gebhart/patrepeval huggingface dataset:
Target-driven DNA association to initiate cyclic assembly of hairpins for biosensing and logic gate operation (2015)

A target-driven DNA association was designed to initiate cyclic assembly of hairpins, which led to an enzyme-free amplification strategy for detection of a nucleic acid or aptamer substrate and flexible construction of logic gates. The cyclic system contained two ssDNA (S1 and S2) and two hairpins (H1 and H2). These ssDNA could co-recognize the target to produce an S1-target-S2 structure, which brought their toehold and branch-migration domains into close proximity to initiate the cyclic assembly of hairpins. The assembly product further induced the dissociation of a double-stranded probe DNA (Q:F) <i>via</i> toehold-mediated strand displacement to switch the fluorescence signal. This method could detect DNA and ATP as model analytes down to 21.6 pM and 38 nM, respectively. By designing different DNA input strands, the "AND", "INHIBIT" and "NAND" logic gates could be activated to achieve the output signal. The proposed biosensing and logic gate operation platform showed potential applications in disease diagnosis.
Radioangiocardiogram monitoring in patients receiving bisantrene (1984)

Due to the tricyclic structural similarity between the anthracyclines and a new anthracene bishydrazone derivative, bisantrene, changes in myocardial function as detected by radionuclide angiography were sought in early phase I-II trials of the drug. Overall, there appear to be no changes in ejection fraction when determined 24 hours postinfusion, or when determined after low cumulative doses of bisantrene.
The development of immunotoxins for the therapy of cancer, AIDS, and immune dysfunctions. (1988)

Immunotoxins (ITs) consist of cell-reactive ligands coupled to toxins or their toxic subunits. The ligands are usually antibodies, hormones, or growth factors and the toxins are of bacterial or plant origin. In the case of the plant toxin, ricin, its structure consists of a ribosome-inactivating A chain of 32 Kd linked by a disulfide bond to a galactose-specific lectin (B chain) of approximately 30 Kd. The A and B chains of ricin can be separated following reduction and the A chain can then be purified and chemically linked to different ligands to generate a cell-reactive conjugate. Studies using A chain-containing ITs to specifically delete tumor cells, or regulatory cells of the immune system began a decade ago. Initial in vitro experiments were successful and led to further experiments in vivo. However, in vivo studies carried out over the past five years in both animals and humans have demonstrated that the efficacy of ITs or conjugates in vivo is often poor due to problems involving instability of the conjugate, inferior potency, inaccessibility of tumor cells, nonspecific binding to cells other than the target cells, and the survival of antigen-negative mutants. In addition, immune responses against both the ligand and the A chain are usually elicited, precluding repeated therapy. During the past several years, there have been attempts to solve these problems and thereby develop more effective ITs. By analogy with conventional chemotherapeutic agents, it could be predicted that immunotoxins will require many years of study to optimize their construction and therapeutic regimens.(ABSTRACT TRUNCATED AT 250 WORDS)
The effect of anastrozole on the single‐dose pharmacokinetics and anticoagulant activity of warfarin in healthy volunteers (2001)

Overall, there was no evidence to suggest that anastrozole has any clinically relevant effects on the pharmacokinetics of warfarin. Anastrozole had no effect on clotting mechanisms or on the pharmacodynamic activity of warfarin, as assessed by prothrombin time, thrombin time, activated partial thromboplastin time, and factor VII.
Influence of experimental hyperglycemia on microvascular blood perfusion of pancreatic islet isografts. (1992)

