gebhart/patrepeval huggingface dataset:
541. Use of Endogenous Viral Elements to Deduce the Sequence of an Ancient Adeno-Associated Virus That Circulated Amongst Australian Marsupials ~30 Million Years Ago (2016)

Vectors based on adeno-associated viruses (AAVs) have been successfully applied in clinical trials and pre-clinical settings. AAV capsid proteins are the primary determinants of vector tropism and immunogenicity, and are continually being developed to impart desirable properties, such as immune evasion and specificity for selected target tissues in humans and those of model organisms. One approach that was recently adopted by at least two groups to generate novel capsid variants is the computational deduction of putative ancestral AAV sequences, based upon observable genetic diversity amongst closely related contemporary AAV isolates. Such inferred ancestral sequences potentially recapitulate the evolutionary history of AAVs for hundreds or possibly thousands of years. Germline endogenous viral elements (EVEs) can compensate for the lack of a viral fossil record by genetically preserving viral nucleotide sequences over a geologic time span. Here we describe an AAV-EVE (mAAV-EVE1) that is lineage-restricted to the germlines of members of the Australian marsupial suborder Macropodiformes (present-day kangaroos, wallabies, and related macropodoids), to the exclusion of other Diprotodontian marsupial lineages. Orthologous mAAV-EVE1 sequences from sixteen macropodoid species, representing a speciation history spanning an estimated 30 million years, facilitated in silico reconstruction of an inferred ancestral AAV sequence. This sequence represents the genome of an ancient marsupial AAV that circulated among Australian metatherian fauna sometime during the late Eocene to early Oligocene. The deduced ancient AAV bears remarkable resemblance to modern AAVs in its predicted structural and non-structural genes, underscoring the concept that despite their relatively rapid mutation rates, AAVs have evolved under tight constraints imposed by both form and function. Moreover, the evolutionary history of mAAV-EVE1 since its integration into the pro-macropodoid lineage reflects that of the respective host species. In addition to providing an inferred ancient AAV capsid sequence for future transduction studies, this sequence can serve as input for the generation of further novel capsids by approaches such as capsid shuffling and directed capsid engineering/evolution. Furthermore, by comparing it to contemporary AAV capsids, this sequence can inform rational capsid design approaches by providing insights into long-term capsid evolution.
Efficient logging for enterprise workloads on column-oriented in-memory databases (2012)

The introduction of a 64 bit address space in commodity operating systems and the constant drop in hardware prices made large capacities of main memory in the order of terabytes technically feasible and economically viable. Especially column-oriented in-memory databases are a promising platform to improve data management for enterprise applications. As in-memory databases hold the primary persistence in volatile memory, some form of recovery mechanism is required to prevent potential data loss in case of failures. Two desirable characteristics of any recovery mechanism are (1) that it has a minimal impact on the running system, and (2) that the system recovers quickly and without any data loss after a failure. This paper introduces an efficient logging mechanism for dictionary-compressed column structures that addresses these two characteristics by (1) reducing the overall log size by writing dictionary-compressed values and (2) allowing for parallel writing and reading of log files. We demonstrate the efficiency of our logging approach by comparing the resulting log-file size with traditional logical logging on a workload produced by a productive enterprise system.
Rosetting Plasmodium falciparum-Infected Erythrocytes Bind to Human Brain Microvascular Endothelial Cells <i>In Vitro</i> , Demonstrating a Dual Adhesion Phenotype Mediated by Distinct P. falciparum Erythrocyte Membrane Protein 1 Domains (2013)

