gebhart/patrepeval huggingface dataset:
A Novel Function of RNAs Arising From the Long Terminal Repeat of Human Endogenous Retrovirus 9 in Cell Cycle Arrest (2012)

The human genome contains approximately 50 copies of the replication-defective human endogenous retrovirus 9 (ERV-9) and thousands of copies of its solitary long term repeat (sLTR) element. While some sLTRs are located upstream of critical genes and have enhancer activity, other sLTRs are located within introns and may be transcribed as RNAs. We found that intronic RNAs arising from U3 sLTRs of ERV-9 were expressed as both sense (S) and antisense (AS) transcripts in all human cells tested but that expression levels differed in malignant versus nonmalignant cells. In nonmalignant cells, AS was expressed at higher levels than S and at higher levels than in malignant cells; in malignant cells, AS was expressed at amounts equivalent to those of S RNA. Critically, U3 AS RNA was found to physically bind to key transcription factors for cellular proliferation, including NF-Y, p53, and sp1, indicating that such RNA transcripts may function as decoy targets or traps for NF-Y and thus inhibit the growth of human cancer cells. Indeed, short U3 oligodeoxynucleotides (ODNs) based on these RNA sequences ably inhibited proliferation of cancer cell lines driven by cyclins B1/B2, the gene targets of NF-Y.
Synthesis of High Quality Phosphorothioate Oligonucleotides as Antisense Drugs. Use of I-Linker in the Elimination of 3′-Terminal Phosphorothioate Monoesters (2003)

Detritylation of a 5'-O-DMT-2'-deoxyadenosine moiety attached to solid support under acidic condition leads to depurination during oligonucleotide synthesis. Deprotection followed by reversed phase HPLC purification leads to desired oligonucleotide contaminated with significant levels of 3'-terminal phosphorothiaote (3'-TPT) monoester (n-1)-mer. However, it is demonstrated that attachment of dA nucleoside through its exocyclic amino group to solid support leads to substantial reduction of 3'-TPT formation thereby improving the quality of oligonucleotide synthesized.
Simultaneous p<scp>H</scp>‐sensitive and oxygen‐sensitive <scp>MRI</scp> of human gliomas at 3 <scp>T</scp> using multi‐echo amine proton chemical exchange saturation transfer spin‐and‐gradient echo echo‐planar imaging (<scp>CEST‐SAGE‐EPI</scp>) (2018)

The CEST-SAGE-EPI technique provides simultaneous pH-sensitive and oxygen-sensitive image contrasts for evaluation of the brain tumor microenvironment. Advantages include fast whole-brain acquisition, in-line B<sub>0</sub> correction, and simultaneous estimation of CEST effects, R<sub>2</sub> , R2*, and R2' at 3 T.
Correction of muscular dystrophies by CRISPR gene editing (2020)

Muscular dystrophies are debilitating disorders that result in progressive weakness and degeneration of skeletal muscle. Although the genetic mutations and clinical abnormalities of a variety of neuromuscular diseases are well known, no curative therapies have been developed to date. The advent of genome editing technology provides new opportunities to correct the underlying mutations responsible for many monogenic neuromuscular diseases. For example, Duchenne muscular dystrophy, which is caused by mutations in the dystrophin gene, has been successfully corrected in mice, dogs, and human cells through CRISPR/Cas9 editing. In this Review, we focus on the potential for, and challenges of, correcting muscular dystrophies by editing disease-causing mutations at the genomic level. Ideally, because muscle tissues are extremely long-lived, CRISPR technology could offer a one-time treatment for muscular dystrophies by correcting the culprit genomic mutations and enabling normal expression of the repaired gene.
Hyper-dimensional analysis for label-free high-throughput imaging flow cytometry (2014)

We present an imaging flow cytometer capable of capturing phase and intensity images of individual unlabeled cells at 36 million frames/second to generate multi-dimensional scatter plots, leading to a considerable enhancement in cell classification sensitivity.
N-Best Optimal Path Ant Routing Algorithm for State-Dependent N Best Quality of service Routes in IP Networks (2007)

As routing mechanism is a key to success of future communication networking, computing constrained shortest paths is fundamental to some important network functions such as QoS routing or traffic engineering. The problem is to And feasible paths satisfying QoS requirements and optimizing resource usage and degrading gracefully during periods of heavy load. This paper introduces a Quality of Service (QoS) routing protocol aimed to offload congested links while optimizing end-to-end delay. The proposed algorithm, called NOPAR "N-best Optimal Paths Ant Routing", extends the earlier N best Optimal path Q Routing Algorithm (NOQRA) by integrating the exploration and reinforcement function inspired by Ant Colony Optimization approaches. NOPAR uses a model combining both a stochastic planned pre-navigation for the exploration phase (forward ant) and a deterministic approach for the backward phase (backward ant). The introduced algorithm is compared with earlier version of NOQRA and the well-known routing algorithms such as SPF or OSPF. The performance analysis under simulation environment using OPNET demonstrates that NOPAR performs better than the classical approach especially over load high networks or link failures conditions.
Penning ionization ternary gas mixtures for diffuse discharge switching applications (1985)

