gebhart/patrepeval huggingface dataset:
Non‐Viral CRISPR/Cas Gene Editing In Vitro and In Vivo Enabled by Synthetic Nanoparticle Co‐Delivery of Cas9 mRNA and sgRNA (2016)

CRISPR/Cas is a revolutionary gene editing technology with wide-ranging utility. The safe, non-viral delivery of CRISPR/Cas components would greatly improve future therapeutic utility. We report the synthesis and development of zwitterionic amino lipids (ZALs) that are uniquely able to (co)deliver long RNAs including Cas9 mRNA and sgRNAs. ZAL nanoparticle (ZNP) delivery of low sgRNA doses (15 nm) reduces protein expression by >90 % in cells. In contrast to transient therapies (such as RNAi), we show that ZNP delivery of sgRNA enables permanent DNA editing with an indefinitely sustained 95 % decrease in protein expression. ZNP delivery of mRNA results in high protein expression at low doses in vitro (<600 pM) and in vivo (1 mg kg<sup>-1</sup> ). Intravenous co-delivery of Cas9 mRNA and sgLoxP induced expression of floxed tdTomato in the liver, kidneys, and lungs of engineered mice. ZNPs provide a chemical guide for rational design of long RNA carriers, and represent a promising step towards improving the safety and utility of gene editing.
Efficient and secure storage of private keys for pseudonymous vehicular communication (2013)

Current standardization efforts for cooperative Intelligent Transportation Systems both in the U.S. and Europe foresee vehicles to use a large number of changeable pseudonyms for privacy protection. Provisioning and storage of these pseudonyms require efficient and secure mechanisms to prevent malicious use of pseudonyms. In this paper we investigate several techniques to improve secure and efficient storage of pseudonyms. Specifically, we propose schemes based on Physical Unclonable Functions (PUFs) that allow to replace expensive secure key storage by regular unsecured memory and still provide fully secure pseudonyms storage.
LPG-Based Fracturing: An Alternate Fracturing Technique in Shale Reservoirs (2014)

Abstract A novel stimulation technique named Liquefied Petroleum Gas (LPG) based fracturing which can be an alternative to conventional water based fracturing technique or hydraulic fracturing. In conventional hydraulic fracturing treatments, it is observed that effective fracture length contributing to the production is fraction of the propped fracture length. In LPG fracturing effective fracture length is more than conventional fracture length hence increasing productivity. If we use gelled LPG as a fracturing fluid, it is highly soluble with the formation hydrocarbon. If natural gas formations are present, then propane and methane will combine to create unique liquid vapour saturation and returns to the surface at ambient conditions which can be separated easily. LPG fracturing eliminates the need of flowback water disposal, which is currently major problem in hydraulic fracturing. In LPG fracturing, a stream of gelled LPG or a mixture of propane and butane is injected into the well. Proppant is supplied in this stream and carried into the formation at frac pressures causing fractures though some precautions are must for the safety issues. It has been observed that with less viscosity, less surface tension and less density, LPG can rapidly and efficiently clean up while reducing the pressure needed to mobilize fracturing fluids. In this paper, effective fracture lengths and rapid cleanup are demonstrated with the help of post fracture pressure transient analysis. Comparison of LPG fracturing with conventional fracturing has been explained critically. Complete recovery of the LPG has also been demonstrated here. Major advantages and disadvantages of this technique along with economics are included in this paper. We can use this technique in order to protect the environment and to increase the productivity. This paper briefly reviews the previous work and explains an overview and applications of LPG fracturing.
A Long-term Prospective Study of Type-Specific Human Papillomavirus Infection and Risk of Cervical Neoplasia Among 20,000 Women in the Portland Kaiser Cohort Study (2011)

The data from this cohort study show the long-term predictive value of HPV testing, particularly in women ≥30, and a possible role for distinguishing particularly carcinogenic types like HPV16.
Potential interventions for the prevention of childhood pneumonia (1995)