Adhesion interactions between Plasmodium falciparum-infected erythrocytes (IE) and human cells underlie the pathology of severe malaria. IE cytoadhere to microvascular endothelium or form rosettes with uninfected erythrocytes to survive in vivo by sequestering IE in the microvasculature and avoiding splenic clearance mechanisms. Both rosetting and cytoadherence are mediated by the parasite-derived IE surface protein family Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1). Rosetting and cytoadherence have been widely studied as separate entities; however, the ability of rosetting P. falciparum strains to cytoadhere has received little attention. Here, we show that IE of the IT/R29 strain expressing a rosette-mediating PfEMP1 variant (IT4var09) cytoadhere in vitro to a human brain microvascular endothelial cell line (HBEC-5i). Cytoadherence was inhibited by heparin and by treatment of HBEC-5i with heparinase III, suggesting that the endothelial receptors for IE binding are heparan sulfate proteoglycans. Antibodies to the N-terminal regions of the IT4var09 PfEMP1 variant (NTS-DBL1α and DBL2γ domains) specifically inhibited and reversed cytoadherence down to low concentrations (<10 μg/ml of total IgG). Surface plasmon resonance experiments showed that the NTS-DBLα and DBL2γ domains bind strongly to heparin, with half-maximal binding at a concentration of ∼0.5 μM in both cases. Therefore, cytoadherence of IT/R29 IE is distinct from rosetting, which is primarily mediated by NTS-DBL1α interactions with complement receptor 1. These data show that IT4var09-expressing parasites are capable of dual interactions with both endothelial cells and uninfected erythrocytes via distinct receptor-ligand interactions.
Chemical Synthesis and Cell-Free Expression of Thiazoline Ring-Bridged Cyclic Peptides and Their Properties on Biomembrane Permeability (2022)

Abstract Cyclic peptides that exhibit biomembrane permeability provide a useful platform in the development of peptide drugs. Here, the reaction characteristics and versatility of a novel type of cyclic peptide having a thiazoline ring structure in the main chain were investigated. The thiazoline ring-bridged cyclic peptides were chemically synthesized by the intramolecular cyclization of linear peptides composed of N-terminal Cys and a non-natural amino acid having a cyano group on the side chain. The thiazoline ring-bridged cyclic peptides had higher model membrane permeability than amide- and thioether-bridged cyclic peptides with similar amino acid sequences. By comparing the solution structures, the factors that contribute to the higher membrane permeability were examined. In addition, the present peptide cyclization was applied to a cell-free translation system. The expression of peptides having the cyanated non-natural amino acids and subsequent spontaneous cyclization were successfully achieved.
Detection of human papillomavirus DNA in formalin-fixed tissues by in situ hybridization after amplification by polymerase chain reaction. (1991)

The authors describe the detection of human papillomavirus (HPV) 16 DNA in paraffin-embedded, formalin-fixed tissues of cervical squamous intraepithelial lesions (SILs) by in situ hybridization after amplification by the polymerase chain reaction (PCR). Using conventional in situ hybridization and a biotin-labeled probe, variable numbers of superficial cells and none of the basal cells in the SILs showed detectable HPV 16 DNA. When the in situ assay was done after amplification, increased numbers of superficial cells had detectable HPV DNA, and the hybridization signal was much more intense. HPV DNA was also detected in basal and parabasal cells at the site of the lesion whereas not detectable in directly adjacent, normal squamous epithelium. Amplified HPV DNA was demonstrated in formalin-fixed SiHa cells using a biotin-labeled probe, demonstrating the ability to detect one copy of HPV 16 DNA. This technique should allow for direct visualization in cells of other DNA sequences of low copy number from achival specimens otherwise undetectable by conventional in situ hybridization analysis.
Conditioning contexts for the arithmetic coding of bit planes (1992)

The arithmetic coding of the bit planes of an image represented either in the conventional weighted binary form or by the Gray code, is investigated. Two-dimensional contexts based on the pixels from the current bit plane and three-dimensional contexts on pixels from both the current and previous bit planes are studied. Results indicate that for binary bit planes, a three-dimensional template results in a significant bit rate reduction compared to a two-dimensional template of the same size. The savings are much less for Gray encoded bit planes; since the final bit rates are similar to the binary case, the need for Gray encoding is eliminated. The effect of the order of encoding the bit planes are also studied. Comparisons to conventional lossless schemes, such as predictive coding followed by Huffman or arithmetic coding, are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Mesenchymal stem cells in neurological diseases (2013)

