gebhart/patrepeval huggingface dataset:
Virus-Enabled Synthesis and Assembly of Nanowires for Lithium Ion Battery Electrodes (2006)

The selection and assembly of materials are central issues in the development of smaller, more flexible batteries. Cobalt oxide has shown excellent electrochemical cycling properties and is thus under consideration as an electrode for advanced lithium batteries. We used viruses to synthesize and assemble nanowires of cobalt oxide at room temperature. By incorporating gold-binding peptides into the filament coat, we formed hybrid gold-cobalt oxide wires that improved battery capacity. Combining virus-templated synthesis at the peptide level and methods for controlling two-dimensional assembly of viruses on polyelectrolyte multilayers provides a systematic platform for integrating these nanomaterials to form thin, flexible lithium ion batteries.
Characterization of glycerate kinase (2-phosphoglycerate forming), a key enzyme of the nonphosphorylative EntnerâDoudoroff pathway, from the thermoacidophilic euryarchaeonPicrophilus torridus (2006)

Picrophilus torridus has been shown to degrade glucose via a nonphosphorylative Entner-Doudoroff (ED) pathway. Here we report the characterization of a key enzyme of this pathway, glycerate kinase (2-phosphoglycerate forming). The enzyme was purified 5,100-fold to homogeneity. The 95 kDa homodimeric protein catalyzed the ATP-dependent phosphorylation of glycerate specifically to 2-phosphoglycerate. The enzyme showed highest activity at 60 degrees C and pH 7.3, with ATP as phosphoryl donor and Mg(2+) as divalent cation. By MALDI-TOF analysis, ORF Pto1442 was identified in the genome of P. torridus as the encoding gene, designated gck. Homologs with high sequence identity were identified in the genomes of the archaea Thermoplasma and Sulfolobus spp. and Thermoproteus tenax, for which the operation of nonphosphorylative ED pathways, involving 2-phosphoglycerate forming glycerate kinases, has been proposed.
Embryonic stem cells and in vitro hematopoiesis (1992)

To study hematopoietic differentiation a variety of in vitro systems have been established using hematopoietic precursors derived from various explanted adult and fetal tissues. In this prospective we describe and discuss the potential of a novel system for studying the earliest stages of hematopoietic development. In addition, some of the applications of this system as a unique in vitro model for studying other developmental systems are discussed. Murine embryonic stem cells (ESC), which are totipotent and can be maintained undifferentiated indefinitely in vitro, have the capacity to differentiate in vitro into hematopoietic precursors of most, if not all, of the colony forming cells found in normal bone marrow. This potential can be exploited to study the control of the early stages of hematopoietic induction and differentiation. Recent results have indicated that there is a strong transcriptional activation, in a well defined temporal order, of many of the hematopoietically relevant genes. Examples of the genes expressed early during the induction of hematopoiesis include erythropoietin (Epo) and its receptor as well as the Steel (SI) factor (SLF) and its receptor (c-kit). Several other genes, including CSF-1, IL-1, and G-CSF were expressed during the later stages of hematopoietic differentiation. Contrasting with these observations, IL-3 and GM-CSF were not expressed during the first 24 days of ES cell differentiation suggesting that neither factor is necessary for the induction of hematopoietic precursors. Although these studies are just beginning, this system is easily manipulated and gives us an approach to understanding the control of the induction and differentiation of the hematopoietic system in ways not previously possible.
Separating access control policy, enforcement, and functionality in extensible systems (2001)