Streptococcus pneumoniae is a leading cause of fatal bacterial pneumonia in young children. Pneumococcal polysaccharide vaccines have not been promoted for use in young children because many constituent serotypes are not immunogenic in children < 2 years old. Conjugating pneumococcal polysaccharide epitopes to a protein carrier would likely increase vaccine immunogenicity in children. We reviewed published and unpublished pneumococcal serotype and serogroup data from 16 countries on 6 continents to determine geographic and temporal differences in serotype and serogroup distribution of sterile site pneumococcal isolates among children and to estimate coverage of proposed and potential pneumococcal conjugate vaccine formulas. The most common pneumococcal serotypes or groups from developed countries were, in descending order, 14, 6, 19, 18, 9, 23, 7, 4, 1 and 15. In developing countries the order was 6, 14, 8, 5, 1, 19, 9, 23, 18, 15 and 7. Development of customized heptavalent vaccine formulas, one for use in all developed countries and one for use in all developing countries, would not provide substantially better coverage against invasive pneumococcal disease than two currently proposed heptavalent formulas. An optimal nanovalent vaccine for global use would include serotypes 1, 5, 6B, 7F, 9V, 14, 18C, 19F and 23F. Geographic and temporal variation in pneumococcal serotypes demonstrates the need for a species-wide pneumococcal vaccine.
Immediate early induction of mRNAs for ethylene‐responsive transcription factors in tobacco leaf strips after cutting (1998)

To investigate the functional relationship between the expression of genes for ethylene-responsive transcription factors (ERFs) and the expression of ethylene-responsive genes, we examined the expression of genes for ERFs and the expression of a reporter gene in transgenic tobacco that carried a gene for β-glucuronidase (GUS) under the control of the ethylene-responsive element, which includes four copies of the 11-bp consensus sequence (designated the GCC-box, TAAGAGCCGCC). In strips of leaves of transgenic tobacco, the GCC-box-mediated expression of the reporter gene was induced in response to treatment with ethylene. We also observed the ethylene-independent immediate early induction of the synthesis of mRNAs for ERFs in wounded leaves and the enhancement of this induction by cycloheximide (CHX). Since CHX suppressed the induction of mRNAs for chitinase and GUS by ethylene, protein synthesis de novo was required for induction of the ethylene-dependent GCC-box-mediated transcription of genes. In contrast, the enhancement by CHX of the wound-induced expression of ERFs suggested that no synthesis of new proteins was required for the wounding signal transduction leading to rapid expression of ERFs. Methyl jasmonate did not stimulate the wounding-responsive accumulation of ERF mRNAs, but it reduced such accumulation of mRNAs for ERF1, ERF2, ERF4 and the ethylene-dependent GCC-box-mediated transcription of the reporter gene. Thus, the immediate early induction of the expression of genes for ERFs in strips of tobacco leaves appears to be a novel type of wound-responsive activation of transcription. These results suggested that the expression of ERFs was not sufficient for activation of the GCC-box-mediated transcription but the expression of ERF1, ERF2 and ERF4, and that conversion of these ERFs by ethylene to their active form might be crucial for the GCC-box-mediated activation of the transcription of defense genes.
Nonpolar InGaN∕GaN emitters on reduced-defect lateral epitaxially overgrown a-plane GaN with drive-current-independent electroluminescence emission peak (2004)

Nonpolar (112¯0) a-plane InGaN∕GaN multiple-quantum-well light-emitting diodes were grown by metalorganic chemical vapor deposition on reduced-defect density hydride-vapor-phase-epitaxy lateral epitaxially overgrown a-plane GaN templates. Direct current output power of 240 μW was measured at 20 mA for a 300×300μm2 device, and dc output powers as high as 1.5 mW were measured at 250 mA. DC electroluminescence (EL) measurements yielded a peak at 413.5 nm, corresponding with the room-temperature photoluminescence peak. The EL peak position was independent of drive current and a 23.5 nm linewidth was realized at 20 mA. The current–voltage characteristics of these diodes showed a forward voltage (Vf) of 3.3 V with a series resistance of 7.8 Ω.
Room temperature observation of electron resonant tunneling through InAs/AlAs quantum dots (2007)

Molecular beam epitaxy is employed to manufacture self-assembled InAs/AlAs quantum-dot resonant tunneling diodes. Resonant tunneling current is superimposed on the thermal current, and they make up the total electron transport in devices. Steps in current-voltage characteristics and peaks in capacitance-voltage characteristics are explained as electron resonant tunneling via quantum dots at 77K or 300K, and this is the first time that resonant tunneling is observed at room temperature in III-V quantum-dot materials. Hysteresis loops in the curves are attributed to hot electron injection/emission process of quantum dots, which indicates the concomitant charging/discharging effect.
Synthesis and antitumor activities of some 4,5-dihydro-1H-1,2,4-triazol-5-ones. (1998)

