gebhart/patrepeval huggingface dataset:
Coordinated Regulation of Iron-Controlling Genes, H-Ferritin and IRP2 , by c-MYC (1999)

The protein encoded by the c-MYC proto-oncogene is a transcription factor that can both activate and repress the expression of target genes, but few of its transcriptional targets have been identified. Here, c-MYC is shown to repress the expression of the heavy subunit of the protein ferritin (H-ferritin), which sequesters intracellular iron, and to stimulate the expression of the iron regulatory protein-2 (IRP2), which increases the intracellular iron pool. Down-regulation of the expression of H-ferritin gene was required for cell transformation by c-MYC. These results indicate that c-MYC coordinately regulates genes controlling intracellular iron concentrations and that this function is essential for the control of cell proliferation and transformation by c-MYC.
Emerging Design Principles in Biomaterials and Scaffolds for Tissue Engineering (2002)

Biomaterials and scaffolds play an essential role in tissue engineering by guiding new tissue growth in vivo and in vitro. While adaptation of existing surgical materials has fulfilled some needs in the field, new applications demand better control of bulk properties such as degradation and of surface properties that control cell interactions. Advances in molecular cell biology are driving the incorporation of new biological moieties into materials, and a set of design principles based on quantitative analysis of key cellular processes involved in regeneration is emerging. At the same time, new materials-processing methodologies are emerging to allow fabrication of these fragile materials into devices appropriate for delivery.
Intraperitoneal α-Particle Radioimmunotherapy of Ovarian Cancer Patients: Pharmacokinetics and Dosimetry of 211At-MX35 F(ab′)2—A Phase I Study (2009)

This study indicates that by intraperitoneal administration of (211)At-MX35 F(ab')(2) it is possible to achieve therapeutic absorbed doses in microscopic tumor clusters without significant toxicity.
A zero-placement technique for designing shaped inputs to suppress multiple-mode vibration (2005)

The performance of many flexible systems can be improved by employing command shaping techniques to reduce machine vibration. The input shaping technique, in particular, has proven to be highly effective for a wide class of systems. Due to the mathematical complexity of higher-order problems, multiple-mode input shapers can be tricky to derive and difficult to understand. This paper proposes a new approach for deriving input shapers using zero-placement in the discrete domain. The flexibility and simplicity inherent in this formulation provide many options for maximizing shaper performance.
Continuous dielectrophoretic bacterial separation and concentration from physiological media of high conductivity (2011)

Biological sample processing involves purifying target analytes from various sample matrices and concentrating them to a small volume from a large volume of crude sample. This complex process is the major obstacle for developing a microfluidic diagnostic platform. In this study, we present a microfluidic device that can continuously separate and concentrate pathogenic bacterial cells from complex sample matrices such as cerebrospinal fluid and whole blood. Having overcome critical limitations of dielectrophoretic (DEP) operation in physiological media of high conductivity, we utilized target specific DEP techniques to incorporate cell separation, medium exchange, and target concentration into an integrated platform. The proposed microfluidic device can uptake mL volumes of crude biological sample and selectively concentrate target cells into a submicrolitre volume, providing ~10(4) fold of concentration. We designed the device based on the electrokinetic theory and electric field simulation, and tested the device performance with different sample types. The separation efficiency of the device was as high as 97.0% for a bead mixture in TAE buffer and 94.3% and 87.2% for E. coli in human cerebrospinal fluid and blood, respectively. A capture efficiency of 100% was achieved in the concentration chamber. With a relatively simple configuration, the proposed device provides a robust method of continuous sample processing, which can be readily integrated into a fully automated microfluidic diagnostic platform for pathogen detection and quantification.
National Academy of Clinical Biochemistry Laboratory Medicine Practice Guidelines: Follow-Up Testing for Metabolic Disease Identified by Expanded Newborn Screening Using Tandem Mass Spectrometry; Executive Summary (2009)

Guidelines are provided for optimal follow-up testing for positive newborn screens using tandem mass spectrometry. The committee regards these tests as reliable and currently optimal for follow-up testing. .
Phenotypes of hypofrontality in older female fragile X premutation carriers (2013)

