gebhart/patrepeval huggingface dataset:
An insight into the Inhibition of HIV‐1 replication by co‐infecting HHV‐6, HHV‐7 or GVB‐C viruses: Role of Mutually Homologous miRNAs in Downregulation of Viral Replication (2009)

In recent years, several reports have documented a better prognosis for HIV‐1‐infected patients co‐infected with HHV‐6, 7 or GBV‐C who may live three times longer as compared to those without these co‐infections. Recent studies have also identified anti‐viral roles of host miRNAs in plants, worms, mammals and possibly humans. To evaluate whether the apparent beneficial effects of the co‐infecting viruses are due to mutually homologous miRNAs, we computationally analyzed miRNAs that have significant homologies to both HIV‐1 and the co‐infecting viruses. We discovered 50 miRNAs that showed >80% homology to HIV‐1 and among these a significant number also mutually targeted co‐infecting viral genomes. We selected four miRNAs based on a tool that detects C +· GC and T.AT triplets which imparts greater stability between miRNA and HIV‐1 provirus. We synthesized four double‐stranded 20‐21mer, fluorophore‐conjugated oligonucleotides, representing HIV‐1 proviral DNA motifs and four homologous, quencher‐conjugated oligonucleotides representing HIV‐specific TF‐miRNA. Each was confirmed for their ability to form highly stable TF as indicated by melting curve data. Next, we developed stably transfected Hela‐CD4+cell lines expressing each of the miRNAs. Two miRNAs exhibited a significant inhibition of HIV‐1 as measured by HIV‐1p24 ELISA and Real Time PCR (>90%; p>0.001). In this study we provide a possible molecular mechanism by which co‐infecting non‐pathogenic viruses impart resistance to HIV‐1, suggest a new miRNA‐based therapeutic strategy for HIV‐1, and demonstrate the anti HIV‐1 protective effects of certain miRNAs that are mutually homologous to HIV‐1 and human herpes virus 6, HHV‐7 or GBV‐C co‐infecting viruses.
The Molecular Biology of Cystic Fibrosis (1993)

Cystic fibrosis afflicts many children and, as the life expectancy for patients with this disease steadily increases, many adults as well. The identification and characterization of the gene responsible for this disorder provide a basis for understanding the pathophysiology of cystic fibrosis. Basic science advances are rapidly being integrated into the diagnostic and therapeutic regimens used by physicians in the care of patients with this disease.
Influence of camera distortions on satellite image registration and change detection applications (2008)

Applications such as change detection and digital elevation model extraction from optical images require a rigorous modeling of the acquisition geometry. We show that the unrecorded satellite jitter during image acquisition, and the uncertainties on the CCD arrays geometry are the current major limiting factors for applications requiring high accuracy. These artifacts are identified and quantified on several optical satellites, i.e., SPOT, ASTER, QuickBird, and HiRISE.
Group Authentication: A New Paradigm for Emerging Applications (2012)

Traditional secure registration protocols rely on client-server authentication procedures. This concept has been extended to support single client registration to multiple servers, using “single sign-on” protocols. In this paper, we design a framework to solve the “reverse single sign-on” problem: How can multiple clients securely register with the same server/network in a single registration procedure? The main advantage of our framework is that it allows multiple clients to register with an infrastructure, such as a cellular network, as a “group,” yet generate individual session keys as well as a group session key. With this, the process of authenticating a large number of clients is greatly simplified, thereby dramatically reducing overheads. With a view towards simplifying the exposition, we describe how our framework can be applied for performing group authentication of devices in the machine-to-machine context. While this is an immediate area of application, we outline other extensions of the framework in the application layer including webcasting in a social networking environment. © 2012 Alcatel-Lucent.
Design, Synthesis, and Biological Evaluation of Cytotoxic 11-Alkenylindenoisoquinoline Topoisomerase I Inhibitors and Indenoisoquinoline−Camptothecin Hybrids (2003)

