gebhart/patrepeval huggingface dataset:
An Azophenol-Based Chromogenic Anion Sensor (2000)

[figure: see text] A new chromogenic azophenol-thiourea based anion sensor, 2, has been developed. This system allows for the selective colorimetric detection of F-, H2PO4-, and AcO-. Selectivity trends turned out to be dependent upon guest basicity and conformational complementarity between 2 and the guest.
Processing of the Notch Ligand Delta by the Metalloprotease Kuzbanian (1999)

Signaling by the Notch surface receptor controls cell fate determination in a broad spectrum of tissues. This signaling is triggered by the interaction of the Notch protein with what, so far, have been thought to be transmembrane ligands expressed on adjacent cells. Here biochemical and genetic analyses show that the ligand Delta is cleaved on the surface, releasing an extracellular fragment capable of binding to Notch and acting as an agonist of Notch activity. The ADAM disintegrin metalloprotease Kuzbanian is required for this processing event. These observations raise the possibility that Notch signaling in vivo is modulated by soluble forms of the Notch ligands.
Debugging with Transactional Memory (2006)

Transactional programming promises to substantially simplify the development of correct, scalable, and efficient concurrent programs. Designs for supporting transactional programming using transactional memory implemented in hardware, software, and a mixture of the two have emerged recently. To our knowledge, nobody has yet addressed issues involved with debugging programs executed using transactional memory. Because transactional memory implementations provide the “illusion ” of multiple memory locations changing value atomically, while in fact they do not, there are challenges involved with integrating debuggers with such programs to provide the user with a coherent view of program execution. This paper shows how to overcome these problems by making the debugger interact with transactional memory implementations in a meaningful way. In addition to describing how “standard” debugging functionality can be integrated with transactional memory implementations, we also describe some powerful new debugging mechanisms that are enabled by transactional memory infrastructure. Our description focuses on how to enable debugging in software and hybrid software-hardware transactional memory systems. 1.
Deuterium Magnetic Resonance Imaging of Rabbit Eye in Vivo (1995)

We used deuterium magnetic resonance imaging (2H MRI) to visualize water movement in the rabbit eye. Dynamic 2H MRI was obtained every 3.5 min at 2 tesla by FLASH pulse sequence (TR, 300 ms; TE, 10 ms; alpha = 90 degrees) with a slice thickness of 10 mm using a surface coil (4 cm in diameter). After topical administration (0.2 ml D2O), only the aqueous chamber was imaged, and the signals decreased mono-exponentially. The flow rate was 0.113/min, in agreement with that already reported. After intravenous administration of deuterated saline (3 ml/kg), the aqueous chamber became visible first during imaging, then by the vitreous body. The signals around the lens were only faintly detected. Thus, deuterium MRI was determined to be useful for visualizing water movement in the eye.
Dietary Factors: Major Regulators of the Gut's Microbiota (2012)

Dietary factors and the associated lifestyle play a major role in the pathophysiology of many diseases. Several diets, especially a Western lifestyle with a high consumption of meat and carbohydrates and a low consumption of vegetables, have been linked to common diseases, such as metabolic syndrome, atherosclerosis, inflammatory bowel diseases, and colon cancer. The gastrointestinal tract harbors a complex and yet mainly molecularly defined microbiota, which contains an enormous number of different species. Recent advances in sequencing technologies have allowed the characterization of the human microbiome and opened the possibility to study the effect of "environmental" factors on this microbiome. The most important environmental factor is probably "what we eat," and the initial studies have revealed fascinating results on the interaction of nutrients with our microbiota. Whereas short-term changes in dietary patterns may not have major influences, long-term diets can affect the microbiota in a substantial manner. This issue may potentially have major relevance for human gastrointestinal health and disease because our microbiota has features to regulate many immune and metabolic functions. Increasing our knowledge on the interaction between nutrients and microbiota may have tremendous consequences and result in a better understanding of diseases, even beyond the gastrointestinal tract, and finally lead to better preventive and therapeutic strategies.
A web-enabled visualization toolkit for geovisual analytics (2011)

