gebhart/patrepeval huggingface dataset:
Interaction of the Gonococcal Porin P.IB with G- and F-Actin (2000)

The invasion of epithelial cells by N. gonorrheae is accompanied by formation of a halo of actin filaments around the enveloped bacterium. The transfer of the bacterial major outer membrane protein, porin, to the host cell membrane during invasion makes it a candidate for a facilitator for the formation of this halo. Western analysis shows here that gonococcal porin P.IB associates with the actin cytoskeleton in infected cells. Using the pyrene-labeled Mg forms of yeast and muscle actins, we demonstrate that under low ionic strength conditions, P.IB causes formation of filamentous actin assemblies, although they, unlike F-actin, cannot be internally cross-linked with N,N'-4-phenylenedimaleimide (PDM). In F-buffer, low porin concentrations appear to accelerate actin polymerization. Higher P.IB concentrations lead to the formation of highly decorated fragmented F-actin-like filaments in which the actin can be cross-linked by PDM. Co-assembly of P.IB with a pyrene-labeled mutant actin, S(265)C, prevents formation of a pyrene excimer present with labeled S(265)C F-actin alone. Addition of low concentrations of porin to preformed F-actin results in sparsely decorated F-actin. Higher P.IB concentrations extensively decorate the filaments, thereby altering their morphology to a state like that observed when the components are copolymerized. With preformed labeled S(265)C F-actin, P.IB quenches the pyrene excimer. This decrease is prevented by the F-actin stabilizers phalloidin and to a lesser extent beryllium fluoride. P.IB's association with the actin cytoskeleton and its ability to interact with and remodel actin filaments support a direct role for porin in altering the host cell cytoskeleton during invasion.
Dynamic Provisioning and Resource Management for Multi-Tier Cloud Based Applications (2013)

Abstract Dynamic capacity provisioning is a useful technique for handling the workload variations seen in cloud environment. In this paper, we propose a dynamic provisioning technique for multi-tier applications to allocate resources efficiently using queueing model. It dynamically increases the mean service rate of the virtual machines to avoid congestion in the multi-tier environments. An optimization model to minimize the total number of virtual machines for computing resources in each tier has been presented. Using the supplementary variable and the recursive techniques, we obtain the system-length distributions at pre-arrival and arbitrary epochs. Some important performance indicators such as blocking probability, request waiting time and number of tasks in the system and in the queue have also been investigated. Finally, computational results showing the effect of model parameters on key performance indicators are presented.
System support for multi-service traffic (2021)

Digital network technology is now capable of supporting the bandwidth requirements of diverse applications such as voice, video and data (so called multi-service traffic). Some media, for example voice, have specific transmission requirements regarding the maximum packet delay and loss which they can tolerate. Problems arise when attempting to multiplex such traffic over a single channel. Traditional digital networks based on the Packet- (PTM) and Synchronous- (STM) Transfer Modes prove unsuitable due to their media access contention and inflexible bandwidth allocation properties respectively. The Asynchronous Transfer Mode (STM) has been proposed as a compromise between the PTM and STM techniques. The current state of multimedia research suggests that a significant amount of multi-service traffic will be handled by computer operating systems. Unfortunately conventional operating systems are largely unsuited to such a task. This dissertation is concerned with the system organisation necessary in order to extend the benefits of ATM networking through the endpoint operating system and up to the application level. A locally developed micro-kernel, with ATM network protocol support, has been used as a testbed for the ideas presented. Practical results over prototype ATM networks, including the 512 MHz Cambridge Backbone Network, are presented.
The Cystic Fibrosis Gene: A Molecular Genetic Perspective (2013)

