gebhart/patrepeval huggingface dataset:
Ionic Permeability and Mechanical Properties of DNA Origami Nanoplates on Solid-State Nanopores (2013)

While DNA origami is a popular and versatile platform, its structural properties are still poorly understood. In this study we use solid-state nanopores to investigate the ionic permeability and mechanical properties of DNA origami nanoplates. DNA origami nanoplates of various designs are docked onto solid-state nanopores where we subsequently measure their ionic conductance. The ionic permeability is found to be high for all origami nanoplates. We observe the conductance of docked nanoplates, relative to the bare nanopore conductance, to increase as a function of pore diameter, as well as to increase upon lowering the ionic strength. The honeycomb lattice nanoplate is found to have slightly better overall performance over other plate designs. After docking, we often observe spontaneous discrete jumps in the current, a process which can be attributed to mechanical buckling. All nanoplates show a nonlinear current-voltage dependence with a lower conductance at higher applied voltages, which we attribute to a physical bending deformation of the nanoplates under the applied force. At sufficiently high voltage (force), the nanoplates are strongly deformed and can be pulled through the nanopore. These data show that DNA origami nanoplates are typically very permeable to ions and exhibit a number of unexpected mechanical properties, which are interesting in their own right, but also need to be considered in the future design of DNA origami nanostructures.
Tolerance to iotrolan after subarachnoid injection in animals. (1989)

Neural tolerance after intracisternal administration of iotrolan was compared with that after iohexol, iopamidol, and metrizamide in mice, rats, and guinea pigs. Around the level of the ED50 (approximately two to four times the human dose) tolerance to iotrolan appeared to be much better than tolerance to the other agents. A study in rabbits comparing iotrolan with iohexol produced approximately the same result. High doses of iotrolan, iohexol, and iopamidol were almost equally well tolerated by rats, as were iotrolan and iohexol by rabbits. Tolerance to metrizamide by rats and to iopamidol by guinea pigs was vastly inferior. In support of this very good general tolerance histologic examinations of the spinal tract and of the brain did not reveal any substance-related changes in beagles after lumbar administration of a high dose. An investigation in rats using mannitol and sorbitol formulations with differing osmotic pressures indicates that contrast tolerance is influenced primarily by the chemotoxicity and not by increased osmotic pressure. As shown by the results of the preclinical investigations, iotrolan should be ideal for use in myelography and also appears highly suitable for the examination of other body cavities.
AN EVALUATION OF DOPPLER ULTRASOUND AND PHOTOPLETHYSMOGRAPHY IN THE INVESTIGATION OF VENOUS INSUFFICIENCY (1992)

Non-invasive methods of venous assessment have been developed to improve diagnostic accuracy in the assessment of venous insufficiency. Of these, continuous wave Doppler (CWD) ultrasound and photoplethysmography are the cheapest and most simple to perform. In this study duplex scanning was used to test the accuracy of these two methods. One hundred and thirty-six patients attending the venous outpatient clinic at Middlesex Hospital, London were examined by all three techniques and a diagnosis was reached using each technique. The technicians performing the examinations were unaware of the diagnoses reached by the other methods. Continuous wave Doppler ultrasound was found to be most accurate in the diagnosis of long saphenous incompetence (sensitivity 73%, specificity 85%). Due to the variability of venous anatomy at the popliteal fossa and the 'blindness' of the technique, it was inaccurate in the diagnosis of short saphenous incompetence (sensitivity 33%) and deep vein reflux (sensitivity 48%). Photoplethysmography was found to be most accurate in the diagnosis of deep vein reflux (sensitivity 79%, specificity 70%) but was inaccurate in identification of the site of superficial vein reflux. Inaccuracies may be attributed to the presence of incompetent perforating veins and variation in arterial inflow.
Probabilistic Posture Classification for Human-Behavior Analysis (2004)

