gebhart/patrepeval huggingface dataset:
Expression of the rotavirus SA11 protein VP7 in the simple eukaryote Dictyostelium discoideum (1995)

The outer capsid protein of rotavirus, VP7, is a major neutralization antigen and is considered a necessary component of any subunit vaccine developed against rotavirus infection. For this reason, significant effort has been directed towards producing recombinant VP7 that maintains the antigenic characteristics of the native molecule. Using a relatively new expression system, the simple eukaryote Dictyostelium discoideum, we have cloned the portion of simian rotavirus SA11 genome segment 9, encoding the mature VP7 protein, downstream of a native D. discoideum secretion signal sequence in a high-copy-number extrachromosomal vector. The majority of the recombinant VP7 expressed by transformants was intracellular and was detected by Western immunoblot following gel electrophoresis as two or three bands with an apparent molecular mass of 35.5 to 37.5 kDa. A small amount of VP7 having an apparent molecular mass of 37.5 kDa was secreted. Both the intracellular VP7 and the secreted VP7 were N glycosylated and sensitive to endoglycosidase H digestion. Under nonreducing electrophoresis conditions, over half the intracellular VP7 migrated as a monomer while the remainder migrated with an apparent molecular mass approximately twice that of the monomeric form. In an enzyme-linked immunosorbent assay, intracellular VP7 reacted with both nonneutralizing and neutralizing antibodies. The monoclonal antibody recognition pattern paralleled that found with VP7 expressed in either vaccinia virus or herpes simplex virus type 1 and confirms that D. discoideum-expressed VP7 is able to form the major neutralization domains present on viral VP7. Because D. discoideum cells are easy and cheap to grow, this expression system provides a valuable alternative for the large-scale production of recombinant VP7 protein.
Rotation sensing based on a slow-light resonating structure with high group dispersion (2007)

The concept of the Sagnac effect in a slow-light medium and resonator structure with a high group dispersion is investigated. It is found that a slow-light medium can be utilized for relative motion sensing, and a slow-light resonator structure is suitable to detect absolute rotation for navigation purposes. It is noted that the high group dispersion leads to a huge enhancement of the rotation sensor's sensitivity in a resonating structure, and an approach to evaluate and design resonator devices with slow-light property is proposed. Moreover, a folded loop-lattice-based structure is numerically simulated to verify the concept.
Maxillary Palps Are Broad Spectrum Odorant Detectors in Culex quinquefasciatus (2007)

A single type of olfactory sensilla on maxillary palps in many species of mosquitoes houses a very sensitive olfactory receptor neuron (ORN) for carbon dioxide reception. We performed extensive single sensillum recordings from this peg sensillum in Culex quinquefasciatus and have characterized the response threshold and kinetics for CO(2) reception, with a detection threshold less than the CO(2) concentration in the atmosphere. This ORN responded in a tonic mode to lower concentrations of CO(2), whereas higher concentrations generated a phasic-tonic mode of action potential firing. Sensillum potentials accurately represented the response magnitude and kinetics of carbon dioxide-elicited excitatory responses. Stimulation of these ORNs with human breath, a complex mixture of mosquito kairomones and up to 4.5% CO(2), elicited excitatory responses that were reliably detected by CO(2)-sensitive ORNs. Another ORN housed in these sensilla responded to 1-octen-3-ol and to various plant-derived compounds, particularly floral and green leaf volatiles. This ORN showed remarkable sensitivity to the natural enantiomer, (R)-(-)-1-octen-3-ol, rivaling pheromone-detecting ORNs in moths. Maximum neuronal response was elicited with a 10 ng dose. A biological, ecological role of maxillary palps in detection of plant- and nectar-related sources is proposed.
PAMAM Dendrimer-Based Multifunctional Conjugate for Cancer Therapy:  Synthesis, Characterization, and Functionality (2006)

