gebhart/patrepeval huggingface dataset:
Current treatment options and the role of peptides as potential therapeutic components for Middle East Respiratory Syndrome (MERS): A review (2017)

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a highly pathogenic respiratory virus with mechanisms that may be driven by innate immune responses. Despite the effort of scientific studies related to this virus, Middle East Respiratory Syndrome (MERS) is still a public health concern. MERS-CoV infection has a high mortality rate, and to date, no therapeutic or vaccine has been discovered, that is effective in treating or preventing the disease. In this review, we summarize our understanding of the molecular and biological events of compounds acting as MERS-CoV inhibitors, the outcomes of existing therapeutic options and the various drugs undergoing clinical trials. Currently, several therapeutic options have been employed, such as convalescent plasma (CP), intravenous immunoglobulin (IVIG), monoclonal antibodies and repurposing of existing clinically approved drugs. However, these therapeutic options have drawbacks, thus the need for an alternative approach. The requirement for effective therapeutic treatment has brought the necessity for additional MERS treatments. We suggest that antimicrobial peptides (AMPs) may be used as alternative therapeutic agents against MERS-CoV infection. In addition, we propose the feasibility of developing effective agents by repurposing the existing and clinically approved anti-coronavirus and anti-viral peptide drugs.
Fabrication of discrete nanoscaled force sensors based on single-walled carbon nanotubes (2006)

We present a fabrication technique for discrete, released carbon-nanotube-based nanomechanical force sensors. The fabrication technique uses prepatterned coordinate markers to align the device design to predeposited single-walled carbon nanotubes (SWNTs): Atomic force microscope (AFM) images are recorded to determine spatial orientation and location of each discrete nanotube to be integrated in a nanoscaled force sensor. Electron beam lithography is subsequently used to pattern the metallic electrodes for the nanoscale structures. Diluted hydrofluoric acid etching followed by critical point drying completes the nanosized device fabrication. We use discrete, highly purified, and chemically stable carbon nanotubes as active elements. We show AFM and scanning electron microscope images of the successfully realized SWNTs embedded nanoelectromechanical systems (NEMS). Finally, we present electromechanical measurements of the suspended SWNT NEMS structures
Synthesis and structure-activity relationships of 7.BETA.-[2-(2-aminothiazol-4-yl)acetamido]-cephalosporin derivatives. III. Synthesis and antibacterial activity of 7.BETA.-[2-amino-2-(2-aminothiazol-4-yl)acetamido]cephalosporins. (1980)

New derivatives of 7β-[2-(2-aminothiazol-4-yl)acetamido]cephalosporins having amino group at the 2-position of the 7-acyl moiety were synthesized in the hope that they would show improved antibacterial activity. Some of these compounds (XXa, XXd, XVb) showed improved activity against Enterobacter cloacae. Replacement of the annular amino group by a methyl group caused loss of activity.
A Novel Cell Penetrating Peptide for the Differentiation of Human Neural Stem Cells (2018)

Retinoic acid (RA) is a bioactive lipid that has been shown to promote neural stem cell differentiation. However, the highly hydrophobic molecule needs to first solubilize and translocate across the cell membrane in order to exert a biological response. The cell entry of RA can be aided by cell penetrating peptides (CPPs), which are short amino acid sequences that are able to carry bioactive cargo past the cell membrane. In this work, a novel cell penetrating peptide was developed to deliver RA to human neural stem cells and, subsequently, promote neuronal differentiation. The novel CPP consists of a repeating sequence, whose number of repeats is proportional to the efficiency of cell penetration. Using fluorescence microscopy, the mode of translocation was determined to be related to an endocytic pathway. The levels of β-III tubulin (Tubb3) and microtubule associated protein 2 (MAP2) expression in neural stem cells treated with RA conjugated to the CPP were assessed by quantitative immunocytochemistry.
Carbon Nanotubes: Synthesis, Integration, and Properties (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Minimal complexity low-latency architectures for Viterbi decoders (2008)