The neuropsychological testing and ERP results of the present study provide support for the hypothesis that executive dysfunction is the primary cognitive impairment among older female premutation carriers both with and without FXTAS, although these deficits are relatively mild compared to those in FXTAS males. These findings are consistent with a synergistic effect of the premutation and aging on cognitive impairment among older female fragile X premutation carriers, even in those without FXTAS symptoms.
MUC16 contributes to the metastasis of pancreatic ductal adenocarcinoma through focal adhesion mediated signaling mechanism (2016)

MUC16, a heavily glycosylated type-I transmembrane mucin is overexpressed in several cancers including pancreatic ductal adenocarcinoma (PDAC). Previously, we have shown that MUC16 is significantly overexpressed in human PDAC tissues. However, the functional consequences and its role in PDAC is poorly understood. Here, we show that MUC16 knockdown decreases PDAC cell proliferation, colony formation and migration in vitro. Also, MUC16 knockdown decreases the tumor formation and metastasis in orthotopic xenograft mouse model. Mechanistically, immunoprecipitation and immunofluorescence analyses confirms MUC16 interaction with galectin-3 and mesothelin in PDAC cells. Adhesion assay displayed decreased cell attachment of MUC16 knockdown cells with recombinant galectin-1 and galectin-3 protein. Further, CRISPR/Cas9-mediated MUC16 knockout cells show decreased tumor-associated carbohydrate antigens (T and Tn) in PDAC cells. Importantly, carbohydrate antigens were decreased in the region that corresponds to MUC16 and suggests for the decreased MUC16-galectin interactions. Co-immunoprecipitation also revealed a novel interaction between MUC16 and FAK in PDAC cells. Interestingly, we observed decreased expression of mesenchymal and increased expression of epithelial markers in MUC16-silenced cells. Additionally, MUC16 loss showed a decreased FAK-mediated Akt and ERK/MAPK activation. Altogether, these findings suggest that MUC16-focal adhesion signaling may play a critical role in facilitating PDAC growth and metastasis.
Cytokine and Ig‐production by CG‐containing sequences with phosphorodiester backbone and dumbbell‐shape (2005)

Our data show an inhibition of IgE production but also enhancement of the inflammatory cytokine response in PBMC from allergic and nonallergic donors by covalently-closed PO-based dSLIM-30L1 with a pattern similar to that of linear PS-based lin-30L1, while avoiding PS-modifications and thus PS-mediated side-effects. Whether such molecules are useful for the treatment of allergic diseases will need further clarification by appropriate in vivo studies.
Effects of neonatal seizures on subsequent seizure-induced brain injury (1999)

Neonatal seizures increase the susceptibility of the developing brain to subsequent seizure-induced injury.
Fidelity of Enzymatic Ligation for DNA Computing (2000)

We describe a convenient assay for rapid qualitative evaluation of hybridization/ligation fidelity. The approach uses randomized probe strands of DNA and restriction enzyme digestion after amplification of reaction products by the polymerase chain reaction (PCR). We report ligation efficiencies and fidelities of two DNA ligases, T4 DNA ligase and Thermus aquaticus (Taq) DNA ligase, over a range of temperatures.
Exact voxel occupancy with graph cuts (2002)

Voxel occupancy is one approach for reconstructing the 3-dimensional shape of an object from multiple views. In voxel occupancy, the task is to produce a binary labeling of a set of voxels, that determines which voxels are filled and which are empty. In this paper, we give an energy minimization formulation of the voxel occupancy problem. The global minimum of this energy can be rapidly computed with a single graph cut, using a result due to D. Greig et al. (1989). The energy function we minimize contains a data term and a smoothness term. The data term is a sum over the individual voxels, where the penalty for a voxel is based on the observed intensities of the pixels that intersect it. The smoothness term is the number of empty voxels adjacent to filled ones. Our formulation can be viewed as a generalization of silhouette intersection, with two advantages: we do not compute silhouettes, which are a major source of errors; and we can naturally incorporate spatial smoothness. We give experimental results showing reconstructions from both real and synthetic imagery. Reconstruction using this smoothed energy function is not much more time consuming than simple silhouette intersection; it takes about 10 seconds to reconstruct a one million voxel volume.
Identification of sex-specific transcripts of theAnopheles gambiae doublesexgene (2005)