The increase in the total ionization produced by high-energy α particles in Ar/C2F6 mixtures, which have conduction and insulation properties appropriate for use in diffuse discharge switching applications by addition of low ionization energy additives has been quantitatively studied. The energy to produce an electron-positive ion pair (ip) W in C2F6 was found to be 34.7 eV/ip; this rather high value is attributed to the large cross section for electron impact-induced dissociation of C2F6. The W values of Ar/C2F6 mixtures have also been measured and are reported; they increase with increasing C2F6 content. The W values of Ar/C2F6 binary gas mixtures have been found to decrease by addition of C2H2 or 2-C4H8. Quantitative measurements of the W values of the ternary gas mixtures are reported. The amounts of C2H2 or 2-C4H8 in Ar/C2F6, which maximize the increase in total ionization have been estimated; some of these ternary gas mixtures may be useful for diffuse discharge switches sustained by external electron beams. The experimental results on the W values for the binary and ternary gas mixtures studied have been modeled and good agreement has been found between the experimental and the calculated results. From an analysis of the data it has been found that the α-particle energy is partitioned between C2F6 and Ar approximately in the ratio 4.2:1. It has also been found that at the argon pressures employed, the probability of deexcitation of excited argon atoms by C2F6 (or C2H2 or 2-C4H8) molecules is more than three orders of magnitude larger than the probability of radiative deexcitation of the excited argon atoms.
Fault tolerant PON topologies (1992)

The authors propose a redundant, tree structured passive optical network (PON) configuration which can withstand all single and most double link failures. The redundant configuration results from the superposition of two physically separate, diverse-routed trees. This redundancy is transparent to the user. It does not require switching elements or special controls inside the network. It permits easy identification of the fault by the network control center. The fault tolerance properties of the proposed solution are evaluated. Power budget, fiber installation cost, and metropolitan coverage issues are investigated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Direct Interaction of a Ligand for the <i>erb</i> B2 Oncogene Product with the EGF Receptor and p185 <sup> <i>erb</i> B2 </sup> (1990)

The erbB2 oncogene encodes a 185-kilodalton transmembrane protein whose sequence is similar to the epidermal growth factor receptor (EGFR). A 30-kilodalton factor (gp30) secreted from MDA-MB-231 human breast cancer cells was shown to be a ligand for p185erbB2. An antibody to EGFR abolished the tyrosine phosphorylation induced by EGF and transforming growth factor-alpha (TGF-alpha) but only partially blocked that produced by gp30 in SK-BR-3 breast cancer cells. In two cell lines that overexpress erbB2 but do not expresss EGFR (MDA-MB-453 breast cancer cells and a Chinese hamster ovary cell line that had been transfected with erbB2), phosphorylation of p185erbB2 was induced only by gp30. The gp30 specifically inhibited the growth of cells that overexpressed p185erbB2. An antibody to EGFR had no effect on the inhibition of SK-BR-3 cell colony formation obtained with gp30. Thus, it appeared that gp30 interacted directly with the EGFR and erbB2. Direct binding of gp30 to p185erbB2 was confirmed by binding competition experiments, where gp30 was found to displace the p185erbB2 binding of a specific antibody to p185erbB2. The evidence described here suggests that gp30 is a ligand for p185erbB2.
Isolation, identification and characterisation of starch‐interacting proteins by 2‐D affinity electrophoresis (2006)

A 2-D affinity electrophoretic technique (2-DAE) has been used to isolate proteins that interact with various starch components from total barley endosperm extracts. In the first dimension, proteins are separated by native PAGE. The second-dimensional gel contains polysaccharides such as amylopectin and glycogen. The migration of starch-interacting proteins in this dimension is determined by their affinity towards a particular polysaccharide and these proteins are therefore spatially separated from the bulk of proteins in the crude extract. Four distinct proteins demonstrate significant affinity for amylopectin and have been identified as starch branching enzyme I (SBEI), starch branching enzyme IIa (SBEIIa), SBEIIb and starch phosphorylase using polyclonal antibodies and zymogram activity analysis. In the case of starch phosphorylase, a protein spot was excised from a 2-DAE polyacrylamide gel and analysed using Q-TOF MS/MS, resulting in the alignment of three internal peptide sequences with the known sequence of the wheat plastidic starch phosphorylase isoform. This assignment was confirmed by the determination of the enzyme's function using zymogram analysis. Dissociation constants (Kd) were calculated for the three enzymes at 4 degrees C and values of 0.20, 0.21 and 1.3 g/L were determined for SBEI, SBEIIa and starch phosphorylase, respectively. Starch synthase I could also be resolved from the other proteins in the presence of glycogen and its identity was confirmed using a polyclonal antibody and by activity analysis. The 2-DAE method described here is simple, though powerful, enabling protein separation from crude extracts on the basis of function.
Discovery of<i>cis</i>-<i>N</i>-(1-(4-(Methylamino)cyclohexyl)indolin-6-yl)thiophene-2-carboximidamide: A 1,6-Disubstituted Indoline Derivative as a Highly Selective Inhibitor of Human Neuronal Nitric Oxide Synthase (nNOS) without Any Cardiovascular Liabilities (2011)