For Viterbi decoders, high throughput rate is achieved by applying look-ahead techniques in the add-compare-select unit, which is the system speed bottleneck. Look-ahead techniques combine multiple binary trellis steps into one equivalent complex trellis step in time sequence, which is referred to as the branch metrics precomputation (BMP) unit. The complexity and latency of BMP increase exponentially and linearly with respect to the look-ahead levels, respectively. For a Viterbi decoder with constraint length K and M-step look-ahead, 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M+K-1</sup> branch metrics need to be computed and compared. In this paper, the computational redundancy in existing branch metric computation approaches is first recognized, and a general mathematical model for describing the approach space is built, based on which a new approach with minimal complexity and latency is proposed. The proof of its optimality is also given. This highly efficient approach leads to a novel overall optimal architecture for M that is any multiple of K. The results show that the proposed approaches can reduce the complexity by up to 45.65% and the latency by up to 72.50%. In addition, the proposed architecture can also be applied when M is any value while achieving the minimal complexity.
A dual-Brillouin-peak optical fiber for simultaneous distributed strain and temperature measurement (2018)

Single mode (SM) optical fiber with multiple Brillouin scattering peaks can be used for simultaneous strain and temperature measurement based on Brillouin frequency shift (BFS), but the measurement uncertainties are high due to the low Brillouin gains of higher-order acoustic modes. A new SM fiber is designed and fabricated with enhanced Brillouin gain of higher-order acoustic modes so that the gains of the multiple Brillouin peaks are at a similar level. The temperature coefficients of the BFSs of the peaks are also made significantly different to improve the accuracy of the measured strain and temperature.
Generation of a Novel Rat Model of Angelman Syndrome with a Complete <i>Ube3a</i> Gene Deletion (2020)

Angelman syndrome (AS) is a rare genetic disorder characterized by severe intellectual disability, seizures, lack of speech, and ataxia. The gene responsible for AS was identified as Ube3a and it encodes for E6AP, an E3 ubiquitin ligase. Currently, there is very little known about E6AP's mechanism of action in vivo or how the lack of this protein in neurons may contribute to the AS phenotype. Elucidating the mechanistic action of E6AP would enhance our understanding of AS and drive current research into new avenues that could lead to novel therapeutic approaches that target E6AP's various functions. To facilitate the study of AS, we have generated a novel rat model in which we deleted the rat Ube3a gene using CRISPR. The AS rat phenotypically mirrors human AS with loss of Ube3a expression in the brain and deficits in motor coordination as well as learning and memory. This model offers a new avenue for the study of AS. Autism Res 2020, 13: 397-409. © 2020 International Society for Autism Research,Wiley Periodicals, Inc. LAY SUMMARY: Angelman syndrome (AS) is a rare genetic disorder characterized by severe intellectual disability, seizures, difficulty speaking, and ataxia. The gene responsible for AS was identified as UBE3A, yet very little is known about its function in vivo or how the lack of this protein in neurons may contribute to the AS phenotype. To facilitate the study of AS, we have generated a novel rat model in which we deleted the rat Ube3a gene using CRISPR. The AS rat mirrors human AS with loss of Ube3a expression in the brain and deficits in motor coordination as well as learning and memory. This model offers a new avenue for the study of AS.
Mass Fusion Splicing Machine for Ribbon-Type Optical Fibers, (1986)

Abstract : A mass fusion splicer was designed and manufactured. Using this splicer, mass fusion splicing of optical fiber ribbons was investigated. 10-fiber ribbon tapes were cut and spliced at an average loss of 0.08 dB for GI and 0.24 dB for SM. They were reinforced by heat-shrinkable tubes with EVA adhesive improved for ribbon tape. An average tensile strength until break was about 3.2 kg soon after splice and about 8.3 kg after reinforcement.
Narrow ( <i>n</i> , <i>m</i> )-Distribution of Single-Walled Carbon Nanotubes Grown Using a Solid Supported Catalyst (2003)

