gebhart/patrepeval huggingface dataset:
Batch Preparation of Linear Au and Ag Nanoparticle Chains via Wet Chemistry (2005)

We present a simple, wet-chemical method for fabricating linear chains of Au and Ag nanoparticles by selectively etching alternating segments from striped metal nanowires. Nanowires composed of sacrificial Ni segments as well as Au and/or Ag segments were prepared by templated electrodeposition in the pores of alumina membranes. After removal from the membrane, wires were coated with SiO2, and selective etching revealed the nanoparticle chains. Extinction spectra are presented as a function of interparticle spacing.
Radiofrequenz‐verschlüsselte kombinatorische Chemie (1995)

Die kombinatorische Peptidsynthese an festen Trägern läßt sich durch Einbau eines Halbleiter‐Speicherchips in Mikroreaktoren, die die Polymerträger enthalten (Bild rechts), exakt verfolgen. Vor dem Kuppeln einer Aminosäure wird ein Signal (z.B. A) auf den Chip übertragen, und vor oder nach dem Abspalten vom Träger liest man die Signalfolge der kompletten Aminosäuresequenz (z.B. A‐B‐A) ab. Auf diese Weise konnte mit 96 Mikroreaktoren eine 24gliedrige Peptidbibliothek aufgebaut werden. magnified image
CpG oligonucleotides: novel regulators of osteoclast differentiation (2002)

The macrophage capability to recognize bacterial DNA is mimicked by oligodeoxynucleotides containing unmethylated CG dinucleotides ('CpG' motifs) in specific sequence contexts (CpG ODN). CpG ODN stimulates NF-kappaB activation in murine macrophages. In light of the pivotal role played by NF-kappaB in osteoclast differentiation, we examined the ability of CpG ODN to modulate osteoclastogenesis. CpG ODN alone induced TRAP-positive cells in bone marrow macrophage (BMM) cultures, but not multinucleation or calcitonin receptor expression. CpG ODN inhibited RANKL-induced osteoclastogenesis when present from the beginning of BMM culture, but strongly increased RANKL-induced osteoclastogenesis in RANKL-pretreated BMMs. CpG ODN enhanced the expression of interleukin 1beta (IL-1beta) and tumor necrosis factor alpha (TNF-alpha). Antibodies to TNF-alpha and the TNF type 1 receptor, but not the addition of IL-1 receptor antagonist, blocked CpG ODN-induced osteoclastogenesis in RANKL-pretreated cultures. On the other hand, CpG ODN reduced expression of the M-CSF receptor, which is critical during the initiation of osteoclast differentiation. These results suggest that CpG ODN, via the induction of TNF-alpha, support osteoclastogenesis in cells that are committed to the osteoclast differentiation pathway but, due to down-modulation of M-CSF receptor, inhibit early steps of osteoclast differentiation. Thus, CpG ODN represents a potential therapeutic tool for treating bone diseases.
CT-guided transthoracic needle biopsy of small solitary pulmonary nodules (1997)

The use of CT guidance in performing transthoracic needle biopsy is well established. We evaluated its accuracy in the diagnosis of small solitary nodules and found it to be highly accurate regardless of size or location. While specific benign diagnoses were uncommon, additional confidence in a benign diagnosis can be gained by careful analysis of needle tip location using strict CT criteria.
The oxazolidinones: past, present, and future (2011)

The success of linezolid stimulated significant efforts to discover new agents in the oxazolidinone class. Over a dozen oxazolidinones have reached the clinic, but many were discontinued due to lack of differentiated potency, inadequate pharmacokinetics, and safety risks that included myelosuppression. Four oxazolidinones are currently undergoing clinical evaluation. The Trius Therapeutics compound tedizolid phosphate (formerly known as torezolid phosphate, TR-701, DA-7218), the most advanced, is in phase 3 clinical trials for acute bacterial skin and skin structure infections. Rib-X completed two phase 2 studies for radezolid (Rx-01_667, RX-1741) in uncomplicated skin and skin structure infections and community-acquired pneumonia. Pfizer and AstraZeneca have each identified antitubercular compounds that have completed phase 1 studies: sutezolid (PNU-100480, PF-02341272) and AZD5847 (AZD2563), respectively. The oxazolidinones share a relatively low frequency of resistance largely due to the requirement of mutations in 23S ribosomal RNA genes. However, maintaining potency against strains carrying the mobile cfr gene poses a challenge for the oxazolidinone class, as well as other 50S ribosome inhibitors that target the peptidyl transferase center.
A noncomparative randomized phase II study of two dose levels of itraconazole in men with metastatic castration-resistant prostate cancer (mCRPC): A DOD/PCCTC trial. (2011)