Poly(amidoamine) (PAMAM) dendrimer-based multifunctional cancer therapeutic conjugates have been designed and synthesized. The primary amino groups on the surface of the generation 5 (G5) PAMAM dendrimer were neutralized through partial acetylation, providing enhanced solubility of the dendrimer (in conjugation of FITC (fluorescein isothiocyanate)) and preventing nonspecific targeting interactions (in vitro and in vivo) during delivery. The functional molecules fluorescein isothiocyanate (FITC, an imaging agent), folic acid (FA, targets overexpressed folate receptors on specific cancer cells), and paclitaxel (taxol, a chemotherapeutic drug) were conjugated to the remaining nonacetylated primary amino groups. The appropriate control dendrimer conjugates have been synthesized as well. Characterization of the G5 PAMAM dendrimer and its nanosize conjugates, including the molecular weight and number of primary amine groups, has been determined by multiple analytical methods such as gel permeation chromatography (GPC), nuclear magnetic resonance spectroscopy (NMR), potentiometric titration, high-performance liquid chromatography (HPLC), and UV spectroscopy. These multifunctional dendrimer conjugates have been tested in vitro for targeted delivery of chemotherapeutic and imaging agents to specific cancer cells. We present here the synthesis, characterization, and functionality of these dendrimer conjugates.
Structure-Based Molecular Design (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure-Based Molecular DesignIrwin D. Kuntz, Elaine C. Meng, and Brian K. ShoichetCite this: Acc. Chem. Res. 1994, 27, 5, 117–123Publication Date (Print):May 1, 1994Publication History Published online1 May 2002Published inissue 1 May 1994https://pubs.acs.org/doi/10.1021/ar00041a001https://doi.org/10.1021/ar00041a001research-articleACS PublicationsRequest reuse permissionsArticle Views1021Altmetric-Citations260LEARN 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
Linker chain L1 of earthworm hemoglobin. Structure of gene and protein: homology with low density lipoprotein receptor (1993)

The extracellular hemoglobins (Hbs) of annelids and tube worms are giant multisubunit proteins of up to approximately 200 polypeptides and molecular masses to at least 3,900 kDa. They differ from all other Hbs in having both O2-binding chains and "linker" chains. The latter are required for assembly and structural integrity of the protein and are deficient in or lack heme. We have determined the nucleotide sequences of the cDNA and gene for linker chain L1 of the hemoglobin of Lumbricus terrestris. The cDNA-derived amino acid sequence has 225 residues and a calculated molecular mass of 25,847 Da. The chain is 21-28% identical to linker chains of the related annelid Tylorrhynchus heterochaetus and the deep-sea tube worm Lamellibrachia sp. A remarkable feature of the linker chains is a conserved 38-39-residue segment that contains a repeating pattern of cysteinyl residues: (Cys-X6)3-Cys-X5-Cys-X10-Cys. This pattern, not present in any globin sequence, corresponds exactly to the cysteine-rich repeats of the ligand binding domains of the low density lipoprotein (LDL) receptors of man and Xenopus laevis. Furthermore, the cysteine-rich segment of linker chain L1 has the sequence Asp-Gly-Ser-Asp-Glu which is characteristic of LDL receptor repeats. Similar cysteine-rich sequences also occur in two other mammalian proteins, complement C9 and renal glycoprotein GP330. The results support the conclusion that the cysteine-rich motif of the LDL receptor and annelid Hbs is a multipurpose protein-binding unit of ancient origin which has been incorporated into diverse unrelated proteins, presumably by the process of exon shuffling.
Common non-synonymous SNPs associated with breast cancer susceptibility: findings from the Breast Cancer Association Consortium (2014)