We introduce a framework and class library (GAV Flash) implemented in Adobe's ActionScript, designed with the intention to significantly shorten the time and effort needed to develop customized web-enabled applications for visual analytics or geovisual analytics tasks. Through an atomic layered component architecture, GAV Flash provides a collection of common geo- and information visualization representations extended with motion behavior including scatter matrix, extended parallel coordinates, table lens, choropleth map and treemap, integrated in a multiple, time-linked layout. Versatile interaction methods are drawn from many data visualization research areas and optimized for dynamic web visualization of spatio-temporal and multivariate data. Based on layered component thinking and the use of programming interface mechanism the GAV Flash architecture is open and facilitates the creation of new or improved versions of existing components so that ideas can be tried out or optimized rapidly in a fully functional environment. Following the Visual Analytics mantra, a mechanism "snapshot" for saving the explorative results of a reasoning process is developed that aids collaboration and publication of gained insight and knowledge embedded as dynamic visualizations in blogs or web pages with associative metadata or "storytelling".
Nonpolar mutagenesis of the ipa genes defines IpaB, IpaC, and IpaD as effectors of Shigella flexneri entry into epithelial cells (1993)

A 31-kb fragment of the large virulence plasmid of Shigella flexneri is necessary for bacterial entry into epithelial cells in vitro. One locus of this fragment encodes the IpaA, -B, -C, and -D proteins, which are the dominant antigens of the humoral immune response during shigellosis. To address the role of the ipa genes, which are clustered in an operon, we constructed a selectable cassette that does not affect transcription of downstream genes and used this cassette to inactivate the ipaB, ipaC, and ipaD genes. Each of these nonpolar mutants was defective in entry and lysis of the phagocytic vacuole but was not impaired in adhesion to the cells. We showed that, like IpaB and IpaC, IpaD is secreted into the culture supernatant and that none of these proteins is necessary for secretion of the other two. This result differentiates the Ipa proteins, which direct the entry process, from the Mxi and Spa proteins, which direct secretion of the Ipa proteins. Moreover, lack of either IpaB or IpaD resulted in the release of larger amounts of the other Ipa polypeptides into the culture medium, which indicates that, in addition to their role in invasion, IpaB and IpaD are each involved in the maintenance of the association of the Ipa proteins with the bacterium.
Electronic Structure and Reactivity of Candidate Conversion Material Iron Oxifluoride (2011)

Abstract not Available.
LightHolder: A Platform for Real-World Mobile Commerce (2006)

Recently, some of cellular phones in the market are equipped with wireless local communication devices such as infrared, Bluetooth, and a contactless IC chip, and several companies are trying to launch real-world mobile commerce services. However, the services have not become widespread yet. In order to realize the market penetration of the services, this research focuses on the mechanism for enhancing users’ convenience and service flexibility. In the architecture proposed in this paper, a service execution engine in a user’s cellular phone works as a common platform for multiple services. It automatically installs and updates service data stored in the cellular phone if necessary (called service plug-and-play). Based on the proposed architecture, we have developed a platform for real-world mobile commerce (called LightHolder) and have evaluated it through the development of several prototype services.
Topological fault-tolerance in cluster state quantum computation (2007)

We describe a fault-tolerant version of the one-way quantum computer using a cluster state in three spatial dimensions. Topologically protected quantum gates are realized by choosing appropriate boundary conditions on the cluster. We provide equivalence transformations for these boundary conditions that can be used to simplify fault-tolerant circuits and to derive circuit identities in a topological manner. The spatial dimensionality of the scheme can be reduced to two by converting one spatial axis of the cluster into time. The error threshold is 0.75% for each source in an error model with preparation, gate, storage and measurement errors. The operational overhead is poly-logarithmic in the circuit size.
Blockade of the Epidermal Growth Factor Receptor Inhibits Transforming Growth Factor α-Induced but Not Estrogen-Induced Growth of Hormone-Dependent Human Breast Cancer (1988)

