gebhart/patrepeval huggingface dataset:
Electron Microscopy of Cytochrome c Oxidase Crystals (1994)

Cytochrome c oxidase was isolated from beef heart mitochondria by detergent extraction yielding two different crystal forms. Extraction with Triton detergents produced vesicular crystals with two-dimensional crystalline arrays of cytochrome c oxidase dimers while extraction with sodium deoxycholate produced crystalline sheets of cytochrome c oxidase monomers. The structures of both crystal forms were determined in two-dimensional projection along an axis normal to the plane of the membrane by cryoelectron microscopy of crystals embedded in vitreous ice (frozen-hydrated). The projection structures of unstained frozen hydrated monomers and of dimers are similar to the structures of the crystals in negative stain. The molecular outline of dimers can be approximated by a parallelogram 44 A by 82 A with an included angle of 80 degrees. Monomers are less regular consisting of two large domains with a smaller domain at one end and a total length of approximately 82 A. Comparison of the two structures reveals the orientation of cytochrome c oxidase monomers within dimers, an orientation which is different from earlier models of monomer-monomer interaction, and suggests a very close interaction between monomers when they associate to form dimers. The crystalline sheets of cytochrome c oxidase monomers bind tightly the small peripheral membrane protein substrate, cytochrome c, and this binding accentuates a tendency of these crystals to stack upon one another. Images of crystals of the cytochrome c oxidase/cytochrome c complex were analyzed by crosscorrelation analysis versus the monomer crystal image. Two types of two-layer crystals have been identified. Both types have one layer rotated by 180 degrees with respect to the other, but they differ in the shifts of origin along crystal axes of the two layers. Difference images formed by subtracting simulated multilayered crystal images (which have no bound cytochrome c) from the complex crystals (cytochrome c oxidase plus cytochrome c) contain one positive difference peak for each cytochrome oxidase monomer within a unit cell. Comparison of the difference peak loci among the different crystal forms is interpreted based upon a consensus cytochrome c binding site in the single layer cytochrome oxidase monomer crystal image.
Characterization of RNA Determinants Recognized by the Arginine- and Proline-Rich Region of Us11, a Herpes Simplex Virus Type 1-Encoded Double-Stranded RNA Binding Protein That Prevents PKR Activation (2002)

The herpes simplex virus Us11 gene product inhibits activation of the cellular PKR kinase and associates with a limited number of unrelated viral and cellular RNA molecules via a carboxyl-terminal 68-amino-acid segment rich in arginine and proline. To characterize the determinants underlying the recognition of an RNA target by Us11, we employed an in vitro selection technique to isolate RNA ligands that bind Us11 with high affinity from a population of molecules containing an internal randomized segment. Binding of Us11 to these RNA ligands is specific and appears to occur preferentially on conformational isoforms that possess a higher-order structure. While the addition of unlabeled poly(I. C) reduced binding of Us11 to a selected radiolabeled RNA, single-stranded homopolymers were not effective competitors. Us11 directly associates with poly(I. C), and inclusion of an unlabeled selected RNA in the reaction reduces poly(I. C) binding, while single-stranded RNA homopolymers have no effect. Finally, Us11 binds to defined, double-stranded RNA (dsRNA) molecules that exhibit greater sequence complexity. Binding to these dsRNA perfect duplexes displays a striking dependence on length, as 39-bp or shorter duplexes do not bind efficiently. Furthermore, this interaction is specific for dsRNA as opposed to dsDNA, implying that the Us11 RNA binding domain can distinguish nucleic acid duplexes containing 2' hydroxyl groups from those that do not. These results establish that Us11 is a dsRNA binding protein. The arginine- and proline-rich Us11 RNA binding domain is unrelated to known dsRNA binding elements and thus constitutes a unique recognition motif that interacts with dsRNA. The ability of Us11 to bind dsRNA may be important for inhibiting activation of the cellular PKR kinase in response to dsRNA.
Replication, integration and stable germ-line transmission of foreign sequences injected into early zebrafish embryos (1988)