The indenoisoquinolines are a novel class of topoisomerase I (top1) inhibitors that are cytotoxic in cancer cell cultures and are therefore under development as potential anticancer agents. As inhibitors of the DNA religation reaction occurring after DNA cleavage by the enzyme, they are classified as top1 poisons, similar to the camptothecins. Two strategies were employed in order to further develop the structure-activity relationships of the indenoisoquinolines and enhance their therapeutic potential. The first strategy involved the synthesis of indenoisoquinoline-camptothecin hybrid molecules to take advantage of a proposed structural analogy between the indenoisoquinolines and camptothecin. The desired hybrids were synthesized by reaction of halogenated phthalides with a dihydropyrroloquinoline. The second strategy involved the attachment of various alkenyl substituents to the C-11 position of the indenoisoquinolines, which were assumed to project into the DNA minor groove. The required C-11-substituted indenoisoquinolines were synthesized by McMurry reactions of 11-ketoindenoisoquinolines with aldehydes, and the geometries of the resulting alkenes were established by nuclear Overhauser effect difference NMR spectroscopy. All of the new indenoisoquinolines were examined for cytotoxicity in human cancer cell cultures as well as for activity vs top1. Although the indenoisoquinoline-camptothecin hybrid molecules proved to be less cytotoxic and displayed less activity against top1, an analogue incorporating a 3'-aminoalkenyl substituent at the C-11 position of the indenoisoquinoline system was significantly more potent than the prototype indenoisoquinoline in both assays. These results indicate that C-11 aminoalkyl substituents that are assumed to project into the minor groove enhance the cytotoxicity and top1 inhibitory activity of the parent indenoisoquinoline system.
Comparative in vivo and ex vivo pacing and sensing performance study using isolated four-chamber working swine heart model (2002)

A study was conducted comparing the pacing and sensing performance of an endocardial pacing lead (5076, Medtronic, Inc., Minneapolis, MN) in vivo to an ex vivo isolated heart model designed to work all four chambers under simulated in vivo physiologic conditions. The lead was implanted in vivo using fluoroscopic guidance. Standard stimulation and sensing parameters were recorded. Using standard cardiac surgical techniques, 8 porcine hearts were excised and reperfused in a working heart model retaining their original lead placement. Following stabilization, the electrical measurements were repeated. Ex vivo electrical values were significantly decreased relative to the in vivo measurements: R-wave amplitude by 39%, P-wave amplitude by 39%, slew rate by 62%, and pacing impedance by 34%. Pacing threshold values were similar in vivo and ex vivo. Variations in performance were in part attributed to local tissue deformation in the isolated heart preparation leading to differences in lead slack and orientation. This comparative study substantiated the value of utilizing the isolated heart model to visualize and simultaneously evaluate lead pacing and sensing performance in comparison with in vivo experimental procedures.
Que Sera Consensus: Simple Asynchronous Agreement with Private Coins and Threshold Logical Clocks (2020)

It is commonly held that asynchronous consensus is much more complex, difficult, and costly than partially-synchronous algorithms, especially without using common coins. This paper challenges that conventional wisdom with que sera consensus QSC, an approach to consensus that cleanly decomposes the agreement problem from that of network asynchrony. QSC uses only private coins and reaches consensus in $O(1)$ expected communication rounds. It relies on "lock-step" synchronous broadcast, but can run atop a threshold logical clock (TLC) algorithm to time and pace partially-reliable communication atop an underlying asynchronous network. This combination is arguably simpler than partially-synchronous consensus approaches like (Multi-)Paxos or Raft with leader election, and is more robust to slow leaders or targeted network denial-of-service attacks. The simplest formulations of QSC atop TLC incur expected $O(n^2)$ messages and $O(n^4)$ bits per agreement, or $O(n^3)$ bits with straightforward optimizations. An on-demand implementation, in which clients act as "natural leaders" to execute the protocol atop stateful servers that merely implement passive key-value stores, can achieve $O(n^2)$ expected communication bits per client-driven agreement.
High Levels of Bioplastic Are Produced in Fertile Transplastomic Tobacco Plants Engineered with a Synthetic Operon for the Production of Polyhydroxybutyrate (2011)