Due to the limited capacity of the CNS for regeneration, more effective treatment of chronic degenerative and inflammatory neurological conditions, but also of acute neuronal damage from injuries or cerebrovascular diseases, could be only achieved, theoretically at least, by stem cells that may have the potential to either regenerate or to support the survival of the existing, partially damaged, cells. A small number of stem cells are found in the adult brain in very specific regions, but this intrinsic stem cell repertoire is rather small and does not contribute significantly to the repair of damaged tissues. Transplantation of stem cells has long been suggested as a possible logical approach for repair of the damaged nervous system. Embryonic cells carrying the pluripotent and self-renewal properties represent the prototype of stem cells, but there are additional somatic stem cells that may be harvested and expanded from various tissues during adult life, such as the mesenchymal stem cells (MSC), which offer several practical advantages for the clinical application. MSC can be obtained from every adult and there are effective culture protocols for their expansion to large numbers for clinical uses. They seem to carry fewer risks for malignancies and some initial indications of their short-term safety (upon system delivery), in clinical settings, exist in the literature. Therefore, in most of the registered clinical trials with stem cells, MSC is the primary stem cell population used. This review summarizes the rationale, the mechanisms and the worldwide clinical experience with MSC, in neurological and other diseases.
Matching colonic polyps using correlation optimized warping (2010)

Computed tomographic colonography (CTC) combined with a computer aided detection system has the potential for improving colonic polyp detection and increasing the use of CTC for colon cancer screening. In the clinical use of CTC, a true colonic polyp will be confirmed with high confidence if a radiologist can find it on both the supine and prone scans. To assist radiologists in CTC reading, we propose a new method for matching polyp findings on the supine and prone scans. The method performs a colon registration using four automatically identified anatomical salient points and correlation optimized warping (COW) of colon centerline features. We first exclude false positive detections using prediction information from a support vector machine (SVM) classifier committee to reduce initial false positive pairs. Then each remaining CAD detection is mapped to the other scan using COW technique applied to the distance along the centerline in each colon. In the last step, a new SVM classifier is applied to the candidate pair dataset to find true polyp pairs between supine and prone scans. Experimental results show that our method can improve the sensitivity to 0.87 at 4 false positive pairs per patient compared with 0.72 for a competing method that uses the normalized distance along the colon centerline (p<0.01).
Recursive and Trellis-Based Feedback Reduction for MIMO-OFDM with Rate-Limited Feedback (2006)

We investigate an adaptive MIMO-OFDM system with a feedback link that can only convey a finite number of bits. We consider three different transmitter configurations: i) beamforming applied per OFDM subcarrier, ii) precoded spatial multiplexing applied per subcarrier, and iii) precoded orthogonal space time block coding applied per subcarrier. Depending on the channel realization, the receiver selects the optimal beamforming vector or precoding matrix from a finite-size codebook on each subcarrier, and informs the transmitter through finite-rate feedback. Exploiting the fact that the channel responses across OFDM subcarriers are correlated, we propose two methods to reduce the amount of feedback. One is recursive feedback encoding that selects the optimal beamforming/precoding choices sequentially across the subcarriers, and adopts a smaller-size time-varying codebook per subcarrier depending on prior decisions. The other is trellis-based feedback encoding that selects the optimal decisions for all subcarriers at once along a trellis structure via the Viterbi algorithm. Our methods are applicable to different transmitter configurations in a unified fashion. Simulation results demonstrate that the trellis-based approach outperforms the recursive method as well as an existing interpolation-based alternative at high signal-to-noise-ratio, as the latter suffers from "diversity loss"
Invited Paper Recent Developments In Reactive Plasma Etching Of III-V Compound Semiconductors (1987)

Reactive plasma etching is being increasingly utilized in the fabrication of III-V - based electronic and optoelectronic devices. The high resolution and control afforded by dry etching processes have led to their rapid move from research to manufacturing applications. This paper will review some of those applications, processes, progress and problems associated with reactive plasma etching of III-V materials.
Synergism between RPBF Dof and RISBZ1 bZIP Activators in the Regulation of Rice Seed Expression Genes (2006)

