gebhart/patrepeval huggingface dataset:
Burn-in failures and local region yield: an integrated field-reliability model (2002)

Defects have long been known to cluster on semiconductor wafers. Recent research has shown that this fact may be exploited to produce die of high reliability, (i.e. decreased infant mortality), by sorting die into bins based on how many of their neighbors test faulty. Die that test good at wafer probe, yet come from neighborhoods with many faulty die, have a higher incidence of infant mortality failure than die from neighborhoods with few faulty die. Analysis of burn-in results from the SEMATECH test methods experiment suggests that such a binning approach has the potential to isolate a high quality bin that displays very few burn-in failures. This paper presents the first analytical model that quantifies the reliability improvement one might expect when binning die based on local region yield.
Molecular targeting of renal inflammation using drug delivery technology to inhibit NF-κB improves renal recovery in chronic kidney disease (2020)

Inflammation is a major determinant for the progression of chronic kidney disease (CKD). NF-κB is a master transcription factor upregulated in CKD that promotes inflammation and regulates apoptosis and vascular remodeling. We aimed to modulate this pathway for CKD therapy in a swine model of CKD using a peptide inhibitor of the NF-κB p50 subunit (p50i) fused to a protein carrier [elastin-like polypeptide (ELP)] and equipped with a cell-penetrating peptide (SynB1). We hypothesized that intrarenal SynB1-ELP-p50i therapy would inhibit NF-κB-driven inflammation and induce renal recovery. CKD was induced in 14 pigs. After 6 wk, pigs received single intrarenal SynB1-ELP-p50i therapy (10 mg/kg) or placebo (<i>n</i> = 7 each). Renal hemodynamics were quantified in vivo using multidetector computed tomography before and 8 wk after treatment. Pigs were then euthanized. Ex vivo experiments were performed to quantify renal activation of NF-κB, expression of downstream mediators of NF-κB signaling, renal microvascular density, inflammation, and fibrosis. Fourteen weeks of CKD stimulated NF-κB signaling and downstream mediators (e.g., TNF-α, monocyte chemoattractant protein-1, and IL-6) accompanying loss of renal function, inflammation, fibrosis, and microvascular rarefaction versus controls. All of these were improved after SynB1-ELP-p50i therapy, accompanied by reduced circulating inflammatory cytokines as well, which were evident up to 8 wk after treatment. Current treatments for CKD are largely ineffective. Our study shows the feasibility of a new treatment to induce renal recovery by offsetting inflammation at a molecular level. It also supports the therapeutic potential of targeted inhibition of the NF-κB pathway using novel drug delivery technology in a translational model of CKD.
Deep-Learning-Based Optimization of the Under-Sampling Pattern in MRI (2020)

In compressed sensing MRI (CS-MRI), k-space measurements are under-sampled to achieve accelerated scan times. CS-MRI presents two fundamental problems: (1) where to sample and (2) how to reconstruct an under-sampled scan. In this article, we tackle both problems simultaneously for the specific case of 2D Cartesian sampling, using a novel end-to-end learning framework that we call LOUPE (Learning-based Optimization of the Under-sampling PattErn). Our method trains a neural network model on a set of full-resolution MRI scans, which are retrospectively under-sampled on a 2D Cartesian grid and forwarded to an anti-aliasing (a.k.a. reconstruction) model that computes a reconstruction, which is in turn compared with the input. This formulation enables a data-driven optimized under-sampling pattern at a given sparsity level. In our experiments, we demonstrate that LOUPE-optimized under-sampling masks are data-dependent, varying significantly with the imaged anatomy, and perform well with different reconstruction methods. We present empirical results obtained with a large-scale, publicly available knee MRI dataset, where LOUPE offered superior reconstruction quality across different conditions. Even with an aggressive 8-fold acceleration rate, LOUPE's reconstructions contained much of the anatomical detail that was missed by alternative masks and reconstruction methods. Our experiments also show how LOUPE yielded optimal under-sampling patterns that were significantly different for brain vs knee MRI scans. Our code is made freely available at https://github.com/cagladbahadir/LOUPE/.
A Versatile Photocleavable Bifunctional Linker for Facile Synthesis of Substrate−DNA Conjugates for the Selection of Nucleic Acid Catalysts (2006)

