gebhart/patrepeval huggingface dataset:
Characterization of infectious Murray Valley encephalitis virus derived from a stably cloned genome-length cDNA (1999)

An infectious cDNA clone of Murray Valley encephalitis virus prototype strain 1-51 (MVE-1-51) was constructed by stably inserting genome-length cDNA into the low-copy-number plasmid vector pMC18. Designated pMVE-1-51, the clone consisted of genome-length cDNA of MVE-1-51 under the control of a T7 RNA polymerase promoter. The clone was constructed by using existing components of a cDNA library, in addition to cDNA of the 3' terminus derived by RT-PCR of poly(A)-tailed viral RNA. Upon comparison with other flavivirus sequences, the previously undetermined sequence of the 3' UTR was found to contain elements conserved throughout the genus FLAVIVIRUS: RNA transcribed from pMVE-1-51 and subsequently transfected into BHK-21 cells generated infectious virus. The plaque morphology, replication kinetics and antigenic profile of clone-derived virus (CDV-1-51) was similar to the parental virus in vitro. Furthermore, the virulence properties of CDV-1-51 and MVE-1-51 (LD(50) values and mortality profiles) were found to be identical in vivo in the mouse model. Through site-directed mutagenesis, the infectious clone should serve as a valuable tool for investigating the molecular determinants of virulence in MVE virus.
Differentiation of Beating Cardiac Muscle Cells from a Derivative of P19 Embryonal Carcinoma Cells. (1996)

A clonal derivative named CL6 has been isolated from pluripotent P19 embryonal carcinoma (EC) cells, after long term culture under conditions for mesodermal differentiation. The CL6 subline has a morphology similar to P19 cells and grows exponentially in standard medium, but unlike P19 cells, it efficiently differentiates into beating cardiac muscle in adherent culture with 1% dimethyl sulfoxide (DMSO). During differentiation, CL6 cells displayed the following general cardiac muscle properties: (1) alpha- and beta-cardiac myosin heavy chain (MHC) transcripts were first detected on day 10 after treatment with DMSO. (2) A sarcomere MHC protein also appeared on day 10, simultaneously with the initiation of contraction. (3) Immunofluorescence analysis showed that vigorously contracting cells have a striated structure. (4) Skeletal muscle specific transcripts, such as myogenin and MyoD, were not detected throughout differentiation. On the other hand, in suspension culture with 1 microM retinoic acid (RA), the condition for neural differentiation of P19 cells, the CL6 cells developed into neurons with poor outgrowth. Taken together, the CL6 subline seems not to be committed to a mesodermal lineage but to represent a developmental stage closer to differentiated cardiac muscle than the P19 cell line. Since CL6 cells directly differentiate into cardiac muscle in adherent culture, it is the most useful cell line for studying the differentiation of cardiac muscle in vitro.
Kohlrausch regulating function and other conservation laws in electrophoresis (2006)

The Kohlrausch regulating function (KRF) is a conservation law (conservation function), which is held in electrophoresis and which enables calculation of the so-called adjusted concentrations of constituents. The KRF is not the only conservation function and, depending on the complexity of the electrophoretic system, other conservation laws may be obeyed having a broader range of applicability. The conservation laws are tightly related to system eigenmobilities and system zones (system peaks). In principle, no system eigenmobility is exactly zero, but in most practical cases at least one system's eigenmobility is close to zero. The existence of the close-to-zero eigenmobility inherently points to the existence of a conservation function and a system zone which is stationary. The stationary system zone is called injection zone, stagnant zone, water peak, or solvent dip. Electrophoretic (electromigration) systems can be divided into two types: (i) conservation systems, in which the absolute value of at least one system eigenmobility is close to zero and where at least one conservation law is obeyed and (ii) nonconservation systems, where no system eigenmobility is close to zero and no conservation law is obeyed. The paper reviews work dealing with conservation functions in electromigration, derives some "historical" conservation functions in a new way, derives several conservation functions for systems of multivalent electrolytes, and discusses electrophoretic systems that have nonconservation behavior. In some typical instances, the conservation functions are simulated by means of a dynamic simulation tool and depicted graphically.
Building Taskable Spaces over Ubiquitous Services (2009)

