gebhart/patrepeval huggingface dataset:
MicC, a Second Small-RNA Regulator of Omp Protein Expression in<i>Escherichia coli</i> (2004)

In a previous bioinformatics-based search for novel small-RNA genes encoded by the Escherichia coli genome, we identified a region, IS063, located between the ompN and ydbK genes, that encodes an approximately 100-nucleotide small-RNA transcript. Here we show that the expression of this small RNA is increased at a low temperature and in minimal medium. Twenty-two nucleotides at the 5' end of this transcript have the potential to form base pairs with the leader sequence of the mRNA encoding the outer membrane protein OmpC. The deletion of IS063 increased the expression of an ompC-luc translational fusion 1.5- to 2-fold, and a 10-fold overexpression of the small RNA led to a 2- to 3-fold repression of the fusion. Deletion and overexpression of the IS063 RNA also resulted in increases and decreases, respectively, in OmpC protein levels. Taken together, these results suggest that IS063 is a regulator of OmpC expression; thus, the small RNA has been renamed MicC. The antisense regulation was further demonstrated by the finding that micC mutations were suppressed by compensatory mutations in the ompC mRNA. MicC was also shown to inhibit ribosome binding to the ompC mRNA leader in vitro and to require the Hfq RNA chaperone for its function. We suggest that the MicF and MicC RNAs act in conjunction with the EnvZ-OmpR two-component system to control the OmpF/OmpC protein ratio in response to a variety of environmental stimuli.
Standards of treatment in chronic hepatitis C. (1999)

Standards of treatment for patients who are infected with the hepatitis C virus have been developed from national and international consensus conferences, from extensive clinical experience with various regimens, from exhaustive literature reviews, and from opinion leaders in the general medical community. From 1987 until very recently, the standard of treatment for non-A, non-B hepatitis, later defined as hepatitis C, had consisted of alpha interferon monotherapy administered for up to 18 to 24 months. Alpha interferon has been used in a variety of regimens with varying success for the initial treatment of chronic hepatitis C, for the retreatment of patients who have relapsed after responding to interferon, and for the retreatment of alpha interferon nonresponders. Treatment standards have evolved as new agents have become available for use in our treatment armamentarium. The current treatment standards, as well as recommendations for the treatment of specific HCV subgroups, are reviewed.
Artemis - an extensible natural language framework for data querying and manipulation (2016)

Filtering and finding items of interest in large volumes of data, such as products in an e-commerce application or invoices in an ERP web platform can be a burdensome task, either for novice users that do not have insights on how the data is modeled or for those users who are already accustomed to the used system, but usually their filtering needs are significantly more complex. Natural language processing provides a way to dramatically improve the search experience for end-users and even though NLP is an AI-complete problem for the moment, based on the underlying data models the user can conduct comprehensive queries in a large set of scenarios guided by powerful context-aware prediction mechanisms. Based on this we have built Artemis, an extensible framework that transforms valid query inputs into filters applicable to underlying data models, stored either in-memory or in RDBMS, along with an extension mechanism to further enrich queries expressiveness via annotations or custom configuration and a context-aware prediction mechanism to direct the user into providing a valid query input, while decreasing the searching time. The conducted usability tests, showed that Artemis yields significantly reduced time-to-search, both for novice or experienced end-users with little or no training and for application developers it provides a straightforward apparatus for further improving expressivity based on custom, business-specific vocabulary.
The developing and senescent inner ear: selected topics and models. (1988)

Development and senescence are not mirror images, reversed, or opposite processes, but instead involve some common, as well as different mechanisms. In this review, we link the themes of development and senescence of the inner ear through the use of models. The inner ear develops in a highly coordinated series of stages. During development, each organ undergoes major structural changes prior to and during the onset of function. Thereafter, patterns of activity change as each sensory organ matures to its normal functional status. The remodeling continues at a slower pace after the onset of function. By comparison, the senescent inner ear loses its functional capacity and displays varying degrees of impairment. Cell degeneration and atrophy are commonly reported. However, in properly preserved specimens, senescent cells display few cytological markers aside from age pigment that can help to identify them.
Tools for Robotics in SME Workcells: Challenges and Approaches for Calibration and Registration (2015)