Covalent photocleavable attachment of small molecules or peptides to oligonucleotides is an integral strategic element in the selection of novel nucleic acid enzymes. Here, we report the synthesis of a multipurpose, photocleavable bifunctional linker (PCBL) suitable for nucleic acid selections and other biotechnology applications. PCBL contains a photocleavable O-nitrobenzyl group flanked on one side by an N-hydroxysuccinimidyl ester (reactive toward primary amines) and on the other side by a sulfhydryl. To demonstrate the utility of PCBL, the linker was used to couple an analog of the antibiotic chloramphenicol (Cam) to the 5' end of an amino-modified 8-mer DNA oligo. Coupling was confirmed by MALDI-TOF spectrophotometry. Decoupling was performed by irradiating the coupled species with near-UV light (approximately 360 nm), regenerating the original amino-modified oligo. Ligation of the Cam-PCBL-DNA conjugate to random-sequence RNA generated a diversity library appropriate for the selection of new ribozymes that catalyze reactions involving the tethered substrate. Coupling and decoupling of the Cam analog from the library was monitored on a trilayered organomercurial polyacrylamide gel. The coupling/decoupling strategy described here is readily generalized to many combinations of macromolecules and small molecules. For example, analogs of this small molecule-DNA conjugate can be generated as synthons for ligation to nucleic acid diversity libraries during each round of novel ribozyme selections, or they can be immobilized onto chips for addresssably reversible microarray analysis.
Observation of Individual DNA Molecules Undergoing Gel Electrophoresis (1989)

Individual DNA molecules undergoing agarose gel electrophoresis were viewed with the aid of a fluorescence microscope. Molecular shape and orientation were studied in both steady and pulsed electric fields. It was observed that (i) DNA macromolecules advanced lengthwise through the gel in an extended configuration, (ii) the molecules alternately contracted and lengthened as they moved, (iii) the molecules often became hooked around obstacles in a U-shape for extended periods, and (iv) the molecules displayed elasticity as they extended from both ends at once. A computer model has been developed that simulates the migration of the molecules in a rotating-field gel electrophoresis experiment.
Imaging the Liver (2004)

Imaging of the liver is undertaken for the detection and characterization of suspected primary or secondary neoplasms, prior to planning a surgery or chemotherapy pump placement, for assessing treatment response, for evaluating biliary pathology, and for screening for liver neoplasms in high-risk groups. In this article, we review the advantages and disadvantages of various imaging modalities in the evaluation of the liver and formulate guidelines for the imaging of common clinical indications. A brief review of imaging findings in focal and diffuse liver disease is also presented.
Distamycin A, a minor groove binder, changes enediyne-induced DNA cleavage sites and enhances apoptosis (2002)

We examined the effects of a minor groove binder, distamycin A, on DNA cleavage and apoptosis induced by an enediyne antitumor antibiotic, C1027, using 32P-labeled DNA fragments obtained from human genes. C1027 alone induced DNA cleavage particularly at the 5'-TTTT-3'/3'-AAAA-5' sequence (cutting sites are underlined). The addition of distamycin A enhanced the double-strand DNA cleavage at the 5'-CCT-3'/3'-GGA-5' and 5'-CCA-3'/3'-GGT-5' sequences, with a two-nucleotide 3'-stagger of the cleaved residues. These results suggest that distamycin A forms a heterodimer with C1027 to bind to DNA at GC-rich regions, resulting in amplification of DNA cleavage at these regions. Distamycin A enhanced C1027-induced DNA ladder formation and cytotoxicity in HL-60 cells. Therefore, amplification of DNA cleavage at GC-rich regions may result in enhancement of apoptosis. The present study on amplifiers of antitumor agents showed a novel approach to the potentially effective antitumor therapy.
An ICE‐like protease is a common mediator of apoptosis induced by diverse stimuli in human monocytic THP.1 cells (1995)