To generate stable lines of transgenic fish, early zebrafish embryos were injected with high concentrations of a linear bacterial plasmid. After injection, the foreign DNA was converted into a high molecular weight form and then amplified approximately tenfold during the initial rapid cleavages characteristic of the early embryo prior to gastrulation. While most of this DNA was subsequently degraded during gastrulation, some of the foreign sequences survived the gastrula stage and could be found in most of the injected fish at 3 weeks of age. Only about 5% of fish analysed 4 months after the injection retained foreign DNA in their fins, usually at less than one copy per cell. One of these fish was also found to contain about 100 copies per cell of foreign DNA in a fraction of its germ cells. Approximately 20% of the F1 offspring from this germ-line-positive parent inherited the foreign DNA, whereas 50% of F2 progeny obtained from an identified F1 individual inherited these sequences. The 50% transmission rate in F2 progeny was as expected for a single, heterozygous genomic insert. These observations indicate that injected DNA can be integrated into the fish genome, that the resulting transgenic fish are mosaic and that some of these mosaic individuals give rise to stable lines of transgenic fish.
Proteome analysis of conditioned medium from mouse embryonic fibroblast feeder layers which support the growth of human embryonic stem cells (2002)

Human embryonic stem (ES) cells are pluripotent cells with the potential to differentiate into a variety of cell types, which could be used for cell transplantation therapies as well as drug discovery studies. However, the large-scale culture of undifferentiated human ES cells is currently limited by their dependency on mouse embryonic fibroblast feeder layers. The proteomics approach was employed to characterize the environment that supports the growth of undifferentiated human ES cells and to identify factors critical for their independent growth. Conditioned medium from mouse embryonic fibroblast feeder layers, STO cell line, was concentrated and subjected to analyses by two-dimensional electrophoresis mass spectrometry. In total, 136 unique protein species were identified which included some that are known to participate in cell growth and differentiation, extracellular matrix formation and remodeling, in addition to the unexpected but interesting finding of many nominally intracellular proteins. This approach has thus revealed the complexity of the environment provided by the feeder cells and provides a useful starting point for future studies. Moreover, candidates from the initial list of identified proteins can be further investigated for their effects on the growth and differentiation of human ES cells in a defined culture environment.
Distribution of telomere-associated sequences on natural chromosomes in Saccharomyces cerevisiae. (1988)

Pulsed-field gel electrophoresis was used to examine the distribution of telomere-associated sequences on individual chromosomes in four strains of Saccharomyces cerevisiae. The pattern of X and Y' distribution was different for each strain. At least one chromosome in each strain lacked Y', and in some strains, chromosome I, the smallest yeast chromosome, lacked detectable amounts of both X and Y'.
Differential regulation of lipopolysaccharide‐induced interleukin 1 and tumor necrosis factor synthesis: effects of endogenous and exogenous glucocorticoids and the role of the pituitary‐adrenal axis (1989)

Intraperitoneal injection of a sublethal dose of lipopolysaccharide (LPS) into mice resulted in the appearance of tumor necrosis factor (TNF) in the serum within 45 min. Maximal serum TNF was detected by 1 h, and by 3-4 h TNF levels were no longer significantly above baseline. Injection of mice with an additional dose of LPS at 4 h resulted in no further increase in serum TNF. The in vivo kinetics of TNF appearance correlated with in vitro studies in which TNF mRNA was detected in murine peritoneal macrophages 30 min after LPS stimulation. The increase in serum TNF was not detected in mice treated with dexamethasone, 3 mg/kg, prior to LPS stimulation. The decrease in TNF correlated with the appearance of significant amounts of endogenous serum corticosterone which were maximal by 3 h. Further evidence for the role of endogenous steroids in the modulation of serum TNF levels was obtained in studies with adrenalectomized or hypophysectomized mice. Compared to sham-operated animals, serum TNF levels remain elevated 5 h post LPS stimulation in adrenalectomized or hypophysectomized mice. In contrast with the transient increase in TNF, serum IL 1 was maximal 4 h post LPS injection and remained elevated at 24 h. In vitro studies with primary cultures of human peripheral blood monocytes and human umbilical cord vein endothelial cells demonstrated that LPS-induced monocyte IL 1 levels were reduced approximately 5-fold by 10(-7) M dexamethasone while dexamethasone had only minimal effects on endothelial cell IL 1. Therefore, the in vitro data would suggest that the maintenance of elevated IL 1 levels coincident with the appearance of endogenous corticosteroids during LPS shock is related to the synthesis of IL 1 by both monocyte-macrophages and non-myeloid cell populations including endothelial cells.
A gene essential for the site-specific excision of actinophage R4 prophage genome from the chromosome of a lysogen. (1995)