Extensible systems, such as Java or the SPIN extensible operating system, allow for units of code, or extensions, to be added to a running system in almost arbitrary fashion. Extensions closely interact through low-latency but type-safe interfaces to form a tightly integrated system. As extensions can come from arbitrary sources, not all of whom can be trusted to conform to an organization's security policy, such structuring raises the question of how security constraints are enforced in an extensible system. In this paper, we present an access control mechanism for extensible systems to address this problem. Our access control mechanism decomposes access control into a policy-neutral enforcement manager and a security policy manager, and it is transparent to extensions in the absence of security violations. It structures the system into protection domains, enforces protection domains through access control checks, and performs auditing of system operations. The access control mechanism works by inspecting extensions for their types and operations to determine which abstractions require protection and by redirecting procedure or method invocations to inject access control operations into the system. We describe the design of this access control mechanism, present an implementation within the SPIN extensible operating systems, and provide a qualitative as well as quantitative evaluation of the mechanism.
The parallel I/O architecture of the high-performance storage system (HPSS) (2002)

Datasets up to terabyte size and petabyte total capacities have created a serious imbalance between I/O and storage-system performance and system functionality. One promising approach is the use of parallel data-transfer techniques for client access to storage, peripheral-to-peripheral transfers, and remote file transfers. This paper describes the parallel I/O architecture and mechanisms, parallel transport protocol (PTP), parallel FTP, and parallel client application programming interface (API) used by the high-performance storage system (HPSS). Parallel storage integration issues with a local parallel file system are also discussed.
Central role of immunoglobulin (Ig) E in the induction of lung eosinophil infiltration and T helper 2 cell cytokine production: inhibition by a non-anaphylactogenic anti-IgE antibody. (1996)

Elevated levels of immunoglobulin (Ig) E are associated with bronchial asthma, a disease characterized by eosinophilic inflammation of the airways. Activation of antigen-specific T helper (Th) 2 cells in the lung with the subsequent release of interleukin (IL) 4 and IL-5 is believed to play an important role in the pathogenesis of this disease. In this study, we have used a non-anaphylactogenic anti-mouse-IgE antibody to investigate the relationship between IgE, airway eosinophil infiltration, and the production of Th2 cytokines. Immunization of mice with house dust mite antigen increased serum levels of IgE and IgG. Antigen challenge of immunized but not control mice induced an infiltration of eosinophils in the bronchoalveolar lavage associated with the production of IL-4 and IL-5 from lung purified Thy1.2+ cells activated through the CD3-T cell receptor complex. Administration of the anti-IgE monoclonal antibody (mAb) 6h before antigen challenge neutralized serum IgE but not IgG and inhibited the recruitment of eosinophils into the lungs and the production of IL-4 and IL-5 but not interferon gamma. Studies performed using an anti-CD23 mAb, CD23 deficient and mast cell deficient mice suggest that anti-IgE mAb suppresses eosinophil infiltration and Th2 cytokine production by inhibiting IgE-CD23-facilitated antigen presentation to T cells. Our results demonstrate that IgE-dependent mechanisms are important in the induction of a Th2 immune response and the subsequent infiltration of eosinophils into the airways. Neutralization of IgE, for example, non-anaphylactogenic anti-IgE mAbs may provide a novel therapeutic approach to the treatment of allergic airway disease.
A Feasibility Study for Imaging Tissue Electroporation With Electrical Impedance Tomography (2002)

In tissue electroporation, electrodes are inserted around the targeted tissue and electrical pulses are applied to permeabilize the cell membrane to macromolecules such as gene constructs in genetic engineering or cancer treatment drugs [1, 2]. For a specific set of voltage parameters (e.g. pulse number, frequency, duration), the effect that the electric field has depends on the voltage gradients that develop across the individual cell [2].
Transient regime of pulsed breakdown in low-conductive water solutions (2001)

The transient regime of pulsed electrical breakdown in both distilled and low-conductive water (σ<15 µS cm-1) has been investigated in a point-to-plane electrode system using quasi-rectangular voltage pulses with a repetition frequency of 25 Hz. Two individual current pulses were observed within the interval of voltages of 18.5-20 kV. The appearance of the transient regime was limited by the minimal capacitance of the storage capacitor C≅4 nF. While the time lag of the first current was not apparently affected by the capacitance of the storage capacitor, a growth in time lag of the second current pulse was observed as the capacitance was increased. The distortion of the electric field at the head and an increase of the leader channel resistance due to accumulation of the electrostatic charge on the inside wall of the gaseous channel are two most likely mechanisms effective in the transient regime. The enhancement of OH radical production in such a regime can be surmised from spectroscopic observations.
Properties of dehydrated human amnion/chorion composite grafts: Implications for wound repair and soft tissue regeneration (2014)