An overview of the challenges associated with robot workcell calibration and registration is presented, with a particular focus on the challenges faced by small-and medium-sized manufacturing enterprises (SMEs). Considerations for the barriers to integrating systemsof-systems workcells are described, and the proposed solutions from literature are presented. We discuss the impacts that calibration and registration have on many common robot applications, and highlight specific use cases of robot-sensor and robot-robot system registration.
Non-utilization of radioactive iodinated uracil, uridine, and orotic acid by animal tissues in vivo. (1953)

Iodouridine, iodoorotic acid, and iodouracil, labeled with I131, were synthesized. The syntheses of iodouridine and iodoorotic acid have not been described previously. The incorporation of these three I131-labeled pyrimidines into normal tissue, regenerating liver, and experimental tumors was investigated, and no significant preferential concentration was observed.
Interaction of Calpactin Light Chain (S100A10/p11) and a Viral NS Protein Is Essential for Intracellular Trafficking of Nonenveloped Bluetongue Virus (2011)

Bluetongue virus (BTV), a member of the Reoviridae family, is an insect-borne animal pathogen. Virus release from infected cells is predominantly by cell lysis, but some BTV particles are also released from the plasma membrane. The nonstructural protein NS3 has been implicated in this process. Using alternate initiator methionine residues, NS3 is expressed as a full-length protein and as a truncated variant that lacks the initial 13 residues, which, by yeast-two hybrid analyses, have been shown to interact with a cellular trafficking protein S100A10/p11. To understand the physiological significance of this interaction in virus-infected cells, we have used reverse genetics to investigate the roles of NS3 and NS3A in virus replication and localization in both mammalian and insect vector-derived cells. A virus expressing NS3 but not NS3A was able to propagate in and release from mammalian cells efficiently. However, growth of a mutant virus expressing only NS3A was severely attenuated, although protein expression, replication, double-stranded RNA (dsRNA) synthesis, and particle assembly in the cytoplasm were observed. Two of three single-amino-acid substitutions in the N-terminal 13 residues of NS3 showed phenotypically similar effects. Pulldown assay and confocal microscopy demonstrated a lack of interaction between NS3 and S100A10/p11 in mutants with poor replication. The role of NS3/NS3A was also assessed in insect cells where virus grew, albeit with a reduced titer. Notably, however, while wild-type particles were found within cytoplasmic vesicles in insect cells, mutant viruses were scattered throughout the cytoplasm and not confined to vesicles. These results provide support for a role for the extreme amino terminus of NS3 in the late stages of virus growth in mammalian cells, plausibly in egress. However, both NS3 and NS3A were required for efficient BTV growth in insect cells.
Automatic IC Hotspot Classification and Detection using Pattern-Based Clustering (2015)

technology have become the major yield detractor of integrated circuit manufacture. Due to inevitable process variations, especially focus and exposure variations in the optical lithography process, many parts of a design layout have bridging, necking or line-end shortening problems after being printed which can cause the circuits to fail certain specifications and therefore become yield detractors. These parts are defined as hotspots. Design rule checking (DRC) was developed to help circuit designers to detect such potential yield detractors by specifying geometric and connectivity restrictions which ensure sufficient margins to account for process variations, but the ever increasing number of rules needed as we move to more advanced technology nodes is becoming cumbersome to maintain. 2
Surgical Management of GH-Secreting Pituitary Adenomas: An Outcome Study Using Modern Remission Criteria (2001)