Apoptosis was induced in THP.1 cells, a human monocytic tumour cell line, by diverse stimuli including cycloheximide, thapsigargin, etoposide and staurosporine. Induction of apoptosis by all these stimuli, except etoposide, was enhanced in the presence of the trypsin-like protease inhibitor, N alpha-tosyl-L-lysinyl chloromethyl ketone (TLCK). Induction of apoptosis, assessed by morphological, flow cytometric and biochemical criteria, including proteolysis of poly(ADP-ribose) polymerase and cleavage of DNA to large kilobasepair fragments, was completely abrogated when cells were pretreated with an ICE-like protease inhibitor, Z-Val-Ala-Asp.fluoromethylketone. This suggested that an ICE homologue was a common mediator of apoptosis in THP.1 cells.
THE KINETICS OF FORMATION OF NATIVE RIBONUCLEASE DURING OXIDATION OF THE REDUCED POLYPEPTIDE CHAIN (1961)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
A 4.5 MGy TID-Tolerant CMOS Bandgap Reference Circuit Using a Dynamic Base Leakage Compensation Technique (2013)

The total-ionizing-dose (TID) radiation tolerance of bandgap references in deep-submicron CMOS technology is generally limited by the radiation introduced leakage current in diodes. An analysis of this phenomenon is given in this paper, and a dynamic base leakage compensation (DBLC) technique is proposed to improve the radiation hardness of a bandgap reference built in a standard 0.13 μm CMOS technology. A temperature coefficient of 15 ppm/ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">°</sup> C from -40 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">°</sup> C to 125 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">°</sup> C is measured before irradiation. The voltage variation from 0 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">°</sup> C to 100 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">°</sup> C is only ±1 mV for an output voltage of 600 mV. Gamma irradiation assessment proves that the bandgap reference is tolerant to a total ionizing dose of at least 4.5 MGy. The output reference voltage exhibits a variation of less than 3% during the entire experiment, when the chip is irradiated by gamma ray at a dose rate of 27 kGy/h.
Write off-loading (2008)

In enterprise data centers power usage is a problem impacting server density and the total cost of ownership. Storage uses a significant fraction of the power budget and there are no widely deployed power-saving solutions for enterprise storage systems. The traditional view is that enterprise workloads make spinning disks down ineffective because idle periods are too short. We analyzed block-level traces from 36 volumes in an enterprise data center for one week and concluded that significant idle periods exist, and that they can be further increased by modifying the read/write patterns using write off-loading . Write off-loading allows write requests on spun-down disks to be temporarily redirected to persistent storage elsewhere in the data center. The key challenge is doing this transparently and efficiently at the block level, without sacrificing consistency or failure resilience. We describe our write off-loading design and implementation that achieves these goals. We evaluate it by replaying portions of our traces on a rack-based testbed. Results show that just spinning disks down when idle saves 28--36% of energy, and write off-loading further increases the savings to 45--60%.
Vascular normalizing doses of antiangiogenic treatment reprogram the immunosuppressive tumor microenvironment and enhance immunotherapy (2012)

