gebhart/patrepeval huggingface dataset:
A comparison of salts for the crystallization of macromolecules (2001)

Thirty-one proteins and viruses that we knew from our own experience could be crystallized, or had been reported to have been crystallized by others, were investigated. In this experiment, each protein or virus was subjected to a crystallization screen of 12 different salts, each titrated to pH 7.2 beforehand, at concentrations ranging from 20% saturation to 90% saturation. Eight macromolecules failed to crystallize at all from any salt and were omitted from consideration. From the remaining 23 proteins, each salt was scored according to how many proteins and viruses it successfully crystallized. Among several results, one was particularly striking. Sodium malonate clearly was much more successful than any other salt, resulting in the crystallization of 19 of the 23 macromolecules, almost twice as effective as the next most successful salt, which was a draw between sodium acetate, sodium tartrate, sodium formate, and ammonium sulfate (11 of 22). The high success rate of sodium malonate in producing crystals was even more impressive when an overall unique success rate with individual macromolecules was considered.
Low Thresholds in Polymer Lasers on Conductive Substrates by Distributed Feedback Nanoimprinting: Progress Toward Electrically Pumped Plastic Lasers (2008)

A light-emitting transistor (LEFET) architecture with a distributed feedback (DFB) resonator structure nanoimprinted into the gain medium offers a route to achieving an electrically pumped plastic laser. A 2D DFB laser provides lower lasing thresholds than a 1D DFB laser under identical conditions. The 2D DFB lasers exhibit excellent characteristics with lasing threshold and slope efficiency of 32 nJ/pulse and 1.2%, respectively.
Mutations within the Putative Membrane-Spanning Domain of the Simian Immunodeficiency Virus Transmembrane Glycoprotein Define the Minimal Requirements for Fusion, Incorporation, and Infectivity (2001)

The membrane-spanning domain (MSD) of a number of retroviral transmembrane (TM) glycoproteins, including those from the human and simian immunodeficiency viruses (HIV and SIV), have been predicted to contain a charged arginine residue. The wild-type SIV TM glycoprotein is 354 amino acids long. The entire putative cytoplasmic domain of SIV (amino acids 193 to 354) is dispensable for virus replication in vitro, and such truncation-containing viruses are capable of reaching wild-type titers after a short delay. We show here that further truncation of eight additional amino acids to TM185 results in a protein that lacks fusogenicity but is, nevertheless, efficiently incorporated into budding virions. By analyzing a series of nonsense mutations between amino acids 193 and 185 in Env expression vectors and in the SIVmac239 proviral clone, a region of the SIV TM that contains the minimum requirement for glycoprotein-mediated cell-to-cell fusion and that for virus replication was identified. Virus entry and infectivity were evident in truncations to a minimum of 189 amino acids, whereas cell-cell fusion was observed for a protein of only 187 amino acids. Glycoprotein was efficiently incorporated into budding virions in truncations up to 185 amino acids, indicating that such proteins are membrane anchored and are transported to the cell surface. However, truncation of the TM to 180 amino acids resulted in a protein that displays a transport defect and may be retained in the endoplasmic reticulum. Based on our analyses of these mutants, an alternative model for the MSD of SIV is proposed. Our model suggests that membrane-imbedded charged residues can be neutralized by side-chain interactions with lipid polar head groups. As a consequence, the membrane-spanning region can be reduced by more than a helical turn. This new model accounts for the ability of truncations within the predicted MSD to remain membrane anchored and maintain biological activity.
An Architecture for Intelligent Interfaces (1988)

Four experiments were conducted to assess procedures for obtaining and testing user-selected terms for task specific concepts in complex, unfamiliar work processing instructions. Experiment 1 tested user-selected terms against both user-nominated and the original technical terms. The final three experiments employed only the user-selected and technical terms. The effect of terminology on subjects' abilities to follow the instructions were evaluated by measuring errors and task completion times during the practice period. Comprehension of the instructions was assessed by performance on a transfer task. Extensive practice produced acceptable and comparable performance for all term types. However, instruction comprehension, as measured by the transfer task, was clearly influenced by terminology. User-selected word processing terms were more understandable than both user-nominated and the original technical terms. In addition, the present study demonstrated that transfer tasks can be a more sensitive (and often a more appropriate) measure of the goodness of a term than learning measures.
Measurement of the mutation rates of animal viruses: influenza A virus and poliovirus type 1 (1986)