Candidate variant association studies have been largely unsuccessful in identifying common breast cancer susceptibility variants, although most studies have been underpowered to detect associations of a realistic magnitude. We assessed 41 common non-synonymous single-nucleotide polymorphisms (nsSNPs) for which evidence of association with breast cancer risk had been previously reported. Case-control data were combined from 38 studies of white European women (46 450 cases and 42 600 controls) and analyzed using unconditional logistic regression. Strong evidence of association was observed for three nsSNPs: ATXN7-K264R at 3p21 [rs1053338, per allele OR = 1.07, 95% confidence interval (CI) = 1.04-1.10, P = 2.9 × 10(-6)], AKAP9-M463I at 7q21 (rs6964587, OR = 1.05, 95% CI = 1.03-1.07, P = 1.7 × 10(-6)) and NEK10-L513S at 3p24 (rs10510592, OR = 1.10, 95% CI = 1.07-1.12, P = 5.1 × 10(-17)). The first two associations reached genome-wide statistical significance in a combined analysis of available data, including independent data from nine genome-wide association studies (GWASs): for ATXN7-K264R, OR = 1.07 (95% CI = 1.05-1.10, P = 1.0 × 10(-8)); for AKAP9-M463I, OR = 1.05 (95% CI = 1.04-1.07, P = 2.0 × 10(-10)). Further analysis of other common variants in these two regions suggested that intronic SNPs nearby are more strongly associated with disease risk. We have thus identified a novel susceptibility locus at 3p21, and confirmed previous suggestive evidence that rs6964587 at 7q21 is associated with risk. The third locus, rs10510592, is located in an established breast cancer susceptibility region; the association was substantially attenuated after adjustment for the known GWAS hit. Thus, each of the associated nsSNPs is likely to be a marker for another, non-coding, variant causally related to breast cancer risk. Further fine-mapping and functional studies are required to identify the underlying risk-modifying variants and the genes through which they act.
Photothermal image flow cytometry in vivo (2005)

The capability of photothermal (PT) microscopy to image moving, unlabeled cells in real time in vivo is demonstrated in a study of circulating red and white blood cells in blood and lymph microvessels of rat mesentery. Potential applications of this optical tool, called PT flow cytometry, are discussed.
The spectrum of genetic defects in a panel of 40 Dutch families with symptomatic protein C deficiency type I: heterogeneity and founder effects (1991)

Heterozygosity for protein C deficiency is associated with thromboembolic episodes, but clinical symptoms are nonrandomly distributed among protein C deficient families. This finding has led to the provisional definition of clinically dominant and clinically recessive protein C deficiency. We report here the molecular basis of hereditary, clinically dominant protein C deficiency in a panel of 40 Dutch probands from apparently independent families. All but one subject was a heterozygote for a point mutation in the protein C gene. These 39 subjects shared 15 mutations, six of which occurred in more than one proband (between two and nine). The diversity in the 15 mutations, together with the observation that the most frequent Dutch mutation was also found in a Swedish family with clinically recessive protein C deficiency, makes it unlikely that the molecular basis of protein C deficiency will be different between the clinically dominant and recessive forms. The recurrence of one of the mutations is most likely due to a founder effect, which suggests that when an additional hereditary factor is involved in the clinical severity of protein C deficiency this factor may remain linked to the protein C gene over many generations.
Resistance of T-Cell Receptor δ-Chain-Deficient Mice to ExperimentalCandidaalbicansVaginitis (2001)

Conditions consistent with tolerance or immunoregulation have been observed in experimental Candida albicans vaginal infections. The present study investigated the role of gamma/delta T cells in experimental vaginal candidiasis. Results showed that T-cell receptor delta-chain-knockout mice had significantly less vaginal fungal burden when compared to wild-type mice, suggesting an immunoregulatory role for gamma/delta T cells in Candida vaginitis.
Impact of laboratory molecular diagnosis on contemporary diagnostic criteria for genetically transmitted cardiovascular diseases: hypertrophic cardiomyopathy, long-QT syndrome, and marfan syndrome : A statement for healthcare professionals from the councils on clinical cardiology, cardiovascular disease in the young, and basic science, american heart association (1998)