An optimized genetic construct for plastid transformation of tobacco (Nicotiana tabacum) for the production of the renewable, biodegradable plastic polyhydroxybutyrate (PHB) was designed using an operon extension strategy. Bacterial genes encoding the PHB pathway enzymes were selected for use in this construct based on their similarity to the codon usage and GC content of the tobacco plastome. Regulatory elements with limited homology to the host plastome yet known to yield high levels of plastidial recombinant protein production were used to enhance the expression of the transgenes. A partial transcriptional unit, containing genes of the PHB pathway and a selectable marker gene encoding spectinomycin resistance, was flanked at the 5' end by the host plant's psbA coding sequence and at the 3' end by the host plant's 3' psbA untranslated region. This design allowed insertion of the transgenes into the plastome as an extension of the psbA operon, rendering the addition of a promoter to drive the expression of the transgenes unnecessary. Transformation of the optimized construct into tobacco and subsequent spectinomycin selection of transgenic plants yielded T0 plants that were capable of producing up to 18.8% dry weight PHB in samples of leaf tissue. These plants were fertile and produced viable seed. T1 plants producing up to 17.3% dry weight PHB in samples of leaf tissue and 8.8% dry weight PHB in the total biomass of the plant were also isolated.
Characterization of the sequences of the human CYP19 (aromatase) gene that mediate regulation by glucocorticoids in adipose stromal cells and fetal hepatocytes. (1995)

The biosynthesis of estrogens is catalyzed by aromatase P450 (P450arom), the product of the CYP19 gene. The tissue-specific expression of the CYP19 gene is regulated by means of tissue-specific promoters through the use of alternative splicing mechanisms. Thus, transcripts containing various 5'-untranslated termini are present in human placenta and other fetal tissues, ovary, brain, and adipose stromal cells. Sequence corresponding to untranslated exon 1.4 is present in 5'-termini of transcripts expressed in adipose tissue and fetal liver, as well as adipose stromal cells in primary culture in the presence of dexamethasone and fetal calf serum (FCS). Identification of hormone-responsive, tissue-specific promoter regions, as well as growth factor-response elements upstream of exon 1.4, may provide insight into the regulation of estrogen biosynthesis in adipose tissue, which is implicated in the development of breast and endometrial cancer. The goals of the present study were to define the 1.4 promoter region with respect to the start of transcription and to characterize the region(s) responsible for conferring glucocorticoid responsiveness on aromatase expression. The transcription initiation site was identified by means of primer extension and S1 nuclease protection analyses. No TATA-like sequence was evident upstream of this site. Various deletion mutations of the upstream flanking region of exon 1.4 and including part of exon 1.4 were made using polymerase chain reaction or restriction enzyme digestion. The genomic fragments were fused upstream of the chloramphenicol acetyltransferase (CAT) reporter gene. These constructs were transfected into adipose stromal cells and fetal hepatocytes in primary culture in medium containing FCS with or without dexamethasone. The -560/+10 base pair (bp) construct expressed CAT activity after a putative silencer element was deleted, and expression was induced by dexamethasone about 3-fold. Transfection of the -330/+170 bp construct, which contains an upstream glucocorticoid response element (GRE) as well as an Sp1-like sequence in untranslated exon 1.4, resulted in an 8-fold stimulation of expression of CAT activity by dexamethasone. The upstream GRE as well as the Sp1-like sequence in untranslated exon 1.4 were mutated separately, and together, to further confirm whether the GRE or Sp1 binding site play a role in the regulation of promoter 1.4-driven transcription. Mutation of either the GRE or Sp1 binding site, or both, in the -330/+170 bp construct, resulted in loss of dexamethasone-induced CAT reporter gene expression.(ABSTRACT TRUNCATED AT 400 WORDS)
Measurement of surface shear stress vectors using liquid crystal coatings (1994)