The influence of hyperglycemia on the microvascular blood perfusion of pancreatic islet isografts of Syrian golden hamsters was analyzed by direct visualization of the islet's microvasculature by means of in vivo fluorescence microscopy. The experiments were performed using the hamster dorsal skinfold preparation, which allows for quantitative analysis of the microcirculation of islets grafted on the striated skin muscle. Islets were isolated from inbred hamsters by collagenase digestion and subsequently transplanted in normoglycemic (controls; n = 8) and hyperglycemic (65 mg/kg streptozotocin intravenously; n = 10) recipients. In both groups, revascularization of the islet grafts was completed on day 10 after transplantation. Quantitative analysis of capillary blood perfusion on days 6, 10, and 14 revealed no differences in functional capillary density and capillary red blood cell velocity of islets grafted into normoglycemic as compared to hyperglycemic animals. However, islet capillaries were significantly wider in hyperglycemic recipients (11.9 +/- 1.3 microns, P < 0.01) as compared to normoglycemic controls (8.9 +/- 0.4 microns). The increase of capillary diameters resulted in a significant rise (P < 0.01) of mean capillary blood perfusion from 1.76 +/- 0.39 nl/min in controls to 2.88 +/- 0.63 nl/min in hyperglycemic recipients, indicating an increase in microvascular blood perfusion due to hyperglycemia. From these results it is concluded that hyperglycemia is associated with higher capillary blood perfusion in revascularized islet isografts, similarly as known for pancreatic islets in situ.
Engineering species-like barriers to sexual reproduction (2017)

Controlling the exchange of genetic information between sexually reproducing populations has applications in agriculture, eradication of disease vectors, control of invasive species, and the safe study of emerging biotechnology applications. Here we introduce an approach to engineer a genetic barrier to sexual reproduction between otherwise compatible populations. Programmable transcription factors drive lethal gene expression in hybrid offspring following undesired mating events. As a proof of concept, we target the ACT1 promoter of the model organism Saccharomyces cerevisiae using a dCas9-based transcriptional activator. Lethal overexpression of actin results from mating this engineered strain with a strain containing the wild-type ACT1 promoter.Genetic isolation of a genetically modified organism represents a useful strategy for biocontainment. Here the authors use dCas9-VP64-driven gene expression to construct a 'species-like' barrier to reproduction between two otherwise compatible populations.
Activation of the c- myb Locus by Viral Insertional Mutagenesis in Plasmacytoid Lymphosarcomas (1984)

Rearrangement in the c-myb locus of each of four independently derived BALB/c plasmacytoid lymphosarcoma (ABPL's) is due to the insertion of a defective Moloney murine leukemia virus (M-MuLV) into a 1.5-kilobase-pair stretch of cellular DNA at the 5' end of the v-myb-related sequences. This retroviral insertion is associated with abnormal transcription of myb sequences and probably represents a step in the neoplastic transformation of ABPL cells.
Actomyosin Cortical Mechanical Properties in Nonadherent Cells Determined by Atomic Force Microscopy (2016)

The organization of filamentous actin and myosin II molecular motor contractility is known to modify the mechanical properties of the cell cortical actomyosin cytoskeleton. Here we describe a novel method, to our knowledge, for using force spectroscopy approach curves with tipless cantilevers to determine the actomyosin cortical tension, elastic modulus, and intracellular pressure of nonadherent cells. We validated the method by measuring the surface tension of water in oil microdrops deposited on a glass surface. We extracted an average tension of T ∼ 20.25 nN/μm, which agrees with macroscopic experimental methods. We then measured cortical mechanical properties in nonadherent human foreskin fibroblasts and THP-1 human monocytes before and after pharmacological perturbations of actomyosin activity. Our results show that myosin II activity and actin polymerization increase cortex tension and intracellular pressure, whereas branched actin networks decreased them. Interestingly, myosin II activity stiffens the cortex and branched actin networks soften it, but actin polymerization has no effect on cortex stiffness. Our method is capable of detecting changes in cell mechanical properties in response to perturbations of the cytoskeleton, allowing characterization with physically relevant parameters. Altogether, this simple method should be of broad application for deciphering the molecular regulation of cell cortical mechanical properties.
Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma (2009)

