gebhart/patrepeval huggingface dataset:
Salmonellosis Outcomes Differ Substantially by Serotype (2008)

Salmonella serotypes are closely related genetically yet differ significantly in their pathogenic potentials. Understanding the mechanisms responsible for this may be key to a more general understanding of the invasiveness of intestinal bacterial infections.
<i>N</i>‐ACYL HOMOSERINE LACTONe LACTONASE, AiiA, INACTIVATION OF QUORUM‐SENSING AGONISTS PRODUCED BY <i>CHLAMYDOMONAS REINHARDTII</i> (CHLOROPHYTA) AND CHARACTERIZATION OF <i>aiiA</i> TRANSGENIC ALGAE<sup>1</sup> (2011)

Eukaryotes such as plants and the unicellular green alga Chlamydomonas reinhardtii P. A. Dang. produce and secrete compounds that mimic N-acyl homoserine lactone (AHL) bacterial quorum-sensing (QS) signals and alter QS-regulated gene expression in the associated bacteria. Here, we show that the set of C. reinhardtii signal-mimic compounds that activate the CepR AHL receptor of Burkholderia cepacia are susceptible to inactivation by AiiA, an AHL lactonase enzyme of Bacillus. Inactivation of these algal mimics by AiiA suggests that the CepR-stimulatory class of mimics produced by C. reinhardtii may have a conserved lactone ring structure in common with AHL QS signals. To examine the role of AHL mimic compounds in the interactions of C. reinhardtii with bacteria, the aiiA gene codon optimized for Chlamydomonas was generated for the expression of AiiA as a chimeric fusion with cyan fluorescent protein (AimC). Culture filtrates of transgenic strains expressing the fusion protein AimC had significantly reduced levels of CepR signal-mimic activities. When parental and transgenic algae were cultured with a natural pond water bacterial community, a morphologically distinct, AHL-producing isolate of Aeromonas veronii was observed to colonize the transgenic algal cultures and form biofilms more readily than the parental algal cultures, indicating that secretion of the CepR signal mimics by the alga can significantly affect its interactions with bacteria it encounters in natural environments. The parental alga was also able to sequester and/or destroy AHLs in its growth media to further disrupt or manipulate bacterial QS.
Surface strain and its impact on the electrical resistivity of GaN channel in AlGaN/GaN high electron mobility transistor (2008)

Localized strain in AlGaN/GaN high electron mobility transistor (HEMT) device structures was studied by high resolution x-ray diffraction and rocking curve measurements, and the results were compared with the corresponding channel sheet resistance measurements. The map of in-plane tensile strain on the HEMT wafer showed a near one-to-one correspondence with the electrical resistivity. The in-plane strain variation in the range of (2.295–3.539)×10−4 resulted in a corresponding sheet resistance variation between 345 and 411 Ω/◻.
Macromolecule Synthesis in Yeast Spheroplasts (1967)

Conditions have been established for the preparation of spheroplasts of Saccharomyces cerevisiae which are able to increase their net content of protein, ribonucleic acid (RNA), and deoxyribonucleic acid (DNA), several-fold upon incubation in a medium stabilized with 1 m sorbitol. The rate of RNA and protein synthesis in the spheroplasts is nearly the same as that occurring in whole cells incubated under the same conditions; DNA synthesis occurs at about half the whole cell rate. The spheroplasts synthesize transfer RNA and ribosomal RNA. The newly synthesized ribosomal RNA is incorporated into ribosomes and polysomes. The polysomes are the site of protein synthesis in these spheroplasts. Greater than 90% of the total RNA can be solubilized by treatment of the spheroplasts with sodium dodecyl sulfate or sodium deoxycholate. These spheroplast preparations appear to be a useful subject for the study of RNA metabolism in yeast.
Perturbation of the autoimmune network. II. Immunization with isologous idiotype induces auto-anti-idiotypic antibodies and suppresses the autoantibody response elicited by antigen: a serologic and cellular analysis. (1986)