4532 Background: The antifungal drug itraconazole inhibits angiogenesis and Hedgehog signaling, and delays tumor growth in murine prostate cancer xenograft models. Unlike ketoconazole, it does not suppress adrenal androgen synthesis. Methods: A phase II study of oral itraconazole in men with chemo-naïve mCRPC (30% ketoconazole-pretreated) was conducted in 4 PCCTC sites. Men were randomized to low dose (LD) or high dose (HD) itraconazole (200 or 600 mg/d) until disease progression or unacceptable toxicity. The primary endpoint was PSA progression-free survival (PPFS) at 24 wk (PSA progression = 25% PSA rise above baseline/nadir; PCWG2 criteria); a 45% success rate in either arm was prespecified as constituting clinical significance. Secondary endpoints were progression-free survival (PFS) at 24 wk (progression = clinical/radiographic progression or death, but not rising PSA; PCWG2 criteria); median PFS; median PPFS; and max PSA decline. Exploratory outcomes were CTC enumeration, and analysis of serum testosterone (T) and DHEA-S. Results: The HD arm enrolled to completion (N=29), but the LD arm closed early (N=17) due to a prespecified futility analysis. After a median follow-up of 21.6 wk (HD arm) and 11.9 wk (LD arm), 24/29 and 17/17 men were evaluable for the primary endpoint. Efficacy results are shown below. In addition, 3/5 men (60%) in the HD arm and 2/3 men (67%) in the LD arm with unfavorable (≥5) CTCs at baseline converted to favorable (<5) CTC counts with treatment. Itraconazole did not reduce serum T or DHEA-S levels. Common toxicities (≥20%) were fatigue, nausea, anorexia, rash, and hypokalemia/hypertension/edema. Conclusions: Only the HD arm met its primary endpoint. Itraconazole 600 mg/d has single-agent activity in men with mCRPC that is not mediated by androgen suppression, and warrants further study. Endpoint Dose Value 95% CI Primary PPFS at 24 wk (%) LD 11.8 3.2–43.2 HD 48.4 32.1–73.0 Secondary PFS at 24 wk (%) LD 18.8 6.8–52.0 HD 61.1 44.1–84.6 Median PFS (wk) LD 11.9 11.9–29.1 HD 35.9 13.0–60+ Median PPFS (wk) LD 11.9 5.6–20.0 HD 17.0 12.4–29.0 ≥30% PSA decline (%) LD 5.9 0.2–28.7 HD 28.6 13.2–48.7 ≥50% PSA decline (%) LD 0 0–19.5 HD 14.3 4.0–32.7
In Situ Kinetics of Self-Assembly by Surface Plasmon Resonance Spectroscopy (1996)

Using surface plasmon resonance (SPR) spectroscopy in the Kretschmann configuration, we followed the self-assembly of organic ultrathin films which resulted from exposure of gold surfaces to solutions of CH3(CH2)n-1SH (n = 8, 12, 16, and 18) in ethanol and heptane. We monitored film growth in situ and continuously for up to 72 h with an overall thickness resolution of <1 Å. Film dielectric constants, necessary for accurately calculating average film thicknesses from SPR spectra, were determined unambiguously for fully formed films by comparing spectra from organic films in different solvents. In addition, we introduce a novel two-color SPR experiment with which we can obtain both film thickness and film dielectric constant without changing solvents. We studied the chain length dependent and concentration dependent kinetics of film formation in ethanol and found that there are at least three distinct kinetics steps. The kinetics of the first, most rapid, step and the third, slowest, step can be described well with Langmuir adsorption models. The kinetics of the second step are zeroth order and depend on alkanethiol chain length, concentration, and partial film thickness. The formation kinetics in heptane can be described with a single step Langmuir adsorption model. We find that films formed by continuous self-assembly in solution are always thicker than films for which the process of self-assembly has been interrupted by rinsing with neat solvents. We also present evidence that, by rinsing the partially formed film before reimmersion into thiol solution, we can change the final film thickness and structure of a hexadecanethiolate film. Our results are most consistent with a formation mechanism involving adsorption of both chemisorbed and physisorbed molecules during film formation in ethanol, with the overall formation kinetics determined by the relative solubility of the alkanethiol in the solvent.
Decanuclear Copper Framework Supported by a Tripodal Adenine Ligand (2010)