A series of 1,6-disubstituted indoline derivatives were synthesized and evaluated as inhibitors of human nitric oxide synthase (NOS) designed to mitigate the cardiovascular liabilities associated with previously reported tetrahydroquinoline-based selective neuronal NOS inhibitors due to higher lipophilicity ( J. Med. Chem. 2011 , 54 , 5562 - 5575 ). This new series produced similar potency and selectivity among the NOS isoforms and was devoid of any cardiovascular liabilities associated with QT prolongation due to hERG activity or endothelial NOS mediated vasoconstriction effect. The SAR studies led to the identification of cis-45, which was shown to reverse thermal hyperalgesia in vivo in the spinal nerve ligation model of neuropathic pain with excellent safety profile (off-target activities at 80 CNS related receptors/ion channels/transporters). The results presented in this report make cis-45 as an ideal tool for evaluating the potential role of selective nNOS inhibitors in CNS related disorders where excess NO produced by nNOS is thought to play a crucial role.
Efficient Lane Detection Based on Spatiotemporal Images (2015)

In this paper, we propose an efficient method for reliably detecting road lanes based on spatiotemporal images. In an aligned spatiotemporal image generated by accumulating the pixels on a scanline along the time axis and aligning consecutive scanlines, the trajectory of the lane points appears smooth and forms a straight line. The aligned spatiotemporal image is binarized, and two dominant parallel straight lines resulting from the temporal consistency of lane width on a given scanline are detected using a Hough transform, reducing alignment errors. The left and right lane points are then detected near the intersections of the straight lines and the current scanline. Our spatiotemporal domain approach is more robust missing or occluded lanes than existing frame-based approaches. Furthermore, the experimental results show not only computation times reduced to as little as one-third but also a slightly improved rate of detection.
A high-frequency, low volume, point-of-load power supply for distributed power systems (1988)

A resonant version of the DC-DC forward converter is presented in which both the primary-side switch and the secondary-side diode are either on or off at the same time. Such a topology is capable of operation in the 10-MHz range, and can be used for very-low volume point-of-load conversion in distributed power systems. This type of converter takes advantage of a very low transformer leakage inductance to achieve zero-voltage switching of all its power semiconductor devices. Its resonant ring is also independent of load current. A 50-W prototype operating at 3.6 MHz is presented along with a discussion of the changes necessary to achieve 10 MHz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Network coding to enhance standard routing protocols in wireless mesh networks (2013)

This paper introduces a design and simulation of a locally optimized network coding protocol, called PlayNCool, for wireless mesh networks. PlayN-Cool is easy to implement and compatible with existing routing protocols and devices. This allows the system to gain from network coding capabilities implemented in software without the need for new hardware. PlayNCool enhances performance by (i) choosing a local helper between nodes in the path to strengthen the quality of each link, (ii) using local information to decide when and how many transmissions to allow from the helper, and (iii) using random linear network coding to increase the usefulness of each transmission from the helpers. This paper focuses on the design details needed to make the system operate in reality and evaluating performance using ns-3 in multi-hop topologies. Our results show that the PlayNCool protocol increases the end-to-end throughput by more than two-fold and up to four-fold in our settings.
An 800-MHz embedded DRAM with a concurrent refresh mode (2005)

An 800-MHz embedded DRAM macro employs a memory cell utilizing a device from the 90-nm high-performance technology menu; a 2.2-nm gate oxide 1.5 V IO device. A concurrent refresh mode is designed to improve the memory utilization to over 99% for a 64 /spl mu/s data retention time. A concurrent refresh scheduler utilizes up-count and down-count registers to identify at least one array to be refreshed at every clock cycle, emulating a classical distributed refresh mode. A command multiplier employs low frequency phased clock signals to generate the clock, commands, and addresses at rates up to 4/spl times/ that of the tester frequency. The macro integrates masked redundancy allocation logic during at speed multibank test. The hardware results show a 312-MHz random access frequency and 800-MHz multibank frequency at 1.2 V, respectively.
Eliminating Unbonded Edges In Explosive Bonding (1991)