The understanding of the molecular mechanisms of sex differentiation in the mosquito Anopheles gambiae could identify important candidate genes for inducing selective male sterility in transgenic lines or for sex-controlled expression of lethal genes. In many insects, doublesex (dsx) is the double-switch gene at the bottom of the somatic sex-determination cascade that determines the differentiation of sexually dimorphic traits. We report here on the identification of the dsx homologue in A. gambiae and on the characterization of its sex-specific transcripts. Agdsx consists of seven exons, distributed over an 85 kb region on chromosome 2R, which are sex-specifically spliced to produce the female and male AgdsxF and AgdsxM transcripts. AgdsxF contains a 795 bp ORF, coding for a protein of 265 amino acids, while AgdsxM comprises a much longer (1866 bp) ORF, coding for a 622 aa protein. Differences in the exon/intron organization suggest that Agdsx sex-specific splicing results from a different mechanism from Drosophila melanogaster dsx. These findings represent an important step towards the understanding of sex differentiation in Anopheles and will facilitate the use of gene transfer technologies to manipulate sex ratios for vector control programs based on the sterile insect technique.
Similarity of Lateralized Rhythmic Delta Activity to Periodic Lateralized Epileptiform Discharges in Critically Ill Patients (2013)

Lateralized rhythmic delta activity in critically ill patients has a similar clinical significance as lateralized periodic discharges. It reflects the presence of a focal lesion and is associated with a high risk of acute seizures, especially nonconvulsive.
Inducers of Interferon and Host Resistance VI. Antiviral Efficacy of Poly I:C in Animal Models (1969)

SummaryStudies were conducted in mice and chicks to measure the prophylactic and therapeutic efficacy of poly I:C in a variety of infections by both DNA and RNA viruses. Drug and virus were given by a variety of routes in a number of different regimens including variable drug and virus dosage. Marked prophylactic protection was obtained against PVM, Columbia SK, vaccinia, and parainfluenza 1 virus infections in mice. Poly I:C was therapeutic against PVM infection in mice when given as late as 3 days after infection and the duration of protective effect induced by poly I:C persisted for almost 7 days in the PVM system. Weak responses were noted against rabies, influenza B, and Rous sarcoma viruses, while the responses to influenza A, yellow fever, and Marek's agent were negative. The highly complex relationships between virus and drug administration will necessitate further study before optimal prophylactic and therapeutic regimens can be developed.The authors are indebted to Carolyn Saydah, Carol Bonoma, Kersti Young, Mary Ellen Davies, and John N. Armstrong, Jr. for technical assistance in these studies.
Formation of high mass carbon cluster ions from laser ablation of polymers and thin carbon films (1990)

Three materials were studied by laser ablation/Fourier transform mass spectrometry, using 266 nm laser radiation: a copolymer of ethylene and tetrafluoroethylene (ETFE), polyphenylene sulfide (PPS), and a diamond-like carbon film (DLC). In each case, positive ion mass spectra exhibit primarily even-numbered, high mass carbon clusters (‘‘fullerenes’’) of the type previously reported for graphite ablation. In the case of ETFE, a large C+60 peak (‘‘buckminsterfullerene’’) was observed. The polymer spectra showed a strong dependence on the number of laser pulses on one spot and the laser power density. For ETFE, the fullerene ion relative intensity first increases and then decreases as a function of the number of laser pulses. For the DLC film, fullerenes are observed with a single laser pulse on a fresh spot of the sample. The results are interpreted in terms of a gas phase growth model for the fullerene ion formation.
DNMT3A mutations in acute myeloid leukemia: stability during disease evolution and clinical implications (2011)