Eight new 3-alkyl(aryl)-4-arylidenamino-4,5-dihydro-1H-1,2,4-triazol-5 - ones were synthesized and characterised by elemental analysis. 1H NMR, IR and UV spectra. Seven new and 34 recently reported derivatives of 4,5-dihydro-1H-1,2,4 triazol-5-one ring were screened for their antitumor activities.
Forecasting gas turbine Exhaust Gas Temperatures using Support Vector Machine Experts and Genetic Algorithm (2010)

One aspect of modern commercial aircraft engine maintenance involves monitoring recorded engine parameters. When these parameters exceed their respective threshold tolerances, appropriate maintenance actions are taken. Reducing these unscheduled maintenance actions would allow maintainers to more effectively plan their maintenance schedules which help in the reduction of costs. One way of accomplishing this is to learn the behavior of the statistics of parameters and the ability to reliably forecast their future values. The parameter studied in this paper is the Exhaust Gas Temperature. A hybrid algorithm called Support Vector Machine Experts and Genetic Algorithm is applied to the task of forecasting a statistic of EGT. The algorithm involves first partitioning the input space according to similar training examples through a procedure that uses a Self Organizing Map. A SVM is regressed onto each partition and the optimal parameters for SVM are found using Genetic Algorithm. This algorithm is shown to have an improved mean absolute error when forecasting EGT values over a single support vector regression machine. The study was conducted for both engines of two Boeing 737 commercial aircrafts.
Synthesis of Fluorinated Fluoresceins (1997)

Several novel fluorinated fluoresceins (Oregon Green dyes) were prepared by the reaction of fluororesorcinols with phthalic anhydride and its derivatives. A novel regiospecific synthesis of fluororesorcinols was key to the successful synthesis of these new fluorophores. (Polyfluoro)nitrobenzenes were reacted with 2 equiv of sodium methoxide followed by reduction, hydrodediazoniation, and demethylation, giving the first straightforward synthesis of 2-fluororesorcinol, 4-fluororesorcinol, 2,4-difluororesorcinol, and 2,4,5-trifluororesorcinol. These fluorinated fluoresceins have higher photostability and ionize at a lower pH (pKa = 3.3−6.1) than fluorescein (pKa = 6.5). Some of the fluorinated fluoresceins have very high quantum yields (0.85−0.97), which, in combination with their lower pKas and high photostability, makes them superior fluorescent dyes for use as reporter molecules in biological systems.
Promoters recognized by Escherichia coli RNA polymerase selected by function: highly efficient promoters from bacteriophage T5 (1985)

Highly efficient promoters of coliphage T5 were identified by selecting for functional properties. Eleven such promoters belonging to all three expression classes of the phage were analyzed. Their average AT content was 75% and reached 83% in subregions of the sequences. Besides the well-known conserved sequences around -10 and -33, they exhibited homologies outside the region commonly considered to be essential for promoter function. Interestingly, the consensus hexamers around -10 (TAT AAT) and -35 (TTG ACA) were never found simultaneously within the sequence of highly efficient promoters. Several of these promoters compete extremely well for Escherichia coli RNA polymerase and can be used for the efficient in vitro synthesis of defined RNA species. In addition, some of these promoters accept 7-mGpppA as the starting dinucleotide, thus producing capped mRNA in vitro which can be utilized in various eucaryotic translation systems.
Three-Dimensional Solid-State Lithium-Ion Batteries Fabricated by Conformal Vapor-Phase Chemistry (2018)