Explosive-bonding technique elminates sharp unbonded notch normally occurring between flyer plate and baseplate. Makes it possible to simply break away unbonded outer extremity of flyer plate; no longer necessary to grind away unbonded edge to prevent collection of corrosive contaminants in edge voids. Method not limited to flat surfaces.
A Concise Total Synthesis of Dysidiolide through Application of a Dioxolenium-Mediated Diels−Alder Reaction (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA Concise Total Synthesis of Dysidiolide through Application of a Dioxolenium-Mediated Diels−Alder ReactionSteven R. Magnuson, Laura Sepp-Lorenzino, Neal Rosen, and Samuel J. DanishefskyView Author Information Department of Chemistry, Columbia University Havemeyer Hall, New York, New York, 10027 Laboratories for Bioorganic Chemistry and Molecular Oncogenesis Sloan-Kettering Institute for Cancer Research 1275 York Avenue, Box 106, New York, New York 10021 Cite this: J. Am. Chem. Soc. 1998, 120, 7, 1615–1616Publication Date (Web):February 5, 1998Publication History Received1 December 1997Published online5 February 1998Published inissue 1 February 1998https://doi.org/10.1021/ja9740428Copyright © 1998 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1604Altmetric-Citations76LEARN 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 Read OnlinePDF (74 KB) Get e-AlertsSUBJECTS:Adducts,Cells,Chemical synthesis,Organic compounds,Pharmaceuticals Get e-Alerts
Leukemia inhibitory factor promotes the neuronal development of spinal cord precursors from the neural tube (1992)

Recent evidence from our laboratory has shown that leukemia inhibitory factor (LIF) can act early in peripheral nervous system development. We have investigated a potential role of LIF in the developing spinal cord. In explants and dissociated cultures of spinal cord primordium, LIF stimulated a profuse neurite outgrowth. To determine if these effects were related to neuronal differentiation, cells were plated at low cell density and stained for neurofilament. LIF stimulated an increase in the number of newly differentiated neurons, without inducing proliferation of the precursors. Given that LIF has previously reported effects as a cholinergic switching factor for sympathetic neurons, we investigated whether LIF had similar effects in these spinal cord cultures. LIF increased the number of cholinergic neurons in proportion to its overall effect on the stimulation of all neurofilament positive neurons in the culture. These data show that LIF stimulates the generation of spinal cord neurons from their precursors and further implicates a role for LIF in nervous system development.
Energy-efficient design of a presbyopia correction wearable powered by mobile GPUs and FPGAs (2022)

Abstract This paper presents an energy-efficient design and evaluation of a novel portable device for the automatic correction of presbyopia in human eyes driven by the use of opto-electronic lenses and based on the dynamic pupil response of the subject. Due to the wearable nature of the proposed Dynamic Auto–Accommodation Glasses, in addition to the real-time requirement, an energy-efficient implementation is critical for the success of the device. In this work, the binocular pupil tracking of a subject, followed by the calculation of the eyes’ vergence, and the control of a pair of opto-electronic lenses are implemented and evaluated on several hardware platforms, including two mobile GPU/SoCs, a high-end FPGA, a low-cost FPGA, and a desktop GPU (as a reference point). The pupil tracking algorithm has been parallelized, applying different platform-specific optimizations for each case, to design a fast yet energy-efficient wearable. The hardware platforms have been evaluated to determine which one is the most appropriate for the presbyopia correction task. The experimental results show that the most energy-efficient platform is a mobile GPU (Samsung Exynos 8890) capable of processing frames at 0.016 Joules/frame, still allowing real-time processing (24 frames/sec).
ChemInform Abstract: New Imidazo[1,2‐a]quinoxaline Derivatives: Synthesis and in vitro Activity Against Human Melanoma. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A Protective and Broadly Cross-Neutralizing Epitope of Human Papillomavirus L2 (2007)

We generated a monoclonal antibody, RG-1, that binds to highly conserved L2 residues 17 to 36 and neutralizes human papillomavirus 16 (HPV16) and HPV18. Passive immunotherapy with RG-1 was protective in mice. Antiserum to the HPV16 L2 peptide comprising residues 17 to 36 (peptide 17-36) neutralized pseudoviruses HPV5, HPV6, HPV16, HPV 18, HPV31, HPV 45, HPV 52, HPV 58, bovine papillomavirus 1, and HPV11 native virions. Depletion of HPV16 L2 peptide 17-36-reactive antibodies from cross-neutralizing rabbit and human L2-specific sera abolished cross-neutralization and drastically reduced neutralization of the cognate type. This cross-neutralization of diverse HPVs associated with cervical cancer, genital warts, and epidermodysplasia verruciformis suggests the possibility of a broadly protective, peptide-based vaccine.