Epidemiologic and genetic evidence suggests that influenza A viruses evolve more rapidly than other viruses in humans. Although the high mutation rate of the virus is often cited as the cause of the extensive variation, direct measurement of this parameter has not been obtained in vivo. In this study, the rate of mutation in tissue culture for the nonstructural (NS) gene of influenza A virus and for the VP1 gene in poliovirus type 1 was assayed by direct sequence analysis. Each gene was repeatedly sequenced in over 100 viral clones which were descended from a single virion in one plaque generation. A total of 108 NS genes of influenza virus were sequenced, and in the 91,708 nucleotides analyzed, seven point changes were observed. A total of 105 VP1 genes of poliovirus were sequenced, and in the 95,688 nucleotides analyzed, no mutations were observed. We then calculated mutation rates of 1.5 X 10(-5) and less than 2.1 X 10(-6) mutations per nucleotide per infectious cycle for influenza virus and poliovirus, respectively. We suggest that the higher mutation rate of influenza A virus may promote the rapid evolution of this virus in nature.
Alkaline-Side Extraction of Cesium from Savannah River Tank Waste Using a Calixarene-Crown Ether Extractant (1998)

Results are presented supporting the viability of the alkaline-side CSEX process as a potential replacement for the In-Tank Precipitation process for removal of cesium from aqueous high-level waste (HLW) at the Savannah River Site (SRS). Under funding from the USDOE Efficient Separations and Crosscutting program, a flowsheet was suggested in early June of 1998, and in the following four months, this flowsheet underwent extensive testing, both in batch tests at ORNL and ANL and in two centrifugal-contactor tests at ANL. To carry out these tests, the initial ESP funding was augmented by direct funds from Westinghouse Savannah River Corporation. The flowsheet employed a solvent containing a calixarene-crown hybrid compound called BoBCalixC6 that was invented at ORNL and can now be obtained commercially for government use from IBC Advanced Technologies. This special extractant is so powerful and selective that it can be used at only 0.01 M, compensating for its expense, but a modifier is required for use in an aliphatic diluent, primarily to increase the cesium distribution ratio D{sub Cs} in extraction. The modifier selected is a relatively economical fluorinated alcohol called Cs3, invented at ORNL and so far available. only from ORNL. For the flowsheet, the modifier is used at 0.2 M in the branched aliphatic kerosene Isopar{reg_sign} L. Testing at ORNL and ANL involved simulants of the SRS HLW. After extraction of the Cs from the waste simulant, the solvent is scrubbed with 0.05 M HNO{sub 3} and stripped with a solution comprised of 0.0005 M HNO{sub 3} and 0.0001 M CsNO{sub 3}. The selection of these conditions is justified in this report, both on the basis of experimental data and underlying theory.
Fabrication of ultra-high aspect ratio silicon nanopores by electrochemical etching (2014)

We report on the formation of ultra-high aspect ratio nanopores in silicon bulk material using photo-assisted electrochemical etching. Here, n-type silicon is used as anode in contact with hydrofluoric acid. Based on the local dissolution of surface atoms in pre-defined etching pits, pore growth and pore diameter are, respectively, driven and controlled by the supply of minority charge carriers generated by backside illumination. Thus, arrays with sub-100 nm wide pores were fabricated. Similar to macropore etching, it was found that the pore diameter is proportional to the etching current, i.e., smaller etching currents result in smaller pore diameters. To find the limits under which nanopores with controllable diameter still can be obtained, etching was performed at very low current densities (several μA cm−2). By local etching, straight nanopores with aspect ratios above 1000 (∼19 μm deep and ∼15 nm pore tip diameter) were achieved. However, inherent to the formation of such narrow pores is a radius of curvature of a few nanometers at the pore tip, which favors electrical breakdown resulting in rough pore wall morphologies. Lowering the applied bias is adequate to reduce spiking pores but in most cases also causes etch stop. Our findings on bulk silicon provide a realistic chance towards sub-10 nm pore arrays on silicon membranes, which are of great interest for molecular filtering and possibly DNA sequencing.
Proxies, application interfaces, and distributed systems (2003)