Task-based abstraction can express user tasks via underlying services with minimal effort. However, developers must first address several issues including task execution transparency, exception handling, ontologies, and abstract architecture design.
The migration of paraxial and lateral plate mesoderm cells emerging from the late primitive streak is controlled by different Wnt signals (2008)

We suggest that the distinct behaviours of paraxial and lateral mesoderm precursors are regulated by the opposing actions of Wnt5a and Wnt3a as they leave the primitive streak in neurula stage embryos. Our data suggests that Wnt5a acts via prickle to cause migration of cells from the posterior streak. In the anterior streak, this is antagonised by Wnt3a to generate non-migratory medial mesoderm.
Reactivity pattern of 92 monoclonal antibodies with 15 human papillomavirus types (2007)

Most anti-human papillomavirus (HPV) capsid antibody assays are based on virus-like particles (VLP). We evaluated glutathione S-transferase (GST)-L1 fusion proteins as ELISA antigens for determining type specificity and cross-reactivity of 92 VLP-specific monoclonal antibodies (mAb) generated against nine mucosal alpha papillomavirus types of species 7, 9 and 10. The antibody panel included 25 new mAb, and 24 previously published mAb are further characterized. We determined the cross-reactivity patterns with 15 different HPV types representing 6 species (alpha1, 2, 4, 7, 9 and 10) and neutralization and cross-neutralization properties with HPV types 6, 11, 16, 18 and 45. Eighty-nine (97 %) of the antibodies including 34, 71 and 14 recognizing neutralizing, conformational and linear epitopes, respectively, reacted with the GST-L1 protein of the HPV type used as immunogen, with log titres ranging from 2.0 to 7.3. Of these 89 antibodies, 52 % were monotypic, 20 % showed intra-species and 28 % inter-species cross-reactivity. Log neutralization titres to the immunogen HPV ranged from 1.7 to 5.6. A single cross-neutralizing mAb (H6.L12) was found. ELISA titres were always higher than neutralization titres. All neutralizing epitopes were conformational and mostly type-specific. Our data show that bacterially expressed, affinity-purified GST-L1 fusion proteins display a broad variety of epitopes and thus are well suited for detection of HPV antibodies. Cross-reactivity is associated with linear as well as conformational epitopes. Distantly related mucosal and skin alpha papillomaviruses share some conformational epitopes and the phylogenetic L1-based species definition may not define a serological unit since no species-specific epitope was found.
Fault Tolerant Communication Library and Applications for High Performance Computing (2003)

With increasing numbers of processors on todays ma-chines, the probability for node or link failures is also in-creasing. Therefore, application level fault-tolerance is be-coming more of an important issue for both end-users and the institutions running the machines. This paper presents the semantics of a fault tolerant version of the Message Passing Interface, the de-facto standard for communication in scientific applications, which gives applications the pos-sibility to recover from a node or link error and continue ex-ecution in a well defined way. The architecture of FT-MPI, an implementation of MPI using the semantics presented above as well as benchmark results with various applica-tions are presented. An example of a fault-tolerant parallel equation solver, performance results as well as the time for recovering from a process failure are furthermore detailed. 1
Ketoconazole and fluconazole drug interactions. (1993)

This article reviews potential drug interactions that exist between ketoconazole or fluconazole and other drugs. English-language data sources included human subjects' computerized databases and published indexes. Case reports and studies demonstrate decreased dosage requirements of cyclosporine sodium, methylprednisolone sodium succinate, and possibly anticoagulants and phenytoin after ketoconazole or fluconazole administration, suggesting hepatic enzyme inhibition. Increased dosage requirements of ketoconazole are necessary after rifampin administration, suggesting rifampin's induction of hepatic microsomal enzymes. Possibly a similar effect may occur with concomitant fluconazole and rifampin. The effect of ketoconazole administration on prednisolone sodium phosphate and theophylline warrants further study. Fluconazole, a more selective agent for fungal P-450, seems to be of less concern regarding the potential for drug interactions than ketoconazole.
Evaluation of a multimodal interface for 3D terrain visualization (2002)