An open reading frame (ORF469) was found near the attP core site of the actinophage R4 which encoded a 469-amino acid polypeptide. A gene disruption experiment suggested that the ORF469 gene was essential for site-specific excision of the prophage R4 genome from its host chromosome. The predicted amino acid sequence of the protein showed a similarity to a resolvase of Tn2501 and SpoIVCA of Bacillus subtilis.
Shift-register synthesis and BCH decoding (1969)

It is shown in this paper that the iterative algorithm introduced by Berlekamp for decoding BCH codes actually provides a general solution to the problem of synthesizing the shortest linear feedback shift register capable of generating a prescribed finite sequence of digits. The shift-register approach leads to a simple proof of the validity of the algorithm as well as providing additional insight into its properties. The equivalence of the decoding problem for BCH codes to a shift-register synthesis problem is demonstrated, and other applications for the algorithm are suggested.
Estimating the Impact of Public and Private Strategies for Controlling an Epidemic: A Multi-Agent Approach (2009)

This paper describes a novel approach based on a combination of techniques in AI, parallel computing, and network science to address an important problem in social sciences and public health: planning and responding in the event of epidemics. Spread of infectious disease is an important societal problem – human behavior, social networks, and the civil infrastructures all play a crucial role in initiating and controlling such epidemic processes. We specifically consider the economic and social effects of realistic interventions proposed and adopted by public health officials and behavioral changes of private citizens in the event of a “flulike” epidemic. Our results provide new insights for developing robust public policies that can prove useful for
Network-based virtual personal overlay networks using programmable virtual routers (2005)

This article explores the use and adaptation of well established VPN technologies to dynamically network at run time devices and services in personal networks. Virtual personal overlay networks are envisaged as an extension of the basic VPN concept to network PN nodes in a secure manner. User managed and provider provisioned-based overlays are analyzed in terms of scalability, management complexity, and security to select the most appropriate VPON deployment and management framework. The dynamic nature of PNs calls for highly flexible self-configuring and self-adaptive VPON architectures. Programmable edge routers and dynamic tunneling mechanisms can be combined to meet the requirements set by PNs. The virtual router model is used in the provider edge to ease the dynamic deployment and management of VPONs. Results of an implementation and a performance evaluation of the VR concept based on open software routers are reported.
Heterogeneous CD52 Expression among Hematologic Neoplasms: Implications for the Use of Alemtuzumab (CAMPATH-1H) (2006)

In contrast with CLL, the variable expression of CD52 among other hematologic malignancies suggests that target validation on a case-by-case basis will likely be necessary to guide the rational analysis of CAMPATH therapy.
Wide-angle, off-axis, see-through head-mounted display (2000)

A 60-deg-field-of-view optical see-through head-mounted display (HMD) using off-axis optics has been designed for 3-D medical imaging visualization. Two basic on-axis optical design concepts for see-though HMDs are reviewed first, to motivate the design of an off-axis optical form. An off-axis design is then presented. Because HMDs are typically designed from the pupil of the eye to the miniature display, it is common to assess final performance according to the display characteristics. Such analysis, however, does not provide information that is easily translated into task-based performance metric. Therefore, we present an analysis of the performance of the design from a usability viewpoint. For this analysis, the optical system is ray-traced from the display to the eye. Three key measures of performance-accommodation, astigmatism, and chromatic blur-are presented over the field of regard using customized graphical output.
Inhibitors ofp38 MAP Kinase: TherapeuticIntervention inCytokine-Mediated Diseases (1999)