The positional cloning of the gene responsible for cystic fibrosis (CF) was the important first step in understanding the basic defect and pathophysiology of the disease. This study aims to provide a historical account of key developments as well as factors that contributed to the cystic fibrosis transmembrane conductance regulator (CFTR) gene identification work. A redefined gene structure based on the full sequence of the gene derived from the Human Genome Project is presented, along with brief reviews of the transcription regulatory sequences for the CFTR gene, the role of mRNA splicing in gene regulation and CF disease, and, various related sequences in the human genome and other species. Because CF mutations and genotype-phenotype correlations are covered by our colleagues (Ferec C, Cutting GR. 2012. Assessing the disease-liability of mutations in CFTR. Cold Spring Harb Perspect Med doi: 10.1101/cshperspect.a009480), we only attempt to provide an introduction of the CF mutation database here for reference purposes.
Surface Proteins ofStreptococcus agalactiaeand Related Proteins in Other Bacterial Pathogens (2005)

Streptococcus agalactiae (group B Streptococcus) is the major cause of invasive bacterial disease, including meningitis, in the neonatal period. Although prophylactic measures have contributed to a substantial reduction in the number of infections, development of a vaccine remains an important goal. While much work in this field has focused on the S. agalactiae polysaccharide capsule, which is an important virulence factor that elicits protective immunity, surface proteins have received increasing attention as potential virulence factors and vaccine components. Here, we summarize current knowledge about S. agalactiae surface proteins, with emphasis on proteins that have been characterized immunochemically and/or elicit protective immunity in animal models. These surface proteins have been implicated in interactions with human epithelial cells, binding to extracellular matrix components, and/or evasion of host immunity. Of note, several S. agalactiae surface proteins are related to surface proteins identified in other bacterial pathogens, emphasizing the general interest of the S. agalactiae proteins. Because some S. agalactiae surface proteins elicit protective immunity, they hold promise as components in a vaccine based only on proteins or as carriers in polysaccharide conjugate vaccines.
Computer modeling and intraoperative navigation in maxillofacial surgery (2007)

Computer modeling and intraoperative navigation is a relatively new tool that can assist surgeons with reconstruction of the maxillofacial skeleton.
Quantum Teleportation Between Distant Matter Qubits (2009)

Quantum teleportation is the faithful transfer of quantum states between systems, relying on the prior establishment of entanglement and using only classical communication during the transmission. We report teleportation of quantum information between atomic quantum memories separated by about 1 meter. A quantum bit stored in a single trapped ytterbium ion (Yb+) is teleported to a second Yb+ atom with an average fidelity of 90% over a replete set of states. The teleportation protocol is based on the heralded entanglement of the atoms through interference and detection of photons emitted from each atom and guided through optical fibers. This scheme may be used for scalable quantum computation and quantum communication.
Field assisted spin switching in magnetic random access memory (2006)

A switching method called by field assisted spin switching has been investigated. A field assisted spin switching consists of a metal line induced magnetic field and a spin switching through a magnetic tunnel junction. It is a variation of a current induced switching and assisted by the magnetic field induced by the current-carrying metal line. Various current paths have been tested to investigate how and how much the spin switching contributes to the overall switching and the results will be explained. A computer simulation has been complemented to measure the degree of the thermal effect in the switching.
Mice lacking the gene encoding tissue-type plasminogen activator show a selective interference with late-phase long-term potentiation in both Schaffer collateral and mossy fiber pathways. (1996)

The gene encoding tissue-type plasminogen activator (t-PA) is an immediate response gene, downstream from CREB-1 and other constitutively expressed transcription factors, which is induced in the hippocampus during the late phase of long-term potentiation (L-LTP). Mice in which the t-PA gene has been ablated (t-PA-/-) showed no gross anatomical, electrophysiological, sensory, or motor abnormalities but manifest a selective reduction in L-LTP in hippocampal slices in both the Schaffer collateral-CA1 and mossy fiber-CA3 pathways. t-PA-/- mice also exhibit reduced potentiation by cAMP analogs and D1/D5 agonists. By contrast, hippocampal-dependent learning and memory were not affected in these mice, whereas performance was impaired on two-way active avoidance, a striatum-dependent task. These results provide genetic evidence that t-PA is a downstream effector gene important for L-LTP and show that modest impairment of L-LTP in CA1 and CA3 does not result in hippocampus-dependent behavioral phenotypes.
Clostridium difficile Colitis (1994)

