aid in optimization of channel performance for capture of rare cells.
The NB protein is an integral component of the membrane of influenza B virus (1996)

The results of biochemical and immunoelectron microscopic studies provide evidence that the NB protein is an integral component of the influenza B virion. Its glycosylation and orientation in the membrane were shown to be equivalent to that of NB in the plasma membrane of virus-infected cells. Sensitivity to proteinase K showed that the N terminus is exterior to the virion and gold immunolabelling of freeze-fractured replicas showed that the C terminus is located in the interior of the virion. The similarities between NB of influenza B and M2 of influenza A viruses in structural features, their presence in the virion and possession of an ion channel activity suggest that, by analogy with the M2 protein, NB may also have a role in virus entry.
Naked RNA vaccine controls tumors with down‐regulated MHC class I expression through NK cells and perforin‐dependent pathways (2004)

One of the major issues facing cancer immunotherapy is that many human cancers down-regulate expression of MHC class I molecules. The understanding of the mechanisms of antitumor effects against tumors with down-regulated MHC class I will facilitate rational design of vaccines and immunotherapeutic strategies to control such tumors. A naked Sindbis RNA replicon vector (SINrep5) encoding the herpes simplex virus type 1 protein VP22 linked to E7 (SINrep5-VP22/E7) generated significant antitumor effects against TC-1 and TC-1 P3(A15), tumors with down-regulated MHC class I expression. Naked SINrep5 RNA without the insert or an E7 vaccine also produced antitumor effects against TC-1 P3(A15) but not TC-1. Mice vaccinated with any of these naked RNA vaccines generated higher percentages of NK cells. In vivo Ab depletion experiments revealed that NK cells were important for the antitumor effects of naked RNA vaccines against TC-1 P3(A15) and that the antitumor effects were perforin-dependent. Poly I:C also increased the percentage of NK cells and generated antitumor effects against the tumors with down-regulated MHC class I. Thus, the SINrep5-VP22/E7 naked RNA vaccine controls MHC class I-positive and MHC class I-down-regulated tumor cells via different mechanisms, and NK cells play an important role in the antitumor effects generated by naked RNA replicon vaccines.
Relationship between parathyroid hormone secretion and cytosolic calcium concentration in dispersed bovine parathyroid cells. (1984)

The parathyroid cell is unusual among exocytotic systems in that low extracellular Ca2+ concentrations stimulate, while high Ca2+ concentrations inhibit, parathyroid hormone (PTH) release, suggesting that this cell might have unique secretory mechanisms. In the present studies, we used the Ca2+-sensitive fluorescent dye QUIN -2 to examine the relationship between cytosolic Ca2+ concentration and PTH release in dispersed bovine parathyroid cells. The secretagogue dopamine, which enhances PTH release 2- to 3-fold in association with 20- to 30-fold increases in cellular cAMP, had no effect on the cytosolic Ca2+ level (261 +/- 28 vs. 236 +/- 22 nM for control cells at 1 mM extracellular Ca2+; P greater than 0.05). Dibutyryl-cAMP, which produces a comparable stimulation of PTH release, likewise did not modify the level of cytosolic Ca2+. Removal of extracellular Ca2+ produced a further decrease of the cytosolic Ca2+ to 82 +/- 10 nM. However, PTH secretion persisted at a near maximal rate despite this decrease of extracellular and cytosolic Ca2+ and was 95 +/- 2.5% of the rate of hormonal release at 0.5 mM extracellular Ca2+. In contrast, addition of the divalent cation ionophore ionomycin to parathyroid cells at 1.0 mM extracellular Ca2+ inhibited PTH secretion in association with an increase in cytosolic Ca2+ from 230 +/- 13 nM to 570 +/- 50 nM. Moreover, the magnitude of the ionomycin-induced reduction in PTH secretion (64 +/- 4% relative to the secretory rate at 0.5 mM Ca2+) was equivalent to the inhibition of PTH release caused by 1.5 mM extracellular Ca2+ (64 +/- 6%), which increased the cytosolic Ca2+ to similar levels (450 +/- 48 nM). Thus, the parathyroid cell differs from secretory cells thought to operate by stimulus-secretion coupling in the following ways: changes in PTH release can occur without detectable alterations in the cytosolic Ca2+ concentration, maximal rates of PTH secretion occur at cytosolic Ca2+ concentrations that fail to support exocytosis in other cell types, and increases in the cytosolic Ca2+ concentration due to ionomycin inhibit rather than stimulate PTH release. Therefore, the control of PTH secretion by Ca2+ and other secretagogues may involve previously undefined mechanisms whereby hormonal release is relatively independent of the cytosolic Ca2+ at low levels of this parameter and is inversely related to cytosolic Ca2+ at higher levels of intracellular Ca2+.
Role of Disulfide Bonds in the Structure and Potassium Channel Blocking Activity of ShK Toxin (1999)