Novel speech and/or gesture interfaces are candidates for use in future mobile or ubiquitous applications. This paper describes an evaluation of various interfaces for visual navigation of a whole Earth 3D terrain model. A mouse driven interface, a speech interface, a gesture interface, and a multimodal speech and gesture interface were used to navigate to targets placed at various points on the Earth. This study measured each participant's recall of target identity, order, and location as a measure of cognitive load. Timing information as well as a variety of subjective measures including discomfort and user preference were taken. While the familiar and mature mouse interface scored best by most measures, the speech interface also performed well. The gesture and multimodal interface suffered from weaknesses in the gesture modality. Weaknesses in the speech and multimodal modalities are identified and areas for improvement are discussed.
Influence of organ site and tumor cell type on MUC1-specific tumor immunity (2001)

We investigated the influence of organ-specific parameters on tolerance and immunity to human MUC1. C57Bl/6 mice (wild-type) and C57Bl/6 transgenic for MUC1 (MUC1.Tg) were challenged in the pancreas with Panc02-MUC1, a C57Bl/6-syngeneic pancreatic cancer cell line expressing human MUC1. Wild-type mice produced immune responses to MUC1 when presented on tumor cells growing in the pancreas; however, the responses to tumors in the pancreas were less effective than responses produced by tumor challenge at the s.c. site. Tumor immunity specific for MUC1 was produced in wild-type mice by two different procedures: (i) s.c. immunization of wild-type mice with a low dose of Panc02-MUC1 or (ii) adoptive transfer of spleen and lymph node cells harvested from wild-type mice previously immunized s.c. with Panc02-MUC1. This demonstrates that immune responses to MUC1 presented at the s.c. site can be detected and adoptively transferred. MUC1.Tg mice were immunologically tolerant to MUC1; however, some immunological protection against orthotopic challenge with Panc02-MUC1 was conferred by adoptive transfer of CD4+ and CD8+ T cells from wild-type mice. These results show that it is more difficult to produce immune responses to tumors growing at the pancreatic site than the s.c. site. Panc02-MUC1 cells growing in the pancreas were accessible to the immune system, and immune responses evoked by s.c. presentation of this molecule in wild-type mice were effective in rejecting tumor cells in the pancreas of both wild-type and MUC1.Tg mice. No effective anti-tumor immune responses against MUC1 were produced in MUC1.Tg mice.
H-2-associated and background genes influence the development of a murine retrovirus-induced immunodeficiency syndrome. (1990)

Host genetic determinants of resistance or susceptibility to a retrovirus-induced immunodeficiency syndrome, termed MAIDS, were evaluated in Fv-1b mice infected with the mixture of ecotropic, MCF, and defective murine leukemia viruses designated LP-BM5 murine leukemia viruses. Genes of the MHC were shown to exert a major influence on the development of disease and the extent of virus spread in mice infected as adults. Strains bearing the b, f, k, q, r, and s haplotypes were moderately to highly susceptible to MAIDS whereas mice of the d haplotype were the most resistant. Resistance to disease was strongly associated with inhibition of mink cell focus-inducing virus spread and, to a lesser extent, with inhibition of ecotropic virus expression. Mapping studies localizing resistance associated with the d haplotype to H-2Dd were confirmed by the demonstration that B6 mice carrying this gene as a transgene or by recombination were resistant to disease. Penetrance of resistance to disease associated with expression of H-2Dd was markedly influenced by MHC genes mapping to the left of H-2D and by non-MHC loci such that some strains bearing this gene were highly susceptible to MAIDS. The combined effects of MHC and background genes among 40 strains examined yielded a remarkably wide spectrum of disease phenotypes with the onset of advanced disease ranging from 10 wk to 72 wk postinfection. Resistance to disease in moderately to highly resistant strains was shown to develop with age. Unexpectedly, the disease resistant phenotype was found to be a recessive trait.
Growth factor-delivery systems for tissue engineering: a materials perspective (2005)