Clostridium difficile, the agent that causes pseudomembranous colitis associated with antibiotic therapy, has been identified in recent years as a common nosocomial pathogen. First described in 1935 by Hall and O'Toole, this gram-positive anaerobic bacillus was named “the difficult clostridium” because it resisted early attempts at isolation and grew very slowly in culture1. Although the organism released potent toxins in broth culture, the fact that it was found in stool specimens from healthy neonates led to its classification as a commensal. C. difficile subsequently passed into obscurity.In the 1960s and 1970s antibiotic-associated pseudomembranous colitis became a major clinical . . .
CRISPR/Cas9‐Directed Gene Editing for the Generation of Loss‐of‐Function Mutants in High‐Throughput Zebrafish F0 Screens (2017)

The ability to perform reverse genetics in the zebrafish model organism has been greatly advanced with the advent of the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated) system. The high level of efficiency in generating mutations when using the CRISPR/Cas9 system combined with the rapid generation time of the zebrafish model organism has made the possibility of performing F<sub>0</sub> screens in this organism a reality. This unit describes a detailed protocol for performing an F<sub>0</sub> screen using the CRISPR/Cas9 system in zebrafish starting with the design and production of custom CRISPR/Cas9 reagents for injection. Next, two approaches for determining the efficiency of mutation induction by the custom CRISPR/Cas9 reagents that are easily performed using standard molecular biology protocols are detailed. Finally, screening for F<sub>0</sub> induced phenotypes using the zebrafish flh gene as an example is discussed. © 2017 by John Wiley & Sons, Inc.
Epigenetic synergy between decitabine and platinum derivatives (2015)

Our results suggest that the combination of decitabine with platinum analogs shows epigenetic synergy that might be exploited in the treatment of different cancers.
Mutations in the trpD gene of Corynebacterium glutamicum confer 5-methyltryptophan resistance by encoding a feedback-resistant anthranilate phosphoribosyltransferase (1995)

The trpD gene from tryptophan-hyperproducing Corynebacterium glutamicum ATCC 21850 was isolated on the basis of its ability to confer resistance to 5-methyltryptophan on wild-type C. glutamicum AS019. Comparative sequence analysis of the genes from the wild-type AS019 and ATCC 21850 trpD genes revealed two amino acid substitutions at the protein level. Further analysis demonstrated that the trpD gene product from ATCC 21850, anthranilate phosphoribosyltransferase, was more resistant to feedback inhibition by either tryptophan or 5-methyltryptophan than its wild-type counterpart. It is proposed that phosphoribosyltransferase insensitivity to tryptophan in ATCC 21850 contributes to an elevated level of tryptophan biosynthesis.
Phenotypic expression of B lymphocytes. III. Marginal zone B cells in the spleen are characterized by the expression of Tac and alkaline phosphatase. (1985)

The marginal zone of the spleen contains lymphocytes with an intermediate morphologic form between small lymphocytes and plasmablasts. The majority of cells can be stained by B cell monoclonal antibodies including B1, Leu-14, and Leu-12. The most significant finding is the expression of an interleukin 2 receptor (Tac) and an enzyme-alkaline phosphatase by the marginal zone B lymphocytes. The Tac antigen is not normally present in B cells, but can be found in a portion of in vitro-activated B lymphocytes. In conjunction with other evidence, the marginal zone B lymphocytes may represent the activated B cells in the early stages of B cells differentiation. Alternatively, the Tac-positive, marginal zone B lymphocytes may be a discrete subpopulation of activated B cells.
Interleukin 2‐Bax: a novel prototype of human chimeric proteins for targeted therapy (1999)