We report on the humoral and cellular events following autologous immunization against an idiotype (Id62) borne on a murine monoclonal autoantibody to thyroglobulin, and their impact on the autoantibody response to thyroglobulin. BALB/c mice with a state of active auto-anti-idiotypic immunity and challenged with thyroglobulin in complete Freund's adjuvant 2 wk after the last immunization with idiotype were found to have a suppressed autoantibody response. This suppression could be adoptively transferred to syngeneic x-irradiated recipients by using whole spleen cells from idiotype-primed mice. Transfer of separate T and B lymphocyte populations proved instrumental in disecting humoral from cellular events and in establishing that whereas B cells were required for transferring an intact anti-idiotype antibody response, T cells from idiotype-primed mice were necessary to transfer suppression. These findings contribute to our understanding of the interrelationship between antigen, idiotype, and anti-idiotype in the immune response to self-antigens, and the role of certain idiotypes in regulating autoimmune responses.
WHOI Cable v2.0 : time domain numerical simulation of moored and towed oceanographic systems (2000)

This report describes version 2.0 of a numerical program for analyzing the statics and dynamics of cable structures commonly encountered in oceanographic engineering practice. The numerical program, WHOI Cable, features a nonlinear solver that includes the effects of geometric and material nonlinearities, bending stiffness for seamless modeling of slack cables, and a model for the interaction of cable segments with the seafloor. The program solves both surface and subsurface single- and multi-point mooring problems, systems with both ends anchored on the bottom, and towing and drifter problems. Forcing includes waves, current, wind, ship speed, and pay-out of cable. The programs that make-up WHOI Cable run under Unix and Windows. There is familiar graphical interface available for Windows platforms. The report includes detailed instructions for formulating problem input files and running the programs.
The antihypertensive hydralazine is an efficient scavenger of acrolein (2000)

Recent work indicates the highly toxic alpha,beta-unsaturated aldehyde acrolein is formed during the peroxidation of polyunsaturated lipids, raising the possibility that it functions as a 'toxicological second messenger' during oxidative cell injury. Acrolein reacts rapidly with proteins, forming adducts that retain carbonyl groups. Damage by this route may thus contribute to the burden of carbonylated proteins in tissues. This work evaluated several amine compounds with known aldehyde-scavenging properties for their ability to attenuate protein carbonylation by acrolein. The compounds tested were: (i) the glycoxidation inhibitors, aminoguanidine and carnosine; (ii) the antihypertensive, hydralazine; and (iii) the classic carbonyl reagent, methoxyamine. Each compound attenuated carbonylation of a model protein, bovine serum albumin, during reactions with acrolein at neutral pH and 37 degrees C. However, the most efficient agent was hydralazine, which strongly suppressed carbonylation under these conditions. Study of the rate of reaction between acrolein and the various amines in a protein-free buffered system buttressed these findings, since hydralazine reacted with acrolein at rates 2-3 times faster than its reaction with the other scavengers. Hydralazine also protected isolated mouse hepatocytes against cell killing by allyl alcohol, which undergoes in situ alcohol dehydrogenase-catalysed conversion to acrolein.
Intracellular Protein Catabolism and its Control During Nutrient Deprivation and Supply (1987)