The transplantation of organs, their surgical reconstruction or implantation of synthetic devices that can perform the function of organs, are the currently available methods for treating loss of tissue/organs in humans. However, the limitations associated with these techniques have led to the development of tissue engineering. One of the primary goals of tissue engineering is to provide growth factor delivery systems that can induce desired cell responses both in vitro and in vivo, in order to cause accelerated tissue regeneration. To make growth factors a more therapeutically viable alternative for the treatment of chronic degenerative diseases, a wide range of natural and synthetic materials have been employed as vehicles for their controlled delivery. The choice of material and design of the carrier device influence the mode of immobilization of growth factors on the scaffolds and their local/systemic administration. From a tissue engineer's perspective, materials could be used for designing scaffolds as well as for delivering single or multiple growth factors. Therefore, this review discusses growth factor delivery systems, with particular reference to carrier-based growth factor delivery systems with a focus on materials.
Human Campylobacteriosis in Developing Countries1 (2002)

Campylobacteriosis is a collective description for infectious diseases caused by members of the bacterial genus Campylobacter. The only form of campylobacteriosis of major public health importance is Campylobacter enteritis due to C. jejuni and C. coli. Research and control efforts on the disease have been conducted more often in developed countries than developing countries. However, because of the increasing incidence, expanding spectrum of infections, potential of HIV-related deaths due to Campylobacter, and the availability of the complete genome sequence of C. jejuni NCTC 11168, interest in campylobacteriosis research and control in developing countries is growing. We present the distinguishing epidemiologic and clinical features of Campylobacter enteritis in developing countries relative to developed countries. National surveillance programs and international collaborations are needed to address the substantial gaps in the knowledge about the epidemiology of campylobacteriosis in developing countries.
EpiSimdemics: an efficient algorithm for simulating the spread of infectious disease over large realistic social networks (2008)

Preventing and controlling outbreaks of infectious diseases such as pandemic influenza is a top public health priority. We describe EpiSimdemics - a scalable parallel algorithm to simulate the spread of contagion in large, realistic social contact networks using individual-based models. EpiSimdemics is an interaction-based simulation of a certain class of stochastic reaction-diffusion processes. Straightforward simulations of such process do not scale well, limiting the use of individual-based models to very small populations. EpiSimdemics is specifically designed to scale to social networks with 100 million individuals. The scaling is obtained by exploiting the semantics of disease evolution and disease propagation in large networks. We evaluate an MPI-based parallel implementation of EpiSimdemics on a mid-sized HPC system, demonstrating that EpiSimdemics scales well. EpiSimdemics has been used in numerous sponsor defined case studies targeted at policy planning and course of action analysis, demonstrating the usefulness of EpiSimdemics in practical situations.
In vivo brain imaging using a portable 39?gram two-photon fluorescence microendoscope (2005)

We introduce a compact two-photon fluorescence microendoscope based on a compound gradient refractive index endoscope probe, a DC micromotor for remote adjustment of the image plane, and a flexible photonic bandgap fiber for near distortion-free delivery of ultrashort excitation pulses. The imaging head has a mass of only 3.9 g and provides micrometer-scale resolution. We used portable two-photon microendoscopy to visualize hippocampal blood vessels in the brains of live mice.
Induced drift currents in circular planar magnetrons (1987)