PURION(®) processed dehydrated human amnion/chorion membrane (dHACM; MiMedx Group, Marietta, GA) tissue products were analyzed for the effectiveness of the PURION(®) process in retaining the native composition of the amniotic membrane and preserving bioactivity in the resulting products. dHACM was analyzed for extracellular matrix (ECM) composition through histological staining and for growth factor content via multiplex ELISA arrays. Bioactivity was assessed by evaluating endogenous growth factor production by human dermal fibroblasts in response to dHACM and for thermal stability by mechanical tests and in vitro cell proliferation assays. Histology of dHACM demonstrated preservation of the native amnion and chorion layers with intact, nonviable cells, collagen, proteoglycan, and elastic fibers distributed in the individual layers. An array of 36 cytokines known to regulate processes involved in inflammation and wound healing were identified in dHACM. When treated with dHACM extracts, bioactivity was demonstrated through an upregulation of basic fibroblast growth factor, granulocyte colony-stimulating factor, and placental growth factor biosynthesis, three growth factors involved in wound healing, by dermal fibroblasts in vitro. After conditioning at temperatures ranging from -78.7 to +73.5°C, dHACM retained its tensile strength and ability to promote proliferation of dermal fibroblasts in vitro. Elution experiments demonstrated a soluble fraction of growth factors that eluted from the tissue and another fraction sequestered within the matrix. The PURION(®) process retains the native composition of ECM and signaling molecules and preserves bioactivity. The array of cytokines preserved in dHACM are in part responsible for its therapeutic efficacy in treating chronic wounds by orchestrating a "symphony of signals" to promote healing.
Intra- and Extracellular β-Galactosidases from Bifidobacterium bifidum and B. infantis : Molecular Cloning, Heterologous Expression, and Comparative Characterization (2001)

Three beta-galactosidase genes from Bifidobacterium bifidum DSM20215 and one beta-galactosidase gene from Bifidobacterium infantis DSM20088 were isolated and characterized. The three B. bifidum beta-galactosidases exhibited a low degree of amino acid sequence similarity to each other and to previously published beta-galactosidases classified as family 2 glycosyl hydrolases. Likewise, the B. infantis beta-galactosidase was distantly related to enzymes classified as family 42 glycosyl hydrolases. One of the enzymes from B. bifidum, termed BIF3, is most probably an extracellular enzyme, since it contained a signal sequence which was cleaved off during heterologous expression of the enzyme in Escherichia coli. Other exceptional features of the BIF3 beta-galactosidase were (i) the monomeric structure of the active enzyme, comprising 1,752 amino acid residues (188 kDa) and (ii) the molecular organization into an N-terminal beta-galactosidase domain and a C-terminal galactose binding domain. The other two B. bifidum beta-galactosidases and the enzyme from B. infantis were multimeric, intracellular enzymes with molecular masses similar to typical family 2 and family 42 glycosyl hydrolases, respectively. Despite the differences in size, molecular composition, and amino acid sequence, all four beta-galactosidases were highly specific for hydrolysis of beta-D-galactosidic linkages, and all four enzymes were able to transgalactosylate with lactose as a substrate.
Other transgenic mutation assays: Parameters affecting the use of thelac repressor system in eukaryotic cells and transgenic animals (1996)