The recent approval of a prostate cancer vaccine has renewed hope for anticancer immunotherapies. However, the immunosuppressive tumor microenvironment may limit the effectiveness of current immunotherapies. Antiangiogenic agents have the potential to modulate the tumor microenvironment and improve immunotherapy, but they often are used at high doses in the clinic to prune tumor vessels and paradoxically may compromise various therapies. Here, we demonstrate that targeting tumor vasculature with lower vascular-normalizing doses, but not high antivascular/antiangiogenic doses, of an anti-VEGF receptor 2 (VEGFR2) antibody results in a more homogeneous distribution of functional tumor vessels. Furthermore, lower doses are superior to the high doses in polarizing tumor-associated macrophages from an immune inhibitory M2-like phenotype toward an immune stimulatory M1-like phenotype and in facilitating CD4(+) and CD8(+) T-cell tumor infiltration. Based on this mechanism, scheduling lower-dose anti-VEGFR2 therapy with T-cell activation induced by a whole cancer cell vaccine therapy enhanced anticancer efficacy in a CD8(+) T-cell-dependent manner in both immune-tolerant and immunogenic murine breast cancer models. These findings indicate that vascular-normalizing lower doses of anti-VEGFR2 antibody can reprogram the tumor microenvironment away from immunosuppression toward potentiation of cancer vaccine therapies. Given that the combinations of high doses of bevacizumab with chemotherapy have not improved overall survival of breast cancer patients, our study suggests a strategy to use antiangiogenic agents in breast cancer more effectively with active immunotherapy and potentially other anticancer therapies.
Characterization of adenosine receptors in bone. Studies on the effect of adenosine analogues on cyclic AMP formation and bone resorption in cultured mouse calvaria (1987)

The effect of different adenosine analogues on cyclic AMP (cAMP) formation and bone resorption in cultured mouse calvarial bones was investigated. 5'-N-ethylcarboxamidoadenosine (NECA), R-N6-phenylisopropyl-adenosine (PIA), N6-cyclohexyl-adenosine (CHA) and 2-chloroadenosine all stimulated cyclic AMP formation with a threshold close to 1 mumol l-1); NECA was the most potent agonist. Theophylline (10, 100 mumol l-1) inhibited the cAMP accumulation induced by NECA and 2-chloroadenosine (30 and 300 mumol l-1), dose dependently. There was no inhibition of cAMP formation by PIA and CHA in forskolin-treated bone tissue. SQ 22, 536 and 2',5'-dideoxyadenosine (100 mumol l-1) both inhibited rolipram-stimulated cAMP formation. Cyclic AMP accumulation in isolated osteoblast-like cells from neonatal mouse calvarial bones was stimulated by NECA (10 and 100 mumol l-1) and 2-chloroadenosine (100 mumol l-1). 2-chloroadenosine (10 and 30 mumol l-1), but not NECA, PIA nor CHA, caused a dose-dependent stimulation of 45Ca release in both 48- and 120-h culture. The effect of 2-chloroadenosine on 45Ca release could not be antagonized by theophylline. Neither NECA, PIA, CHA nor 2-chloroadenosine could affect PTH-stimulated 45Ca release in short term cultures (6, 24 h). By contrast, stimulation of cAMP formation by forskolin or dibutyryl cAMP caused a rapid (6 h) inhibition of PTH-stimulated bone resorption. The results demonstrate functional A2 and P-site receptors in mouse calvaria and osteoblast-like cells, but no A1-receptor was detected. These adenosine receptors regulate cAMP, but are not intimately linked to bone resorption. The calcium mobilization induced by 2-chloroadenosine appears to be unrelated to adenosine receptors.
Finite element method-simulation of the human lens during accommodation (2005)

A finite-element-method model with ANSYS 8.0 of a 29 year old human lens during accommodation will be presented. The required data, to draw and calculate a two dimensional, axis-symmetric model of the human lens is inherited from various sources. Furthermore the analysis premises all lens materials to be linear elastic and allows large displacements. A first analysis of a possible method for the treatment of presbyopia by fs-laser induced microcuts is accomplished. Therefore a mechanical analysis of an untreated and a treated lens are compared. As a result an improvement of the flexibility of the lens tissue is found and as its consequence a change of the lens' radii of curvature is established. After a suitable processing of the output data a linear Gaussian ray trace is performed and a minor change in the optical power between the untreated and treaded human lens is perceived. By calculation of the discrete optical power of the anterior and posterior surface on the one hand and the overall optical power on the other hand an interpretation of the effectiveness resulting from the treatment is offered. It is ascertained that the change in optical power of the anterior lens surface is increased while the optical power of the posterior lens surface is decreased, almost compensating each other. A possible explanation for this phenomenon is given and a suggestion of how to increase the effectiveness of the treatment is discussed.
A novel CD18 genomic deletion in a patient with severe leucocyte adhesion deficiency: a possible CD2/lymphocyte function‐associated antigen‐1 functional association in humans (2000)