Computer vision and ubiquitous multimedia access nowadays make feasible the development of a mostly automated system for human-behavior analysis. In this context, our proposal is to analyze human behaviors by classifying the posture of the monitored person and, consequently, detecting corresponding events and alarm situations, like a fall. To this aim, our approach can be divided in two phases: for each frame, the projection histograms (Haritaoglu et al., 1998) of each person are computed and compared with the probabilistic projection maps stored for each posture during the training phase; then, the obtained posture is further validated exploiting the information extracted by a tracking module in order to take into account the reliability of the classification of the first phase. Moreover, the tracking algorithm is used to handle occlusions, making the system particularly robust even in indoors environments. Extensive experimental results demonstrate a promising average accuracy of more than 95% in correctly classifying human postures, even in the case of challenging conditions.
Learning mid-level features for recognition (2010)

Many successful models for scene or object recognition transform low-level descriptors (such as Gabor filter responses, or SIFT descriptors) into richer representations of intermediate complexity. This process can often be broken down into two steps: (1) a coding step, which performs a pointwise transformation of the descriptors into a representation better adapted to the task, and (2) a pooling step, which summarizes the coded features over larger neighborhoods. Several combinations of coding and pooling schemes have been proposed in the literature. The goal of this paper is threefold. We seek to establish the relative importance of each step of mid-level feature extraction through a comprehensive cross evaluation of several types of coding modules (hard and soft vector quantization, sparse coding) and pooling schemes (by taking the average, or the maximum), which obtains state-of-the-art performance or better on several recognition benchmarks. We show how to improve the best performing coding scheme by learning a supervised discriminative dictionary for sparse coding. We provide theoretical and empirical insight into the remarkable performance of max pooling. By teasing apart components shared by modern mid-level feature extractors, our approach aims to facilitate the design of better recognition architectures.
Quantitative Proteomic Analysis of the Metastasis-Inhibitory Mechanism of miR-193a-3p in Non-Small Cell Lung Cancer (2015)

miR-193a-3p inhibited the metastasis of lung cancer cells by deregulating the expression of tumor-related proteins. These findings may improve the understanding of the molecular mechanisms underlying the metastatic-inhibitory effect of miR-193a-3p on lung cancer cells.
Synthesis and biological activity of C-3' ortho dihydroxyphthalimido cephalosporins. (1993)

A series of C-3' ortho dihydroxyphthalimido cephalosporins 3-7 has been prepared by reaction of C-3' aminomethyl cephalosporin 41 with the corresponding N-carboethoxyphthalimides 23-25, 37, 38. These new cephalosporins exhibit excellent in vitro Gram-negative activities, including Pseudomonas aeruginosa, excellent beta-lactamases stability and pharmacokinetics equivalent or better than ceftriaxone.
A case example of human factors in product definition: needs finding for a voice output workstation for the blind (1986)

Human factors efforts can contribute to product design at every design phase from conception through evaluation of a product in the field. Early human factors involvement has certain advantages. The major advantage is that it can have greater “leverage” by influencing more far-reaching aspects of a product. Input at later design phases, on the other hand, may delay product schedules or require a major re-design effort. Input at earlier stages can diminish these problems. As a case example, a needs finding study for a voice output workstation for the blind is described. Users of these workstations participated in a semi-structured interview to determine their needs. Results identified specific features needed. The findings also indicated that the original scope of the project, word processing, should be broadened to include other applications.
An inexpensive and simple method for DNA purifications on silica particles (1993)

Journal Article An inexpensive and simple method for DNA purifications on silica particles Get access M. J. Carter, M. J. Carter Department of Virology, The Medical School, University of Newcastle upon TyneNE2 4HH, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar I. D. Milton I. D. Milton Department of Virology, The Medical School, University of Newcastle upon TyneNE2 4HH, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 21, Issue 4, 25 February 1993, Page 1044, https://doi.org/10.1093/nar/21.4.1044 Published: 25 February 1993 Article history Received: 11 January 1993 Accepted: 11 January 1993 Published: 25 February 1993
Chemistry and biology of khafrefungin. Large-scale synthesis, design, and structure–activity relationship of khafrefungin, an antifungal agent (2003)