Under normal white light illumination and oblique observation, liquid crystal coating (LCC) color-change response to shear depends on both shear stress magnitude as well as the direction of the applied shear relative to the observer's line of sight. These color-change responses were quantified by subjecting a LCC to a wall-jet shear flow and measuring scattered-light spectra using a fiber optic probe and spectrophotometer. At any fixed shear stress magnitude, the maximum color change was measured when the shear vector was aligned with and directed away from the observer; changes in the relative in-plane view angle to either side of this vector/observer aligned position resulted in symmetric Gaussian reductions in measured color change. Based on these results, a surface shear stress vector measurement methodology, involving multiple oblique-view observations of the test surface, was formulated. Under present test conditions, the measurement resolution of this technique was found to be ±1 deg for vector orientations and ±5% for vector magnitudes. An approach to extend the present methodology to full-surface applications is proposed. Nomenclature Cf = skin friction coefficient D = jet exit diameter / = spectral scattering intensity N = number of data points used in curve fits or in datareduction technique V = velocity W = white light X, Y = chromaticity coordinates a = above-plane view angle, measured positive upward from zero in plane of test surface
Helix Stabilized, Thermostable, and Protease-Resistant Self-Assembled Peptide Nanostructures as Potential Inhibitors of Protein–Protein Interactions (2013)

Self-assembled peptide nanostructures with actively folded secondary structures have potential to mimic the function of proteins. We here show that α-helix-stabilized self-assembled peptide nanostructures (αSSPNs), whose sizes are comparable to those of proteins, have potential to be developed as protein-protein interaction (PPI) inhibitors along with several unprecedented properties. Using p53-MDM2 PPI as a model system, the molecular recognition and modulation of PPIs by αSSPN grafted with a p53 α-helix (p53 αSSPN) were investigated. The competition assay showed that the p53 αSSPN can inhibit the p53-MDM2 interaction. Interestingly, the p53 αSSPN was far more resistant to degradation by the protease chymotrypsin than the monomeric p53 peptide and had high thermal stability. These results suggest that the αSSPN scaffold holds great potential to be developed as a novel class of PPI inhibitors.
Metasurfaces for polarization sensing and imaging (Conference Presentation) (2019)

Metasurfaces, nanophotonic arrays of subwavelength phase shifting elements, hold promise for the miniaturization of a variety of bulk optical elements. Owing to the flexibility with which their constituent elements may be engineered, metasurfaces allow for point-to-point polarization control on a subwavelength scale. Metasurfaces, then, represent an exciting new platform for polarization optics. A single metasurface may combine many different polarization-dependent functionalities that would ordinarily be spread out over many optical elements. We describe how, through relatively simple optimization methods, a metasurface producing arbitrarily specified polarization states can be designed. This functionality is equivalent to a traditional diffraction grating with individual waveplate optics on each order; here, all the necessary polarization optics can be integrated into a flat, efficient, and ultrathin metasurface optical element. Moreover, such a metasurface can be used in a reverse configuration as a parallel snapshot polarimeter with no need for additional polarization optics. We present a detailed experimental characterization of this device in the visible spectral region and a comparison of the performance of the metasurface to a commercially available rotating waveplate polarimeter. Metasurfaces can enable compact, miniaturized sensors for polarimetry and polarization imaging. We will conclude with a perspective on these possibilities and their implications for remote sensing. Metasurface polarization optics can overcome limitations of previous diffractive/grating based polarimetry schemes are potentially of significant interest to the imaging polarimetry community.
Shift-variant digital holographic microscopy: inaccuracies in quantitative phase imaging (2013)

Inaccuracies introduced in quantitative phase digital holographic microscopy by the use of nontelecentric imaging systems are analyzed. Computer modeling of the experimental result shows that even negligible errors in the radius and center of curvature of the numerical compensation needed to get rid of the remaining quadratic phase factor introduce errors in the phase measurements; these errors depend on the position of the object in the field-of-view. However, when a telecentric imaging system is utilized for the recording of the holograms, the numerical modeling and experimental results show the shift-invariant behavior of the quantitative-phase digital holographic microscope.
PIDISC: pattern independent design independent seed compression technique (2006)

A novel scheme for compressing the seeds of a linear feedback shifter register (LFSR) is presented. Instead of storing the seeds of the LFSR in the tester, the scheme compresses the seeds and stores them in the tester. The compression scheme can be used with any variation of static LFSR reseeding. An important feature of the proposed scheme is that the decompressor is test pattern and design independent and can be implemented with very little area overhead. Experimental results show that seed compression can improve overall compression by a factor of 7/spl times/ for large industrial circuits.
Active CMOS Sensor Array for Electrochemical Biomolecular Detection (2008)

