gebhart/patrepeval huggingface dataset:
Integrated Nanoparticle–Biomolecule Hybrid Systems: Synthesis, Properties, and Applications (2004)

Nanomaterials, such as metal or semiconductor nanoparticles and nanorods, exhibit similar dimensions to those of biomolecules, such as proteins (enzymes, antigens, antibodies) or DNA. The integration of nanoparticles, which exhibit unique electronic, photonic, and catalytic properties, with biomaterials, which display unique recognition, catalytic, and inhibition properties, yields novel hybrid nanobiomaterials of synergetic properties and functions. This review describes recent advances in the synthesis of biomolecule-nanoparticle/nanorod hybrid systems and the application of such assemblies in the generation of 2D and 3D ordered structures in solutions and on surfaces. Particular emphasis is directed to the use of biomolecule-nanoparticle (metallic or semiconductive) assemblies for bioanalytical applications and for the fabrication of bioelectronic devices.
High-frequency capacitive disk gyroscopes in (100) and (111) silicon (2007)

This paper reports on the design and implementation of capacitive bulk acoustic wave (BAW) disk gyroscopes in single crystal silicon. The capacitive BAW disk gyroscopes are stationary devices operating in their degenerative MHzfrequency bulk acoustic modes with very small vibration amplitudes (≪20nm). They can achieve very high quality factors (Q) in moderate vacuum and even under atmospheric pressure, which substantially simplifies their wafer-level packaging. In addition, their small operating voltages simplify the interface circuit design and implementation in standard CMOS.
Estimation of cell survival by flow cytometric quantification of fluorescein diacetate/propidium iodide viable cell number. (1989)

We report a flow cytometric method to quantify the number of viable cells remaining in suspension culture following exposure to cytotoxic drugs. Cell viability is assessed by flow cytometric measurement of cellular fluorescence after staining with fluorescein diacetate and propidium iodide in isotonic solution. The number of viable cells per ml of culture is determined by a timed count of viable cells and from knowledge of the flow cytometer sample flow rate. P388 murine or HL-60 human leukemia cells in culture were used as model systems. This method can quantify accurately viable cell concentrations in suspension culture from 100 cells/ml to 1 million cells/ml. The sensitivity of the method as a cytotoxicity assay increases if, following brief (1-4-h) exposure to drug, greater time is allowed for cell death and lysis to occur prior to flow cytometric counting of viable cells. If the viability assessment is deferred for at least 72 h following drug (daunorubicin, actinomycin D, vincristine) exposure, results were obtained approximating those obtained from the soft agar clonogenic assay or the colorimetric 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. In studying the cytotoxic effects of vincristine, actinomycin D, 1-beta-D-arabinofuranosylcytosine, and daunorubicin on P388 or HL-60 cells sensitive and resistant to these agents, reasonable results were obtained by flow cytometric counting of viable cell number. We have been able to perform this flow cytometric viability assay with ease using bone marrow blast cells obtained from patients with acute myelogenous leukemia. The method is facile, relatively rapid, and since it is ideal for studying cells in suspension culture, its potential as a predictor of chemotherapeutic response in leukemia warrants further evaluation.
Metal-coordination: using one of nature's tricks to control soft material mechanics (2013)

Growing evidence supports a critical role of dynamic metal-coordination crosslinking in soft biological material properties such as self-healing and underwater adhesion<sup>1</sup>. Using bio-inspired metal-coordinating polymers, initial efforts to mimic these properties have shown promise<sup>2</sup>. Here we demonstrate how bio-inspired aqueous polymer network mechanics can be easily controlled via metal-coordination crosslink dynamics; metal ion-based crosslink stability control allows aqueous polymer network relaxation times to be finely tuned over several orders of magnitude. In addition to further biological material insights, our demonstration of this compositional scaling mechanism should provide inspiration for new polymer material property-control designs.
National survey of quality assurance activities for pharmacy-compounded sterile preparations (2003)