Unusually structure-selective growth of single-walled carbon nanotubes (SWNTs) has been attained using a CVD method with a solid supported catalyst. In this method, CO feedstock disproportionates on silica-supported catalytic nanoclusters of Co that are formed in situ from mixed salts of Co and Mo. The nanotube products are analyzed by spectrofluorimetry to reveal distributions resolved at the level of individual (n,m) structures. Two structures, (6,5) and (7,5), together dominate the semiconducting nanotube distribution and comprise more than one-half of that population. The average diameter of produced SWNTs is only 0.81 nm, and a strong propensity is found favoring chiral angles near the armchair limit.
Delta 6-desaturases From Primulaceae (Patent GB 2385852 A) (2003)

An improved method for the specific production of unsaturated l -3 fatty acids and a method for the production of triglycerides having an increased content of unsaturated fatty acids, in particular l -3 fatty acids having more than three double bonds. The invention relates to the production of a transgenic organism, preferably a transgenic plant or a transgenic microorganism, having an increased content of fatty acids, oils or lipids having W 6 double bonds due to the expression of a W 6-desaturase from Primulaceae. The invention additionally relates to expression cassettes containing a nucleic acid sequence, a vector and organisms containing at least one nucleic acid sequence or an expression cassette. The invention further relates to unsaturated fatty acids and triglycerides having an increased content of unsaturated fatty acids and use thereof.
A third-order multistage sigma-delta modulator with reduced sensitivity to nonidealities (1991)

A multistage third-order sigma-delta modulator, which is unconditionally stable and has a low sensitivity to component mismatch and op-amp performance limitations, has been designed and fabricated in a 1.2- mu m CMOS double-poly technology. The modulator, consisting of cascaded second- and first-order stages, is scaled to prevent performance degradation from integrator overload. In addition, the first-stage integrator output is used directly, instead of its quantization error, to facilitate ratioless input circuitry in the second stage. Experimental results indicate a signal-to-noise ratio of 93 and 90 dB at a signal-to-distortion ratio of 93 dB for sample rates of 24 and 80 kHz, respectively.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
MicroRNA Biomarkers in Traumatic Brain Injury (2018)

Traumatic brain injury (TBI) is currently considered one of the major causes of disability and death worldwide. The cellular and molecular changes of TBI pathology are dynamic and complex in nature. MicroRNAs (miRNA) are small endogenous RNA molecules that regulate gene expression at the posttranscriptional level. Several studies have shown a critical role of miRNAs in the development of long- and short-term TBI pathology. Circulating miRNAs are of great interest as blood-based biomarkers in TBI diagnosis. In this chapter, the authors review recent reports that aim to understand the role of miRNAs in TBI pathophysiology and their potential use as a therapeutic target. Additionally, the authors discuss the potential use of miRNAs as blood-based diagnostic markers for TBI and their possible association with other neurodegenerative diseases.
Low-leakage asymmetric-cell SRAM (2002)

We introduce a novel family of asymmetric dual-Vt SRAM cell designs that reduce leakage power in caches while maintaining low access latency. Our designs exploit the strong bias towards zero at the bit level exhibited by the memory value stream of ordinary programs. Compared to conventional symmetric high-performance cells, our cells offer significant leakage reduction in the zero state and in some cases also in the one state albeit to a lesser extend. A novel sense-amplifier, in coordination with dummy bitlines, allows for read times to be on par with conventional symmetric cells. With one cell design, leakage is reduced by 7X (in the zero state) with no performance degradation. An alternative cell design reduces leakage by 40X (in the zero state) with a performance degradation of 5%.
Optimizing fiber coatings for interferometric acoustic sensors (1982)