Elements of the lactose operon were used to study parameters affecting gene expression in cultured cells and transgenic animals. A Lac repressor protein containing a nuclear transport signal was shown to inhibit expression of a reporter gene by interacting with lac operator sequences. In cultured cells, operator sequence, operator placement and induction parameters were all shown to be important for obtaining tight repression of a reporter gene followed by high level expression upon induction. Induction levels were also dependent on the reporter gene, with the luciferase gene yielding higher induction levels than the chloramphenicol acetyltransferase gene. In transgenic animals, the lacI mRNA was not detected in the C57BL/6 mouse strain until the animal was exposed to a demethylating agent. After 5-azacytidine treatment, expression of lacI mRNA was detected in the brain, heart, kidney, lung and ovary. In the FVB transgenic mouse strain, expression of lacI mRNA was detected without 5-azacytidine treatment in the kidney, liver, lung, and testes. Preliminary experiments with double transgenic animals containing both lacI and operator/luciferase transgenes showed a decrease in luciferase expression compared to the luciferase-only animals in both tissue extracts and transgenic fetal primary cultures, although IPTG induction was not achieved in these animals or primary cultures. The applicability and challenges of the system for regulation of gene expression are discussed.
Effect of Secondary Structure on the Thermodynamics and Kinetics of PNA Hybridization to DNA Hairpins (2001)

The binding of a series of PNA and DNA probes to a group of unusually stable DNA hairpins of the tetraloop motif has been observed using absorbance hypochromicity (ABS), circular dichroism (CD), and a colorimetric assay for PNA/DNA duplex detection. These results indicate that both stable PNA-DNA and DNA-DNA duplexes can be formed with these target hairpins, even when the melting temperatures for the resulting duplexes are up to 50 degrees C lower than that of the hairpin target. Both hairpin/single-stranded and hairpin/hairpin interactions are considered in the scope of these studies. Secondary structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands. The thermodynamic and kinetic obstacles to hybridization imposed by both target and probe secondary structure are significant concerns for the continued development of antisense agents and especially diagnostic probes.
Efficient Partitioning of Fragment Shaders for Multipass Rendering on Programmable Graphics Hardware (2002)

Real-time programmable graphics hardware has resource constraints that prevent complex shaders from rendering in a single pass. One way to virtualize these resources is to partition shading computations into multiple passes, each of which satisfies the given constraints. Many such partitions exist for a shader, but it is important to find one that renders efficiently. We present Recursive Dominator Split (RDS), a polynomial-time algorithm that uses a cost model to find near-optimal partitions of arbitrarily complex shaders. Using a simulator, we analyze partitions for architectures with different resource constraints and show that RDS performs well on different graphics architectures. We also demonstrate that shader partitions computed by RDS can run efficiently on programmable graphics hardware available today.
A systems approach for collaborative decision support in water resources planning (2002)

The paper presents a decision support system (DSS) for collaborative group planning of hydroelectric development projects. The framework for planning is described with a systems approach for dynamic evaluation. Systems involving human frailties will always be complex, and that complexity will always be intimidating from a systems perspective. However, systems thinking is evolving into concepts that may help us understand how to approach complex technical problems that affect or involve people. There are currently two types of dynamic modelling paradigms understood by systems analysis. One is negative feedback, which forces system transformation toward an external goal. The second paradigm is the concept of positive feedback. Positive feedback behaves in a similar manner to many natural growth processes in which the system feedback instigates growth away from an external goal or reference point. Positive feedback systems approach initiates changes to a proposal away from the initial reference point of conflict or disjoint value systems. Its direction and pace are flexible, which may be desirable properties for group behaviour. A framework for planning hydroelectric water management policy is demonstrated as a positive system feedback approach. A decision support system is designed for interaction and participation of a group of stakeholders with a project proponent. Planning within the group setting assumes an iterative, flexible, modelling posture. Stakeholders are able to interactively adjust the system to visualize changes, designed to improve understanding of system behaviour. Experimental alternatives are compared in terms of decision robustness relative to apparent issues and preference structures. Overall, the positive feedback mechanisms of iteration and experimentation allow alternatives to be generated, assessed, and improved.
The Noncoding RNA MALAT1 Is a Critical Regulator of the Metastasis Phenotype of Lung Cancer Cells (2012)