Leucocyte adhesion deficiency (LAD) is an autosomal-recessive genetic disease that is characterized clinically by severe bacterial infections and caused by mutations in the CD18 gene that codes for the beta2 integrin subunit. A patient with a severe LAD phenotype was studied and the molecular basis of the disease was identified as a single homozygous defect in a Herpes virus saimiri (HVS)-transformed T-cell line. The defect identified involves a deletion of 171 bp in the cDNA that encodes part of the proteic extracellular domain. This genetic abnormality was further studied at the genomic DNA level and found to consist of a deletion of 169 bp (from -37 of intron 4 to +132 of exon 5), which abolishes the normal splicing and results in the total skipping of exon 5. The 171-bp shortened 'in-frame' mRNA not only resulted in the absence of CD18 expression on the cell surface but also in its absence in the cytoplasm of HVS T-cell lines. Functionally, the LAD-derived HVS T-cell lines showed a severe, selective T-cell activation impairment in the CD2 (but not in the CD3) pathway. This defect was not reversible when exogenous interleukin-2 (IL-2) was added, suggesting that there is also a functional interaction of the lymphocyte function-associated antigen-1 (LFA-1) protein in the CD2 signal transduction pathway in human T cells, as has been previously reported in mice and in the human Papillon-Lefèvre syndrome. Thus, HVS transformation is not only a suitable model for T-cell immunodeficiency studies and characterization, but is also a good system for investigating the immune system in pathological conditions. It may also be used in the future in cellular models for in vitro gene-therapy trials.
The Fas Signaling Pathway: More Than a Paradigm (2002)

Apoptosis and related forms of cell death have central importance in development, homeostasis, tumor surveillance, and the function of the immune system. Apoptosis is initiated by two principal pathways. The intrinsic pathway emerges from mitochondria, whereas the extrinsic pathway is activated by the ligation of death receptors. This Viewpoint introduces the basic mechanisms of the extrinsic pathway, using the example of the prototypical death receptor Fas and its role in apoptosis, but it also points out the increasingly understood importance of this receptor as a non-apoptotic signal transducer.
Effects of carbon‐nanotube doping on the performance of a TN‐LCD (2005)

Abstract— The electro‐optical characteristics of a 90° twisted‐nematic liquid‐crystal display (TN‐LCD) were analyzed. The test cell was composed of a minute amount of dopant, multiwalled carbon nanotubes, and a standard nematic mixture, E7, used in TN‐LCDs with direct addressing. Under the experimental conditions, no hystereses in optical transmittance were observed in either the doped cell or a neat counterpart under an applied ac voltage. Experimental results show that doping with nanotubes rectifies the electro‐optical properties of the cells by reducing the driving voltage as well as the rise time. Similar results were found in a TN cell of a TFT‐grade liquid crystal instead of the mixture consisting completely of polar compounds.
Assembly of Phenylacetylene-Bridged Silver and Gold Nanoparticle Arrays (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTAssembly of Phenylacetylene-Bridged Silver and Gold Nanoparticle ArraysJames P. Novak and Daniel L. FeldheimView Author Information Department of Chemistry, North Carolina State University Raleigh, North Carolina 27695 Cite this: J. Am. Chem. Soc. 2000, 122, 16, 3979–3980Publication Date (Web):April 8, 2000Publication History Received8 February 2000Published online8 April 2000Published inissue 1 April 2000https://pubs.acs.org/doi/10.1021/ja000477ahttps://doi.org/10.1021/ja000477arapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views2264Altmetric-Citations181LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Gold,Metal nanoparticles,Nanoparticles,Oligomers,Silver Get e-Alerts