gebhart/patrepeval huggingface dataset:
Proteome Analysis of Pitcher Fluid of the Carnivorous Plant Nepenthes alata (2008)

The genus Nepenthes comprises carnivorous plants that digest insects in pitcher fluid to supplement their nitrogen uptake. In a recent study, two acid proteinases (nepenthesins I and II) were purified from the pitcher fluid. However, no other enzymes involved in prey digestion have been identified, although several enzyme activities have been reported. To identify all the proteins involved, we performed a proteomic analysis of Nepenthes pitcher fluid. The secreted proteins in pitcher fluid were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and several protein bands were detected by silver staining. The proteins were identified by in-gel tryptic digestion, de novo peptide sequencing, and homology searches against public databases. The proteins included homologues of beta-D-xylosidase, beta-1,3-glucanase, chitinase, and thaumatin-like protein, most of which are designated "pathogenesis-related proteins". These proteins presumably inhibit bacterial growth in the pitcher fluid to ensure sufficient nutrients for Nepenthes growth.
Human Immune Response to a Plague Vaccine Comprising Recombinant F1 and V Antigens (2005)

The human immune response to a new recombinant plague vaccine, comprising recombinant F1 (rF1) and rV antigens, has been assessed during a phase 1 safety and immunogenicity trial in healthy volunteers. All the subjects produced specific immunoglobulin G (IgG) in serum after the priming dose, which peaked in value after the booster dose (day 21), with the exception of one individual in the lowest dose level group, who responded to rF1 only. Three subjects, found to have an anti-rV titer at screening, were excluded from the overall analysis. Human antibody functionality has been assessed by quantification of antibody competing for binding to rV in vitro and also by the transfer of protective immunity in human serum into the naive mouse. Human and macaque IgG competed for binding to rV in vitro with a mouse monoclonal antibody, previously shown to protect mice against challenge with plague, suggesting that this protective B-cell epitope on rV is conserved between these three species. Total IgG to rV in individuals and the titer of IgG competing for binding to rV correlated significantly at days 21 (r = 0.72; P < 0.001) and 28 (r = 0.82; P < 0.001). Passive transfer of protective immunity into mice also correlated significantly with total IgG titer to rF1 plus rV at days 21 (r(2) = 98.6%; P < 0.001) and 28 (r(2) = 76.8%; P < 0.03). However, no significant vaccination-related change in activation of peripheral blood mononuclear cells was detected at any time. Potential serological immune correlates of protection have been investigated, but no trends specific to vaccination could be detected in cellular markers.
Promoter domains required for expression of plasmid-borne copies of the herpes simplex virus thymidine kinase gene in virus-infected mouse fibroblasts and microinjected frog oocytes. (1985)

A transient expression assay was used to measure the relative template activities of mutated tk genes in mouse L cells induced in trans by herpes simplex virus (HSV). In this assay, expression of the wild-type HSV type 1 tk gene is induced at least 200-fold by the superinfecting virus. Genetic lesions that were assayed include 5' deletions, clustered base substitutions, single base substitutions, intrapromoter inversions, and intrapromoter recombinants with the HSV type 2 tk gene. Roughly half of the mutations that were tested were found to weaken tk expression efficiency, and the remaining mutations did not alter expression. The spatial distribution of mutations that reduce expression efficiency in trans-induced mouse fibroblasts facilitated the construction of a map of promoter domains. The most gene-proximal promoter domain is located between 16 and 32 base pairs (bp) upstream of the tk mRNA cap site and contains a TATA homology. Two more distally located promoter domains were mapped to discrete locations upstream from the TATA homology. One of these distal domains is located between 47 and 79 bp upstream from the mRNA cap site, and the other is located between 84 and 105 bp upstream from the tk gene. The boundaries of these three promoter domains, with one exception, coincided with the set of domains delineated previously in a frog oocyte microinjection assay. The concordant behavior of tk promoter mutants in microinjected frog oocytes and trans-induced mouse fibroblasts leads us to propose that recognition and activation of the HSV tk promoter is mediated by cellular transcription factors that are common to frogs and mice.
Fluid Bed Technology in Materials Processing (1998)