Transforming growth factor alpha (TGF alpha), a polypeptide that binds to the epidermal growth factor (EGF) receptor, is expressed and secreted by human breast cancer cells and has been proposed as an autocrine growth factor and as a mediator of the mitogenic effect of estrogen. We investigated the potential importance of secreted TGF alpha in estrogen-responsive MCF-7 human breast cancer cells using monoclonal (528ab and 225ab) and polyclonal antibodies that block the EGF/TGF alpha receptor. Confirming other studies, these MCF-7 cells expressed TGF alpha with mRNA transcripts of 4.8 kilobases identified by Northern analysis, and they secreted TGF alpha activity measured by normal rat kidney colony-forming assay and an EGF RRA of conditioned medium. This activity was increased 3-fold by 1 nM 17 beta-estradiol and decreased by 1 microM tamoxifen. 528ab and 225ab bound to EGF receptors in MCF-7 cells with high affinity [dissociation constant (Kd) 0.1-0.5 nM] and blocked the binding of EGF/TGF alpha. These antibodies failed to inhibit baseline DNA synthesis or growth of MCF-7 cells although they were potent inhibitors of EGF/TGF alpha-induced growth of these cells. We hypothesized that if secreted TGF alpha mediates estrogen-induced growth, then EGF/TGF alpha receptor blockade should inhibit estrogen stimulation. MCF-7 cells were first treated with tamoxifen to inhibit growth and to reduce TGF alpha expression. Under these conditions, estrogen replenishment induced a marked dose-dependent rescue of TGF alpha secretion, DNA synthesis, and cell proliferation. Exogenous TGF alpha also partially restored growth of tamoxifen-inhibited cells. Although the simultaneous addition of 528ab or 225ab blocked TGF alpha-induced rescue of MCF-7 cells, it had no effect on rescue by estradiol.(ABSTRACT TRUNCATED AT 250 WORDS)
Cell segmentation and pipette identification for automated patch clamp recording (2014)

Abstract A visual-based approach for identifying living cells and performing the automated patch clamp recording was reported. Based on the image processing and blob detection algorithm, the vision-based method was developed for the detection and identification of biological cells and micropipette. The method was implemented in a micromanipulation system that enabled the identification of the boundary and the center of the target cell and separation from its neighboring cells. The method successfully identified a batch of neuroblastoma cells with the highest yield of 90%. The results demonstrated that the visual-based approach can be integrated to the micromanipulation system to automatically manipulate the patch pipette tip to the center of the target cell, and as a result, the whole-cell recording can be performed precisely and effectively.
Treatment with a Histone Deacetylase Inhibitor after Nuclear Transfer Improves the Preimplantation Development of Cloned Bovine Embryos (2010)