During the past few years many chimeric proteins have been developed to target and kill cells expressing specific surface molecules. Generally, these molecules carry a bacterial or plant toxin that destroys the unwanted cells. The major obstacle in the clinical application of such chimeras is their immunogenicity and non-specific toxicity. We have developed a new generation of chimeric proteins, taking advantage of apoptosis-inducing proteins, such as the human Bax protein, as novel killing components. The first prototype chimeric protein, IL2-Bax, directed toward IL2R-expressing cells, was constructed, expressed in Escherichia coli and partially purified. IL2-Bax increased the population of apoptotic cells in a variety of target T cell lines, as well as in human fresh PHA-activated lymphocytes, in a dose-dependent manner and had no effect on cells lacking IL2R expression. The IL2-Bax chimera represents an innovative approach for constructing chimeric proteins comprising a molecule that binds a specific cell type and an apoptosis-inducing protein. Such new chimeric proteins could be used for targeted treatment of human diseases.
Deficiency of methylthioadenosine phosphorylase in human leukemic cells in vivo (1982)

Cells from 20 patients with leukemia and 9 with solid tumors were assayed for the enzyme methylthioadenosine phosphorylase, which function in both purine and polyamine metabolism in rapidly dividing cells. As determined by autoradiography of viable cells, and by direct enzymatic analysis, samples from one individual with pre-T-cell acute lymphoblastic leukemia and one with common acute lymphoblastic leukemia were methylthioadenosine phosphorylase deficient. In contrast, other leukemias of similar antigenic phenotype, as well as normal peripheral blood lymphocytes, thymic lymphocytes, and normal bone marrow cells, had substantial methylthioadenosine phosphorylase activity. This evidence suggests that the complete absence of methylthioadenosine phosphorylase distinguishes some leukemic cells in vivo from their nonmalignant counterparts.
Uncemented STAR Total Ankle Prostheses (2004)

Total ankle replacement may be a realistic alternative to arthrodesis, provided that the components are correctly positioned and are of the correct size. However, the risks of loosening and failure are still higher than are such risks after total hip or total knee replacement.
Risk Factors for Community-Associated Methicillin-Resistant Staphylococcus aureus Infections in an Outbreak of Disease among Military Trainees in San Diego, California, in 2002 (2004)

An outbreak of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) skin infections was observed in a population of U.S. military trainees in the summer of 2002. A questionnaire was developed and administered to 206 trainees, 22 of whom had MRSA infections. Factors associated with infection were described by multivariable logistic regression modeling and included having a roommate in training with a prior skin infection (odds ratio [OR] = 3.44) or having a family member or friend who worked in a health care setting (OR = 2.79). Previous antibiotic use, hospitalization, or health problems were not associated with MRSA infection. This outbreak of MRSA skin infections in an otherwise-healthy, well-defined, military population provided an opportunity to describe risk factors for CA-MRSA which may help focus prevention efforts in this and other communities.
Peptide-derived self-assembled monolayers: Assorption of N-stearoylL-systeine methyl ester on gold (1997)

The work reported herein concerns the assembly of N-stearoyl L-cysteine methyl ester [CH3(CH2)16COCysOMe, 1] on the surface of gold. This compound serves as a simple model of a related polypeptide, which has been designed to adopt a beta-sheet architecture on metallic and oxide surfaces. We describe the preparation of monolayers of 1, and characterization of these layers via ellipsometry, vibrational spectroscopy and X-ray photoelectron spectroscopy. The results are most consistent with a disordered array of the alkyl chains, in which close packing is frustrated by a mismatch in the cross-sectional areas of the cysteinyl ester head group and the stearoyl chains of the thiol. Despite the disorder, the alkyl chains form a hydrophobic surface layer, with an advancing contact angle for water comparable to that observed for octadecanethiol on gold.
Effect of enzyme supplementation of broiler diets based on corn and soybeans (1999)