Reliable identification of cancer-related mutations in TP53 is often problematic, as these mutations can be randomly distributed throughout numerous codons and their relative abundance in clinical samples can fall below the sensitivity limits of conventional sequencing. To ensure the highest sensitivity in mutation detection, we adapted the recently described coamplification at lower denaturation temperature-PCR (COLD-PCR) method to employ two consecutive rounds of COLD-PCR followed by Sanger sequencing. Using this highly sensitive approach we screened 48 nonmicrodissected lung adenocarcinoma samples for TP53 mutations. Twenty-four missense/frameshift TP53 mutations throughout exons 5 to 8 were identified in 23 out of 48 (48%) lung adenocarcinoma samples examined, including eight low-level mutations at an abundance of approximately 1 to 17%, most of which would have been missed using conventional methodologies. The identified alterations include two rare lung adenocarcinoma mutations, one of which is a "disruptive" mutation currently undocumented in the lung cancer mutation databases. A sample harboring a low-level mutation ( approximately 2% abundance) concurrently with a clonal mutation (80% abundance) revealed intratumoral TP53 mutation heterogeneity. The ability to identify and sequence low-level mutations in the absence of elaborate microdissection, via COLD-PCR-based Sanger sequencing, provides a platform for accurate mutation profiling in clinical specimens and the use of TP53 as a prognostic/predictive biomarker, evaluation of cancer risk, recurrence, and further understanding of cancer biology.
Primary Structure of the β Subunit of the DHP-Sensitive Calcium Channel from Skeletal Muscle (1989)

Complementary DNAs for the beta subunit of the dihydropyridine-sensitive calcium channel of rabbit skeletal muscle were isolated on the basis of peptide sequences derived from the purified protein. The deduced primary structure is without homology to other known protein sequences and is consistent with the beta subunit being a peripheral membrane protein associated with the cytoplasmic aspect of the sarcolemma. The protein contains sites that might be expected to be preferentially phosphorylated by protein kinase C and guanosine 3',5'-monophosphate-dependent protein kinase. A messenger RNA for this protein appears to be expressed in brain.
Edoxaban versus Warfarin in Patients with Atrial Fibrillation (2013)

Both once-daily regimens of edoxaban were noninferior to warfarin with respect to the prevention of stroke or systemic embolism and were associated with significantly lower rates of bleeding and death from cardiovascular causes. (Funded by Daiichi Sankyo Pharma Development; ENGAGE AF-TIMI 48 ClinicalTrials.gov number, NCT00781391.).
A Recurrent Chromosome Breakpoint in Breast Cancer at the NRG1 / Neuregulin 1 / Heregulin Gene (2004)

Most studies of genomic rearrangements in common cancers have focused on regional gains and losses, but some rearrangements may break within specific genes. We previously reported that five breast cancer cell lines have chromosome translocations that break in the NRG1 gene and that could cause abnormal NRG1 expression. NRG1 encodes the Neuregulins 1 (formerly the Heregulins), ligands for members of the ErbB/epidermal growth factor-receptor family, which includes ErbB2/HER2. We have now screened for breaks at NRG1 in paraffin sections of breast tumors. Tissue microarrays were screened by fluorescence in situ hybridization, with hybridization probes proximal and distal to the expected breakpoints. This screen detects breaks but does not distinguish between translocation or deletion breakpoints. The screen was validated with array-comparative genomic hybridization on a custom 8p12 high-density genomic array to detect a lower copy number of the sequences that were lost distal to the breaks. We also precisely mapped the breaks in five tumors with different hybridization probes. Breaks in NRG1 were detected in 6% (19 of 323) of breast cancers and in some lung and ovarian cancers. In an unselected series of 213 cases with follow-up, breast cancers where the break was detected tended to be high-grade (65% grade III compared with 28% of negative cases). They were, like breast tumors in general, mainly ErbB2 low (11 of 13 were low) and estrogen receptor positive (11 of 13 positive).
Representation of pre-grasp strategies for object manipulation (2010)

In this paper, we present a method for representing and re-targeting manipulations for object adjustment before final grasping. Such pre-grasp manipulation actions bring objects into better configurations for grasping through e.g. object rotation or object sliding. For this purpose, we propose a scaling-invariant and rotation-invariant representation of the hand poses, which is then automatically adapted to the target object to perform the selected pre-grasp manipulations. We show that pre-grasp strategies such as sliding manipulations not only enable more robust object grasping, but also significantly increase the success rate for grasping.
Characterisation of PV modules of new generations : results of tests and simulations (2000)