This Communication describes the synthesis, crystal structure, and magnetic properties of a unique decanuclear copper complex of a tripodal adenine ligand built around a phenyl ring core. This complex comprises two mu(4)-oxo tetranuclear copper(II) units of the type Cu(4)OCl(6)L(4), bridged together by two pentacoordinated copper centers. Variable-temperature magnetic susceptibility data reveal the possibility of interaction between copper sites.
A Catalytic Nanoreactor Based on in Vivo Encapsulation of Multiple Enzymes in an Engineered Protein Nanocompartment (2016)

Bacterial protein compartments concentrate and sequester enzymes, thereby regulating biochemical reactions. Here, we generated a new functional nanocompartment in Escherichia coli by engineering the MS2 phage capsid protein to encapsulate multiple cargo proteins. Sequestration of multiple proteins in MS2-based capsids was achieved by SpyTag/SpyCatcher protein fusions that covalently crosslinked with the interior surface of the capsid. Further, the functional two-enzyme indigo biosynthetic pathway could be targeted to the engineered capsids, leading to a 60 % increase in indigo production in vivo. The enzyme-loaded particles could be purified in their active form and showed enhanced long-term stability in vitro (about 95 % activity after seven days) compared with free enzymes (about 5 % activity after seven days). In summary, this engineered in vivo encapsulation system provides a simple and versatile way for generating highly stable multi-enzyme nanoreactors for in vivo and in vitro applications.
A broad-spectrum human lung fibroblast-derived mitogen is a variant of hepatocyte growth factor. (1991)

A heparin-binding mitogen was isolated from conditioned medium of human embryonic lung fibroblasts. It exhibited broad target-cell specificity whose pattern was distinct from that of any known growth factor. It rapidly stimulated tyrosine phosphorylation of a 145-kDa protein in responsive cells, suggesting that its signaling pathways involved activation of a tyrosine kinase. Purification identified a major polypeptide with an apparent molecular mass of 87 kDa under reducing conditions. Partial amino acid sequence analysis and cDNA cloning revealed that it was a variant of hepatocyte growth factor, a mitogen thought to be specific for hepatic cells and structurally related to plasminogen. Recombinant expression of the cDNA in COS-1 cells established that it encoded the purified growth factor. Its site of synthesis and spectrum of targets imply that this growth factor may play an important role as a paracrine mediator of the proliferation of melanocytes and endothelial cells, as well as cells of epithelial origin.
Mapping the theories of preeclampsia and the role of angiogenic factors: a systematic review. (2007)

Third-trimester increases in sFlt-1 and decreases in placental growth factor levels are associated with preeclampsia, specifically severe disease, based on retrospective data. The evidence is insufficient to recommend these markers to be used for screening, and prospective studies employing rigorous laboratory and study design criteria are needed to determine the clinical usefulness of these tests.
The flagellar anti-ς factor FlgM actively dissociates Salmonella typhimurium ς28 RNA polymerase holoenzyme (1998)