The pressure sensitivity of the phase of light propagating in an optical fiber is studied both analytically and experimentally. The analysis, which takes into account the exact composition and geometry of multilayer fibers, is utilized to identify coating properties which optimize the fiber acoustic sensitivity. In order to predict the fiber acoustic sensitivity, the elastic parameters of commonly used coating materials, thermoplastics, and UV curable elastomers have been studied in bulk samples as a function of frequency ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10^{2}-10^{4}</tex> Hz) and temperature ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0-35\deg</tex> C). The analytically predicted frequency dependence of the acoustic sensitivity is found to be in agreement with that obtained experimentally from fibers with coatings of various materials.
Effect of Temperature on the Capacitance of Carbon Nanotube Supercapacitors (2009)

The effect of temperature on the kinetics and the diffusion mechanism of the ions in a supercapacitor assembled with single-walled carbon nanotube (SWNT) film electrodes and an organic electrolyte were thoroughly investigated. An improved room temperature performance of the supercapacitor was observed due to the combined effects of an increase in the conductivity of the SWNT films and surface modifications on the SWNT films by repeatedly heating and cooling the supercapacitor between the temperatures of 25 and 100 °C. Modified Randles equivalent circuit was employed to carry out an extensive analysis of the Nyquist spectra measured at different temperatures between 25 and 100 °C in order to understand the fundamentals of the capacitive and resistive variations in the supercapacitor. The experimental results and their thorough analysis will have significant impact not only on the fundamental understanding of the temperature-dependent electrode/electrolyte interfacial properties but also on supercapacitor design with appropriate electrode materials for numerous industrial and consumer applications. The supercapacitor with SWNT film electrodes was capable of withstanding current densities as high as 100 A/g, yielding eminent specific power density values of about 55 kW/kg. Ultralong galvanostatic charge−discharge cycling over 200 000 cycles with a constant current density of 20 A/g at 25 and 100 °C, respectively, showed excellent stability in capacitance with more than 80% efficiency. The usage of such a supercapacitor potentially enables far-reaching advances in backup energy storage and high pulse power applications.
Spectral and temporal stealthy fiber-optic communication using sampling and phase encoding (2011)

We propose a method for covert fiber-optic communication in both frequency and time domains. The power spectral density of the pulse sequence bearing the information is spread in the frequency domain below the noise level by means of sampling. In addition, temporal phase encryption prevents the coherent addition of the various pulses in the frequency domain, further reducing the signal power spectral density. Thus, there is no need to transmit the signal within the bandwidth of a public user in order to spectrally conceal the signal. Temporal spreading of the pulse sequence is achieved by spectral phase encoding, resulting in a stealthy temporal and spectral transmission.
Piranha (2000)

The microprocessor industry is currently struggling with higher development costs and longer design times that arise from exceedingly complex processors that are pushing the limits of instruction-level parallelism. Meanwhile, such designs are especially ill suited for important commercial applications, such as on-line transaction processing (OLTP), which suffer from large memory stall times and exhibit little instruction-level parallelism. Given that commercial applications constitute by far the most important market for high-performance servers, the above trends emphasize the need to consider alternative processor designs that specifically target such workloads. The abundance of explicit thread-level parallelism in commercial workloads, along with advances in semiconductor integration density, identify chip multiprocessing (CMP) as potentially the most promising approach for designing processors targeted at commercial servers.
Intravenously Injected Human Fibroblasts Home to Skin Wounds, Deliver Type VII Collagen, and Promote Wound Healing (2007)

Patients with dystrophic epidermolysis bullosa (DEB) have incurable skin fragility, blistering, and multiple skin wounds because of mutations in the gene that encodes for type VII collagen (C7), which holds together the epidermal and dermal layers of human skin. The intradermal injection of gene-corrected DEB fibroblasts, recombinant C7 protein, or lentiviral vectors expressing C7 is a potential therapy for DEB. Nevertheless, severe DEB causes widespread wounds and treatment would require multiple injections. An alternative strategy might be to inject genetically engineered cells into the patient's circulation that home to the skin wounds and deposit the transgene product. In this study, we demonstrated that intravenously (IV) injected, molecularly engineered DEB fibroblasts (overexpressing human C7) homed to murine skin wounds and continuously delivered C7 at the wound site, where it incorporated into the skin's basement membrane zone and formed anchoring fibril structures. Wounds made on murine or grafted human skin demonstrated accelerated healing when the animals were IV injected with gene-corrected DEB fibroblasts. Our data demonstrate that abundant C7 promotes wound healing. This is also the first evidence that IV injected, molecularly engineered skin fibroblasts can deliver C7 to skin wounds. This strategy could be useful for treating DEB patients.
CPU Frequency Tuning to Improve Energy Efficiency of MapReduce Systems (2016)

