gebhart/patrepeval huggingface dataset:
Journey mapping (2014)

If you've been in the field of user experience design, usability testing, or marketing for anytime at all, you've almost certainly come across the use of personas to help members of a cross functional design team communicate with one another about the impacts that design decisions will have on a particular user demographic. As Adlin and Pruitt (2006) explain, personas are useful because they put an individual, human face on demographic and ethnographic data which would otherwise be difficult to explain to software engineers, project managers, information product developers, and other stakeholders in a way they can easily conceptualize and apply. Usually on one sheet of paper, a persona will provide a photo of the character for the persona; a memorable name for the persona; a short bio or background information about the persona; the persona's goals for using the product being developed; a short and memorable quote from the persona which usually conveys their ethos ; and other information relevant to the use of the product being designed such as training; previous experience with similar products, or physical disabilities (such as arthritis or poor eye sight---see http://www.clemson.edu/caah/caah_mockups/persona_clemsongrad.html for an example of personas developed for the redesign of a College's website).
Windowing time in digital libraries (2006)

This paper discusses the specification, organization, and utility of time references identified in digital library materials, emphasizing how to treat date references that cannot be resolved to a single day. The HistoryMakers oral history archive is used to illustrate the concept of windowing such time in digital library interfaces.
Induction of Plasmodium falciparum Transmission-blocking Antibodies by Recombinant Vaccinia Virus (1991)

Many candidate antigens of malaria vaccines have limited immunological recognition. One exception is Pfs25, a cysteine-rich, 25-kilodalton sexual stage surface protein of Plasmodium falciparum. Pfs25 is a target of monoclonal antibodies that block transmission of malaria from vertebrate host to mosquito vector. The surface of mammalian cells infected with a recombinant vaccinia virus that expressed Pfs25 specifically bound transmission-blocking monoclonal antibodies. Furthermore, major histocompatibility complex-disparate congenic mouse strains immunized with recombinant Pfs25 elicited transmission-blocking antibodies, demonstrating that the capacity to develop transmission-blocking antibodies is not genetically restricted in mice. Live recombinant viruses may provide an inexpensive, easily administered alternative to subunit vaccines prepared from purified recombinant proteins to block transmission of malaria in developing countries.
Use of controlled reactive spreading of liquid alkanethiol on the surface of gold to modify the size of features produced by microcontact Printing (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTUse of controlled reactive spreading of liquid alkanethiol on the surface of gold to modify the size of features produced by microcontact PrintingYounan Xia and George M. WhitesidesCite this: J. Am. Chem. Soc. 1995, 117, 11, 3274–3275Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://pubs.acs.org/doi/10.1021/ja00116a033https://doi.org/10.1021/ja00116a033research-articleACS PublicationsRequest reuse permissionsArticle Views837Altmetric-Citations147LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Fluorinated Aryl Sulfonimide Tagged (FAST) salts: modular synthesis and structure–property relationships for battery applications (2018)

Fluorinated Aryl Sulfonimide Tag (FAST) anions provide a new class of modular salts with tunable properties for potential battery applications.
Human mannose-binding protein activates the alternative complement pathway and enhances serum bactericidal activity on a mannose-rich isolate of Salmonella. (1989)

The human mannose-binding protein (MBP) is a multimeric serum protein that is divided into three domains, a cysteine-rich NH2-terminal domain that stabilizes the collagen alpha helix of the second domain and a third COOH-terminal carbohydrate recognition domain. Previous studies have shown that both native and recombinant human MBP bind to wild-type virulent Salmonella montevideo that expresses a mannose-rich lipopolysaccharide. Interaction with MBP results in opsonization and killing by phagocytes. In this report we show that low concentration of MBP (less than 10 micrograms/ml) markedly enhance complement deposition via the alternative complement pathway on S. montevideo. Despite structural similarities between MBP and the C1q subcomponent of the first complement component, MBP did not restore classical pathway activity to C1q-deficient serum, nor did it activate C1s when added to a mixture of C1r and C1s. In the presence of MBP the C3 bound to S. montevideo during incubation in serum was in the form of C3b and iC3b at a ratio of 1:2. Presensitization of S. montevideo with MBP rendered this normally serum resistant organism susceptible to complement-mediated killing. These results emphasize that MBP and complement cooperate in first line defense of the nonimmune host.
A Phase II Study of Single Agent Bortezomib in Patients with Metastatic Breast Cancer: A Single Institution Experience (2007)