The anti-sigma factor FlgM of Salmonella typhimurium inhibits transcription of class 3 flagellar genes through a direct interaction with the flagellar-specific sigma factor, sigma28. FlgM is believed to prevent RNA polymerase (RNAP) holoenzyme formation by sequestering free sigma28. We have analyzed FlgM-mediated inhibition of sigma28 activity in vitro. FlgM is able to inhibit sigma28 activity even when sigma28 is first allowed to associate with core RNAP. Surface plasmon resonance (SPR) was used to evaluate the interaction between FlgM and both sigma28 and sigma28 holoenzyme (Esigma28). The Kd of the sigma28-FlgM complex is approximately 2 x 10(-10) M; missense mutations in FlgM that cause a defect in sigma28 inhibition in vivo increase the Kd of this interaction by 4- to 10-fold. SPR measurements of Esigma28 dissociation in the presence of FlgM indicate that FlgM destabilizes Esigma28, presumably via an interaction with the sigma subunit. Our data provide the first direct evidence of an interaction between FlgM and Esigma28. We propose that this secondary activity of FlgM, which we term holoenzyme destabilization, enhances the sensitivity of the cell to changes in FlgM levels during flagellar biogenesis.
Computation of buffer capacities for throughput constrained and data dependent inter-task communication (2008)

Streaming applications are often implemented as task graphs. Currently, techniques exist to derive buffer capacities that guarantee satisfaction of a throughput constraint for task graphs in which the inter-task communication is data-independent, i.e. the amount of data produced and consumed is independent of the data values in the processed stream. This paper presents a technique to compute buffer capacities that satisfy a throughput constraint for task graphs with data dependent inter-task communication, given that the task graph is a chain. We demonstrate the applicability of the approach by computing buffer capacities for an MP3 playback application, of which the MP3 decoder has a variable consumption rate. We are not aware of alternative approaches to compute buffer capacities that guarantee satisfaction of the throughput constraint for this application.
A novel approach to raspberry-like particles for superhydrophobic materials (2009)

A new strategy was developed to prepare raspberry-like particles by introducing poly(acrylic acid) (PAA)-functionalized polystyrene (PS) particles into hydrolysis reaction of tetraethoxysilane (TEOS). The monodisperse PAA-functionalized PS particles were used as cores and nanosized silica particles were then assembled on the surface of PS particles to construct raspberry-like particles during the hydrolysis process. With the increase of PAA content from 11% to 20% (wt) at the surface of latexes, the diameter of the silica particles assembled at the surface of cores decreased from 124 nm to 36 nm. The structure, morphology and constitution of the PAA-functionalized PS particles and the raspberry-like particles were characterized by Fourier transform infrared spectroscopy (FT-IR), field-emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS). In addition, the particulate films were constructed by assembling these raspberry-like particles on glass substrates. After surface modification with dodecyltrichlorosilane, superhydrophobic surfaces can be obtained and the contact angle of water on the dual-sized structured surface can be adjusted by the scale ratio of the micro/nano surface structure of raspberry-like particles.
Effect of prophylactic administration of recombinant human granulocyte colony-stimulating factor (filgrastim) on the frequency of nosocomial infections in patients with acute traumatic brain injury or cerebral hemorrhage (1998)

In this patient population, use of filgrastim was safe and the agent appeared to reduce the risk of primary bacteremias but had no beneficial effects on mortality, length of stay, or other nosocomial infections.
Introduction to Cancer Chemotherapeutics (2009)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTIntroduction to Cancer ChemotherapeuticsDonna S. Shewach and Robert D. KuchtaView Author Information Guest Editor, University of Michigan School of Medicine Issue Editor, University of Colorado, BoulderCite this: Chem. Rev. 2009, 109, 7, 2859–2861Publication Date (Web):July 8, 2009Publication History Received1 June 2009Published online8 July 2009Published inissue 8 July 2009https://pubs.acs.org/doi/10.1021/cr900208xhttps://doi.org/10.1021/cr900208xeditorialACS PublicationsCopyright © 2009 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views13872Altmetric-Citations190LEARN 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 PDF (99 KB) Get e-AlertscloseSUBJECTS:Cancer,Cells,Genetics,Peptides and proteins,Pharmaceuticals Get e-Alerts
Effects of Inactivation and Constitutive Expression of the Unfolded- Protein Response Pathway on Protein Production in the Yeast Saccharomyces cerevisiae (2003)