Large-scale synthesis, design, and structure-activity relationships of khafrefungin are reported. Khafrefungin is an antifungal agent that inhibits inositol phosphorylceramide (IPC) synthase, an enzyme involved in fungal sphingolipid biosynthesis. Unlike other inhibitors that inhibit the corresponding enzyme in fungi and mammals to the same extent, khafrefungin does not impair sphingolipid synthesis in mammals. We have developed an efficient method for large-scale synthesis of khafrefungin, and various khafrefungin derivatives were synthesized based on this method. While most of the khafrefungin derivatives lost antifungal activity, a lactone-type derivative had almost the same activity as khafrefungin. We also designed and synthesized derivatives which contain a five- or six-membered ring at the central part of the structure based on NOE experiments of khafrefungin. A macrocyclic khafrefungin derivative was also synthesized, but the antifungal activity was lost. These results suggest that the structure of khafrefungin might be strictly recognized in fungi.
[Study on enzyme-assisted extraction of polysaccharides from Dioscorea opposita]. (2008)

To carry out an enzyme treatment before ultrasound--assisted extraction elevated the yield of polysaccharides.
GATA4 Mutations in 357 Unrelated Patients with Congenital Heart Malformation (2010)

Congenital heart disease (CHD) represents one of the most common birth defects, but the genetic causes remain largely unknown. Mutations in GATA4, encoding a zinc finger transcription factor with a pivotal role in heart development, have been associated with CHD in several familial cases and a small subset of sporadic patients. To estimate the pathogenetic role of GATA4 in CHD, we screened for mutations in 357 unrelated patients with different congenital heart malformations. In addition to nine synonymous changes, we identified two known (A411V and D425N) and two novel putative mutations (G69D and P163R) in five patients with atrial or ventricular septal defects that were not seen in control subjects. The four mutations did not show altered GATA4 transcriptional activity in synergy with the transcription factors NKX2-5 and TBX20. Our data expand the spectrum of mutations associated with cardiac septal defects but do not support GATA4 mutations as a common cause of CHD.
Bovine CNS Myelin Contains Neurite Growth-Inhibitory Activity Associated with Chondroitin Sulfate Proteoglycans (1999)

The absence of fiber regrowth in the injured mammalian CNS is influenced by several different factors and mechanisms. Besides the nonconducive properties of the glial scar tissue that forms around the lesion site, individual molecules present in CNS myelin and expressed by oligodendrocytes, such as NI-35/NI-250, bNI-220, and myelin-associated glycoprotein (MAG), have been isolated and shown to inhibit axonal growth. Here, we report an additional neurite growth-inhibitory activity purified from bovine spinal cord myelin that is not related to bNI-220 or MAG. This activity can be ascribed to the presence of two chondroitin sulfate proteoglycans (CSPGs), brevican and the brain-specific versican V2 splice variant. Neurite outgrowth of neonatal cerebellar granule cells and of dorsal root ganglion neurons in vitro was strongly inhibited by this myelin fraction enriched in CSPGs. Immunohistochemical staining revealed that brevican and versican V2 are present on the surfaces of differentiated oligodendrocytes. We provide evidence that treatment of oligodendrocytes with the proteoglycan synthesis inhibitors beta-xylosides can strongly influence the growth permissiveness of oligodendrocytes. beta-Xylosides abolished cell surface presentation of brevican and versican V2 and reversed growth cone collapse in encounters with oligodendrocytes as demonstrated by time-lapse video microscopy. Instead, growth cones were able to grow along or even into the processes of oligodendrocytes. Our results strongly suggest that brevican and versican V2 are additional components of CNS myelin that contribute to its nonpermissive substrate properties for axonal growth. Expression of these CSPGs on oligodendrocytes may indicate that they participate in the restriction of structural plasticity and regeneration in the adult CNS.
Drosophila melanogaster as an Animal Model for the Study of Pseudomonas aeruginosa Biofilm Infections In Vivo (2011)