Electrochemical sensing of biomolecules eliminates the need for the bulky and expensive optical instrumentation required in traditional fluorescence-based sensing assays. Integration of the sensor interface electrodes and active electrochemical detection circuitry on a CMOS substrate miniaturizes the sensing platform, enhancing its portability for use in point-of-care applications, while enabling the high-throughput, highly parallel analysis characteristic of traditional microarrays. This paper describes the design of a four-by-four active sensor array for multiplexed electrochemical biomolecular detection in a standard 0.25-mum CMOS process. Integrated potentiostats, comprised of control amplifiers and dual-slope analog-to-digital converters, stimulate the electrochemical cell and detect the current flowing through the on-chip gold electrodes at each sensor site that results from biomolecular reactions occurring on the chip surface. Post-processing steps needed to fabricate a biologically-compatible surface-electrode array in CMOS that can withstand operation in a harsh electrochemical environment are also described. Experimental results demonstrating the proper operation of the active CMOS array for biomolecular detection include cyclic voltammetry of a reversible redox species, DNA probe density characterization, as well as quantitative and specific DNA hybridization detection.
Fat‐Specific Protein 27 Regulation of Vascular Function in Human Obesity (2019)

Background Pathophysiological mechanisms that connect obesity to cardiovascular disease are incompletely understood. FSP27 (Fat-specific protein 27) is a lipid droplet-associated protein that regulates lipolysis and insulin sensitivity in adipocytes. We unexpectedly discovered extensive FSP27 expression in human endothelial cells that is downregulated in association with visceral obesity. We sought to examine the functional role of FSP27 in the control of vascular phenotype. Methods and Results We biopsied paired subcutaneous and visceral fat depots from 61 obese individuals (body mass index 44±8 kg/m<sup>2</sup>, age 48±4 years) during planned bariatric surgery. We characterized depot-specific FSP27 expression in relation to adipose tissue microvascular insulin resistance, endothelial function and angiogenesis, and examined differential effects of FSP27 modification on vascular function. We observed markedly reduced vasodilator and angiogenic capacity of microvessels isolated from the visceral compared with subcutaneous adipose depots. Recombinant FSP27 and/or adenoviral FSP27 overexpression in human tissue increased endothelial nitric oxide synthase phosphorylation and nitric oxide production, and rescued vasomotor and angiogenic dysfunction (P<0.05), while siRNA-mediated FSP27 knockdown had opposite effects. Mechanistically, we observed that FSP27 interacts with vascular endothelial growth factor-A and exerts robust regulatory control over its expression. Lastly, in a subset of subjects followed longitudinally for 12±3 months after their bariatric surgery, 30% weight loss improved metabolic parameters and increased angiogenic capacity that correlated positively with increased FSP27 expression (r=0.79, P<0.05). Conclusions Our data strongly support a key role and functional significance of FSP27 as a critical endogenous modulator of human microvascular function that has not been previously described. FSP27 may serve as a previously unrecognized regulator of arteriolar vasomotor capacity and angiogenesis which are pivotal in the pathogenesis of cardiometabolic diseases linked to obesity.
A small derivative of the broad-host-range plasmid RK2 which can be switched from a replicating to a non-replicating state as a response to an externally added inducer (1999)

TrfA is the only plasmid-encoded protein required for RK2 replication. We report here the construction and characterization of an RK2-based vector in which trfA is expressed from the inducible promoter Pm. The resulting construct, pJBSD1, was found to replicate in Escherichia coli DH5a (recA(-)) only in the presence of a Pm inducer. In two tested E. coli recA(+) strains pJBSD1 could replicate in the absence of inducer, but a replication inducer-dependent phenotype was obtained in these strains by introducing a mutation known to reduce the trfA expression level. The plasmid construct could be used as a conditional suicide vector system for targeted chromosomal integration via homologous recombination. This feature may potentially be used for many types of studies in microbial molecular biology.
High efficiency resonant cavity microwave optical modulator (1985)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text N. H. Tran, T. F. Gallagher, J. P. Watjen, G. R. Janik, and C. B. Carlisle, "High efficiency resonant cavity microwave optical modulator," Appl. Opt. 24, 4282-4284 (1985) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article