The circulating E×B drift currents in a circular planar magnetron have been measured as a function of discharge parameters. The drift current was calculated from the magnetic field measured at a probe located over the center of the drift loop. The drift current was found to vary almost linearly with magnetron discharge current over the entire range of the magnetron power capability. The drift current-to-discharge ratio ranged from 2.5–9 and was dependent on gas pressure, and to some extent on gas species and cathode material. This ratio was derived using both classical two-body relations and also Bohm diffusion considerations. The results of the Bohm diffusion calculations are in close agreement with the experimental measurements. An additional feature confirming the Bohm diffusion results is the weak dependence of the observed drift current on gas species. Bohm diffusion is based on turbulent, collective interactions between electrons and the choice of gas species should only have an indirect effect through the electron density and temperature.
Cleome monophylla essential oil and its constituents as tick (Rhipicephalus appendiculatus) and maize weevil (Sitophilus zeamais) repellents (1995)

Abstract The repellency of the essential oil of the shrub Cleome monophylla (Family: Capparidaceae) and identified constituents of the oil were evaluated against the livestock tick, Rhipicephalus appendiculatus and the maize weevil, Sitophillus zeamais. In a tick climbing repellency bioassay, the oil of C. monophylla exhibited repellency which, at the highest dose, was comparable to that of the commercial arthropod repellent N, N‐diethyl toluamide (DEET). In a Y‐tube olfactometer bioassay, C. monophylla oil showed higher or comparable repellency against S. zeamais relative to DEET at all the doses tested. 14 Compounds were identified in the C. monophylla oil by GC, GC‐MS and coinjection with authentic samples. Terpenolene was found to occur in largest quantity (14%) followed by 1‐α‐terpeneol (10%), pentacosane (9%), (α + β)‐humulene (8%), phytol (5%) and 2‐dodecanone (4%). The most repellent components against R. appendiculatus and S. zeamais were 1‐α‐terpeneol and 2‐dodecanone. The overall pattern of repellency activity of the C. monophylla constituents with respect to the two arthropods was, however, different. The potential of C. monophylla in tick and maize weevil control is discussed.
Novel high-κ dielectrics for next-generation electronic devices screened by automated ab initio calculations (2015)

As the scale of transistors and capacitors in electronics is reduced to less than a few nanometers, leakage currents pose a serious problem to the device’s reliability. To overcome this dilemma, high-κ materials that exhibit a larger permittivity and band gap are introduced as gate dielectrics to enhance both the capacitance and block leakage simultaneously. Currently, HfO2 is widely used as a high-κ dielectric; however, a higher-κ material remains desired for further enhancement. To find new high-κ materials, we conduct a high-throughput ab initio calculation for band gap and permittivity. The accurate and efficient calculation is enabled by newly developed automation codes that fully automate a series of delicate methods in a highly optimized manner. We can, thus, calculate >1800 structures of binary and ternary oxides from the Inorganic Crystal Structure Database and obtain a total property map. We confirm that the inverse correlation relationship between the band gap and permittivity is roughly valid for most oxides. However, new candidate materials exhibit interesting properties, such as large permittivity, despite their large band gaps. Analyzing these materials, we discuss the origin of large κ values and suggest design rules to find new high-κ materials that have not yet been discovered. Automated ab initio calculations have been used to screen 1,800 oxides to find those with both a high dielectric constant (κ) and bandgap. High-κ dielectrics are needed to miniaturize microelectronic devices such as CPU, DRAM and flash memory. Ideally, they should also have a large bandgap, but no dielectric has yet been found that simultaneously has both a high κ and a large bandgap. Now, researchers in South Korea have performed first-principles calculations on almost all binary and tertiary oxides identified to date. They found that while a roughly inverse relation exists between permittivity and bandgap for most oxides, several oxides buck this trend. Based on the calculation results, they compiled a list of 13 oxides that show promise for CPU, DRAM and flash memory applications. Novel high-κ dielectric materials are identified by automated ab initio calculations on ~1800 oxides. The cubic BeO is found to possess an unprecedented material property of 10 eV for band gap and 275 for dielectric constant. Candidate high-κ oxides are suggested for microelectronic devices such as CPU, DRAM and flash memory.