One strategy to obtain better yields of secreted proteins has been overexpression of single endoplasmic reticulum-resident foldases or chaperones. We report here that manipulation of the unfolded-protein response (UPR) pathway regulator, HAC1, affects production of both native and foreign proteins in the yeast Saccharomyces cerevisiae. The effects of HAC1 deletion and overexpression on the production of a native protein, invertase, and two foreign proteins, Bacillus amyloliquefaciens alpha-amylase and Trichoderma reesei endoglucanase EGI, were studied. Disruption of HAC1 caused decreases in the secretion of both alpha-amylase (70 to 75% reduction) and EGI (40 to 50% reduction) compared to the secretion by the parental strain. Constitutive overexpression of HAC1 caused a 70% increase in alpha-amylase secretion but had no effect on EGI secretion. The invertase levels were twofold higher in the strain overexpressing HAC1. Also, the effect of the active form of T. reesei hac1 was tested in S. cerevisiae. hac1 expression caused a 2.4-fold increase in the secretion of alpha-amylase in S. cerevisiae and also slight increases in invertase and total protein production. Overexpression of both S. cerevisiae HAC1 and T. reesei hac1 caused an increase in the expression of the known UPR target gene KAR2 at early time points during cultivation.
Mechanism-Based Profiling of Enzyme Families (2006)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanism-Based Profiling of Enzyme FamiliesMichael J. Evans and Benjamin F. CravattView Author Information The Skaggs Institute for Chemical Biology and Departments of Cell Biology and Chemistry, The Scripps Research Institute, La Jolla, California 92037 Cite this: Chem. Rev. 2006, 106, 8, 3279–3301Publication Date (Web):July 15, 2006Publication History Received6 February 2006Published online15 July 2006Published inissue 1 August 2006https://pubs.acs.org/doi/10.1021/cr050288ghttps://doi.org/10.1021/cr050288gresearch-articleACS PublicationsCopyright © 2006 American Chemical SocietyRequest reuse permissionsArticle Views8290Altmetric-Citations504LEARN 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 SUBJECTS:Inhibitors,Labeling,Monomers,Peptides and proteins,Probes Get e-Alerts
ASC-J9 Suppresses Renal Cell Carcinoma Progression by Targeting an Androgen Receptor–Dependent HIF2α/VEGF Signaling Pathway (2014)

Males have a higher incidence of renal cell carcinoma (RCC) than females, but the reason for this gender difference is unknown. Addressing this question, we report the discovery of an androgen receptor (AR)-induced HIF2α/VEGF signal that drives RCC progression. AR attenuation or augmentation in RCC cells altered their proliferation, migration, and invasion in multiple models in vitro and in vivo. Mechanistic investigations revealed that AR targeting inhibited RCC cell migration and invasion by modulating HIF2α/VEGF signals at the level of mRNA and protein expression. Interrupting HIF2α/VEGF signals with inhibitors of either HIF2α or VEGF was sufficient to suppress RCC progression. Similarly, the specific AR degradation enhancer ASC-J9 was sufficient to suppress AR-induced HIF2α/VEGF signaling and RCC progression in multiple models in vitro and in vivo. Taken together, our results revealed a novel role for AR in RCC initiation and progression with implications for novel therapeutic strategies.
Interaction between chlorhexidine digluconate and sodium monofluorophosphate in vitro (1988)

The aim of the present study was to investigate the compatibility of chlorhexidine digluconate and sodium monofluorophosphate since these agents are potential ingredients in future products in preventive dentistry. Varying combinations of chlorhexidine digluconate and sodium monofluorophosphate in water, covering the possible ranges of clinically relevant concentrations of both compounds, were made, incubated for 24 h and observed for precipitation of insoluble salts. The mixtures were analyzed for presence of free chlorhexidine and monofluorophosphate after incubation. The results showed that chlorhexidine digluconate and sodium monofluorophosphate are not compatible in clinically relevant concentrations. A chlorhexidine-monofluorophosphate salt of low solubility in water is presumably formed.
Missense Mutations in the MEFV Gene Are Associated with Fibromyalgia Syndrome and Correlate with Elevated IL-1β Plasma Levels (2009)

Background: Fibromyalgia syndrome (FMS), a common, chronic, widespread musculoskeletal pain disorder found in 2% of the general population and with a preponderance of 85% in females, has both genetic and environmental contributions. Patients and their parents have high plasma levels of the chemokines MCP-1 and eotaxin, providing evidence for both a genetic and an immunological/inflammatory origin for the syndrome Biol. Med. 233: 1171-1180).