Proxy objects are local representatives of remote objects in a distributed system. The authors use proxies to construct a transparent application programming interface (API) for the Choices distributed operating system. In earlier work, proxies were used in Choices to provide a protected, object-oriented interface to system objects. The addition of Remote Proxies allows applications to access all resources in a uniform way by simply invoking methods on objects, irrespective of whether they are local, in the kernel, in a different user virtual address space or remote. They also extend proxies to optimize access to remote and protected objects and to provide support for changing server interfaces. They describe a new remote procedure call (RPC) facility for invoking methods on remote objects through the proxy mechanism. The API is made dynamically reconfigurable by using table lookup to perform all functions normally provided by stubs in conventional RPC implementations. The API permits new versions of a service to be introduced without requiring recompilation of application client code.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A novel synthetic, nonpsychoactive cannabinoid acid (HU‐320) with antiinflammatory properties in murine collagen‐induced arthritis (2004)

Our studies show that the novel synthetic cannabinoid acid HU-320 has strong antiinflammatory and immunosuppressive properties while demonstrating no psychoactive effects. The profound suppressive effects on cellular immune responses and on the production of proinflammatory mediators all indicate its usefulness as a novel nonpsychoactive, synthetic antiinflammatory product.
Effects of cell cycle dependent histone H1 phosphorylation on chromatin structure and chromatin replication (1996)

We have reconstituted salt-treated SV40 minichromosomes with differentially phosphorylated forms of histone H1 extracted from either G0-, S- or M-phase cells. Sedimentation studies revealed a clear difference between minichromosomes reconstituted with S-phase histone H1 compared with histone H1 from G0- or M-phase cells, indicating that the phosphorylation state of histone H1 has a direct effect on chromatin structure. Using reconstituted minichromosomes as substrate in the SV40 in vitro replication system, we measured a higher replication efficiency for SV40 minichromosomes reconstituted with S-phase histone H1 compared with G0- or M-phase histone H1. These data indicate that the chromatin structure induced by the phosphorylation of histone H1 influences the replication efficiency of SV40 minichromosomes in vitro.
Strategic management process design and the systemic thought: The emergency of new design management methodologies (2009)

A partir de um contexto historico em crescente complexifi­cacao e das limitacoes do pensamento analitico da Ciencia Moderna, na compreensao de fenomenos processuais nao lineares nem redutiveis a poucas variaveis de partes atomiza­das, alcanca-se o paradigma do pensamento sistemico. Com fundamento neste paradigma, reflete-se sobre o design na contemporaneidade, suas multiplas interacoes mercadologi­cas, sua funcao estrategica nas organizacoes e a necessidade de processos e gestao orientados pelo e para o design. Me­diante uma revisao geral e sucinta das metodologias basea­das na epistemologia analitica, adentra-se no escopo princi­pal deste artigo, que e tentar esbocar um metodo sistemico de design estrategico. Palavras-chave: design estrategico, gestao de design, meto­dologia, pensamento sistemico.
B Cell Antigen Receptor Signaling: Roles in Cell Development and Disease (2002)

Signals propagated through the B cell antigen receptor (BCR) are vital for the development and survival of B lymphocytes in both the bone marrow and the periphery. These signals not only guide maturation and activation but also affect the removal of potentially self-reactive B lymphocytes. Interestingly, these signals are known to be either ligand-independent ("tonic" signals) or induced by ligand (antigen) binding to the BCR. We focus on the problems that occur in B cell development due to defects in signals emanating from the BCR. In addition, we present the B Cell Antigen Receptor Pathway, an STKE Connections Map that illustrates the events involved in B cell signaling.
Cancer-derived immunoglobulin G promotes tumor cell growth and proliferation through inducing production of reactive oxygen species (2013)