p38 MAP kinase is a member of the family of kinases which mediate intracellular transduction pathways. The activation of this particular MAP kinase pathway is in response to a broad variety of extracellular stimuli. Subsequent downstream events triggered by p38 activation result in the production of IL-1 and TNF-a, suggesting that inhibition of this enzyme may provide a useful therapeutic target for intervention in various diseases mediated by these cytokines. Understanding the biological consequences of p38 activation and inhibition has been the subject of intensive research over the past several years and there is now ample evidence to suggest that inhibition of this enzyme represents a valid approach for target intervention in various cytokine-mediated diseases. Crystal structures of both apo enzyme and enzyme bound to various ligands in conjunction with site specific mutagenesis studies have provided a wealth of information regarding the interactions necessary to result in potent inhibition and selectivity from other kinases. This information has proven useful towards the analysis of previously reported compounds and will provide additional insight towards the design of new compounds and building upon existing SAR.
Anti-progestins suppress the growth of established tumors induced by 7,12-dimethylbenz(a)anthracene: Comparison between RU486 and a new 21-substituted-19-nor-progestin (2007)

In this report, we evaluate the effects of a 21-substituted-19-nor-progestin, CDB-4124, on 7,12,-dimethylbenz(a)anthracene (DMBA)-induced mammary carcinogenesis in rats in comparison with RU486. Sprague-Dawley female rats were treated with DMBA at 50 days of age in order to induce mammary tumors. When the tumors reached the size of 10-12 mm, the animals were treated for 28 days with the vehicle, RU486, progesterone, CDB-4124 at various doses, or CDB-4124 plus progesterone. Anti-progestins resulted in the regression in the size of the existing tumors, and in the suppressed development of new tumors and tumor multiplicity. Progesterone treatment, however, increased the size and multiplicity. Progesterone rendered an increased number of growing tumors as compared to the regression in the anti-progesterone treatment groups. The combination of CDB-4124 and high doses of progesterone opposed the efficacy of CDB-4124. The growth inhibitory effects of the anti-progestins were correlated with increased apoptosis and reduced cell proliferation. These results indicate that anti-progestins should be developed for the chemoprevention and treatment of hormone-responsive breast cancer.
A System for Video Surveillance and Monitoring (2000)

The Robotics Institute at Carnegie Mellon University (CMU) and the Sarnoff Corporation are developing a system for autonomous Video Surveillance and Monitoring. The technical objective is to use multiple, cooperative video sensors to provide continuous coverage of people and vehicles in cluttered environments. This paper presents an overview of the system and significant results achieved to date. 1 Introduction The DARPA Image Understanding (IU) program is funding basic research in the area of Video Surveillance and Monitoring (VSAM) to provide battlefield awareness. The thrust of CMU&amp;apos;s VSAM research is to develop automated video understanding algorithms that allow a network of active video sensors to automatically monitor objects and events within a complex, urban environment. We have developed video understanding technology that can automatically detect and track multiple people and vehicles within cluttered scenes, and to monitor their activities over long periods of time. Human an...
2-Year Efficacy, Immunogenicity, and Safety of Vigoo Enterovirus 71 Vaccine in Healthy Chinese Children: A Randomized Open-Label Study (2016)

NCT01508247.
The Behavior of Dynamic Channel-Assignment Mobile Communications Systems as a Function of Numbers of Radio Channels (1972)

Dynamic channel assignment in mobile communications systems is able to cope with varying nonuniform spatial user demand. It also readily handles the normal randomness in offered traffic. This study presents system performance data for radio systems having 8, 20, 40, 80, and 120 radio channels available and a radio-channel reuse interval of 4 base-station coverage areas. Data are also presented that compare performance of a 30 radiochannel system with a reuse interval of 3 base stations, a 40 radiochannel system with a reuse interval of 4 base stations, and a 50 radio-channel system with a reuse interval of 5 base stations. The results are obtained from a computer simulation of a onedimensional network laid out along a line. As the number of radio channels available to a communication system increases, the system becomes more efficient in handling the fluctuations in offered traffic. Changing the radio-channel reuse interval also affects the per-channel traffic carried by a dynamic-channel-assignment system.
Silicon–Polymer Hybrid Materials for Drug Delivery (2009)