The work was carried out under NOVEM contract 146.230-016.1 "Karakterisering PV modules van nieuwe generaties".This report includes only part of the activities of the above-mentioned contract, namely the results
Microbubble ultrasound contrast agents: A review (2003)

The superior scattering properties of gas bubbles compared with blood cells have made microbubble ultrasound contrast agents important tools in ultrasound diagnosis. Over the past 2 years they have become the focus of a wide and rapidly expanding field of research, with their benefits being repeatedly demonstrated, both in ultrasound image enhancement, and more recently in drug and gene delivery applications. However, despite considerable investigation, their behaviour is by no means fully understood and, while no definite evidence of harmful effects has been obtained, there remain some concerns as to their safety. In this review the existing theoretical and experimental evidence is examined in order to clarify the extent to which contrast agents are currently understood and to identify areas for future research. In particular the disparity between the conditions considered in theoretical models and those encountered both in vitro, and more importantly in vivo is discussed, together with the controversy regarding the risk of harmful bio-effects.
The Cell Wall-Associated Kinase (WAK) andWAK-Like Kinase Gene Family (2002)

We have identified a large family of genes with sequence similarity to the cell wall-associated kinase ( WAK ) genes ([He et al., 1999][1]). Like the WAK s, these genes exist in multiple gene clusters, and our analyses suggest that they encode functional protein kinases that are associated with the
Inhibition of FOXC2 restores epithelial phenotype and drug sensitivity in prostate cancer cells with stem-cell properties (2016)

Advanced prostate adenocarcinomas enriched in stem-cell features, as well as variant androgen receptor (AR)-negative neuroendocrine (NE)/small-cell prostate cancers are difficult to treat, and account for up to 30% of prostate cancer-related deaths every year. While existing therapies for prostate cancer such as androgen deprivation therapy (ADT), destroy the bulk of the AR-positive cells within the tumor, eradicating this population eventually leads to castration-resistance, owing to the continued survival of AR<sup>-/lo</sup> stem-like cells. In this study, we identified a critical nexus between p38MAPK signaling, and the transcription factor Forkhead Box Protein C2 (FOXC2) known to promote cancer stem-cells and metastasis. We demonstrate that prostate cancer cells that are insensitive to ADT, as well as high-grade/NE prostate tumors, are characterized by elevated FOXC2, and that targeting FOXC2 using a well-tolerated p38 inhibitor restores epithelial attributes and ADT-sensitivity, and reduces the shedding of circulating tumor cells in vivo with significant shrinkage in the tumor mass. This study thus specifies a tangible mechanism to target the AR<sup>-/lo</sup> population of prostate cancer cells with stem-cell properties.
Site-Specific Incorporation of Fluorescent Probes into Protein:  Hexahistidine-Tag-Mediated Fluorescent Labeling with (Ni2+:Nitrilotriacetic Acid)n−Fluorochrome Conjugates (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSite-Specific Incorporation of Fluorescent Probes into Protein: Hexahistidine-Tag-Mediated Fluorescent Labeling with (Ni2+:Nitrilotriacetic Acid)n−Fluorochrome ConjugatesAchillefs N. Kapanidis, Yon W. Ebright, and Richard H. EbrightView Author Information Howard Hughes Medical Institute, Waksman Institute and Department of Chemistry, Rutgers University Piscataway New Jersey 08854Cite this: J. Am. Chem. Soc. 2001, 123, 48, 12123–12125Publication Date (Web):November 9, 2001Publication History Received13 September 2001Published online9 November 2001Published inissue 1 December 2001https://pubs.acs.org/doi/10.1021/ja017074ahttps://doi.org/10.1021/ja017074arapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views3317Altmetric-Citations171LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information SUBJECTS:Fluorescence,Genetics,Labeling,Peptides and proteins,Titration Get e-Alerts
Nanoporous Anodic Alumina Film on Glass: Improving Transparency by an Ion-Drift Process (2005)