The Dof (DNA binding with one finger) transcriptional activator rice (Oryza sativa) prolamin box binding factor (RPBF), which is involved in gene regulation of rice seed storage proteins, has been isolated from rice cDNA expressed sequence tag clones containing the conserved Dof. RPBF is found as a single gene per haploid genome. Comparison of RPBF genomic and cDNA sequences revealed that the genomic copy is interrupted by one long intron of 1,892 bp in the 5' noncoding region. We demonstrated by transient expression in rice callus protoplasts that the isolated RPBF trans-activated several storage protein genes via an AAAG target sequence located within their promoters, and with methylation interference experiments the additional AAAG-like sequences in promoters of genes expressed in maturing seeds were recognized by the RPBF protein. Binding was sequence specific, since mutation of the AAAG motif or its derivatives decreased both binding and trans-activation by RPBF. Synergism between RPBF and RISBZ1 recognizing the GCN4 motif [TGA(G/C)TCA] was observed in the expression of many storage protein genes. Overexpression of both transcription factors gave rise to much higher levels of expression than the sum of individual activities elicited by either RPBF or RISBZ1 alone. Furthermore, mutation of recognition sites suppressed reciprocal trans-activation ability, indicating that there are mutual interactions between RISBZ1 and RPBF. The RPBF gene is predominantly expressed in maturing endosperm and coordinately expressed with seed storage protein genes, and is involved in the quantitative regulation of genes expressed in the endosperm in cooperation with RISBZ1.
Highly Stable Organosilicon Electrolytes for Li-ion Batteries (2014)

During the last two decades, a large effort has been devoted to improve the safety and performance of Li-ion batteries. Current commercial electrolytes are based on highly flammable solvents that make them dangerous for certain applications. Organosilicon (OS) electrolytes are a good alternative to conventional carbonate electrolytes. Silatronix has developed many organosilanes containing ethylene oxide units for \(Li^+\) coordination. These OS have properties suitable for their use in electrolytes including high thermal stability, high flash point, low vapor pressure and relatively low viscosities. The OS electrolytes are less flammable than commercial electrolytes, hence improving the safety of the batteries and have shown a performance comparable with the current standard electrolytes when used in Li-ion coin cells. Fluoroorganosilanes (FOS) have been found to be the best candidates for commercial application and have been successfully tested in coin cells at high temperature.
Inhibition of IL-6 and IL-8 production in human fibroblast cell lines by 1,25 (OH)2 vitamin D3 and two of its analogs with lower calcemic activity. (1994)

In human fibroblast cultures TPA increased IL-6 and IL-8 production. This was reduced by vitamin D3 metabolites and analogs. The two analogs employed: 1,25 (OH)2-22 (E)-dehydro-24-monohomo vitamin D3 (Compound A) and 1,25 (OH)2 -22 (E)-dehydro-24 dihomo-vitamin D3 (Compound B) may be useful in the therapy of pathologic proliferative disorders including psoriasis, particularly since they are less toxic and have less effect on calcium metabolism than vitamin D3.
Hierarchical nanotwins in single-crystal-like nickel with high strength and corrosion resistance produced<i>via</i>a hybrid technique (2019)

High-density growth nanotwins enable high-strength and good ductility in metallic materials. However, twinning propensity is greatly reduced in metals with high stacking fault energy. Here we adopted a hybrid technique coupled with template-directed heteroepitaxial growth method to fabricate single-crystal-like, nanotwinned (nt) Ni. The nt Ni primarily contains hierarchical twin structures that consist of coherent and incoherent twin boundary segments with few conventional grain boundaries. In situ compression studies show the nt Ni has a high flow strength of ∼2 GPa and good deformability. Moreover, the nt Ni has superb corrosion behavior due to the unique twin structure in comparison to coarse grained and nanocrystalline counterparts. The hybrid technique opens the door for the fabrication of a wide variety of single-crystal-like nt metals with unique mechanical and chemical properties.
Guided acoustic-surface-wave filters (1976)