The long noncoding RNA MALAT1 (metastasis-associated lung adenocarcinoma transcript 1), also known as MALAT-1 or NEAT2 (nuclear-enriched abundant transcript 2), is a highly conserved nuclear noncoding RNA (ncRNA) and a predictive marker for metastasis development in lung cancer. To uncover its functional importance, we developed a MALAT1 knockout model in human lung tumor cells by genomically integrating RNA destabilizing elements using zinc finger nucleases. The achieved 1,000-fold MALAT1 silencing provides a unique loss-of-function model. Proposed mechanisms of action include regulation of splicing or gene expression. In lung cancer, MALAT1 does not alter alternative splicing but actively regulates gene expression including a set of metastasis-associated genes. Consequently, MALAT1-deficient cells are impaired in migration and form fewer tumor nodules in a mouse xenograft. Antisense oligonucleotides (ASO) blocking MALAT1 prevent metastasis formation after tumor implantation. Thus, targeting MALAT1 with ASOs provides a potential therapeutic approach to prevent lung cancer metastasis with this ncRNA serving as both predictive marker and therapeutic target. Finally, regulating gene expression, but not alternative splicing, is the critical function of MALAT1 in lung cancer metastasis. In summary, 10 years after the discovery of the lncRNA MALAT1 as a biomarker for lung cancer metastasis, our loss-of-function model unravels the active function of MALAT1 as a regulator of gene expression governing hallmarks of lung cancer metastasis.
Transient measurements of SOI body contact effectiveness (1998)

A technique for characterizing the effectiveness of SOI MOSFET body contacts under transient conditions, by measuring the transient lateral bipolar current in a SOI pass gate, is demonstrated. Using this technique, the minimum rise or fall edge rate required to guarantee that the body potential over the device width follows the contact potential is defined. While this technique is applied specifically to a Schottky body tie, it can be generalized to other technologies and other body ties.
Neuropsychiatric Adverse Events of Varenicline (2012)

Varenicline is associated with an increased risk of serious neuropsychiatric AEs, especially in patients with a psychiatric illness. It is strongly recommended that varenicline be administered only to mentally stable patients and under close monitoring.
Do Nitroxide Antioxidants Act as Scavengers of O2−˙or as SOD Mimics? (1996)

Stable nitroxide radicals were reported to act as SOD mimics and catalyze the dismutation of O2-. through two different catalytic pathways including reductive and oxidative reaction mechanisms (Samuni, A., Krishna, C. M., Riesz, P., Finkelstein, E. & Russo, A. (1988) J. Biol Chem. 263, 17921-17924). Recent studies directly monitoring O2-. and employing kinetics analysis did not reveal SOD activity of nitroxides (Weiss, R. H., Flickinger, A. G., Rivers, W. J., Hardy, M. M., Aston, K. W., Ryan, U. S. & Riley, D. P. (1993) J. Biol. Chem. 268, 23049-23054). Such discrepancy may result in cases where distinction of stoichiometric scavengers from catalytic detoxifiers of O2-. is not readily feasible. Nitroxides are effective antioxidants that protect against oxidative injury in various pathological processes. The distinction of their SOD mimic activity from O2-. scavenging was established by examining the validity of direct and indirect methods employed to assay SOD-like catalytic activity. Kinetics analysis along with direct EPR monitoring were used to study the mechanism underlying nitroxide reactions with O2-.. The nitroxide EPR signal decayed in the presence of NADH but otherwise did not decrease with time, thus substantiating its catalytic role in O2-. dismutation. The catalytic rate constants for O2-., dismutation, determined for the nitroxides tested, were found to increase with [H+], indicating that .OOH rather than O2-. is oxidizing the nitroxide. The results demonstrate the limitations associated with direct kinetics analysis in evaluating SOD mimic activity, underscoring the need for independent assays for valid discrimination of SOD mimics from stoichiometric scavengers of O2-..