gebhart/patrepeval huggingface dataset:
Cytokine-based high log-scale expansion of functional human dendritic cells from cord-blood CD34-positive cells (2011)

Dendritic cells (DCs) play a crucial role in maintaining the immune system. Though DC-based cancer immunotherapy has been suggested as a potential treatment for various kinds of malignancies, its clinical efficacies are still insufficient in many human trials. Issues that limit the clinical efficacy of DC-based immunotherapy, as well as the difficulty of the industrial production of DCs, are largely due to the limited number of autologous DCs available from each patient. We here established a possible breakthrough, a simple cytokine-based culture method to expand the log-scale order of functional human DCs. Floating cultivation of cord-blood CD34(+) cells under an optimized cytokine cocktail led these progenitor cells to stable log-scale proliferation and to DC differentiation. The expanded DCs had typical features of conventional myeloid DCs in vitro. Therefore, the concept of DC expansion should contribute significantly to the progress of DC immunotherapy.
Targeted inactivation of transcription factors by overexpression of their truncated forms in plants (2012)

Transcription factors are central constituents of gene regulatory networks that control diverse aspects of plant development and environmental adaptability. Therefore they have been explored for decades as primary targets for agricultural biotechnology. A gene of interest can readily be introduced into many crop plants, whereas targeted gene inactivation is practically difficult in many cases. Here, we developed an artificial small interfering peptide (a-siPEP) approach, which is based on overexpression of specific protein domains, and evaluated its application for the targeted inactivation of transcription factors in the dicot model, Arabidopsis, and monocot model, Brachypodium. We designed potential a-siPEPs of two representative MADS box transcription factors, SUPPRESSOR OF OVEREXPRESSOR OF CONSTANS 1 (SOC1) and AGAMOUS (AG), and a MYB transcription factor, LATE ELONGATED HYPOCOTYL (LHY). Transgenic plants overproducing the a-siPEPs displayed phenotypes comparable to those of gene-deficient mutants. The a-siPEPs attenuate nuclear import and DNA-binding of target transcription factors. Our data demonstrate that the a-siPEP tool is an efficient genetic means of inactivating specific transcription factors in plants.
Recognition of Modern Arabic Poems (2015)

We propose a machine learning method for recognizing modern Arabic poems based on the common poetic features of modern Arabic poetry. The poetic features include: rhyming, repetition, use of diacritics and punctuations, and text alignment. The method can classify text documents as poem or non-poem documents with a very high accuracy of 99.81%.
Design, Efficient Synthesis, and Anti‐HIV Activity of 4′‐<i>C</i>‐Cyano‐ and 4′‐<i>C</i>‐Ethynyl‐2′‐deoxy Purine Nucleosides (2004)

Some 4'-C-ethynyl-2'-deoxy purine nucleosides showed the most potent anti-HIV activity among the series of 4'-C-substituted 2'-deoxynucleosides whose 4'-C-substituents were methyl, ethyl, ethynyl and so on. Our hypothesis is that the smaller the substituent at the C-4' position they have, the more acceptable biological activity they show. Thus, 4'-C-cyano-2'-deoxy purine nucleosides, whose substituent is smaller than the ethynyl group, will have more potent antiviral activity. To prove our hypothesis, we planned to develop an efficient synthesis of 4'-C-cyano-2'-deoxy purine nucleosides (4'-CNdNs) and 4'-C-ethynyl-2'-deoxy purine nucleosides (4'-EdNs). Consequently, we succeeded in developing an efficient synthesis of six 2'-deoxy purine nucleosides bearing either a cyano or an ethynyl group at the C-4' position of the sugar moiety from 2'-deoxyadenosine and 2,6-diaminopurine 2'-deoxyriboside. Unfortunately, 4'-C-cyano derivatives showed lower activity against HIV-1, and two 4'-C-ethynyl derivatives suggested high toxicity in vivo.
Reference Axis Selection: Subcommittee Report of the OSA Working Group to Establish Standards for Measurement and Reporting of Optical Aberrations of the Eye (2000)

It is the committee's recommendation that the ophthalmic community use the line of sight as the reference axis for the purposes of calculating and measuring the ocular optical aberrations.
Permuting streaming data using RAMs (2009)

This article presents a method for constructing hardware structures that perform a fixed permutation on streaming data. The method applies to permutations that can be represented as linear mappings on the bit-level representation of the data locations. This subclass includes many important permutations such as stride permutations (corner turn, perfect shuffle, etc.), the bit reversal, the Hadamard reordering, and the Gray code reordering. The datapath for performing the streaming permutation consists of several independent banks of memory and two interconnection networks. These structures are built for a given streaming width (i.e., number of inputs and outputs per cycle) and operate at full throughput for this streaming width. We provide an algorithm that completely specifies the datapath and control logic given the desired permutation and streaming width. Further, we provide lower bounds on the achievable cost of a solution and show that for an important subclass of permutations our solution is optimal. We apply our algorithm to derive datapaths for several important permutations, including a detailed example that carefully illustrates each aspect of the design process. Lastly, we compare our permutation structures to those of Järvinen et al. [2004], which are specialized for stride permutations.
Context-Aware Synthesis for Video Frame Interpolation (2018)