Digestibility of diets based on corn and soybean meal or soybeans treated by roasting or extrusion, with or without an enzyme supplementation, was measured by "true" (Sibbald) methods, by analysis of excreta, and by analysis of ileal digesta. Only analysis of ileal digesta was able to consistently measure differences between soybean and enzyme treatments in the digestibility of CP, starch, fat, and ME. The amino acid (AA) digestibility of the diets was measured by analysis of the ileal contents. Whereas enzyme supplementation improved overall CP digestibility by 2.9%, this improvement was not equal for all AA. Of the AA most important for broilers fed corn-soybean diets, the digestibilities of Lys, Met, and Arg were not improved or not improved significantly by the enzyme supplementation; however, that of Val was improved by 2.3% and that of Thr was improved by 3.0%. A performance trial demonstrated that enzyme supplementation with equal diet formulation improved BW and the feed conversion ratio by 1.9 and 2.2%, respectively. A second performance trial compared standard diet formulations with formulations using enzyme supplementation and energy levels that were reduced by the amount of improvement provided by the inclusion of enzyme in the first performance trial. No difference was seen between treatments, showing that the improvement of nutrient utilization brought about by enzyme supplementation completely compensated for the reduced energy content. Whereas enzyme supplementation should allow a reduction in CP formulation as well, individual AA were not improved equally by supplementation and should also be balanced.
Switch networks for photonic fusion-based quantum computing (2021)

Fusion-based quantum computing (FBQC) offers a powerful approach to building a fault-tolerant universal quantum computer using photonic components -- single-photon sources, linear-optical circuits, single-photon detectors, and optical switching with feedforward control. Both individual optical switches and sophisticated switch networks are needed where it is necessary to perform operations conditionally, using feedforward of previous photon-detection outcomes, within the lifetime of remaining photons. Most visibly, feedforward switching is required for fault-tolerant operations at the level of logical qubits, which are needed in turn for useful quantum algorithms. However, switch networks are also required for multiplexing ("muxing") stages that are needed for generating specific small entangled resource states, where it is used to boost the probabilities for allocating quantum states to fusion gates and other operations -- a task which dominates the footprint of photonic FBQC. Despite their importance, limited attention has been paid to exploring possible designs of switch networks in this setting. Here we present a wide range of new techniques and schemes which enable major improvements in terms of muxing efficiency and reductions in hardware requirements. Since the use of photonic switching heavily impacts qubit losses and errors, our schemes are constructed with low switch depth. They also exploit specific features of linear-optical circuits which are commonly used to generate entanglement in proposed quantum computing and quantum network schemes.
Making information flow explicit in HiStar (2006)

HiStar is a new operating system designed to minimize the amount of code that must be trusted. HiStar provides strict information flow control, which allows users to specify precise data security policies without unduly limiting the structure of applications. HiStar's security features make it possible to implement a Unix-like environment with acceptable performance almost entirely in an untrusted user-level library. The system has no notion of superuser and no fully trusted code other than the kernel. HiStar's features permit several novel applications, including an entirely untrusted login process, separation of data between virtual private networks, and privacy-preserving, untrusted virus scanners.
Combustion Powered Actuator with Integrated High Frequency Oscillator (2009)

A new actuation concept for flow control has been tested combining the high jet strength of chemically-based, combustion powered actuation with the high frequency of fluidic oscillators. The device exhausts the jet from a combustion powered actuator through a fluidic oscillator and embeds a high frequency [∼ O(1-10) kHz] oscillation into the lower frequency [∼ O(10-100) Hz] of the repetitively ignited combustion bursts. The present work includes characterization of the fluidic oscillator in steady operation for the properties which vary over the combustion burst (pressure, temperature, and gas composition) and results from test firing of the fully integrated device successfully indicating high frequency oscillation in the high speed actuation jet while maintaining a no moving parts design.
Monocyte‐derived dendritic cells in innate and adaptive immunity (2008)

Monocytes have been classically considered essential elements in relation with innate immune responses against pathogens, and inflammatory processes caused by external aggressions, infection and autoimmune disease. However, although their potential to differentiate into dendritic cells (DCs) was discovered 14 years ago, their functional relevance with regard to adaptive immune responses has only been uncovered very recently. Studies performed over the last years have revealed that monocyte-derived DCs play an important role in innate and adaptive immunity, due to their microbicidal potential, capacity to stimulate CD4(+) and CD8(+) T-cell responses and ability to regulate Immunoglobulin production by B cells. In addition, monocyte-derived DCs not only constitute a subset of DCs formed at inflammatory foci, as previously thought, but also comprise different subsets of DCs located in antigen capture areas, such as the skin and the intestinal, respiratory and reproductive tracts.