Three-dimensional thin-film solid-state batteries (3D TSSB) were proposed by Long et al. in 2004 as a structure-based approach to simultaneously increase energy and power densities. Here, we report experimental realization of fully conformal 3D TSSBs, demonstrating the simultaneous power-and-energy benefits of 3D structuring. All active battery components-electrodes, solid electrolyte, and current collectors-were deposited by atomic layer deposition (ALD) onto standard CMOS processable silicon wafers microfabricated to form arrays of deep pores with aspect ratios up to approximately 10. The cells utilize an electrochemically prelithiated LiV<sub>2</sub>O<sub>5</sub> cathode, a very thin (40-100 nm) Li<sub>2</sub>PO<sub>2</sub>N solid electrolyte, and a SnN <sub>x</sub> anode. The fabrication process occurs entirely at or below 250 °C, promising compatibility with a variety of substrates as well as integrated circuits. The multilayer battery structure enabled all-ALD solid-state cells to deliver 37 μAh/cm<sup>2</sup>·μm (normalized to cathode thickness) with only 0.02% per-cycle capacity loss. Conformal fabrication of full cells over 3D substrates increased the areal discharge capacity by an order of magnitude while simulteneously improving power performance, a trend consistent with a finite element model. This work shows that the exceptional conformality of ALD, combined with conventional semiconductor fabrication methods, provides an avenue for the successful realization of long-sought 3D TSSBs which provide power performance scaling in regimes inaccessible to planar form factor cells.
Generation of 10 nJ picosecond pulses from a modelockedfibre laser (1995)

Wavelength-tunable very high power soliton fibre lasers are constructed using chirped fibre Bragg gratings. Near-bandwidth-limited pulses with widths of 4.0 ps and pulse energies up to 10 nJ are generated directly from passively modelocked erbium fibre lasers. A stable pulse repetition rate of 17 MHz is obtained, giving rise to an average modelocked output power of 170 mW.
The Survival Kinase Mirk/dyrk1B Is Activated through Rac1-MKK3 Signaling (2005)

The serine/threonine kinase Mirk/dyrk1B is activated in several solid tumors where it mediates cell survival, but the mechanism by which Mirk is activated in tumors is unknown. We now demonstrate that Mirk is activated as a kinase by signaling from Rac1 to the mitogen-activated protein kinase kinase MKK3. Rac is a Ras superfamily GTPase that, when activated, functions downstream of Ras oncoproteins to promote cell survival, transformation, and membrane ruffling. The constitutively active mutant Rac1QL activated Mirk in several cell types through MKK3, which in turn activated Mirk by phosphorylation. Dominant negative Rac1, dominant negative MKK3, and knockdown of MKK3 by RNA interference inhibited the kinase activity of co-expressed Mirk. E-cadherin ligation in confluent Madin-Darby canine kidney (MDCK) epithelial cells is known to transiently activate Rac1. Mirk was activated by endogenous Rac1 following E-cadherin ligation in confluent MDCK epithelial cells, whereas treatment of confluent MDCK cells with an Rac1 inhibitor decreased Mirk activity. Disruption of cadherin ligation by EGTA or prevention of cadherin ligation by maintenance of cells at subconfluent density blocked activation of Mirk. Engagement of cadherin molecules on subconfluent cells by an E-cadherin/Fc chimeric molecule transiently activated both Rac1 and Mirk with a similar time course. Rac activity is up-regulated in many human tumors and mediates survival signals, which enable tumor cells to evade apoptosis. This study characterizes a new anti-apoptotic signaling pathway that connects Rac1 with a novel downstream effector, Mirk kinase, which has recently been demonstrated to mediate survival in human tumors.
Incidence of Alzheimer’s disease in a rural community in India (2001)

These are the first AD incidence rates to be reported from the Indian subcontinent, and they appear to be among the lowest ever reported. However, the relatively short duration of follow-up, cultural factors, and other potential confounders suggest caution in interpreting this finding.
Mixed excitation for HMM-based speech synthesis (2001)

This paper describes improvements on the excitation model of an HMM-based text-to-speech system. In our previous work, natural sounding speech can be synthesized from trained HMMs. However, it has a typical quality of “vocoded speech” since the system uses a traditional excitation model with either a periodic impulse train or white noise. In this paper, in order to reduce the synthetic quality, a mixed excitation model used in MELP is incorporated into the system. Excitation parameters used in mixed excitation are modeled by HMMs, and generated from HMMs by a parameter generation algorithm in the synthesis phase. The result of a listening test shows that the mixed excitation model significantly improves quality of synthesized speech as compared with the traditional excitation model.
Isolation, characterization and comparison of bacteria from swine faeces and manure storage pits (2003)