ShK toxin, a potassium channel blocker from the sea anemone Stichodactyla helianthus, is a 35 residue polypeptide cross-linked by three disulfide bridges: Cys3-Cys35, Cys12-Cys28, and Cys17-Cys32. To investigate the role of these disulfides in the structure and channel-blocking activity of ShK toxin, a series of analogues was synthesized by selective replacement of each pair of half-cystines with two alpha-amino-butyrate (Abu) residues. The remaining two disulfide pairs were formed unambiguously using an orthogonal protecting group strategy of Cys(Trt) or Cys(Acm) at the appropriate position. The peptides were tested in vitro for their ability to block Kv1.1 and Kv1.3 potassium channels and their ability to displace [(125)I]dendrotoxin binding to rat brain synaptosomal membranes. The monocyclic peptides showed no activity in these assays. Of the dicyclic peptides, [Abu12,28]ShK(3-35,17)(-)(32) (where the subscript indicates disulfide connectivities) had weak activity on Kv1.3 and Kv1.1. [Abu17,32]ShK(3-35,12)(-)(28) blocked Kv1.3 with low nanomolar potency, but was less effective (being comparable to [Abu12,28]ShK(3-35,17)(-)(32)) against Kv1.1. [Abu3, 35]ShK(12-28,17)(-)(32), retained high picomolar affinity against both channels. Corroborating these results, [Abu3,35]ShK(12-28, 17)(-)(32) had an IC(50) ratio relative to native toxin of 18 in the displacement assay, whereas [Abu17,32]ShK(3-35,12)(-)(28) and [Abu12, 28]ShK(3-35,17)(-)(32) had ratios of 69 and 390, respectively. Thus, the disulfide bond linking the N- and C-terminal regions is less important for activity than the internal disulfides. NMR analysis of the [Abu12,28] and [Abu17,32] analogues indicated that they had little residual structure, consistent with their significantly reduced activities. By contrast, [Abu3,35]ShK(12-28,17)(-)(32) had a moderately well-defined solution structure, with a mean pairwise root-mean-square deviation of 1.33 A over the backbone heavy atoms. This structure nevertheless showed significant differences from that of native ShK toxin. The possible interactions of this analogue with the channel and the distinction between native secondary and tertiary structure on one hand and global topology imposed by the disulfide bridges on the other are discussed.
Ribavirin and interferon‐α combination therapy vs interferon‐α alone in the retreatment of chronic hepatitis C: a randomized clinical trial (1997)

Interferon-alpha (IFN-alpha) induces sustained remission of chronic hepatitis C in approximately 25% of patients. In patients who are non-responders to the first course of therapy, retreatment with IFN-alpha is of limited efficacy. Ribavirin has also been used to treat chronic hepatitis C, but it induces only a transient response. In this study, we evaluated the efficacy of ribavirin and IFN-alpha combination therapy for IFN-alpha resistant chronic hepatitis C. Twenty-four IFN-alpha non-responders and 24 relapsers were randomized to receive either ribavirin (1000 mg per day) together with IFN-alpha (3-6 million units (MU) thrice weekly) or the same dose of IFN-alpha alone, for 6 months. Both at the end of treatment and 6 months later, normal transaminase levels were more common in the patients receiving combination therapy than in the group receiving IFN-alpha alone: 17 (70.8%) vs seven (29.2%) patients (P = 0.009) and six (25%) vs one (4.2%) patient (P = 0.034), respectively. At the end of treatment and 6 months later, serum HCV RNA was no longer detectable in eight (33.3%) and five (20.8%) patients in the combination therapy group and in six (25%) and one (4.2%) patient in the IFN-alpha therapy group, respectively. Three patients (12.5%) were withdrawn prematurely from combination therapy because of side-effects; ribavirin therapy was ceased or dosage reduced in six other patients (25%), again because of side-effects. In conclusion, this combination treatment was more effective than retreatment with IFN-alpha, alone, in inducing sustained biochemical remission of chronic hepatitis C that was resistant to a previous course of IFN-alpha. The combination treatment, however, was frequently associated with significant side-effects.
Superflick: a natural and efficient technique for long-distance object placement on digital tables (2006)

Moving objects past arms' reach is a common action in both real-world and digital tabletops. In the real world, the most common way to accomplish this task is by throwing or sliding the object across the table. Sliding is natural, easy to do, and fast: however, in digital tabletops, few existing techniques for long-distance movement bear any resemblance to these real-world motions. We have designed and evaluated two tabletop interaction techniques that closely mimic the action of sliding an object across the table. Flick is an open-loop technique that is extremely fast. Superflick is based on Flick, but adds a correction step to improve accuracy for small targets. We carried out two user studies to compare these techniques to a fast and accurate proxy-based technique, the radar view. In the first study, we found that Flick is significantly faster than the radar for large targets, but is inaccurate for small targets. In the second study, we found no differences between Superflick and radar for either time or accuracy. Given the simplicity and learnability of flicking, our results suggest that throwing-based techniques have promise for improving the usability of digital tables.
Thy1-positive mesenchymal cells promote the maturation of CD49f-positive hepatic progenitor cells in the mouse fetal liver (2004)