PS-341, now known as bortezomib (Velcade[Millenium Pharmaceuticals, Inc., Cambridge, MA; and Johnson & Johnson Pharmaceutical Research & Development, LLC, Spring house, PA]), is a proteasome inhibitor approved for the treatment of refractory multiple myeloma. Preclinical and early clinical studies showed PS-341 to be effective in solid tumors, one of which was breast cancer. We conducted a single institution, phase II study using PS-341 in the treatment of patients with metastatic breast cancer. The primary objective of this study was to determine the objective tumor response in patients with metastatic breast cancer (MBC) receiving PS-341. The secondary objectives were to estimate progression-free survival of patients receiving single-agent PS-341 and to evaluate toxicity related to PS-341. In all 12 patients who met criteria for enrollment, there were no observed objective responses. Further, all 12 patients progressed while receiving therapy with PS-341. This study was terminated after the first stage due to the lack of any objective response.
The effects of anti‐nerve growth factor monoclonal antibodies on developing basal forebrain neurons are transient and reversible (1998)

In order to reassess the role of nerve growth factor (NGF) on rat basal forebrain cholinergic neurons (BFCNs) survival and/or phenotype maturation during the early postnatal life, we immunoneutralized NGF in vivo. Hybridoma cells producing the neutralizing anti-NGF monoclonal antibody alphaD11 were implanted in the lateral ventricle of the rat at different postnatal ages (P2, P8 and P15) and the effects on the number and the soma size of cholinacetyltransferase (ChAT) positive neurons were analysed 1, 2 or 3 weeks after the injection. A marked decrease in the number and in the soma size of BFCNs was observed implanting hybridoma cells at P2 and performing the analysis 1 week later. These effects are reversed 3 weeks after the implant of hybridoma cells at P2. At this time point, the levels of alphaD11 antibodies in the brain parenchyma are still in a vast molar excess over endogenous NGF. No effects on BFCNs were observed implanting alphaD11 cells at P15 while LGN neurons showed marked shrinkage. Our results demonstrate that the reduction in the number of ChAT-positive neurons during the first two postnatal weeks of anti-NGF treatment is not due to cell death. We conclude that NGF is not a survival factor for BFCNs, and that the influence of NGF on BFCNs cell maturation during the first 2 postnatal weeks is transient and reversible. Our results on tyrosine kinase (Trk) coexpression, suggest that NGF may cooperate with other factors in the cholinergic phenotype differentiation and maintenance after the second postnatal week.
Bone marrow transplantation for chronic lymphocytic leukemia. (1998)

The use of bone marrow transplant (BMT) for patients with chronic lymphocytic leukemia (CLL) is a relatively new approach when compared to the use of this therapy for other hematologic malignancies. The long natural history of CLL and significant procedure-related mortality initially deterred the use of BMT for CLL. However, improvement in transplantation procedures and supportive care paved the way for the use of BMT in patients with CLL. There are now multiple reports showing complete remissions with both autologous and allogeneic BMT. The follow-up remains short, therefore, the durability of these remissions remains to be determined. Several innovative approaches to BMT for CLL are now being explored and include non-myeloablative preparative regimens for allogeneic transplants, purging autologous grafts, and induction of graft-versus-leukemia effects. Ultimately, however, long-term disease-free and overall survival will need to be shown before BMT for CLL will gain widespread acceptance.
Mechanism by Which Exosites Promote the Inhibition of Blood Coagulation Proteases by Heparin-activated Antithrombin (2007)

Heparin activates the serpin, antithrombin, to inhibit its target blood-clotting proteases by generating new protease interaction exosites. To resolve the effects of these exosites on the initial Michaelis docking step and the subsequent acylation and conformational change steps of antithrombin-protease reactions, we compared the reactions of catalytically inactive S195A and active proteases with site-specific fluorophore-labeled antithrombins that allow monitoring of these reaction steps. Heparin bound to N,N'-dimethyl-N-(acetyl)-N'-(7-nitrobenz-3-oxa-1,3-diazol-4-yl)ethylenediamine (NBD)-fluorophore-labeled antithrombins and accelerated the reactions of the labeled inhibitor with thrombin and factor Xa similar to wild type. Equilibrium binding of NBD-labeled antithrombins to S195A proteases showed that exosites generated by conformationally activating antithrombin with a heparin pentasaccharide enhanced the affinity of the serpin for S195A factor Xa minimally 100-fold. Moreover, additional bridging exosites provided by a hexadecasaccharide heparin activator enhanced antithrombin affinity for both S195A factor Xa and thrombin at least 1000-fold. Rapid kinetic studies showed that these exosite-mediated enhancements in Michaelis complex affinity resulted from increases in k(on) and decreases in k(off) and caused antithrombin-protease reactions to become diffusion-controlled. Competitive binding and kinetic studies with exosite mutant antithrombins showed that Tyr-253 was a critical mediator of exosite interactions with S195A factor Xa; that Glu-255, Glu-237, and Arg-399 made more modest contributions to these interactions; and that exosite interactions reduced k(off) for the Michaelis complex interaction. Together these results show that exosites generated by heparin activation of antithrombin function both to promote the formation of an initial antithrombin-protease Michaelis complex and to favor the subsequent acylation of this complex.
Characterization of the porins of Campylobacter jejuni and Campylobacter coli and implications for antibiotic susceptibility (1989)