Cancer cells have been found to express immunoglobulin G (IgG), but the exact functions and underlying mechanisms of cancer-derived IgG remain elusive. In this study, we first confirmed that downregulation of IgG restrained the growth and proliferation of cancer cells in vitro and in vivo. To elucidate its mechanism, we carried out a co-immunoprecipitation assay in HeLa cells and identified 27 potential IgG-interacting proteins. Among them, receptor of activated protein kinase C 1 (RACK1), ras-related nuclear protein (RAN) and peroxiredoxin 1 (PRDX1) are closely related to cell growth and oxidative stress, which prompted us to investigate the mechanism of action of IgG in the above phenomena. Upon confirmation of the interactions between IgG and the three proteins, further experiments revealed that downregulation of cancer-derived IgG lowered levels of intracellular reactive oxygen species (ROS) by enhancing cellular total antioxidant capacity. In addition, a few ROS scavengers, including catalase (CAT), dimethylsulfoxide (DMSO), n-acetylcysteine (NAC) and superoxide dismutase (SOD), further inhibited the growth of IgG-deficient cancer cells through suppressing mitogen-activated protein kinase/extracellular-regulated kinase (MAPK/ERK) signaling pathway induced by a low level of intracellular ROS, whereas exogenous hydrogen peroxide (H2O2) at low concentration promoted their survival via increasing intracellular ROS levels. Similar results were obtained in an animal model and human tissues. Taken together, our results demonstrate that cancer-derived IgG can enhance the growth and proliferation of cancer cells via inducing the production of ROS at low level. These findings provide new clues for understanding tumor proliferation and designing cancer therapy.
A Novel Method for Determining the Chelation Ability of the Cysteine-Containing Peptides with 3,4-Toluenedithiol. Application to [2Fe–2S]-Ferredoxin Model Systems (1987)

Abstract The chelating ability of a bidentate ligand, Cys–X–Y–Cys (X, Y=amino acid residue), in 2Fe–2S peptide model complexes was examined by a ligand-exchange method using 3,4-toluenedithiol (tdt-H2) or o-xylene-α,α′-dithiol. The addition of tdt-H2 to an N,N-dimethylformamide solution of [Fe2S2(Z–cys–Ala–Ala–cys–OMe)2]2− results in the cleavage pf Fe–S* (S*=inorganic sulfur) bond and in the formation of hydrogen sulfide and mononuclear Fe(III) peptide thiolate complex, [Fe(Z–cys–Ala–Ala–cys–OMe)(tdt)]1−. In the case of [Fe2S2(Z–Ala–cys–OMe)4]2−, [Fe2S2(tdt)2]2− was obtained by the substitution of Z–Ala–Cys–OMe with the chelating reagent. On the other hand, o-xylene-α,α′-dithiol expels both Z–Cys–Ala–Ala–Cys–OMe and Z–Ala–Cys–OMe ligands from these complexes.
High-performance micro scale thermoelectric cooler: An optimized 6-stage cooler (2009)

We report the design, fabrication and testing of an optimized 6-stage planar thermoelectric (TE) micro cooler producing a DeltaT = 22.3degC at a power consumption of 26 mW, the best performance reported to date for a thermoelectric microcooler. This microcooler has a compact chip-scale design, and utilizes Bi <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Te <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> and Sb <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Te <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> thermoelectric thin films deposited on thermally isolating silicon oxide bridges. The fabricated cooler incorporates a total of 126 thermocouples across 6-stages within a volume of 5 times 5 times 1 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> .
Wnt signaling in idiopathic carpal tunnel syndrome (2016)