DNMT3A mutations are associated with poor prognosis in acute myeloid leukemia (AML), but the stability of this mutation during the clinical course remains unclear. In the present study of 500 patients with de novo AML, DNMT3A mutations were identified in 14% of total patients and in 22.9% of AML patients with normal karyotype. DNMT3A mutations were positively associated with older age, higher WBC and platelet counts, intermediate-risk and normal cytogenetics, FLT3 internal tandem duplication, and NPM1, PTPN11, and IDH2 mutations, but were negatively associated with CEBPA mutations. Multivariate analysis demonstrated that the DNMT3A mutation was an independent poor prognostic factor for overall survival and relapse-free survival in total patients and also in normokaryotype group. A scoring system incorporating the DNMT3A mutation and 8 other prognostic factors, including age, WBC count, cytogenetics, and gene mutations, into survival analysis was very useful in stratifying AML patients into different prognostic groups (P < .001). Sequential study of 138 patients during the clinical course showed that DNMT3A mutations were stable during AML evolution. In conclusion, DNMT3A mutations are associated with distinct clinical and biologic features and poor prognosis in de novo AML patients. Furthermore, the DNMT3A mutation may be a potential biomarker for monitoring of minimal residual disease.
16×16 Non-blocking Silicon Electro-optic Switch Based on Mach-Zehnder Interferometers (2016)

A non-blocking 16×16 silicon electro-optic switch based on Benes network was demonstrated. The extinction ratios of the switch are 20.2~29.8 dB. It consists of 56 MZI switch units, whose switching time are 1 nanosecond.
Water Wetting Transition Parameters of Perfluorinated Substrates with Periodically Distributed Flat-Top Microscale Obstacles (2007)

Superhydrophobicity is obtained on photolithographically structured silicon surfaces consisting of flat-top pillars after a perfluorosilanization treatment. Systematic static contact angle measurements were carried out on these surfaces as a function of pillar parameters that geometrically determine the surface roughness, including pillar height, diameter, top perimeter, overall filling factor, and disposition. In line with thermodynamics models, two regimes of static contact angles are observed varying each parameter independently: the "Cassie" regime, in which the water drop sits suspended on top of the pillars (referred to as composite), corresponding to experimental contact angles greater than 140-150 degrees, and the "Wenzel" regime, in which water completely wets the asperities (referred to as wetted), corresponding to lower experimental contact angles. A transition between the Cassie and Wenzel regimes corresponds to a set of well-defined parameters. By smoothly depositing water drops on the surfaces, this transition is observed for surface parameter values far from the calculated ones for the thermodynamic transition, therefore offering evidence for the existence of metastable composite states. For all studied parameters, the position of the experimental transition correlates well with a rough estimation of the energy barrier to be overcome from a composite metastable state in order to reach the thermodynamically favored Wenzel state. This energy barrier is estimated as the surface energy variation between the Cassie state and the hypothetical composite state with complete filling of the surface asperities by water, keeping the contact angle constant.
Marginal zone macrophages identified by a monoclonal antibody: characterization of immuno- and enzyme-histochemical properties and functional capacities. (1985)

In the present study, the non-lymphoid cell of the marginal zone is described: the marginal zone macrophage, identified by a monoclonal antibody, ERTR9. The characteristics of these cells were investigated by use of a two-step immunoperoxidase method (on light and ultrastructural level) in combination with enzyme-cytochemical techniques and functional tests. The marginal zone macrophage appears to be a large cell with close contacts between its cell processes and surrounding marginal zone B cells, and with a well-developed phagocytic capacity. These ERTR9-positive macrophages are capable of selective uptake and retention of i.v. injected FITC-Ficoll and are negative for Ia antigen as well as for the macrophage-related F4/80 antigen. By these characteristics, they constitute a subpopulation of non-lymphoid cells of spleen unique for the marginal zone.
Potentiation by aminopeptidase P of blood pressure response to bradykinin (1995)