The compliance of hospitals' quality assurance practices for pharmacy-compounded sterile preparations with the American Society of Health-System Pharmacists (ASHP) Guidelines on Quality Assurance for Pharmacy-Prepared Sterile Products was studied. A survey based on the 2000 ASHP guidelines was developed to determine current practices for compounding sterile preparations in hospital pharmacies. Practices were compared with those identified in a 1995 ASHP survey. The survey was mailed in July 2002 to a stratified random sample of 600 hospital pharmacy directors. There were a total of 182 usable responses, for a net response rate of 30.3%. Quality assurance practices for some quality domains showed low compliance with the 2000 ASHP guidelines. Only 5.2% of pharmacies that compounded risk level 1 preparations were compliant with garb requirements. Only 4.7% of pharmacies compounding risk level 3 preparations were compliant with recommendations for documentation. Compliance with guidelines on the use of resources to determine expiration dates was high (95.5%). Hospitals were moderately compliant with guidelines related to personnel training (62.7%) and labeling (61.1%). Although some improvements were observed, hospital pharmacies in 2002 were still not fully compliant with the ASHP Guidelines on Quality Assurance for Pharmacy-Prepared Sterile Products.
Degradation of the LDL receptors by PCSK9 is not mediated by a secreted protein acted upon by PCSK9 extracellularly (2007)

Degradation of the LDLR by PCSK9 is not mediated by a secreted protein acted upon by PCSK9 extracellularly. Also the PCSK9-mediated degradation of the LDLR does not take place on the cell surface. Rather, the PCSK9-mediated degradation of the LDLR appears to take place intracellularly and occurs even when endocytosis through clathrin-coated pits is blocked by hypertonic medium.
AN IMPROVED SYNTHESIS OF INDOLE-3-CARBOXYLIC ACIDS (1970)

(1970). AN IMPROVED SYNTHESIS OF INDOLE-3-CARBOXYLIC ACIDS. Organic Preparations and Procedures: Vol. 2, No. 4, pp. 297-303.
Regulation of the Bacillus subtilis acetate kinase gene by CcpA (1993)

The Bacillus subtilis gene encoding acetate kinase was identified on the basis of sequence similarity to the Escherichia coli ackA gene and to a second E. coli gene closely related to ackA. Insertional inactivation of this region of the B. subtilis chromosome resulted in the disappearance of acetate kinase enzyme activity in cell extracts. The ackA gene was mapped to a site close to the ccpA gene, at 263 degrees. The transcriptional start site for B. subtilis ackA was located 90 bp upstream from the start of the coding region, and expression was increased by growth in the presence of excess glucose. Growth of the AckA- mutant was inhibited by glucose, suggesting that acetate kinase is important for excretion of excess carbohydrate. The stimulation of ackA expression by glucose was blocked in a CcpA- mutant, indicating that CcpA, which is required for glucose repression of certain carbon source utilization genes, including amyE, may also be involved in activation of carbon excretion pathways. Two sequences resembling the amyO operator site were identified upstream of the ackA promoter; removal of this region resulted in loss of glucose activation of ackA expression.
Can Brain SPECT Be Used to Cost-effectively Triage Which Patients Require PET for the Investigation of Dementia? (2010)

Aim: Increasing demand for 18F-FDG PET brain studies for investigation of dementia in a financially capped environment resulted in a prolonged waiting list for appointments. Our Department instituted a policy where all patients were to be triaged using brain SPECT prior to receiving a PET appointment. This study reviews the cost-effectiveness of this policy. Method: 222 consecutive patients referred for SPECT/PET brain studies for dementia in a six month period were included. Scan reports were classified into 4 grades: Normal, No diagnostic pattern, Suggestive of dementia, or Abnormal. Patients with diagnostic abnormality on SPECT did not proceed to PET. 114 patients proceeded to PET and these results were compared to SPECT. Reporting for both SPECT and PET was performed using 3-plane slices and Neurostat 3D-SSP (Stereotactic Surface Projection). Sub-analysis for age was performed for patients 65 years and under compared over 65 years. Results : Brain SPECT provided definitively abnormal results in 66 of 222 patients (30%). In patients aged 65 years and under, the percentage rose to 33%, compared to 29% in those over 65. Non diagnostic or suggestive patterns were seen in 133 of 222 (60%) with SPECT compared to only 18 of 114 patients (16%) with PET. In patients 65 years and under, PET provided equally high levels of Normal and Abnormal scans (approximately 40% each), whilst in those over 65 years, Abnormal scans were found in 63% and Normal scans in 23%. The potential Medicare cost of SPECT + PET triage was $232,080 compared to $203,796 for PET only, if FDG PET for dementia were funded at the same rate as 18F-FDG PET for epilepsy. Conclusion: Brain SPECT imaging provides definitive diagnosis in around 30% of patients regardless of age, producing a modest impact on the waiting list. 18F-FDG PET provides greater diagnostic certainty with most patients receiving either a clear Normal or Abnormal result. Additionally, if 18F-FDG PET for dementia were Medicare funded, SPECT triage would not be cost-effective.
Carbon-fluorine bond formation. (2008)