Fluid Bed Technology in Materials Processing comprehensively covers the various aspects of fluidization engineering and presents an elaborate examination of the applications in a multitude of materials processing techniques.This singular resource discusses:All the basic aspects of fluidization essential to understand and learn about various techniquesThe range of industrial applicationsSeveral examples in extraction and process metallurgyFluidization in nuclear engineering and nuclear fuel cycle with numerous examplesInnovative techniques and several advanced concepts of fluidization engineering, including use and applications in materials processing as well as environmental and bio-engineeringPros and cons of various fluidization equipment and specialty of their applications, including several examplesDesign aspects and modelingTopics related to distributors effects and flow regimesA separate chapter outlines the importance of fluidization engineering in high temperature processing, including an analysis of the fundamental concepts and applications of high temperature fluidized bed furnaces for several advanced materials processing techniques.Presenting information usually not available in a single source, Fluid Bed Technology in Materials Processing servesFluidization engineersPracticing engineers in process metallurgy, mineral engineering, and chemical metallurgyResearchers in the field of chemical, metallurgical, nuclear, biological, environmental engineeringEnergy engineering professionalsHigh temperature scientists and engineersStudents and professionals who adopt modeling of fluidization in their venture for design and scale up
Biodistribution and Pharmacokinetics of EGFR-Targeted Thiolated Gelatin Nanoparticles Following Systemic Administration in Pancreatic Tumor-Bearing Mice (2013)

The objective of this study was to evaluate qualitative and quantitative biodistribution of epidermal growth factor receptor (EGFR)-targeted thiolated type B gelatin nanoparticles in vivo in subcutaneous human pancreatic adenocarcinoma (Panc-1) bearing female SCID Beige mice. EGFR-targeted nanoparticles showed preferential and sustained accumulation in the tumor mass, especially at early time points. Higher blood concentrations and higher tumor accumulations were observed with PEG-modified and EGFR-targeted nanoparticles during the study (AUClast: 17.38 and 19.56%ID/mL·h in blood, 187 and 322%ID/g·h in tumor for PEG-modified and EGFR-targeted nanoparticles, respectively), as compared to control, unmodified particles (AUClast: 10.71%ID/mL·h in blood and 138%ID/g·h in tumor). EGFR-targeted nanoparticles displayed almost twice tumor targeting efficiency than either PEG-modified or the unmodified nanoparticles, highlighting the efficacy of the active targeting strategy. In conclusion, this study shows that EGFR-targeted and PEG-modified nanoparticles were suitable vehicles for specific systemic delivery in subcutaneous Panc-1 tumor xenograft models.
Firefly luciferin-activated rose bengal: in vitro photodynamic therapy by intracellular chemiluminescence in transgenic NIH 3T3 cells. (2003)

Photodynamic therapy (PDT) of cancer (1, 2) is a well-established treatment modality that uses light excitation of a photosensitive substance to produce oxygen-related cytotoxic intermediates, such as singlet oxygen or free radicals (3, 4). Although PDT is advantageous over other forms of cancer treatments because of its limited side effects, its main disadvantage is the poor accessibility of light to more deeply lying malignancies. External light sources such as lasers or lamps can be applied either noninvasively to reach tumors that lie well within the penetration depth of the light or in a minimally invasive fashion (interstitial treatments) in which optical fibers are placed intratumorally through needles. Even with the second approach, light distribution over the tumor is not homogeneous and nonidentified metastatic disease is left untreated. CL, the chemical production of light, is exemplified by firefly light emission mediated by the enzymatic (luciferase + ATP) oxidation of D-luciferin to oxyluciferin (5). This mobile light source is a targetable alternative to external sources of illumination. Here we show the in vitro photodynamic effect of rose bengal activated by intracellular generation of light, in luciferase-transfected NIH 3T3 murine fibroblasts.
Adult-onset calorie restriction and fasting delay spontaneous tumorigenesis in p53-deficient mice (2002)

Heterozygous p53-deficient (p53 +/– ) mice, a potential model for human Li-Fraumeni Syndrome, have one functional allele of the p53 tumor suppressor gene. These mice are prone to spontaneous neoplasms, most commonly sarcoma and lymphoma; the median time to death of p53+/– mice is 18 months. We have shown previously that juvenile-onset calorie restriction (CR) to 60% of ad libitum (AL) intake delays tumor development in young p53-null (–/–) mice by a p53-independent and insulin-like growth factor 1 (IGF-1)-related mechanism. To determine whether CR is effective when started in adult p53-deficient mice, and to compare chronic CR with an intermittent fasting regimen, male p53+/– mice (7–10 months old, 31–32 mice/group) were randomly assigned to the following regimens: (i) AL (AIN-76A diet), (ii) CR to 60% of AL intake or (iii) 1 day/week fast. Food availability on non-fasting days was controlled to prevent compensatory over feeding. Relative to the AL group, CR significantly delayed ( P =; 0.001) the onset of tumors in adult mice, whereas the 1 day/week fast caused a moderate delay ( P =; 0.039). Substantial variation in longevity and maximum body weight within treatments was not correlated with variation in growth characteristics of individual mice. In a separate group of p53+/– mice treated for 4 weeks ( n =; five mice per treatment), plasma IGF-1 levels in CR versus AL mice were reduced by 20% ( P < 0.01) and leptin levels were reduced by 71% ( P < 0.01); fasted mice had intermediate levels of leptin and IGF-1. Our findings that CR or a 1 day/week fast suppressed carcinogenesis—even when started late in life in mice predestined to develop tumors due to decreased p53 gene dosage—support efforts to identify suitable interventions influencing energy balance in humans as a tool for cancer prevention.
Tissue-mimicking agar/gelatin materials for use in heterogeneous elastography phantoms (2005)