Storage of swine manure is associated with the microbiological production of a variety of odorous chemicals including ammonia, organic acids and alcohols, and sulphides. Although largely the product of microbiological activity, little is known about the microorganisms present in swine manure. In order to gain a better understanding of the types and activities of the microorganisms present, representative strains of microorganisms were isolated from faeces and stored manure slurry, identified, and physiologically characterized. For swine manure slurry samples, total anaerobe colony counts were greatest when a non-selective, habitat simulating medium containing clarified swine manure slurry was used whereas the highest counts for faecal anaerobes were obtained on rumen fluid containing medium. Faecal and slurry samples were also plated onto the appropriate medium containing the antibiotics tetracycline, erythromycin and tylosin (10 micro g ml-1, individually) and the proportional counts of organisms capable of growing in the presence of these antibiotics determined. Randomly selected isolates from the highest dilutions were identified by 16 s rDNA sequence analysis, and selected physiological characteristics were determined. The results of these examinations indicate that the predominant culturable microorganisms from these environments are obligately anaerobic, low mol percentage G + C Gram positive bacteria (Firmicutes) who are members of Clostridial, Eubacterial, and Lactobacillus/Streptococcus phylogenetic groups. Isolates similar to Sporomusa and Flexibacter/Cytophaga/Bacteroides (CFB or Bacteroidetes) groups were also obtained. Although similar overall, faecal and slurry samples differed in bacterial composition. Manure slurry samples were dominated by organisms similar to Clostridium coccoides and Enterococcus species whereas the distribution of species present in faeces appeared much broader. Whereas most of the pure cultures could be assigned to known phylogenetic groupings, few could be identified as known species. Examination of some growth and physiological characteristics of faecal and slurry isolates showed these to be primarily carbohydrate fermenters, although some were able to ferment lactate and amino acids. When the ability of manure and faecal isolates to ferment protein, peptides and amino acids was examined, a relatively small percentage of these were able to do so and most of these fermented carbohydrates in addition to the amino acid sources provided. The predominant amino acid fermenters were most closely related to C. coccoides and C. botulinum, but representatives of the Bacteroides, Staphylococcus, Enterococcus and other phylogenetic groups were also found. The results reported here are compared with those obtained from clone libraries prepared from the same environmental samples.
Antibody Pretargeting Advances Cancer Radioimmunodetection and Radioimmunotherapy (2005)

This article reviews the methods of pretargeting, which involve separating the targeting antibody from the subsequent delivery of an imaging or therapeutic agent that binds to the tumor-localized antibody. This provides enhanced tumor:background ratios and the delivery of a higher therapeutic dose than when antibodies are directly conjugated with radionuclides, as currently practiced in cancer radioimmunotherapy. We describe initial promising clinical results using streptavidin-antibody constructs with biotin-radionuclide conjugates in the treatment of patients with malignant gliomas, and of bispecific antibodies with hapten-radionuclides in the therapy of tumors expressing carcinoembryonic antigen, such as medullary thyroid and small-cell lung cancers.
SoftNIC: A Software NIC to Augment Hardware (2015)

As the main gateway for network traffic to a server, the network interface card (NIC) is an ideal place to incorporate diverse network functionality, such as traffic control, protocol offloading, and virtualization. However, the slow evolution and inherent inflexibility of NIC hardware have failed to support evolving protocols, emerging applications, and rapidly changing system/network architectures. The traditional soft- ware approach to this problem—implementing NIC features in the host network stack—is unable to meet increasingly challenging performance requirements. In this paper we present SoftNIC, a hybrid software-hardware architecture to bridge the gap between limited hardware capabilities and ever changing user demands. SoftNIC provides a programmable platform that allows applications to leverage NIC features implemented in software and hard- ware, without sacrificing performance. Our evaluation results show that SoftNIC achieves multi-10G performance even on a single core and scales further with multiple cores. We also present a variety of use cases to show the potential of software NIC augmentation.
PEROXISOME PROLIFERATOR-ACTIVATED RECEPTORS: A Nuclear Receptor Signaling Pathway in Lipid Physiology (1996)

Peroxisome proliferator-activated receptors (PPARs) are lipid-activated transcription factors that belong to the steroid/thyroid/retinoic acid receptor superfamily. All their characterized target genes encode proteins that participate in lipid homeostasis. The recent finding that antidiabetic thiazolidinediones and adipogenic prostanoids are ligands of one of the PPARs reveals a novel signaling pathway that directly links these compounds to processes involved in glucose homeostasis and lipid metabolism including adipocyte differentiation. A detailed understanding of this pathway could designate PPARs as targets for the development of novel efficient treatments for several metabolic disorders.