Energy efficiency is a major concern in today's data centers that house large scale distributed processing systems such as data parallel MapReduce clusters. Modern power aware systems utilize the dynamic voltage and frequency scaling mechanism available in processors to manage the energy consumption. In this paper, we initially characterize the energy efficiency of MapReduce jobs with respect to built-in power governors. Our analysis indicates that while a built-in power governor provides the best energy efficiency for a job that is CPU as well as IO intensive, a common CPU-frequency across the cluster provides best the energy efficiency for other types of jobs. In order to identify this optimal frequency setting, we derive energy and performance models for MapReduce jobs on a HPC cluster and validate these models experimentally on different platforms. We demonstrate how these models can be used to improve energy efficiency of the machine learning MapReduce applications running on the Yarn platform. The execution of jobs at their optimal frequencies improves the energy efficiency by average 25% over the default governor setting. In case of mixed workloads, the energy efficiency improves by up to 10% when we use an optimal CPU-frequency across the cluster.
Adenovirus DNA Binding Protein Interacts with the SNF2-Related CBP Activator Protein (SrCap) and Inhibits SrCap-Mediated Transcription (2001)

The SNF2-related CBP activator protein, SrCap (pronounced "sir cap"), shares homology with the SNF2/SWI2 protein family. SrCap was cloned through its ability to bind CBP. SrCap can function as a CBP coactivator and can activate transcription in a reporter assay when expressed as a Gal-SrCap fusion protein. A monoclonal antibody raised against the carboxyl terminus of SrCap coimmunoprecipitates CBP/p300, supporting the model that SrCap is a CBP binding protein and that these proteins can be found together in a cellular protein complex. In addition, several cellular proteins are coimmunoprecipitated by the SrCap-specific antibody. Since adenovirus E1A proteins interact with CBP/p300 proteins, we examined what proteins could be copurified in a SrCap-specific coimmunoprecipitation assay from lysates of adenovirus-infected cells. While E1A proteins were not detected in this complex, to our surprise, we observed the presence of an infected-cell-specific band of 72 kDa, which we suspected might be the adenovirus DNA binding protein, DBP. The adenovirus DBP is a multifunctional protein involved in several aspects of the adenovirus life cycle, including an ability to modulate transcription. The identity of DBP was confirmed by DBP-specific Western blot analysis and by reimmunoprecipitating DBP from denatured SrCap-specific protein complexes. Using in vitro-translated DBP and SrCap proteins, we demonstrated that these proteins interact. To determine whether this interaction could affect SrCap-mediated transcription, we tested whether increasing amounts of DBP could modulate the Gal-SrCap transcription activity. We observed that DBP inhibited Gal-SrCap transcription activity in a dose-dependent manner. These data suggest a novel mechanism of adenovirus host cell control by which DBP binds to and inactivates SrCap, a member of the SNF2 chromatin-remodeling protein family.
<title>Concept annotation and search space decrement of digital photos using optical context information</title> (2007)

A modern digital camera is not just a single sensor capturing light. It is an ensemble of different sensors which capture independent contextual information about the photo shooting event. This is stored as metadata in the image. In this paper, we demonstrate how the optical metadata (data related to the optics of the camera) can be retrieved, interpreted and used along with content information for organizing and indexing digital photos. Our model is based on the physics of vision and operation of a camera. We use our algorithm on images from personal photo albums. Our results show that the optical metadata improves annotation performance and decreases the search space for retrieval.