The continuous turnover of intracellular protein and other macromolecules is a basic cellular process that serves, among other functions, to regulate cytoplasmic content and provide amino acids for ongoing oxidative and biosynthetic reactions during nutrient deprivation. The intensity of breakdown and pattern of regulation, though, vary widely among cells. Rat hepatocytes, for example, exhibit high absolute rates of proteolysis and regulatory effects that diminish during starvation, while corresponding responses in skeletal and cardiac muscle move in the opposite direction. It is also becoming apparent that effects of insulin and other acute regulatory agents on muscle breakdown are limited to nonmyofibrillar components. The latter may be sequestered and degraded within autophagic vacuoles, whereas myofibrillar proteins require an initial attack by calcium-dependent proteases in the cytosol. By contrast, most if not all of the breakdown of resident (long-lived) proteins as well as RNA in the hepatocyte can be explained by lysosomal mechanisms. The uptake of cytoplasmic components by lysosomes can be divided into two major categories, macroautophagy and micro- or basal autophagy. The first is induced by amino acid or insulin/serum deprivation. In the hepatocyte, amino acids alone can regulate this process almost instantaneously over two thirds of the full range of proteolysis, 4.5% to 1.5% per hour. Glucagon, cyclic AMP, and beta-agonists also stimulate macroautophagy in hepatocytes but have opposite effects in skeletal and cardiac myocytes. Basal autophagy differs from the macro type in that the cytoplasmic "bite" is smaller and sequestration is not acutely regulated. It is, however, adaptively decreased during starvation in parallel with absolute rates of basal turnover. Since endoplasmic reticulum comprises an appreciable fraction of the vacuolar content, volume sequestration would be compatible with the known heterogeneity of individual protein turnover if some proteins (or altered proteins) selectively bind to membranes. The amino acid control of macroautophagy in the hepatocyte is accomplished by a small group of direct inhibitors (Leu, Tyr/Phe, Gln, Pro, Met, Trp, and His) and the permissive effect of alanine whereas only leucine is involved in myocytes and adipocytes. Of unusual interest is the fact that the inhibitory amino acid group alone evokes responses in perfused livers that are identical to those of a complete plasma mixture at 0.5 and 4 times normal plasma levels but loses effectiveness almost completely at normal concentrations.(ABSTRACT TRUNCATED AT 400 WORDS)
Molecular characterization of flgM, a gene encoding a negative regulator of flagellin synthesis in Salmonella typhimurium (1991)

The expression of flagellin in Salmonella typhimurium is coupled to the assembly of complete flagella. Mutations which disrupt this coupling define a gene, flgM, which represses the expression of the flagellin genes in strains with mutations in the basal body, switch, or hook flagellar gene (K. L. Gillen and K. T. Hughes, J. Bacteriol. 173:2301-2310, 1991). Complementation studies demonstrated that the flgM gene is contained within a 600-bp cloned DNA fragment. Sequence analysis revealed that this fragment carries a small open reading frame corresponding to a 97-amino-acid protein. The FlgM protein observed in a T7-mediated expression system showed an apparent molecular mass of 9.5 kDa, similar to the predicted size of 10.6 kDa. Upstream of the flgM coding region is a putative promoter sequence which shows strong homology to that thought to be recognized by the flagellin-specific sigma factor (FliA). Consistent with the use of this promoter in vivo, promoter mapping by primer extension demonstrated a transcriptional start site 11 bases downstream from the center of the putative -10 promoter element, which was dependent on functional FliA for full expression.
Midgut Bacteria in Anopheles gambiae and An. funestus (Diptera: Culicidae) from Kenya and Mali (1998)

Field studies in Kenya and Mali investigated the prevalence of bacteria in the midguts of malaria vectors, and the potential relationship between gram-negative bacteria species and Plasmodium falciparum sporozoites. Midguts were dissected from 2,430 mosquitoes: 863 Anopheles funestus Giles and 1,037 An. gambiae s.l. Giles from Kenya, and 530 An. gambiae s.l. from Mali. An. funestus had a higher prevalence of gram-negative bacteria (28.5%) compared with An. gambiae collected in Kenya and Mali (15.4 and 12.5%, respectively). Twenty different genera of bacteria were identified by gas chromatography from 73 bacterial isolates from mosquito midguts. Pantoea agglomerans (Enterobacter agglomerans) was the most common species identified. There was no association between gram-negative bacteria in the midgut and P. falciparum sporozoites in field-collected An. gambiae s.l. and An. funestus. However, An. funestus females that harbored gram positive bacteria were more likely to be infected with sporozoites compared with those with no cultivable bacteria or gram negative bacteria in their midguts. Habitat-related variation in the prevalence of diverse types of bacteria in mosquitoes could influence malaria parasite development in mosquitoes and corresponding sporozoite prevalence.
Large-Scale Isolation and Crystallization of Epothilone D From <i>Myxococcus </i><i>x</i><i>anthus</i> Cultures (2002)