A selection of carbon-fluorine bond-forming reactions that have been developed in the recent past are presented. An overview of the most common fluorination reagents is followed by descriptions of fluorination reactions that are organized by reactivity. The distinction between nucleophilic and electrophilic fluorinations is highlighted, as well as between aliphatic and aromatic fluorinations. Each section is divided into more specific reaction classes and examples for the synthesis of pharmaceuticals, [18F]radiolabeling and mechanistic investigations are provided.
Conserved and Divergent Rhythms of Crassulacean Acid Metabolism-Related and Core Clock Gene Expression in the Cactus Opuntia ficus-indica (2011)

The cactus Opuntia ficus-indica is a constitutive Crassulacean acid metabolism (CAM) species. Current knowledge of CAM metabolism suggests that the enzyme phosphoenolpyruvate carboxylase kinase (PPCK) is circadian regulated at the transcriptional level, whereas phosphoenolpyruvate carboxylase (PEPC), malate dehydrogenase (MDH), NADP-malic enzyme (NADP-ME), and pyruvate phosphate dikinase (PPDK) are posttranslationally controlled. As little transcriptomic data are available from obligate CAM plants, we created an expressed sequence tag database derived from different organs and developmental stages. Sequences were assembled, compared with sequences in the National Center for Biotechnology Information nonredundant database for identification of putative orthologs, and mapped using Kyoto Encyclopedia of Genes and Genomes Orthology and Gene Ontology. We identified genes involved in circadian regulation and CAM metabolism for transcriptomic analysis in plants grown in long days. We identified stable reference genes for quantitative polymerase chain reaction and found that OfiSAND, like its counterpart in Arabidopsis (Arabidopsis thaliana), and OfiTUB are generally appropriate standards for use in the quantification of gene expression in O. ficus-indica. Three kinds of expression profiles were found: transcripts of OfiPPCK oscillated with a 24-h periodicity; transcripts of the light-active OfiNADP-ME and OfiPPDK genes adapted to 12-h cycles, while transcript accumulation patterns of OfiPEPC and OfiMDH were arrhythmic. Expression of the circadian clock gene OfiTOC1, similar to Arabidopsis, oscillated with a 24-h periodicity, peaking at night. Expression of OfiCCA1 and OfiPRR9, unlike in Arabidopsis, adapted best to a 12-h rhythm, suggesting that circadian clock gene interactions differ from those of Arabidopsis. Our results indicate that the evolution of CAM metabolism could be the result of modified circadian regulation at both the transcriptional and posttranscriptional levels.
Oral recombinant human lactoferrin induces systemic immune responses and inhibits the growth of established tumors (2004)

Proc Amer Assoc Cancer Res, Volume 45, 2004

4689 

We investigated the immunomodulatory function and anti-cancer activity of orally administered recombinant human lactoferrin (rhLF), alone and in combination with chemotherapy in tumor-bearing mice. Oral rhLF (300 mg/kg/day for three days) administered to naive Balb/C mice resulted in statistically significant changes with respect to placebo including: (i) increased production of IL-18 in the intestinal tract (8.4 vs. 1.0 ng/ml); (ii) systemic NK activation (34.0 vs. 9.9 lytic units); and (iii) CD8+ T cell expansion in peripheral blood (26% relative increase). IL-18 is known to induce the production of Th1 cytokines including INF-γ, and to enhance cell-mediated immune cytotoxicity via NK and CD8+ T cell activation. We then investigated rhLF’s ability to inhibit tumor growth in syngeneic mice. Monotherapy with oral rhLF (1,000 mg/kg) induced partial or complete regression in mammary adenocarcinoma (TUBO) tumors. Oral rhLF (200 mg/kg) also caused tumor growth inhibition (TGI) in a head and neck squamous cell carcinoma (SCC VII) model: monotherapy with oral rhLF caused a 61% TGI relative to placebo (p<0.001), comparable to Cis-platinum (5 mg/kg) alone (66%). Animals receiving both rhLF (200 mg/kg) and Cis-platinum (5 mg/kg) had a 79% TGI, a statistically significant improvement over either agent alone. These findings suggest that oral rhLF is active against cancer as a single agent and in combination with chemotherapy, and exerts its systemic effect through stimulation of cytokines such as IL-18 from the gut enterocytes. RhLF has been shown to be safe in human clinical trials. Thus, rhLF shows promise as a safe and well-tolerated novel immunomodulatory anticancer agent.
Silicon microring resonators (2011)