A number of filter structures utilizing acoustic surface waveguides and periodic arrays of reflecting strips to form multimoded resonant configurations are described. The devices described are analogous to the monolithic crystal filter in that an array of acoustically coupled resonators is obtained from a structure placed on a single substrate. The coupling between resonators is described in terms of trapped energy modes of the surface-waveguiding structures.
EHMTI-0191. A novel approach for the treatment of cluster headache – onabotulinumtoxina block of the sphenopalatine ganglion (2014)

Aim The aim of this pilot study was to explore the safety aspects and therapeutic potential of SphenoBlock. Method After signing written confirmed consent ten patients with iCCH were injected with 25 U (n=5) or 50 U (n=5) onabotulinumtoxinA towards the sphenopalatine ganglion in an observational study, approved by the Institutional Review Board, with 6 months follow-up. The procedure was performed with a novel imageguided technique. The primary endpoint was to evaluate safety of the procedure, but change in attack
Arbitrarily-shaped bursts of picosecond pulses from a fiber laser source for high-throughput applications (2011)

Increasing the ablation efficiency of picosecond laser sources can be performed by bunching pulses in bursts<sup>1</sup> and benefit from heat accumulation effects<sup>2-5</sup> in the target. Pulsed fiber lasers are well suited for such a regime of operation, as the single pulse energy in a fiber is limited by the onset of nonlinear effects (SPM, SRS). Increasing the number of pulses to form a burst of pulses allows for average power scaling of picosecond fiber lasers. We are presenting in this paper a high-power fiber laser emitting arbitrarily-shaped bursts of picosecond pulses at 20 W of average output power. Burst duration can be varied from 2.5 ns to 80 ns. The burst repetition rate is externally triggered and can be varied from 100 kHz to 1 MHz. The single pulse duration is 60 ps and the repetition rate within a burst is 1.8 GHz. The output beam is linearly polarized (PER > 20 dB) and its M<sup>2</sup> value is smaller than 1.15. The laser source has a tunable central wavelength around 1064 nm and a spectral linewidth compatible with frequency conversion. Conversion efficiency higher than 60% has been obtained at 10 W of 1064-nm output power.
Integrated Microstrip Antennas and Phased Arrays with Mode-Free Electromagnetic Bandgap Materials for Scan Blindness Elimination (2017)

This article discusses the investigation of the use of mode-free electromagnetic bandgap materials, a novel bandgap-antenna structure, to eliminate scan blindness from two-dimensional infinite microstrip phased arrays. This electromagnetic bandgap material is multi-functional; in addition to suppressing both surface and leaky waves, it also radiates to broadside direction as an antenna element within the mode-free bandgap region. A strip line impedance matching network is used to match the bandgap-antenna element’s input impedance to 50 Ω, so that the actual bandgap behavior of the structure on the array can be obtained since the strip line does not allow couplings within the matching network. In addition, internal couplings within the unit element of the bandgap-antenna structure, which is composed of four metallic layers, are analyzed in detail; these internal couplings vary with array element’s excitation phase or scan angles, therefore, an optimum structure must consider scan behavior as well.
Performance enhancements on a pulsed detonation engine (2003)

A major problem applying detonations into aero-propulsive devices is the transition of deflagration and weak detonation into CJ detonation. The longer this transition, the longer the physical length of the engine must be to facilitate the propagation of the flame. However, lengthening of the detonation chamber can significantly increase weight, rendering the reduction of DDT (deflagration to detonation) and weak detonation transition length of great importance. One of the most common means of shortening these lengths is with the aid of a Shchelkin spiral. A simple helical apparatus, it was used in early single-shot detonation investigations to over-exaggerate wall roughness effects
Decoder for variable-number of channel presentation of multidimensional sound fields (1995)

First Page
Test apparatus for determination of vibration characteristics of piezoelectric transducers (1985)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Friedrich Ruckenbauser, Peter Krempl; Test apparatus for determination of vibration characteristics of piezoelectric transducers. J. Acoust. Soc. Am. 1 May 1985; 77 (5): 1979. https://doi.org/10.1121/1.391789 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAcoustical Society of AmericaThe Journal of the Acoustical Society of America Search Advanced Search |Citation Search