The results of transsphenoidal surgery as initial therapy for GH-secreting pituitary adenomas in 57 acromegalic patients were analyzed retrospectively. Patients with prior surgery or radiation therapy were excluded from the study. Three different criteria were used to define remission: glucose-suppressed (nadir) GH less than 1.0 microg/liter, a normal sex- and age-adjusted IGF-I level, and postoperative random GH levels of 2.5 microg/liter or less. Additionally, we analyzed the neuropathological data, including immunohistochemistry and ultrastructural categorization, and the surgical complications. The short-term remission rate (6-wk postoperative follow-up visit), as determined by a random GH measurement of 2.5 microg/liter or less, was 48.8%; the remission rate, as determined by nadir GH, was 51.4%. For 57 patients followed for 12 months or more after surgery (mean, 37.7 months), surgical remission was achieved in 70.2%, 66.7%, and 61.1%, respectively, for patients assessed by normal IGF-I, random GH, and nadir GH. One patient (1.1%) developed recurrence of active acromegaly 81 months after initially successful surgical therapy. Extrasellar growth of the tumor (P = 0.04) and dural invasion by the adenoma (P = 0.008) were significant univariate predictors of a poor outcome. Tumor size was significantly greater in patients with persistent or recurrent acromegaly (P = 0.02). Patients with tumors of the ultrastructural categories of mixed GH/PRL cell and mammosomatotroph adenomas had the lowest remission rates (50% and 42.9%, respectively). There were no perioperative deaths, and there was no serious morbidity. The permanent complication rate was 3.3% (1 permanent DI and 2 nasal septal perforations). Surgical management of acromegaly currently provides prompt, effective, and satisfactory initial treatment for the majority of patients. Using stringent criteria for remission, primary transsphenoidal surgery for GH-secreting pituitary adenomas is effective and often definitive therapy for acromegaly. These results provide a benchmark for the contemporary results of surgical management as assessed by modern outcome criteria.
Disintegration and reorganization of fibrin networks during tissue-type plasminogen activator-induced clot lysis (2001)

In this study, we investigated tissue-type plasminogen activator (tPA)-induced lysis of glutamic acid (glu)-plasminogen-containing or lysine (lys)-plasminogen-containing thrombin-induced fibrin clots. We measured clot development and plasmin-mediated clot disintegration by thromboelastography, and used scanning electron microscopy (SEM) to document the structural changes taking place during clot formation and lysis. These events occurred in three overlapping stages, which were initiated by the addition of thrombin, resulting first in fibrin polymerization and clot network organization (Stage I). Autolytic plasmin cleavage of glu-plasminogen at lys-77 generates lys-plasminogen, exposing lysine binding sites in its kringle domains. The presence of lys-plasminogen within the thrombin-induced fibrin clot enhanced network reorganization to form thicker fibers as well as globular complexes containing fibrin and lys-plasminogen having a greater level of turbidity and a higher elastic modulus (G) than occurred with thrombin alone. Lys-plasminogen or glu-plasminogen that had been incorporated into the fibrin clot was activated to plasmin by tPA admixed with the thrombin, and led directly to clot disintegration (Stage II) concomitant with fibrin network reorganization. The onset of Stage III (clot dissolution) was signaled by a sustained secondary rise in turbidity that was due to the combined effects of lys-plasminogen presence or its conversion from glu-plasminogen, plus clot network reorganization. SEM images documented dynamic structural changes in the lysing fibrin network and showed that the secondary turbidity rise was due to extensive reorganization of severed fibrils and fibers to form wide, occasionally branched fibers. These degraded structures contributed little, if anything, to the structural integrity of the residual clot, and eventually collapsed completely during the course of progressive clot dissolution. These results provide new perspectives on the major structural events that occur in the fibrin clot matrix during fibrinolysis.
Development of Scavenger-Free Three-Way Automotive Emission Control Catalysts with Reduced Hydrogen Sulfide Formation (1989)

<div class="htmlview paragraph">Fundamental research work was undertaken to elucidate the mechanism of hydrogen sulfide formation on three-way automotive exhaust catalysts during the lean to rich engine operation sequence and to identify the role of the different catalyst components in this phenomenon.</div> <div class="htmlview paragraph">Based upon this knowledge, new catalysts were developed with reduced ability to form hydrogen sulfide by minimizing the storage of sulfur oxides. Engine dynamometer tests confirmed that the suppression of the hydrogen sulfide formation was obtained without loss of catalyst activity or aging stability. The role of the catalyst's age in the hydrogen sulfide formation is discussed.</div> <div class="htmlview paragraph">The development presented shows that it is possible to avoid “scavengers” to minimize the emission of hydrogen sulfide from three-way emission control catalysts.</div>
TGF-β–Activated Kinase 1 Signaling Maintains Intestinal Integrity by Preventing Accumulation of Reactive Oxygen Species in the Intestinal Epithelium (2010)