The introduction of the epothilone polyketide synthase (PKS) into Myxococcus xanthus has enabled the heterologous production of epothilone D (1) on a large scale. To isolate this valuable product from the fermentation medium, an economical, scalable, and high-yielding purification process was developed. With the crystallization of 1 from a binary solvent system that consisted of ethanol and water, the product was recovered as white crystals with a final purity of > or =97% (w/w). This is the first reported crystallization of 1.
Video fingerprinting based on moment invariants capturing appearance and motion (2009)

In this paper, we propose two video fingerprinting methods that are robust to both geometric and non-geometric modifications on content. Both of the proposed methods are based on computation of moment invariants as features from concentric circular regions. The two methods differ in the way they capture appearance and motion information from video. In one method, we capture motion information by computing a difference image between the current video frame and a temporal average video frame computed from a past window of video frames. This method captures appearance by computing moment invariants from concentric circular regions of a video frame. In the second method, we capture appearance and motion by projecting features onto two sets of basis functions and explicitly capture how the moment invariants change over the regions and over time. We present experimental results on both of these video fingerprinting comparing their performance in terms of robustness against attacks and sensitivity to content.
General Rules for the Optimal External Porosity of LC Supports (2004)

We present a series of numerically calculated plate height and flow resistance data obtained for an idealized chromatographic support mimic with variable bed porosity (0.3 </= epsilon </= 0.9), yielding a unique insight into how the main chromatographic performance parameters can be expected to vary with the external bed porosity, unbiased by any differences in molecular diffusivity or retention factor. The influence of pore heterogeneity effects is considered as well. It is found that the product h(min)nu(opt) depends only very weakly on epsilon and on the degree of pore heterogeneity. It is also found that the minimal separation impedance E(min) decreases monotonically with epsilon. This shows that the minimal plate height increase that can be expected for large porosity systems is always more than compensated by their reduced flow resistance, in agreement with the current observations in real silica monolith columns. Using the computed plate height data in an optimization analysis, it is found that large porosity supports can always potentially yield shorter analysis times or larger plate numbers than small porosity supports but need submicrometer feature sizes to actually achieve this. Assuming a lower limit on the producible or useable structural feature sizes, it is found that small N separations can best be performed with a small porosity packing, whereas large N separations require a large porosity packing if the column length (L) is left free. A plot yielding epsilon(opt) as a function of the required plate number has been established, showing that roughly epsilon(opt) approximately log(N) in both the ordered and the disordered support cases. It is also shown that the maximal increase in peak capacity ever to be expected from the use of high porosity supports is a factor of 2 (if the mobile-phase viscosity can be kept constant), potentially to be increased by a factor of 1.5 by increasing the homogeneity of the packing.
Pore‐structure optimization of calcium carbonate for enhanced sulfation (1997)

Abstract A modified CaCO 3 sorbent with an open internal pore structure is prepared and its sulfation characteristics are investigated in an entrained flow reactor at high temperatures (900‐1,100°C) and short contact times (20–600 ms) using small particle sizes (&lt; 5 μm). The most distinguishing feature of this modified carbonate (MC) is its 70–75% sulfation conversion within 0.5 s, which is substantially higher than any other sorbents published. The MC is prepared by carbonation‐precipitation from a calcium hydroxide suspension by optimizing the operating parameters to generate carbonate particles of the desired pore structural properties. The high initial surface area combined with its open pore structure and pore‐size distribution of its calcine contribute to its high reactivity. The calcined MC possesses a significant portion of its pore volume in the 50‐200 Å range. This size range represents an optimum pore size for sulfation since it provides a reasonably high surface area and is less susceptible than &lt; 50 Å pore sizes, to pore filling, or pore‐mouth plugging due to the formation of higher molar volume CaSO 4 . Investigation with other carbonates reveals that a much higher portion of their calcines' porosity lies in the smaller pores, which leads to premature termination of sulfation. Results show the impact of internal pore structure on initial reactivity and ultimate sorbent conversion.
Principles of dataspace systems (2006)