Five 9 cm x 9 cm x 9 cm phantoms, each with a 2-cm-diameter cylindrical inclusion, were produced with various dry-weight concentrations of agar and gelatin. Elastic contrasts ranged from 1.5 to 4.6, and values of the storage modulus (real part of the complex Young's modulus) were all in the soft tissue range. Additives assured immunity from bacterial invasion and can produce tissue-mimicking ultrasound and NMR properties. Monitoring of strain ratios over a 7 to 10 month period indicated that the mechanical properties of the phantoms were stable, allowing about 1 month for the phantom to reach chemical equilibrium. The only dependable method for determining the storage moduli of the inclusions is to make measurements on samples excised from the phantoms. If it is desired to produce and accurately characterize a phantom with small inclusions with other shapes, such as an array of small spheres, an auxiliary phantom with the geometry of the cylindrical inclusion phantoms or the equivalent should be made at the same time using the same materials. The elastic contrast can then be determined using samples excised from the auxiliary phantom. A small increase of about 10% in volume of the cylindrical inclusions occurred-a tolerable increase. Interestingly, the smallest increase (about 5%) occurred in the phantom with the largest elastic contrast.
Efficient Organic Solar Cells with Solution‐Processed Silver Nanowire Electrodes (2011)

An effective method for reducing interelectrode shorting in silver nanowire (AgNW) based organic solar cells is reported. The method is applied to standard and inverted devices based on poly(3-hexylthiophene) and [6,6]-phenyl-C61-butyric acid methyl ester. The best results are obtained using an inverted architecture with a 200 nm buffer layer of nanostructured titania (TiOx) on top of the AgNWs, yielding power conversion efficiencies of up to 3.5%.
Influence of DNA on Volatile Generation from Maillard Reaction of Cysteine and Ribose (2003)

The effects of DNA on thermal flavor generation were investigated using the Maillard reaction model system containing cysteine and ribose, which were heated to the roasting temperature of 180 °C for 2 hours at pH 5 and pH 8.5. The volatiles and semi-volatile compounds identified from the liquid phase of the reaction systems of ribose and cysteine with or without DNA indicated that DNA affected volatile formation in a complex manner. A typical compound derived from DNA-involved thermal reaction was 2-furfuryl alcohol, which elicits a sugary aroma. DNA mitigated the sulfurous, meaty aroma by reducing the concentration of some well-known meaty flavor compounds such as 2-methyl-3-furanthiol, 2-methyl-3-thiophenethiol, 2-furfurylthiol and their associated dimers as well as some thiophenes. On the other hand, DNA promoted the formation of several important nitrogen-containing volatiles such as methylpyrazine, 2-acetylthiazole, cyclopentapyrazine and 2,6-dimethylpyrazine, which are known to elicit roasty, nutty flavor notes. Although DNA can act as a nitrogenous source, it should not be regarded as a major donor in the formation of nitrogen-containing compounds.
Tau proteins with FTDP‐17 mutations have a reduced ability to promote microtubule assembly (1998)

Recently exonic and intronic mutations in the gene for microtubule-associated protein tau have been discovered in cases of familial frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17). Intronic mutations have been shown to lead to an abnormal preponderance of four-repeat tau isoforms. The effects of the exonic mutations are unknown. We report here that the G272V, P301L, V337M and R406W mutations lead to a marked reduction in the ability of tau to promote microtubule assembly. This partial loss-of-function may be the primary effect of the known missense mutations in tau.
Differences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors (2005)

The up-regulation of these gene types in both tissue types is an unexpected finding and suggests that normal appearing prostate tissue can undergo genetic changes in response to or in expectation of morphologic cancer. A possible field effect surrounding prostate cancers and the implications of these findings for characterizing gene expression changes in prostate tumors are discussed.
Role of inducible cyclooxygenase (COX-2) in inflammation. (1994)