The major outer membrane protein was extracted from Campylobacter coli by Triton X-100/EDTA fractionation of cell envelopes. This heat-modifiable protein was shown to have pore-forming activity in black lipid bilayers. The C. coli porin formed a relatively small cation-selective pore with a mean single-channel conductance of 0.53 +/- 0.16 nS in 1.0 M KCl. There was no evidence of oligomer formation, which suggested that each protein monomer formed a pore. Pore-forming activity of the C. coli porin and similarly prepared Campylobacter jejuni porin was also measured in liposome-swelling assays. These results confirmed the cation selectivity of both pores. The C. coli porin formed a small pore, which hindered the penetration of solutes with a molecular weight of 262, and a larger pore, which hindered the penetration of solutes with a molecular weight of 340, in a protein-concentration-dependent manner. C. jejuni formed one size of pore that was slightly larger than the C. coli pore and just permitted the passage of solutes, with a molecular weight of 340. A review of the literature concerning in vitro screening of antimicrobial agents tended to confirm the low permeability of the C. jejuni outer membrane to hydrophilic antimicrobial agents except when the molecules had molecular weights of less than 360. The porins of C. jejuni and C. coli may contribute to intrinsic resistance to antimicrobial agents, whereas alternative (nonporin) routes of antimicrobial agent uptake may be more important determinants of susceptibility to antimicrobial agents.
Automated Upgrades in a Lab Environment (1994)

Back in the late 80s and early 90s, when disk drives were expensive, it was more economical to buy one server and configure it with enough disk space to support several diskless workstations. Now that disks are cheaper, most workstations now come with internal disks which contain an entire bootable operating system.

Most vendors provide ways of automatically upgrading multiple diskless workstations; unfortunately, the same is not true for diskfull configurations. Upgrading diskfull workstations typically involves either a lot of manpower or a lot of tedious, repetitive work. In any moderate to large sized network, something needs to be done to automate the upgrade process.

This paper describes a scheme which we use to upgrade our various networks of Silicon Graphics workstations. Interestingly, it relies on the same technology that allows diskless workstations to boot over the network.
Oncolytic Vaccinia Virus Disrupts Tumor-Associated Vasculature in Humans (2013)

Efforts to selectively target and disrupt established tumor vasculature have largely failed to date. We hypothesized that a vaccinia virus engineered to target cells with activation of the ras/MAPK signaling pathway (JX-594) could specifically infect and express transgenes (hGM-CSF, β-galactosidase) in tumor-associated vascular endothelial cells in humans. Efficient replication and transgene expression in normal human endothelial cells in vitro required either VEGF or FGF-2 stimulation. Intravenous infusion in mice resulted in virus replication in tumor-associated endothelial cells, disruption of tumor blood flow, and hypoxia within 48 hours; massive tumor necrosis ensued within 5 days. Normal vessels were not affected. In patients treated with intravenous JX-594 in a phase I clinical trial, we showed dose-dependent endothelial cell infection and transgene expression in tumor biopsies of diverse histologies. Finally, patients with advanced hepatocellular carcinoma, a hypervascular and VEGF-rich tumor type, were treated with JX-594 on phase II clinical trials. JX-594 treatment caused disruption of tumor perfusion as early as 5 days in both VEGF receptor inhibitor-naïve and -refractory patients. Toxicities to normal blood vessels or to wound healing were not evident clinically or on MRI scans. This platform technology opens up the possibility of multifunctional engineered vaccinia products that selectively target and infect tumor-associated endothelial cells, as well as cancer cells, resulting in transgene expression, vasculature disruption, and tumor destruction in humans systemically.
Leukemia Viruses Associated with Mouse Myeloma Cells (1970)

Myeloma cells derived from BALB/c and C3H mice show evidence of infection by a murine leumemia virus. The immunoglobulin-producing myelomas secrete an RNA-containing virus with a density of 1.20 to 1.22 gm/cm(3). RNA with a sedimentation coefficient of 74 S in 0.1 M sodium sodium chloride has been isolated from secreted virus particles and has a base composition similar to that found for other murine leukemia virus RNA. An intracellular virus particle has been partially purified and has a density of 1.29 to 1.32 gm/cm(3). Both extracellular and intracellular virus particles contain the leukemia virus group-specific antigen.
Hypoxic postconditioning reduces cardiomyocyte loss by inhibiting ROS generation and intracellular Ca2+ overload (2004)