We examined the effects of treatment with histone deacetylase inhibitors (HDACi), trichostatin A (TSA) and scriptaid (SCR), on the blastocyst formation rate in bovine somatic cell nuclear transferred (SCNT) embryos derived from fibroblast cells. Three fibroblast cell lines (L1, L2 and L3) were used as somatic cell donors to produce SCNT embryos (L1, L2 and L3 embryos, respectively). In Experiment 1, we compared the in vitro developmental competence of L1 embryos treated with various concentrations of TSA for different time periods following chemical activation. Embryos treated with 5 nM TSA for 20 h showed a significantly increased blastocyst formation rate compared with untreated controls. In Experiment 2, we examined the effect of TSA (5 nM) treatment of L1, L2 and L3 embryos as well as the effect of treatment of L1, L2 and L3 embryos with various concentrations of SCR on in vitro developmental competence. It was found that 5 nM TSA treatment significantly increased the blastocyst formation rate in L1 and L3 embryos but did not have an influence on the development of L2 embryos. On the other hand, 5 nM SCR treatment significantly increased the blastocyst formation rates of L1 and L2 embryos compared with controls. However, there was no significant increase in the blastocyst formation rate of L3 embryos when they were treated with SCR. In Experiment 3, acetylation of H4K12 was examined in donor cells and pronuclear-stage L1, L2 and L3 embryos treated with 5 nM TSA or 5 nM SCR by immunostaining. The level of H4K12 acetylation was different among donor cells. The staining intensities in the TSA-treated L1 and L3 embryos and SCR-treated L2 embryos were significantly higher than those of untreated embryos. These results suggest that HDACi treatment of bovine SCNT embryos improves the blastocyst formation rate; however, the optimal treatment conditions may differ among donor cell lines.
Antimicrobial Susceptibility Patterns of KPC-Producing or CTX-M-Producing Enterobacteriaceae (2010)

Enterobacteriaceae clinical isolates harboring KPC-(178 strains) or CTX-M-encoding (67 strains) genes were collected during surveillance programs in the 2000-2007 period; and susceptibility was tested by broth microdilution methods. Organisms were dominantly collected in U.S. hospitals (93%). CTX-M-15 and -14 were the most prevalent CTX-M types (97%), all collected from the United States. KPC producers were isolated in the United States (160/178), Israel, China, and Argentina. bla(CTX-M)-carrying isolates were 95.5 and 98.5%, susceptible to Imipenem and meropenem respectively, and were all susceptible to tigecycline, whereas KPC-producing isolates were highly resistant to all antimicrobials tested except polymyxin B and tigecycline (90.6% and 99.4% susceptibility, respectively). The occurrence of KPC-producing and CTX-M-producing isolates has rapidly increased especially in U.S. hospitals, and expanded therapeutic options are needed to treat infections caused by these emerging organisms.
Formation of highly porous biodegradable scaffolds for tissue engineering (2000)

In recent years, lack of donor organs has caused many to consider tissue engineering methods as means to replace diseased or damaged organs. This newly-emerging field uses tissue-specific cells in a three-dimensional organization, provided by a scaffolding material, to return functionality of the organ. For these applications, the choice of scaffolding material is crucial to the success of the technique. In addition to the chemical properties of the material, physical properties such as surface area for cell attachment are essential. Various methods of creating pores in these materials to increase surface area are reviewed here. Scaffolds formed using the different techniques, which include fiber bonding, solvent casting/particulate leaching, gas foaming and phase separation, are compared on the basis of porosity, pore size, and promotion of tissue growth.
Processable Multipurpose Conjugated Polymer for Electrochromic and Photovoltaic Applications (2010)

A benzotriazole and 3-hexylthiophene (3HT) bearing a donor acceptor donor (D-A-D) type conjugated polymer (PHTBT) was synthesized. The polymer is both p and n-dopable, fluorescent, soluble in common organic solvents, and processable. Electrochemical and spectroelectrochemical characterization of PHTBT and its photovoltaic performance in organic bulk heterojunction (BHJ) solar cells (SC) have been measured. Using PHTBT as donor material in BHJ solar cells resulted in increased open circuit voltage (V-oc) up to 0.85 V.
Phase-locked arrays of antiguides: model content and discrimination (1990)

Three classes of array modes of closely spaced antiguides are analyzed: coupled fundamental (element) modes, coupled first-order (element) modes, and modes adjacent to coupled fundamental modes. The behavior of coupled fundamental modes as a function of lateral index step is analyzed and explained from a ray-optics point of view. It is found that at resonance, for both coupled fundamental and first-order modes, the array-mode propagation constant is virtually identical to the propagation constant of the mode of a single, unperturbed antiguide. Several types of mode discrimination mechanisms are discussed. For devices with 3- mu m-wide antiguide cores and 1- mu m interelement spacing, intermodal discrimination values of 15-20 cm/sup -1/ can be achieved. Excellent agreement is found between experimental data and theoretical predictions based on the effective-index method.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Current perspectives on control of equine influenza (2004)