Nonsteroidal anti-inflammatory drugs (NSAIDs) are potent anti-inflammatory agents that act through the inhibition of the cyclooxygenase (COX) enzyme and the subsequent inhibition of prostaglandins at the site of inflammation. Unfortunately, inhibition of gastrointestinal or renal prostaglandins is associated with mechanism-based toxicities that limit the usefulness of these otherwise potent and efficacious drugs. Recently two forms of the COX enzyme have been identified: COX-1, which is constitutively expressed in many cells and tissues, and COX-2, which is selectively induced by proinflammatory cytokines at the site of inflammation. The discovery of a second COX enzyme led to the hypothesis that toxicity associated with the clinically useful NSAIDs is caused by the inhibition of COX-1, whereas the anti-inflammatory properties were caused by the inhibition of inducible COX-2. In support of this hypothesis, expression of the inducible COX-2 enzyme is selectively blocked by the potent anti-inflammatory drug dexamethasone. Selective inhibition of COX-2 may produce superior anti-inflammatory drugs with substantial safety over existing NSAIDs.
Amino Acid-Protecting Groups (2009)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTAmino Acid-Protecting GroupsAlbert Isidro-Llobet†, Mercedes Álvarez*†‡§, and Fernando Albericio*†‡∥View Author Information Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain; CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain; Laboratory of Organic Chemistry, Faculty of Pharmacy, University of Barcelona, 08028 Barcelona, Spain; and Department of Organic Chemistry, University of Barcelona, Martı́ i Franqués 1, 08028 Barcelona, Spain* To whom correspondence should be addressed. Fax: 34 93 403 71 26. E-mail: [email protected]; [email protected];†Institute for Research in Biomedicine.‡CIBER-BBN.§Laboratory of Organic Chemistry, Faculty of Pharmacy, University of Barcelona.∥Department of Organic Chemistry, University of Barcelona.Cite this: Chem. Rev. 2009, 109, 6, 2455–2504Publication Date (Web):April 13, 2009Publication History Received28 April 2008Published online13 April 2009Published inissue 10 June 2009https://pubs.acs.org/doi/10.1021/cr800323shttps://doi.org/10.1021/cr800323sreview-articleACS PublicationsCopyright © 2009 American Chemical SocietyRequest reuse permissionsArticle Views92893Altmetric-Citations636LEARN 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:Catalytic reactions,Monomers,Peptides and proteins,Protective groups,Redox reactions Get e-Alerts
Sample size determination in combinatorial chemistry. (1995)

Combinatorial chemistry is gaining wide appeal as a technique for generating molecular diversity. Among the many combinatorial protocols, the split/recombine method is quite popular and particularly efficient at generating large libraries of compounds. In this process, polymer beads are equally divided into a series of pools and each pool is treated with a unique fragment; then the beads are recombined, mixed to uniformity, and redivided equally into a new series of pools for the subsequent couplings. The deviation from the ideal equimolar distribution of the final products is assessed by a special overall relative error, which is shown to be related to the Pearson statistic. Although the split/recombine sampling scheme is quite different from those used in analysis of categorical data, the Pearson statistic is shown to still follow a chi2 distribution. This result allows us to derive the required number of beads such that, with 99% confidence, the overall relative error is controlled to be less than a pregiven tolerable limit L1. In this paper, we also discuss another criterion, which determines the required number of beads so that, with 99% confidence, all individual relative errors are controlled to be less than a pregiven tolerable limit L2 (0 < L2 < 1).
CADD: predicting the deleteriousness of variants throughout the human genome (2018)

Combined Annotation-Dependent Depletion (CADD) is a widely used measure of variant deleteriousness that can effectively prioritize causal variants in genetic analyses, particularly highly penetrant contributors to severe Mendelian disorders. CADD is an integrative annotation built from more than 60 genomic features, and can score human single nucleotide variants and short insertion and deletions anywhere in the reference assembly. CADD uses a machine learning model trained on a binary distinction between simulated de novo variants and variants that have arisen and become fixed in human populations since the split between humans and chimpanzees; the former are free of selective pressure and may thus include both neutral and deleterious alleles, while the latter are overwhelmingly neutral (or, at most, weakly deleterious) by virtue of having survived millions of years of purifying selection. Here we review the latest updates to CADD, including the most recent version, 1.4, which supports the human genome build GRCh38. We also present updates to our website that include simplified variant lookup, extended documentation, an Application Program Interface and improved mechanisms for integrating CADD scores into other tools or applications. CADD scores, software and documentation are available at https://cadd.gs.washington.edu.
Biomechanics of the Lumbar Intervertebral Disk: A Review (1980)

This article reviews the literature on the biomechanics of the lumbar intervertebral disk according to: 1) disk structure and properties, 2) biomechanical principles and their application to the disk, 3) biomechanics and intradiskal pressures as they relate to posture, work, and exercise, and 4) prophylactic measures.