We have shown that intermittent interruption of immediate reflow at reperfusion (i.e., postconditioning) reduces infarct size in in vivo models after ischemia. Cardioprotection of postconditioning has been associated with attenuation of neutrophil-related events. However, it is unknown whether postconditioning before reoxygenation after hypoxia in cultured cardiomyocytes in the absence of neutrophils confers protection. This study tested the hypothesis that prevention of cardiomyocyte damage by hypoxic postconditioning (Postcon) is associated with a reduction in the generation of reactive oxygen species (ROS) and intracellular Ca(2+) overload. Primary cultured neonatal rat cardiomyocytes were exposed to 3 h of hypoxia followed by 6 h of reoxygenation. Cardiomyocytes were postconditioned after the 3-h index hypoxia by three cycles of 5 min of reoxygenation and 5 min of rehypoxia applied before 6 h of reoxygenation. Relative to sham control and hypoxia alone, the generation of ROS (increased lucigenin-enhanced chemiluminescence, SOD-inhibitable cytochrome c reduction, and generation of hydrogen peroxide) was significantly augmented after immediate reoxygenation as was the production of malondialdehyde, a product of lipid peroxidation. Concomitant with these changes, intracellular and mitochondrial Ca(2+) concentrations, which were detected by fluorescent fluo-4 AM and X-rhod-1 AM staining, respectively, were elevated. Cell viability assessed by propidium iodide staining was decreased consistent with increased levels of lactate dehydrogenase after reoxygenation. Postcon treatment at the onset of reoxygenation reduced ROS generation and malondialdehyde concentration in media and attenuated cardiomyocyte death assessed by propidium iodide and lactate dehydrogenase. Postcon treatment was associated with a decrease in intracellular and mitochondrial Ca(2+) concentrations. These data suggest that Postcon treatment reduces reoxygenation-induced injury in cardiomyocytes and is potentially mediated by attenuation of ROS generation, lipid peroxidation, and intracellular and mitochondrial Ca(2+) overload.
ISMB-2000: Bioinformatics enters a new millennium (2000)

The huge success of the 8th International Conference on Intelligent Systems for Molecular Biology, ISMB-2000 (http://ismb2000.sdsc.edu),indicates that bioinformatics and computational biology have truly come of age.The ISMB-2000 meeting attracted over 1200 attendees from 44 countries and registration had to be closed due to lack of space.We believe the incredible demand for this conference reflects the growing acceptance of bioinformatics as a scientific discipline, as well as the still growing need for trained professionals to deal with the growth in biological data.The completion of the human genome marks a unique point in time for biology.The reductionist paradigm will soon have been pushed to its ultimate limit, in which we will have identified every gene, every message, and every protein in the cell.The challenge now is to build synthetic and predictive models that will enable us to understand the complexity of living organisms as holistic systems.ISMB-2000 placed special emphasis on knowledge discovery from the modeling and simulation of complex biological systems.This included, but was not limited to, interpretation of large-scale gene expression data, whole genome comparative analysis, and mathematical modeling of biochemical pathways.This seemed appropriate given the completion of the human genome and thus the continual reference to the post-genomic era.Bioinformatics remains a notably international discipline.Over 140 papers were received, with approximately 60% coming from the US, 30% from Europe and 10% from other parts of the world.Forty-two papers were selected for oral presentation.
Complete Oxidation of Methanol in Biobattery Devices Using a Hydrogel Created from Three Modified Dehydrogenases (2012)

Enzyme catalysis: Three dehydrogenases have been engineered to self-assemble into a hydrogel that supports a synthetic metabolic network. The new catalytic biomaterial was used as an anode modification in two enzymatic biobatteries capable of the complete oxidation of methanol to CO2 (see picture).
Synthesis of chain-extended and C-6' functionalized precursors of the nucleoside antibiotic sinefungin (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of chain-extended and C-6' functionalized precursors of the nucleoside antibiotic sinefunginJohn W. Lyga and John A. Secrist IIICite this: J. Org. Chem. 1983, 48, 12, 1982–1988Publication Date (Print):June 1, 1983Publication History Published online1 May 2002Published inissue 1 June 1983https://doi.org/10.1021/jo00160a008Request reuse permissionsArticle Views388Altmetric-Citations23LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (945 KB) Get e-Alertsclose Get e-Alerts
System Identification and Nonlinear Factor Analysis for Discovery and Visualization of Dynamic Gene Regulatory Pathways (2005)

DNA microarray time-series provide the information vital to estimate the dynamic regulatory pathways and therefore predict the dynamic interaction among genes in time. While dynamic system identification theory has been applied to many fields of study, due to some practical limitations, this theory has been widely used to analyze DNA microarray time series. In this paper, we describe some of these limitations and propose a hierarchical model utilizing nonlinear factor analysis methods to analyze time-series DNA microarray data and identify the dynamic regulatory pathways. The proposed model is applied to model the eukaryotic cell cycle process using a popular dataset of cell cycle time-series. The results indicate that the proposed method can successfully predict the dynamic pathway involved in the process.