The most acute information management challenges today stem from organizations relying on a large number of diverse, interrelated data sources, but having no means of managing them in a convenient, integrated, or principled fashion. These challenges arise in enterprise and government data management, digital libraries, "smart" homes and personal information management. We have proposed dataspaces as a data management abstraction for these diverse applications and DataSpace Support Platforms (DSSPs) as systems that should be built to provide the required services over dataspaces. Unlike data integration systems, DSSPs do not require full semantic integration of the sources in order to provide useful services. This paper lays out specific technical challenges to realizing DSSPs and ties them to existing work in our field. We focus on query answering in DSSPs, the DSSP's ability to introspect on its content, and the use of human attention to enhance the semantic relationships in a dataspace.
Parallel Assignments in Software Model Checking (2006)

In this paper we investigate how formal software verification systems can be improved by utilising parallel assignment in weakest precondition computations. We begin with an introduction to modern software verification systems. Specifically, we review the method in which software abstractions are built using counterexample-guided abstraction refinement (CEGAR). The classical NP-complete parallel assignment problem is first posed, and then an additional restriction is added to create a special case in which the problem is tractable with an O(n2) algorithm. The parallel assignment problem is then discussed in the context of weakest precondition computations. In this special situation where statements can be assumed to execute truly concurrently, we show that any sequence of simple assignment statements without function calls can be transformed into an equivalent parallel assignment block. Results of compressing assignment statements into a parallel form with this algorithm are presented for a wide variety of software applications. The proposed algorithms were implemented in the ComFoRT reasoning framework [J. Ivers and N. Sharygina. Overview of ComFoRT: A model checking reasoning framework. Technical Report CMU/SEI-2004-TN-018, Carnegie Mellon Software Engineering Institute, 2004] and used to measure the improvement in the verification of real software systems. This improvement in time proved to be significant for many classes of software.
High Expression of lncRNA-PCNA-AS1 in Human Gastric Cancer and its Clinical Significances (2015)

These data indicated that IncRNA-PCNA-AS1 may participate in the gastric cancer carcinogenesis and development and may serve as a new biomarker for patients with gastric cancer.
Auditory images. How complex sounds are represented in the auditory system. (2000)

When an event occurs in the world around us, say a lion roars or a cat meows, information about the event flows to us in light waves and sound waves.Our eyes form a visual image of the event, our ears form an auditory image of the event, and the two are combined with any other sensory inputs to produce our initial experience of the event.The purpose of this paper is to describe:1)the three natural categories of sounds:noises, transients, and tones, 2)a computer model designed to explain how the auditory system converts sounds into auditory images, 3)the characteristics of the auditory images of noises, transients and tones, and 4)the role of auditory image construction in the initial segregation of tones and noises.
Ex Vivo Purging of Stem Cell Autografts Using Cytotoxic Cells (2001)

Autologous stem cell transplantation (SCT) is the treatment alternative offered to patients that cannot benefit from allogeneic transplantation due to lack of suitable donor or age limitations. However, the outcome of autologous SCT is largely hindered by the high relapse rate. Two major factors can account for relapse after autologous SCT: the persistence of residual malignant cells resistant to chemo/radiotherapy left either in the body or in the autograft. Therefore, the rationale for purging autografts of residual malignant cells comes from the limitations of conventional high-dose chemo/radiotherapy in achieving a complete eradication of residual tumor cells in the marrow. To date, different purging modalities have been exploited. Immunological methods of purging present the advantage of being non-cross-reactive with conventional chemotherapy. These immunologic methods include depletion using antibody targeting of the malignant cells, ex vivo activation/generation of the autologous cytotoxic cells, in particular that of natural killer/lymphokine-activated killer (NK/LAK) and cytokine-induced killer (CIK) cells, and ex vivo purging of autografts using cytotoxic cell lines. The generation of ex vivo-expanded and activated autologous cytotoxic cells (CTL or NK) has generated increasing interest for the treatment of different malignancies. Unfortunately, the isolation and expansion of these cells have proven to be technically difficult. As an alternative, the use of cytotoxic cell lines as immune effectors has been proposed. The two available human cytotoxic cell lines TALL104 and NK-92 are currently in clinical trials and a number of studies have suggested their effectiveness as an immunotherapeutic agent including for ex vivo purging of autografts.