The intestinal epithelium is constantly exposed to inducers of reactive oxygen species (ROS), such as commensal microorganisms. Levels of ROS are normally maintained at nontoxic levels, but dysregulation of ROS is involved in intestinal inflammatory diseases. In this article, we report that TGF-β-activated kinase 1 (TAK1) is a key regulator of ROS in the intestinal epithelium. tak1 gene deletion in the mouse intestinal epithelium caused tissue damage involving enterocyte apoptosis, disruption of tight junctions, and inflammation. Disruption of TNF signaling, which is a major intestinal damage inducer, rescued the inflammatory conditions but not apoptosis or disruption of tight junctions in the TAK1-deficient intestinal epithelium, suggesting that TNF is not a primary inducer of the damage noted in TAK1-deficient intestinal epithelium. We found that TAK1 deficiency resulted in reduced expression of several antioxidant-responsive genes and reduced the protein level of a key antioxidant transcription factor NF-E2-related factor 2, which resulted in accumulation of ROS. Exogenous antioxidant treatment reduced apoptosis and disruption of tight junctions in the TAK1-deficient intestinal epithelium. Thus, TAK1 signaling regulates ROS through transcription factor NF-E2-related factor 2, which is important for intestinal epithelial integrity.
Loss of arm function after stroke: measurement, frequency, and recovery (1986)

This study aims to establish the frequency of paralysis and other arm problems after stroke; the recovery of lost function; and to compare various tests of the affected arm. Thirteen per cent of the sample had no arm paralysis when first seen within 14 days. At 3 months 24 per cent of survivors had moderate or severe paralysis; 57 per cent could place nine pegs into holes within 50 seconds; 19 per cent had significant sensory disturbance; 5 per cent had shoulder pain; 8 per cent had restricted passive shoulder movement; and 17 per cent had some paralysis of the dominant arm. Between 3 and 6 months, improvement of motor power was seen in 40 per cent of patients, and 13 per cent of patients improved their function. Severity of initial paralysis was an important prognostic factor.
Prophetic dialogue as a practical theological category (2007)

Stephen Bevans and Roger Schroeder suggest that “prophetic dialogue” is the most appropriate category or metaphor for Christian mission today.2 This paper explores the significance and implications of “prophetic dialogue” for the task of practical theology. Whereas “prophecy” gives priority to the Word of God in scripture and tradition, “dialogue” highlights the importance of respectful human, cultural and religious encounter. Both components are necessary; their relationship is dialectical. Whether we are concerned with worship and liturgy, prayer and contemplation, justice and peace, the integrity of creation, interreligious dialogue, evangelization, inculturation or reconciliation, prophetic dialogue is a significant category for gauging the effectiveness and authenticity of the theological task. Panikkar’s “cosmotheandric” dialogue and the “triple dialogue” advocated by the Federation of the Asian Bishops’ Conferences are two possible avenues for advancing “prophetic dialogue.”
Nonlinear optical properties of silicon nanoclusters (1997)

The nonlinear and linear optical responses of Si nanoclusters at λ=355 nm were measured. The nanoclusters were laser ablated on quartz substrates. χ(3) values as high as 2.28×10−5 esu (as measured by the Z-scan technique) and lifetime as long as 143 ns were measured for clusters of an average size of 11 nm. The optical properties were strongly correlated with the clusters’ sizes.
Identification of a Differentially Expressed Oligopeptide Binding Protein (OppA2) in <i>Streptococcus uberis</i> by Representational Difference Analysis of cDNA (2003)