Influenza A viruses of the H3N8 subtype are a major cause of respiratory disease in horses. Subclinical infection with virus shedding can occur in vaccinated horses, particularly where there is a mismatch between the vaccine strains and the virus strains circulating in the field. Such infections contribute to the spread of the disease. Rapid diagnostic techniques are available for detection of virus antigen and can be used as an aid in control programmes. Improvements have been made to methods of standardising inactivated virus vaccines, and a direct relationship between vaccine potency measured by single radial diffusion and vaccine-induced antibody measured by single radial haemolysis has been demonstrated. Improved adjuvants and antigenic presentation systems extend the duration of immunity induced by inactivated virus vaccines, but high levels of antibody are required for protection against field infection. In addition to circulating antibody, infection with influenza virus stimulates mucosal and cellular immunity; unlike immunity to inactivated virus vaccines, infection-induced immunity is not dependent on the presence of circulating antibody to HA. Live attenuated or vectored equine influenza vaccines, which may better mimic the immunity generated by influenza infection than inactivated virus vaccines, are now available. Mathematical modelling based upon experimental and field data has been applied to examine issues relating to vaccine efficacy at the population level. A vaccine strain selection system has been implemented and a more global approach to the surveillance of equine influenza is being developed.
DWMS: Data Warehouse Management System (1996)

After a thorough investigation of end user requirement differences from a Database and a Data Warehouse, a strong case is made for specific Data Warehouse Management Systems (DWMS), in contrast to the trend of utilizing DBMS for Data Warehouse construction. The three type (Temporal, Nested Relational, Multidimensional) DWMS hypothesis, an original concept of Yoshioki Ishii, President, Software AG of Far East, Inc. is explained in detail. Customer solutions and related products are introduced.
[Animal studies on neuropathic pain: the role of cytokines and cytokine receptors in pathogenesis and therapy]. (1999)

When pain becomes chronic this is a process that takes place at several levels of the peripheral and central nervous systems. In recent years, proinflammatory substances like bradykinin, prostaglandins and signal molecules like cytokines have been identified as allogenic factors. In the present paper we examined whether cytokines play a role also in non-inflammatory peripheral nerve lesions, i.e. whether they are of importance in the causation of pain in general and whether their antagonists can be used therapeutically. The development of pain after peripheral nerve lesion in animal models follows the process of Wallerian degeneration. During Wallerian degeneration the expression of proinflammatory cytokines in the nerve is upregulated. Here we studied the temporal course of cytokine expression with several different analytical methods, analyzing tumor necrosis factor-alpha (TNF) and interleukin-beta (IL-beta) in the mouse model of chronic constrictive injury (CCI) of the sciatic nerve. This model is associated with reproducible pain related behavior in the animals. We found an early increase of TNF 12 hours after injury. Neutralizing antibodies to TNF were able to reduce the hyperalgesia that evolved due to the nerve injury. As TNF exerts its effects via two receptors, TNF receptor 1 (TNF-R1) and TNF receptor 2 (TNF R2), we also investigated, which of the receptors is relevant to the causation of pain in this model. It turned out that antibodies to TNF-R1, but not to TNF-R2 reduced hyperalgesia, indicating that TNF-R1 is the receptor concerned. Neutralizing antibodies to IL-1 receptor and to IL-6 receptor also reduced pain related behavior. These results lead to the conclusion that proinflammatory cytokines are involved not only in inflammatory pain but also in neuropathic pain. Therapeutic strategies involving cytokine inhibition have been tested experimentally and are already being used in preliminary clinical studies in immune-mediated diseases. In the future, they might be a useful addition to the range of treatments for patients with neuropathic pain.