Pseudomonas aeruginosa is an opportunistic pathogen capable of causing both acute and chronic infections in susceptible hosts. Chronic P. aeruginosa infections are thought to be caused by bacterial biofilms. Biofilms are highly structured, multicellular, microbial communities encased in an extracellular matrix that enable long-term survival in the host. The aim of this research was to develop an animal model that would allow an in vivo study of P. aeruginosa biofilm infections in a Drosophila melanogaster host. At 24 h post oral infection of Drosophila, P. aeruginosa biofilms localized to and were visualized in dissected Drosophila crops. These biofilms had a characteristic aggregate structure and an extracellular matrix composed of DNA and exopolysaccharide. P. aeruginosa cells recovered from in vivo grown biofilms had increased antibiotic resistance relative to planktonically grown cells. In vivo, biofilm formation was dependent on expression of the pel exopolysaccharide genes, as a pelB::lux mutant failed to form biofilms. The pelB::lux mutant was significantly more virulent than PAO1, while a hyperbiofilm strain (PAZHI3) demonstrated significantly less virulence than PAO1, as indicated by survival of infected flies at day 14 postinfection. Biofilm formation, by strains PAO1 and PAZHI3, in the crop was associated with induction of diptericin, cecropin A1 and drosomycin antimicrobial peptide gene expression 24 h postinfection. In contrast, infection with the non-biofilm forming strain pelB::lux resulted in decreased AMP gene expression in the fly. In summary, these results provide novel insights into host-pathogen interactions during P. aeruginosa oral infection of Drosophila and highlight the use of Drosophila as an infection model that permits the study of P. aeruginosa biofilms in vivo.
Identification of HLA DR7-restricted epitopes from human telomerase reverse transcriptase recognized by CD4+ T-helper cells. (2002)

CD4+ T cells play critical roles in initiating, regulating, and maintaining antitumor immune responses. One way to improve current tumor vaccines that mainly induce CTLs would be to activate antigen-specific CD4+ T cells that recognize MHC class II restricted tumor associated antigens. Human telomerase reverse transcriptase (hTRT) is preferentially expressed by various tumors and, therefore, could be a universal tumor antigen. In this study, we used a combined approach of using the prediction software TEPITOPE to select class II epitope candidates and in vitro T-cell biological analysis to identify class II-restricted epitope(s) in hTRT. We first identified several HLA-DR7-restricted class-II epitope candidates in hTRT by examining human T-cell responses to synthetic peptides. We then characterized these HLA-DR7-restricted hTRT epitope candidates by establishing and analyzing peptide-specific T-cell clones. It was demonstrated that CD4+ T cells specific for the HLA-DR7-restricted hTRT(672) epitope (RPGLLGASVLGLDDI) can respond to naturally processed hTRT proteins. Furthermore, the hTRT(672)-specific T cells recognized hTRT antigen from various tumors, including prostate cancer, breast cancer, melanoma, and leukemia. Thus, the identification of the naturally processed HLA-DR7-restricted hTRT epitope, together with the previous finding of class I-restricted hTRT epitopes, provide a basis for the combined application of class I- and II-restricted hTRT epitopes to induce potent, long-term CD4+ and CD8+ T-cell responses against a broad spectrum of tumors.
Medical Therapy Can Improve the Biological Properties of the Chronically Failing Heart (1996)

Abstract Myocardial failure has been considered to be an irreversible and progressive process characterized by ventricular enlargement, chamber geometric alterations, and diminished pump performance. However, more recent evidence has suggested that certain types of medical therapy may lead to retardation and even reversal of the cardiomyopathic process. In the failing heart, long-term neurohormonal/autocrine-paracrine activation results in abnormalities in myocyte growth, energy production and utilization, calcium flux, and receptor regulation that produce a progressively dysfunctional, mechanically inefficient heart. Interventions such as ACE inhibition and β-blockade result in a reduction in the harmful long-term consequences of neurohormonal/autocrine-paracrine effects and retard the progression of left ventricular dysfunction or ventricular remodeling. Furthermore, in subjects with idiopathic dilated or ischemic cardiomyopathy, antiadrenergic therapy with β-blocking agents appears to be able to partially reverse systolic dysfunction and ventricular remodeling. Although the precise mechanisms underlying this latter effect have not yet been elucidated, the general mechanism appears to be via improvement in the biological function of the cardiac myocyte. Such an improvement in the intrinsic defect(s) responsible for myocardial failure will likely translate into important clinical benefits.
A Novel in Vitro Replication System for Dengue Virus (1999)