Abstract An overview is presented of the current state‐of‐the‐art in silicon nanophotonic ring resonators. Basic theory of ring resonators is discussed, and applied to the peculiarities of submicron silicon photonic wire waveguides: the small dimensions and tight bend radii, sensitivity to perturbations and the boundary conditions of the fabrication processes. Theory is compared to quantitative measurements. Finally, several of the more promising applications of silicon ring resonators are discussed: filters and optical delay lines, label‐free biosensors, and active rings for efficient modulators and even light sources.
Genetic Encoding and Labeling of Aliphatic Azides and Alkynes in Recombinant Proteins via a Pyrrolysyl-tRNA Synthetase/tRNACUA Pair and Click Chemistry (2009)

We demonstrate that an orthogonal Methanosarcina barkeri MS pyrrolysyl-tRNA synthetase/tRNA(CUA) pair directs the efficient, site-specific incorporation of N6-[(2-propynyloxy)carbonyl]-L-lysine, containing a carbon-carbon triple bond, and N6-[(2-azidoethoxy)carbonyl]-L-lysine, containing an azido group, into recombinant proteins in Escherichia coli. Proteins containing the alkyne functional group are labeled with an azido biotin and an azido fluorophore, via copper catalyzed [3+2] cycloaddition reactions, to produce the corresponding triazoles in good yield. The methods reported are useful for the site-specific labeling of recombinant proteins and may be combined with mutually orthogonal methods of introducing unnatural amino acids into proteins as well as with chemically orthogonal methods of protein labeling. This should allow the site specific incorporation of multiple distinct probes into proteins and the control of protein topology and structure by intramolecular orthogonal conjugation reactions.
History and Evolution (1990)

We have discussed the aesthetic standards that might legitimately be applied to theatre for the young and the factors, in general, that might influence its shape. In trying to account for its various manifestations at present in evidence, it is necessary to take a backward glance at its evolution. We shall have to look at social and political developments and at the status accorded to children at different times. Changes in educational theory and practice have had a profound effect on the range of dramatic experiences which have been offered. Developments in the theatre itself have provided a backdrop and, to some extent, supplied examples of possible content, form, organisation and philosophy. Funding, a crucial consideration in talking about any of the arts, is of peculiar significance in talking about a vulnerable phenomenon like theatre for young people. The esteem in which it is held is partially reflected in the willingness shown by sponsors, public or private, to bestow their patronage. Related to this is the attractiveness of working in this area to stage artists and playwrights of merit.
A meta‐analysis of the MTHFR C677T polymorphism and schizophrenia risk (2005)

Epigenetic mechanisms such as methylation of DNA, could lead to abnormal neurodevelopment and may be important in the etiology of schizophrenia. Maternal dietary folate intake may play a role in determining methylation levels. The MTHFR gene C677T polymorphism influences folate metabolism and intracellular availability of folate metabolites for methylation. We carried out a meta-analysis of MTHFR C677T genotype and schizophrenia risk, and found that TT homozygotes had a significantly increased risk, OR 1.48 (1.18-1.86). This supports the hypothesis that folate status is a determinant of schizophrenia risk. Larger studies of this issue are required, together with studies of maternal genotype which could identify whether maternal folate status during pregnancy is important.
Sparse geometric image representations with bandelets (2005)

This paper introduces a new class of bases, called bandelet bases, which decompose the image along multiscale vectors that are elongated in the direction of a geometric flow. This geometric flow indicates directions in which the image gray levels have regular variations. The image decomposition in a bandelet basis is implemented with a fast subband-filtering algorithm. Bandelet bases lead to optimal approximation rates for geometrically regular images. For image compression and noise removal applications, the geometric flow is optimized with fast algorithms so that the resulting bandelet basis produces minimum distortion. Comparisons are made with wavelet image compression and noise-removal algorithms.
Quantitative evaluation of siRNA delivery in vivo (2010)