Previously, we reported a system to enrich mouse fetal hepatic progenitor cells (HPCs) by forming cell aggregates. In this study, we sorted two cell populations, CD49f(+)Thy1(-)CD45(-) cells (CD49f-positive cells) and CD49f(+/-)Thy1(+)CD45(-) cells (Thy1-positive cells), from the cell aggregates using a flow cytometer. CD49f-positive cells stained positive for endodermal specific markers such as alpha-fetoprotein (AFP), albumin (ALB), and cytokeratin 19 (CK19), and are thus thought to be HPCs. However, Thy1-positive cells were a morphologically heterogeneous population; reverse-transcription polymerase chain reaction (RT-PCR) and immunocytochemical analyses revealed the expression of mesenchymal cell markers such as alpha-smooth muscle actin, desmin, and vimentin, but not of AFP, ALB, or CK19. Therefore, Thy1-positive cells were thought to be of a mesenchymal lineage. When these two cell populations were co-cultured, the CD49f-positive colonies matured morphologically and stored a significant amount of glycogen. Furthermore, real-time RT-PCR demonstrated an increased expression of tyrosine amino transferase and tryptophan oxygenase mRNA, and transmission electron microscopy confirmed that co-cultured cells produced mature hepatocytes. However, when CD49f-positive cells were cultured alone or when the two populations were cultured separately, the CD49f-positive cells did not mature. These results indicate that CD49f-positive cells are primitive hepatic endodermal cells with the capacity to differentiate into hepatocytes, and that Thy1-positive cells promote the maturation of CD49f-positive cells by direct cell-to-cell contact. In conclusion, we were able to isolate CD49f-positive primitive hepatic endodermal cells and Thy1-positive mesenchymal cells and to demonstrate the requirement of cell-to-cell contact between these cell types for the maturation of the hepatic precursors.
Docosahexaenoic Acid (DHA), a Primary Tumor Suppressive Omega-3 Fatty Acid, Inhibits Growth of Colorectal Cancer Independent of p53 Mutational Status (2007)

Human colon carcinoma COLO 205, carrying wild type p53, grown subcutaneously in athymic mice was inhibited 80% by a high fat menhaden oil diet containing a mixture of omega-3 fatty acids compared to the low fat corn oil diet containing omega-6 fatty acids. Feeding a high fat diet of golden algae oil containing docosahexaenoic acid (DHA) as the sole long chain omega-3 fatty acid resulted in 93% growth inhibition. Similar findings were previously reported for WiDr colon carcinoma containing mutated p53 (His237). In vitro, 125 muM DHA inhibited COLO 205 growth by 81%, WiDr by 42%, while eicosapentaenoic acid (EPA) marginally inhibited growth of both lines by approximately 30%. DHA inhibited cell proliferation by 41% in WiDr but did not significantly inhibit proliferation in COLO 205. Cell cycle analysis revealed that DHA arrested cell cycle at Resting/Gap 1 (G0/G1 phase) in WiDr and at Gap 2/Mitosis (G2/M) phase in COLO 205. DHA induced apoptosis in COLO 205 but not in WiDr, and EPA did not induce apoptosis in either line. Taken together, these findings suggest DHA is the primary tumor suppressive omega-3 fatty acid in vivo and in vitro and inhibits cancer growth by p53 dependent and independent pathways, while the marginal inhibition by EPA is p53 independent.
The Sverdlovsk Anthrax Outbreak of 1979 (1994)

In April and May 1979, an unusual anthrax epidemic occurred in Sverdlovsk, Union of Soviet Socialist Republics. Soviet officials attributed it to consumption of contaminated meat. U.S. agencies attributed it to inhalation of spores accidentally released at a military microbiology facility in the city. Epidemiological data show that most victims worked or lived in a narrow zone extending from the military facility to the southern city limit. Farther south, livestock died of anthrax along the zone's extended axis. The zone paralleled the northerly wind that prevailed shortly before the outbreak. It is concluded that the escape of an aerosol of anthrax pathogen at the military facility caused the outbreak.
Expert Answers: Multistreamer/multisource acquisition (2005)

This article first appeared in the June 2004 issue of the CSEG Recorder. Editor Satinder Chopra submitted two sets of questions to different experts. The topic of multistreamers and multisources was broached by Guillaume Cambois (CGG), Helmut Jakubowicz (Veritas DGC), Nick Moldoveanu (WesternGeco), and Thorbjorn Rekdahl (PGS). A single question about feathering and poor repeatability in 4D acquisition was posed to Ola Eiken (Statoil) and Tony Curtis (WesternGeco). The answers have been condensed and adapted to TLE style. Reproduced with permission of CSEG. [Refer to Recorder for details, references, and figures in PDF format: http://www.cseg.ca/recorder/pdf/2004/06jun/06jun_03.pdf]
A scientific workflow solution to the archiving of digital media (2006)

This work explores the challenges of embedding long-term preservation processes into existing video production workflows. The challenges are many: size of video data, bulk and parallel transfer into the archive, automation of the processes, elimination of human steps, automatic triggering of the preservation workflows, replication of content, automatic extraction of metadata, and most important mechanisms to “harden” the automation by providing recovery mechanisms in case of errors and discrepancies. We present production-quality solutions that automate this process and make use of Kepler scientific workflows and Storage Resource Broker (SRB) data grid environments.