Positive strand viral replicases are membrane-bound complexes of viral and host proteins. The mechanism of viral replication and the role of host proteins are not well understood. To understand this mechanism, a viral replicase assay that utilizes extracts from dengue virus-infected mosquito (C6/36) cells and exogenous viral RNA templates is reported in this study. The 5'- and 3'-terminal regions (TR) of the template RNAs contain the conserved elements including the complementary (cyclization) motifs and stem-loop structures. RNA synthesis in vitro requires both 5'- and 3'-TR present in the same template molecule or when the 5'-TR RNA was added in trans to the 3'-untranslated region (UTR) RNA. However, the 3'-UTR RNA alone is not active. RNA synthesis occurs by elongation of the 3'-end of the template RNA to yield predominantly a double-stranded hairpin-like RNA product, twice the size of the template RNA. These results suggest that an interaction between 5'- and 3'-TR of the viral RNA that modulates the 3'-UTR RNA structure is required for RNA synthesis by the viral replicase. The complementary cyclization motifs of the viral genome also seem to play an important role in this interaction.
Monolayer transformation by nucleophilic substitution: Applications to the creation of new monolayer assemblies (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMonolayer transformation by nucleophilic substitution: Applications to the creation of new monolayer assembliesNatarajan Balachander and Chaim N. SukenikCite this: Langmuir 1990, 6, 11, 1621–1627Publication Date (Print):November 1, 1990Publication History Published online1 May 2002Published inissue 1 November 1990https://pubs.acs.org/doi/10.1021/la00101a001https://doi.org/10.1021/la00101a001research-articleACS PublicationsRequest reuse permissionsArticle Views2066Altmetric-Citations304LEARN 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
Use of Magnetic Beads for Plasma Cell-free DNA Extraction: Toward Automation of Plasma DNA Analysis for Molecular Diagnostics (2003)

Urine, breast milk, plasma, and serum have been shown to contain cell-free DNA (1)(2)(3)(4)(5)(6)(7). For plasma DNA detection, several recent studies addressed the need for careful evaluation and standardization of preanalytical processes (8)(9)(10)(11)(12). Key problems appear, such as possible contamination of plasma by white blood cells; the generally low and variable amount of circulating DNA, making extraction/quantification difficult and time-consuming; poor DNA quality; and the presence of PCR inhibitors. In any case, automation of DNA extraction, which is a prerequisite for introduction of these diagnostic approaches in clinical laboratories, is difficult to achieve because of the volumes of plasma necessary to get sufficient DNA.

In this study (summarized in Fig. 1⇓ ), we propose a new semiautomated, time-saving process for extraction of plasma cell-free DNA that provides high yields and is suitable for PCR amplification.

Two 5-mL blood samples from each of 23 patients being monitored for lung (n = 19) or colon cancer (n = 4) and 20 healthy controls were collected in EDTA-containing tubes. Informed consent was obtained for each. Blood was centrifuged at 800 g for 10 min, and the collected plasma was transferred to a 15-mL BD FalconTM polypropylene tube for an additional centrifugation step of 10 min at 1500 g to remove any remaining leukocytes and platelets. An equal volume of 2× concentrated proteolytic buffer (2×: 20 mmol/L Tris-HCl, 50 mmol/L EDTA, 200 mmol/L NaCl, 10 g/L sodium dodecyl sulfate, and 400 mg/L proteinase K) was added to the plasma, mixed, and incubated 1 h at 37 °C. After digestion, plasma samples were concentrated by centrifugation at room temperature (to avoid sodium dodecyl sulfate precipitation) for 20 min at 2600 g in Amicon …