Effective small interfering RNA (siRNA)-mediated therapeutics require the siRNA to be delivered into the cellular RNA-induced silencing complex (RISC). Quantitative information of this essential delivery step is currently inferred from the efficacy of gene silencing and siRNA uptake in the tissue. Here we report an approach to directly quantify siRNA in the RISC in rodents and monkey. This is achieved by specific immunoprecipitation of the RISC from tissue lysates and quantification of small RNAs in the immunoprecipitates by stem-loop PCR. The method, expected to be independent of delivery vehicle and target, is label-free, and the throughput is acceptable for preclinical animal studies. We characterized a lipid-formulated siRNA by integrating these approaches and obtained a quantitative perspective on siRNA tissue accumulation, RISC loading, and gene silencing. The described methodologies have utility for the study of silencing mechanism, the development of siRNA therapeutics, and clinical trial design.
Binding of 111In-labeled HDL to platelets from normolipemic volunteers and patients with heterozygous familial hypercholesterolemia. (1992)

High density lipoproteins (HDLs; d = 1.063 - 1.21 g/ml) were isolated by ultracentrifugation and radiolabeled with 111In. The in vitro binding onto platelets from healthy volunteers (n = 15) and patients (n = 36) with heterozygous familial hypercholesterolemia (FH) was investigated. Binding was saturable and indicated high-affinity binding sites, which bound 1,882 +/- 361 ng protein of 111In-HDL/10(9) platelets (dissociation constant [Kd] = 7 +/- 3 micrograms protein/ml) in healthy volunteers and significantly (p less than 0.01) lower amounts in the FH patients (1,012 +/- 439 ng protein of 111In-HDL/10(9) platelets [Kd = 12 +/- 4 micrograms protein/ml]; p less than 0.01). The capacity to displace one half of the bound ligand (IC50) amounted to 14 +/- 3 micrograms protein/ml in healthy volunteers and 22 +/- 9 micrograms protein/ml in FH patients (p less than 0.001). Treatment with lipid-lowering drugs (gemfibrozil, alone or in combination with cholestyramine) in 10 patients resulted in an increased HDL binding capacity: before treatment, 1,280 +/- 883; after 2 months of treatment, 2,052 +/- 873 (p less than 0.05); and after 6 months of treatment, 2,127 +/- 812 ng protein/10(9) platelets (p less than 0.01). There was a significant (p less than 0.001) correlation between 111In-HDL binding data and plasmatic lipid and lipoprotein values. Furthermore, those FH patients with the additional risk factors of smoking (p less than 0.05) and hypertension (p less than 0.01) showed significantly lower 111In-HDL binding onto platelets. The findings indicate specific 111In-HDL binding sites for human platelets, which may be decreased in patients with heterozygous FH. Upregulation of HDL binding sites during lipid-lowering medication therapy supports the hypothesis that high-affinity HDL binding is involved in hyperlipemic disorders and is possibly related to the reactivity of platelets.
Randomized Controlled Trial of Azacitidine in Patients With the Myelodysplastic Syndrome: A Study of the Cancer and Leukemia Group B (2002)

Aza C treatment results in significantly higher response rates, improved quality of life, reduced risk of leukemic transformation, and improved survival compared with supportive care. Aza C provides a new treatment option that is superior to supportive care for patients with the MDS subtypes and specific entry criteria treated in this study.
Uranium-loaded apoferritin with antibodies attached: molecular design for uranium neutron-capture therapy. (1992)

A method is described to deliver 235U to tumors; the isotope would then be fissioned by incident neutrons, producing localized lethal radiation sufficient for therapy. Apoferritin was loaded with an average of approximately 800 238U atoms per molecule. Stability of the loaded apoferritin in solution was improved, so that only 8% loss of uranium occurred after 8 days at pH 7. Fab' antibody fragments were covalently attached to the uranium-loaded apoferritin, and the immunoreactivity of the conjugate was 92% of that for antibody alone. Such bio-uranium constructions should provide significant advantages over boronated antibodies to meet the requirements for clinical neutron-capture therapy.