We examined whether a specific aminopeptidase P (APP) inhibitor, apstatin, increases vasodepressor responses to bradykinin in anaesthetized rats, and whether it would augment blood pressure responses further after treatment with the angiotensin-converting enzyme inhibitor (ACEi), lisinopril. Apstatin doubled the maximum blood pressure response to bradykinin. The area under the curve (AUC), which incorporates both peak blood pressure changes and duration of response, was doubled in apstatin-treated rats vs controls and in the apstatin+lisinopril group vs lisinopril alone. These data demonstrate that APP is an important kinase in vivo.
Ionic Liquids (2007)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTIonic LiquidsRobin D. Rogers and Gregory A. VothView Author Information The Queenʼs University of Belfast/The University of Alabama and University of UtahCite this: Acc. Chem. Res. 20072007, 40, 11, 1077–1078Publication Date (Web):November 20, 2007Publication History Published online20 November 2007Published inissue 20 November 2007https://doi.org/10.1021/ar700221nCopyright © 2007 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views5664Altmetric-Citations233LEARN 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 InReddit PDF (70 KB) Get e-AlertsSUBJECTS:Ions,Liquids,Mixtures,Salts,Solvents Get e-Alerts
Entrapment of Flaxseed Oil Within Gelatin‐Gum Arabic Capsules (2010)

Abstract The aim of this study was to optimize the encapsulation of flaxseed oil within a gelatin‐gum Arabic (GA) matrix via complex coacervation. The effect of homogenization rates (3,000–15,000 rpm) and total biopolymer concentrations (1–2% w/v) on emulsion efficiency was studied in order to optimize the wall matrix. The physicochemical properties of the dried powder, and the capsule's ability to inhibit oxidation during storage were assessed. As homogenization rates increased from 3,000 to 9,000 rpm, the structure of the capsule transitioned from a spherical mononuclear‐type to irregular‐shaped multinuclear capsules. The size of the capsules and amount of non‐encapsulated oil was found to increase as the total biopolymer concentration was raised from 1 to 2% (w/v). Subsequently, gelatin‐GA capsules were produced with a 1:1 core‐to‐wall ratio at a total biopolymer concentration of 2% (w/v) and at a homogenization rate of 9,000 rpm. Formed capsules had an encapsulation efficiency of 84% and showed a protective effect against the production of primary and secondary oxidative products versus non‐encapsulated oil during 25 days of room temperature storage.
Manufacture of photonics components with a deep UV laser source at 255nm (2001)

Fiber bragg gratings (FBG) are manufactured by inducing a periodic refractive index change and are used for DWDM, gain flattening and frequency locking telecoms components. The frequency doubled copper vapor laser is a high power deep-UV (255nm) source capable of efficiently inducing the required photorefractive index change for the manufacture of FGBs. The writing of FBGs with the frequency doubled copper vapor laser has been demonstrated in a wide range of optical fiber materials, with high growth rates and high reflectivity gratings. Growth rates as high as 60 dB in 2 seconds have been seen in boron/germanium/hydrogen doped silica fibers and typical growth rates for hydrogen doped standard telecom fiber of 10 dB in 30 seconds. The high average power (up to 1000 mW), high repetition rate (6 kHz), low pulse energy (&amp;lt;0.2 mJ) and long coherence length (40 mm), of the UV copper vapor laser make it highly suited to the manufacture of a range of photonics components. These include the production of Bragg gratings in both optical fibers and planar waveguides and the trimming of optical circuits. This paper will report typical growth rates and grating profiles that can be achieved using this source.
Heparan Sulfate 6-O-Sulfotransferase Is Essential for Muscle Development in Zebrafish (2003)

Heparan sulfate proteoglycans function in development and disease. They consist of a core protein with attached heparan sulfate chains that are altered by a series of carbohydrate-modifying enzymes and sulfotransferases. Here, we report on the identification and characterization of a gene encoding zebrafish heparan sulfate 6-O-sulfotransferase (hs6st) that shows high homology to other heparan sulfate 6-O-sulfotransferases. When expressed as a fusion protein in cultured cells, the protein shows specific 6-O-sulfotransferase activity and preferentially acts on the iduronosyl N-sulfoglycosamine. In the developing embryo, hs6st is expressed in the brain, the somites, and the fins; the same structures that were affected upon morpholino-mediated functional knockdown. Morpholino injections significantly inhibited 6-O- but not 2-O-sulfation as assessed by HPLC. Morphants display disturbed somite specification independent of the somite oscillator mechanism and have impaired muscle differentiation. In conclusion, our results show that transfer of sulfate to specific positions on glycosaminoglycans is essential for muscle development.