Streptococcus uberis is an increasingly significant cause of intramammary infection in the dairy cow, presently responsible for approximately 33% of all cases of bovine mastitis in the United Kingdom. Following experimentally induced infection of the lactating mammary gland, S. uberis is found predominantly in the luminal areas of secretory alveoli and ductular tissue, indicating that much of the bacterial growth occurs in residual and newly synthesized milk. With the objective of identifying potential virulence determinants in a clinical isolate of S. uberis, we have used representational difference analysis of cDNA to identify genes that show modified expression in milk. We have identified a number of differentially expressed genes that may contribute to the overall pathogenicity of the organism. Of these, a transcript encoding a putative oligopeptide binding protein (OppA) was further characterized. We have found that S. uberis possesses two oppA-like open reading frames, oppA1 and oppA2, which are up-regulated to different degrees following growth in milk. Mutants lacking either oppA1 or oppA2 are viable and have an increased resistance to the toxic peptide derivative aminopterin; however, only mutants lacking oppA1 display a lower rate of growth in milk. In addition, expression of the oppA genes appears to be coordinated by different mechanisms. We conclude that the oppA genes encode oligopeptide binding proteins, possibly displaying different specificities, required for the efficient growth of S. uberis in milk.
Automated Provisioning of Back-end Databases in Shared Dynamic Content Server Clusters (2005)

This thesis describes Vivaldi, a self-configuring architecture for scaling the database tier of dynamic content web services. We design an automatic and transparent provisioning algorithm that provides a unified approach to load and fault management in a database cluster. Our algorithm is based on dynamic data replication and provides strong consistency guarantees (i.e., 1-copy serializability) for the database cluster. Our algorithm dynamically allocates tasks to commodity databases across workloads in response to peak loads or failure conditions thus providing quality of service to clients. We investigate our transparent provisioning mechanisms in the database tier using two dynamic content applications: the TPC-W e-commerce benchmark and the RUBIS auction site benchmark. We demonstrate that our techniques provide both high resource usage and quality of service under different load and failure scenarios. ii Acknowledgements First, I would like to thank my advisor, Professor Cristiana Amza, for her support and guidance in my research efforts. Secondly, I would like to thank my parents for their emotional support and for encouraging me to explore new ideas.
The Impact of Tumor Necrosis Factor α Inhibitors on Radiographic Progression in Ankylosing Spondylitis (2013)

Treatment with TNFα inhibitors appears to reduce radiographic progression in AS patients, especially with early initiation and with longer duration of followup.
DOM: a scalable multicast protocol for next-generation internet (2010)

In this article we propose a scalable and efficient destination-oriented multicast protocol for next-generation Internet. With DOM, each packet carries explicit destinations information, instead of an implicit group address, to facilitate the multicast data delivery; and each router leverages the unicast IP routing table to determine necessary multicast copies and next-hop interfaces. The fundamental issue is that we need to limit the bandwidth overhead for such explicit addressing, since it is impractical to attach all the destination addresses to each packet. We resort to the Bloom filter technique to encode the destination information carried by each packet for bandwidth efficiency, with elaborated design to accommodate the features of the practical Internet including longest-prefix matching, route aggregation, and asymmetric interdomain routing. Moreover, DOM enables a fast group joining approach to minimize the joining delay perceived by receivers. The scalability and efficiency of DOM are demonstrated with simulation results.
A linear transconductance amplifier obtained by realizing a floating resistor (1998)

A novel circuit-design technique for bipolar and CMOS linear transconductance amplifiers is presented. The proposed linear transconductance amplifier consists of a differential pair of constant-current-biased transistors with a degeneration resistor and emitter- or source-followed-augmented current mirrors. The fundamental characteristics of the bipolar linear transconductance amplifier at a 1.9 V supply voltage are verified using bipolar transistor arrays and discrete resistors. The obtained linear input-voltage range is 320 mV r.m.s. (=0.905 V/sub p-p/ for less than 1% total harmonic distortion (THD) or 285 mV r.m.s. (=0.806 V/sub p-p/ for less than 0.1% THD when the input frequency is 1 kHz.
Development of infective larvae of Onchocerca volvulus in diffusion chambers implanted into Mastomys natalensis. (1985)

Diffusion chambers containing vector-derived infective larvae of O. volvulus were implanted into male Mastomys natalensis and removed after periods up to 100 days. Nearly all chambers contained motile living parasites. After two weeks lengths and diameters of the larvae had increased significantly and after 100 days one juvenile worm showed well developed papillae at the posterior end.