Over the last several years, substantial progress has been achieved in defining the molecular basis for several genetically transmitted, nonatherosclerotic cardiovascular diseases. These advances in molecular biology have enhanced our understanding of the primary defects and basic mechanisms responsible for the pathogenesis of these conditions and their phenotypic expression, and in the process, new perspectives on cardiac diagnosis have been formulated. In the course of this scientific evolution, a certain measure of uncertainty has also arisen regarding the implications of genetic analysis for clinical diagnostic criteria. New subgroups of genetically affected individuals without conventional clinical diagnostic findings have been identified solely by virtue of access to molecular laboratory techniques, creating a number of medical and ethical concerns regarding the possible clinical implications. Indeed, the extent to which such individuals should receive sequential evaluations and/or therapy or be subjected to employment or insurance discrimination, psychological harm, loss of privacy, or unnecessary withdrawal from competitive athletics is uncertain but remains a legitimate source of concern. It is therefore particularly timely and appropriate to analyze these issues in detail, specifically the extent to which molecular biology has revised traditional diagnostic criteria. The role of genetic testing in assessing prognosis and identifying high-risk subgroups or in defining basic disease mechanisms and pathophysiology is, however, largely beyond the scope of this scientific statement. As models for the present critique, we selected the 3 most common familial cardiovascular diseases for which gene defects have been identified, each of which is associated with autosomal dominant inheritance and a risk for sudden cardiac death: hypertrophic cardiomyopathy (HCM), long-QT syndrome (LQTS), and Marfan syndrome (MFS).
Synapsis and catalysis by activated Tn3 resolvase mutants (2008)

The serine recombinase Tn3 resolvase catalyses recombination between two 114 bp res sites, each of which contains binding sites for three resolvase dimers. We have analysed the in vitro properties of resolvase variants with 'activating' mutations, which can catalyse recombination at binding site I of res when the rest of res is absent. Site I x site I recombination promoted by these variants can be as fast as res x res recombination promoted by wild-type resolvase. Activated variants have reduced topological selectivity and no longer require the 2-3' interface between subunits that is essential for wild-type resolvase-mediated recombination. They also promote formation of a stable synapse comprising a resolvase tetramer and two copies of site I. Cleavage of the DNA strands by the activated mutants is slow relative to the rate of synapsis. Stable resolvase tetramers were not detected in the absence of DNA or bound to a single site I. Our results lead us to conclude that the synapse is assembled by sequential binding of resolvase monomers to site I followed by interaction of two site I-dimer complexes. We discuss the implications of our results for the mechanisms of synapsis and regulation in recombination by wild-type resolvase.
Toward Rapid, High-Sensitivity, Volume-Constrained Biomarker Quantification and Validation using Backscattering Interferometry (2014)

Realizing personalized medicine, which promises to enable early disease detection, efficient diagnostic staging, and therapeutic efficacy monitoring, hinges on biomarker quantification in patient samples. Yet, the lack of a sensitive technology and assay methodology to rapidly validate biomarker candidates continues to be a bottleneck for clinical translation. In our first direct and quantitative comparison of backscattering interferometry (BSI) to fluorescence sensing by ELISA, we show that BSI could aid in overcoming this limitation. The analytical validation study was performed against ELISA for two biomarkers for lung cancer detection: Cyfra 21-1 and Galectin-7. Spiked serum was used for calibration and comparison of analytical figures of merit, followed by analysis of blinded patient samples. Using the ELISA antibody as the probe chemistry in a mix-and-read assay, BSI provided significantly lower detection limits for spiked serum samples with each of the biomarkers. The limit of quantification (LOQ) for Cyrfa-21-1 was measured to be 230 pg/mL for BSI versus 4000 pg/mL for ELISA, and for Galectin-7, it was 13 pg/mL versus 500 pg/mL. The coefficient of variation for 5 day, triplicate determinations was <15% for BSI and <10% for ELISA. The two techniques correlated well, ranging from 3-29% difference for Cyfra 21-1 in a blinded patient sample analysis. The label-free and free-solution operation of BSI allowed for a significant improvement in analysis speed, with greater ease, improved LOQ values, and excellent day-to-day reproducibility. In this unoptimized format, BSI required 5.5-fold less sample quantity needed for ELISA (a 10 point calibration curve measured in triplicate required 36 μL of serum for BSI vs 200 μL for ELISA). The results indicate that the BSI platform can enable rapid, sensitive analytical validation of serum biomarkers and should significantly impact the validation bottleneck of biomarkers.
Taxol: a history of pharmaceutical development and current pharmaceutical concerns. (1993)