A novel method for increasing the transparency of an anodic aluminum oxide film on glass is demonstrated. The residual aluminum layer, which limits the transparency of the porous aluminum oxide film, was fully converted to its oxide by the ion-drift process. The transmittance of the film was improved more than 20% over the visible-near infrared range and was similar to that of a glass substrate. This ion-drift process also improved the adhesion of the anodic alumina film to the glass substrate. © 2005 The Electrochemical Society. All rights reserved.
Repetitive Transcranial Magnetic Stimulation for Major Depressive Disorder: A Review (2008)

Several studies demonstrated that repetitive transcranial magnetic stimulation (rTMS) is an efficacious treatment for treatment-resistant major depressive disorder (TRD). Recent metaanalyses and more recent large multicentre studies provided evidence suggesting that rTMS is indeed a promising treatment; however, its efficacy has often been shown to be modest, compared with sham stimulation. We review these lines of evidence and discuss several reasons that may explain the modest therapeutic efficacy in most of these studies, including: most involved left-sided treatment alone to the dorsolateral prefrontal cortex (DLPFC) only, which may be less optimal than applying bilateral stimulation; suboptimal methods were used to target the DLPFC (that is, the 5-cm anterior method), limiting the treatment potential of inherently a targeted form of treatment; some treatment durations were short (that is, 2 to 4 weeks); and stimulation intensity might have been insufficient by not considering coil-to-cortex distance, which has been linked to rTMS-induced antidepressant response. Future studies attempting to address the above-mentioned limitations are necessary to potentially optimize the efficacy of this already promising treatment option in TRD. Finally, it is also essential that research investigate the mechanisms of therapeutic efficacy, thus increases in understanding can be translated into enhanced treatment. For several reasons that will be reviewed, cortical excitability may represent an important mechanism, linked to the therapeutic efficacy of this disorder.
Catalytic Activity of Administered Gulonolactone OxidasePolyethylene Glycol Conjugates (1989)

Scurvy in guinea pigs provides a convenient model of inborn metabolic disease for the investigation of enzyme therapy protocols. Gulonolactone oxidase, the enzyme in ascorbic acid biosynthesis that is missing from the scurvy-prone species, was modified by attachment of polyethylene glycol. The catalytic properties of this enzyme were affected little by the modification. Intravenous injection of this modified form of the enzyme elicited ascorbic acid synthesis in a dose-dependent manner. The modified enzyme was stabilized to incubation at 37 degrees C but was not protected from inactivation by trypsin. The circulating half-life of enzyme activity was not prolonged by this modification. Further, attachment of polyethylene glycol did neither abolish the enzyme's ability to react with preformed antibodies nor eliminate its immunogenicity.
Separation distance dependent fluorescence enhancement of fluorescein isothiocyanate by silver nanoparticles (2006)

Nanocomposites consisting of a metal core, a silica-spacer shell with controlled thickness, and a dye-labelled shell were synthesized and separation distance dependent fluorescence enhancement of fluorescein isothiocyanate by silver nanoparticles was studied; the results indicated an optimum enhancement of 4.8 times with a spacer shell thickness of 21 nm.
Aging and senescence of the budding yeast Saccharomyces cerevisiae (1990)

The budding yeast Saccharomyces cerevisiae has a limited life span, defined by the number of times an individual cell divides. Longevity in this organism involves a genetic component. Several morphological and physiological changes are associated with yeast aging and senescence. One of these, an increase in generation time with age, provides a 'biomarker' for the aging process. This increase in generation time has revealed the operation of a 'senescence factor(s)', which is likely to be a product of age-specific gene expression. The Cell Spiral Model indicates coordination of successive cell cycles to be inherent in the determination of life span. It is proposed that life expectancy depends on the function of a stochastic trigger during aging that sets in motion a programme leading to cell senescence and death.