Silicon and its oxides are widely used in biomaterials research, tissue engineering and drug delivery. These materials are highly biocompatible, easily surface functionalized, degrade into nontoxic silicic acid and can be processed into various forms such as micro- and nano-particles, monoliths, membranes and micromachined structures. The large surface area of porous forms of silicon and silica (up to 1200 m2/g) permits high drug loadings. The degradation kinetics of silicon- and silica-based materials can be tailored by coating or grafting with polymers. Incorporation of polymers also improves control over drug-release kinetics. The use of stimuli-responsive polymers has enabled environmental stimuli-triggered drug release. Simultaneously, silicon microfabrication techniques have facilitated the development of sophisticated implantable drug-delivery microdevices. This paper reviews the synthesis, novel properties and biomedical applications of silicon-polymer hybrid materials with particular emphasis on drug delivery. The biocompatible and bioresorptive properties of mesoporous silica and porous silicon make these materials attractive candidates for use in biomedical applications. The combination of polymers with silicon-based materials has generated a large range of novel hybrid materials tailored to applications in localized and systemic drug delivery.
Differential regulation of transforming growth factor beta and interleukin 2 genes in human T cells: demonstration by usage of novel competitor DNA constructs in the quantitative polymerase chain reaction. (1991)

The regulation of mRNA encoding transforming growth factor beta (TGF-beta) and interleukin 2 (IL-2) in normal human T cells was explored using novel competitor DNA constructs in the quantitative polymerase chain reaction and accessory cell-independent T cell activation models. Our experimental design revealed the following: (a) TGF-beta mRNA and IL-2 mRNA are regulated differentially in normal human T cells, quiescent or signaled with the synergistic combinations of: sn-1,2-dioctanoylglycerol and ionomycin or anti-CD3 monoclonal antibody (mAb) and anti-CD2 mAb; (b) the steady-state level of TGF-beta mRNA in the stimulated T cells, in contrast to that of IL-2 mRNA, is increased by the immunosuppressant cyclosporine (CsA); and (c) the paradoxical effect of CsA on TGF-beta mRNA levels is also appreciable at the level of production of functionally active TGF-beta protein. Our findings, in addition to demonstrating the utility of the competitor DNA constructs for the precise quantification of immunoregulatory cytokines, suggest a novel and unifying mechanistic basis for the immunosuppression and some of the complications (e.g., renal fibrosis) associated with CsA usage.
Genetic analysis of a human rotavirus that belongs to subgroup I but has an RNA pattern typical of subgroup II human rotaviruses (1987)

We have previously found (O. Nakagomi, T. Nakagomi, H. Oyamada, and T. Suto, J. Med. Virol. 17:29-34, 1985), during an epidemiological study in Japan, a novel human rotavirus that belongs to subgroup I but has a long RNA pattern typical of subgroup II human rotaviruses. From the stool specimen containing this virus, we successfully isolated in MA104 cells a rotavirus, designated AU-1, which possesses these novel characteristics. The possibility that strain AU-1 was a laboratory contaminant of an animal rotavirus previously adapted to tissue culture cells was ruled out, and the identity of the AU-1 strain was established. Genetic analysis by RNA-RNA hybridization revealed that the AU-1 strain is not a simple reassortant between subgroup I and II human rotaviruses but that it shares a high level of sequence homology only with the gene encoding VP7 (the major neutralization protein) of serotype 3 human rotaviruses. Weak homology of the genomic RNA segments was also observed between the AU-1 strain and animal rotavirus strains, including rhesus rotavirus strain RRV and bovine rotavirus strain NCDV. These results suggest that the AU-1 strain may be an animal rotavirus that infected a human.