Taxol, a unique diterpene anticancer compound derived from the bark of the Taxus brevifolia (Pacific yew) tree, induces cytotoxicity by a novel mechanism of action. An antimicrotubule agent, Taxol promotes the formation and stabilization of the tubulin polymer unlike other anticancer agents that induce microtubule disassembly. Because of its poor aqueous solubility, Taxol is formulated as a solution in 50% Cremophor EL and 50% dehydrated alcohol, USP. The Cremophor EL and dehydrated alcohol vehicle used in the formulation of Taxol creates some interesting challenges for its preparation and administration. The pharmaceutical concerns associated with the preparation and administration of Taxol are discussed.
Brain and ocular metastases from a transmissible venereal tumour in a dog (2000)

A five-year-old crossbred dog was referred with rapidly growing masses over its penis and right popliteal lymph node. The dog had severe blepharospasm, congestion of episcleral vessels and rubeosis iridis of the left eye. A presumptive diagnosis of transmissible venereal tumour (TVT) and iridocyclitis was made based on the results of fine needle aspiration. Chemotherapy with vincristine and prednisolone was initiated and after four months the dog made a complete recovery. However, the dog subsequently relapsed, showing miosis, blepharospasm and a well defined mass within the anterior chamber of the left eye. In addition, the dog exhibited generalised 'grand mal' type seizures. Computed tomographic (CT) examination of the brain revealed two distinct masses in the left frontal lobe. Because of the poor prognosis, the owners elected to have the dog euthanased. On histopathology, metastases of TVT in the left eye and left cerebral hemisphere were found, showing no specific staining for CD3, immunoglobulin (Ig) G, IgM and lambda light chains. It was therefore concluded that the tumour growth was progressive, and that there was an absence of local humoral immune response against TVT in this case.
Gastric Residuals and Their Relationship to Necrotizing Enterocolitis in Very Low Birth Weight Infants (2004)

VLBW infants who developed NEC had more gastric residuals. However, there was overlap with the normal control subjects. Of the gastric residual data, the maximum residual seems to be the best predictor for NEC in the subsequent days.
Optimal surface functionalization of silicon quantum dots (2008)

Surface functionalization is a critical step for Si nanocrystals being used as biological probes and sensors. Using density-functional tight-binding calculations, we systematically investigate the optical properties of silicon quantum dots (SiQDs) with various termination groups, including H, CH(3), NH(2), SH, and OH. Our calculations reveal that capping SiQDs with alkyl group (-Si-C-) induces minimal changes in the optical spectra, while covering the surface with NH(2), SH, and OH results in evident changes compared to hydrogenated SiQDs. The structural deformations and electronic property changes due to surface passivation were shown to be responsible for the above-described features. Interestingly, we find that the optical properties of SiQDs can be controlled by varying the S coverage on the surface. This tuning effect may have important implications in device fabrications.
The expression of toll‐like receptors 3 and 7 in rheumatoid arthritis synovium is increased and costimulation of toll‐like receptors 3, 4, and 7/8 results in synergistic cytokine production by dendritic cells (2005)

TLRs are involved in the regulation of DC activation and cytokine production. We hypothesize that various TLR ligands in the joint trigger multiple TLRs simultaneously, favoring the breakthrough of tolerance in RA.
Molecular Adaptors for Vascular-Targeted Adenoviral Gene Delivery (2000)

Gene therapy would be considerably more effective if vectors could be targeted to specific organs or tissues after systemic administration. We previously developed an in vivo selection system to isolate organ- and tumor-homing peptides from phage display peptide libraries. The peptides isolated by this approach bind to receptors expressed in vascular endothelia. We describe here the development of molecular adaptors to target adenoviral gene therapy vectors to selective vascular "addresses." The adaptor design consists of an organhoming peptide conjugated to an adenovirus-binding moiety. We isolated and characterized several monoclonal antibodies that bind to adenovirus type 5 (Ad5). Two of the antibodies neutralized Ad5 infection. We linked the Fab fragments of one of these antibodies to a synthetic lung-homing peptide (CGFECVRQCPERC or GFE-1 peptide) and tested the ability of the resulting bispecific conjugate to retarget Ad5. Cells that express the receptor for the GFE-1 peptide and are resistant to Ad5 infection were sensitized to recombinant Ad5 vectors in the presence of the Fab-GFE adaptor. Our findings indicate that selective gene therapy delivery may be developed on the basis of our vascular targeting technology.