Carpal tunnel syndrome (CTS) is the most frequently reported entrapment neuropathy; however, the exact pathological mechanism of CTS remains unknown. In a recent paper published in the Journal of Orthopaedic Research, we investigated the associations between Wnt signaling and the etiology of idiopathic CTS (ICTS). We compared the expression levels of genes encoding Wnt1, 2, 3, 4, 5a, 5b, 6, 7a, 7b, 8a, 8b, 9a, 9b, 10a, 10b, 11, and 16 in the flexor tenosynovium between ICTS patients and controls, and we also evaluated whether an association exists between Wnt signaling and cell proliferation factors, such as estrogen-responsive finger protein, epidermal growth factor receptor, heparin binding-epidermal growth factor-like growth factor, insulin-like growth factor-1, and vascular endothelial growth factor (VEGF). To compare the cell proliferation potency, expression levels of MIB-1 protein were also measured. We found that Wnt9a gene expression in the flexor tenosynovium is more prominent in ICTS patients. A positive correlation was observed in only ICTS patient group for the gene expression of Wnt9a and VEGF in the flexor tenosynovium. There were no relationships between the expression levels of Wnt9a and fibroblast proliferation in either group. These results indicate that Wnt9a may be involved in the expression of VEGF in ICTS.
Hierarchical multicast routing in ATM networks (2002)

In this paper, we extend the hierarchical PNNI (private network node interface or private network network interface) point-to-point routing protocols [Dykeman, 1995] to support multicast routing in ATM networks. Our idea is based on the core-based tree idea for inter-domain multicast routing in the Internet [Ballardie et al., 1993]. Our idea uses multiple core nodes connected on a backbone tree. The destination nodes attach to the core nodes using the shortest path. Our algorithm is scalable because the multicast tree is shared among all senders. Also, only the core node information has to be flooded within each peer group. Our algorithm supports dynamic changes to the set of destinations. The backbone tree itself can be reconstructed depending on the current link and node states, thus, guaranteeing quality-of-service requirements. The cost of the multicast tree built incrementally for a given set of destinations is comparable to the cost of the Steiner tree constructed using standard heuristics. Using simulations, we show that the process of addition or deletion nodes is simplified, thereby reducing overheads. Moreover, the routing algorithm is recursive, that is, the nodes at each level of hierarchy execute the same algorithm. This makes the algorithm suitable for a distributed implementation.
Reducing the Cost of Frequent Hospital Admissions for Congestive Heart Failure (2001)

Substantial reductions in hospital readmissions, emergency visits, and cost of care for patients with CHF might be achieved by widespread deployment of distance technologies to provide posthospitalization monitoring. Home telecare may not offer incremental benefit beyond telephone follow-up and is more expensive.
Disruption of Rxra gene in thymocytes and T lymphocytes modestly alters lymphocyte frequencies, proliferation, survival and T helper type 1/type 2 balance (2007)

Retinoid X receptor (RXR) agonists, including the vitamin A metabolite 9-cis retinoic acid, decrease T-lymphocyte apoptosis and promote T helper type 2 (Th2) development ex vivo. To examine the in vivo role of RXR-alpha in T-lymphocyte development and function, we disrupted the Rxra gene in thymocytes and T lymphocytes using cyclization recombinase (Cre)-loxP-mediated excision of Rxra exon 4. Expression of Cre was targeted to these cells using the Lck promoter. Successful disruption of exon 4 was seen in thymus and T lymphocytes. Mice were healthy and the thymus, spleen and lymph nodes appeared normal. However, knockout mice had a lower percentage of double-positive (CD4(+) CD8(+)) and a higher percentage of double-negative thymocytes than wild-type mice. The percentage of splenic B lymphocytes was lower in unimmunized and ovalbumin-immunized knockout mice and the percentage of T lymphocytes was lower in immunized knockout mice. Ex vivo proliferation was decreased and apoptosis was increased in T lymphocytes from knockout mice. Memory CD4(+) T lymphocytes from knockout mice produced more interferon-gamma and interleukin-2 (IL-2) and less IL-5 and IL-10 than memory cells from wild-type mice, indicating a Th1 bias in vivo. However, Rxra disruption did not similarly bias ex vivo differentiation of naive CD4(+) T lymphocytes, nor did Rxra disruption alter the serum immunoglobulin G1/immunoglobulin G2a response to immunization. In summary, disruption of Rxra altered the percentages of T and B lymphocytes, produced a Th1 bias in vivo, and altered T-lymphocyte proliferation and apoptosis ex vivo. These differences were modest in magnitude and their impact on disease resistance is yet to be examined.