Video frame interpolation algorithms typically estimate optical flow or its variations and then use it to guide the synthesis of an intermediate frame between two consecutive original frames. To handle challenges like occlusion, bidirectional flow between the two input frames is often estimated and used to warp and blend the input frames. However, how to effectively blend the two warped frames still remains a challenging problem. This paper presents a context-aware synthesis approach that warps not only the input frames but also their pixel-wise contextual information and uses them to interpolate a high-quality intermediate frame. Specifically, we first use a pre-trained neural network to extract per-pixel contextual information for input frames. We then employ a state-of-the-art optical flow algorithm to estimate bidirectional flow between them and pre-warp both input frames and their context maps. Finally, unlike common approaches that blend the pre-warped frames, our method feeds them and their context maps to a video frame synthesis neural network to produce the interpolated frame in a context-aware fashion. Our neural network is fully convolutional and is trained end to end. Our experiments show that our method can handle challenging scenarios such as occlusion and large motion and outperforms representative state-of-the-art approaches.
Engineered membrane protein antigens successfully induce antibodies against extracellular regions of claudin-5 (2018)

The production of antibodies against the extracellular regions (ECR) of multispanning membrane proteins is notoriously difficult because of the low productivity and immunogenicity of membrane proteins due to their complex structure and highly conserved sequences among species. Here, we introduce a new method to generate ECR-binding antibodies utilizing engineered liposomal immunogen prepared using a wheat cell-free protein synthesis system. We used claudin-5 (CLDN-5) as the target antigen, which is a notoriously difficult to produce and poorly immunogenic membrane protein with two highly conserved extracellular loops. We drastically improved the productivity of CLDN-5 in the cell-free system after suppressing and normalizing mRNA GC content. To overcome its low immunogenicity, two engineered antigens were designed and synthesized as proteoliposomes: a human/mouse chimeric CLDN-5, and a CLDN-5-based artificial membrane protein consisting of symmetrically arranged ECRs. Intraperitoneal immunization of both engineered CLDN-5 ECR antigens induced ECR-binding antibodies in mice with a high success rate. We isolated five monoclonal antibodies that specifically recognized CLDN-5 ECR. Antibody clone 2B12 showed high affinity (<10 nM) and inhibited CLDN-5-containing tight junctions. These results demonstrate the effectiveness of the methods for monoclonal antibody development targeting difficult-to-produce membrane proteins such as CLDNs.
Crosstalk in multicore fibers with randomness: gradual drift vs short-length variations (2012)

Random perturbations play an important role in the crosstalk of multicore fibers, and can be captured by statistical coupled-mode calculations. In this approach, phase matching contributes a multiplicative factor to the average crosstalk, depending on the perturbation statistics and any intentional heterogeneity of neighboring cores. The impact of perturbations is shown to be qualitatively different depending on whether they are gradually varying, or have short-length (centimeter-scale) variations. This insight implies a novel crosstalk suppression strategy: fast modulation of a bend perturbation by spinning the fiber can disrupt the bend-induced phase matching.
Association of herpes simplex virus regulatory protein ICP22 with transcriptional complexes containing EAP, ICP4, RNA polymerase II, and viral DNA requires posttranslational modification by the U(L)13 proteinkinase (1997)

The expression of herpes simplex virus 1 gamma (late) genes requires functional alpha proteins (gamma1 genes) and the onset of viral DNA synthesis (gamma2 genes). We report that late in infection after the onset of viral DNA synthesis, cell nuclei exhibit defined structures which contain two viral regulatory proteins (infected cell proteins 4 and 22) required for gamma gene expression, RNA polymerase II, a host nucleolar protein (EAP or L22) known to be associated with ribosomes and to bind small RNAs, including the Epstein-Barr virus small nuclear RNAs, and newly synthesized progeny DNA. The formation of these complexes required the onset of viral DNA synthesis. The association of infected cell protein 22, a highly posttranslationally processed protein, with these structures did not occur in cells infected with a viral mutant deleted in the genes U(L)13 and U(S)3, each of which specifies a protein kinase known to phosphorylate the protein.
Forty Years of Xylene Isomerization Technology Deployment at <scp>ExxonMobil</scp> (Case Study) (2023)

Paraxylene is by far the most industrially significant of the three xylene isomers yet the least abundant (∼24% only) in equilibrium xylenes. Commercial processes re-isomerizing paraxylene-depleted streams are therefore of paramount importance in the polyester chain. This chapter surveys 40 years of xylene isomerization process development and deployment by ExxonMobil. The two routes for ethylbenzene (EB) conversion, namely, xylenes (EB reforming) or benzene (EB dealkylation), are described and discussed. This chapter focuses on the EB-dealkylation route (the industry dominant process) and its evolution, initially from single- to dual-bed catalytic systems and later to dual-bed technologies using an ex situ selectivated catalyst in the first bed. The recent commercialization of a new liquid-phase xylene isomerization process, with associated energy savings and debottleneck capacity, is also presented.
Partial cloning and expression of the bovine leptin gene (1998)

The product of the leptin (i.e., obese) gene may be an important regulator of energy metabolism, adiposity, and reproduction, and is perhaps linked to meat quality determinants such as marbling. Molecular probes were developed using polymerase chain reaction (PCR) technology to evaluate leptin expression in adipose depots and to evaluate the tissue-dependent nature of expression reported in other species. A 438 bp fragment representing the coding region of the bovine leptin gene excluding the N-terminal secretory signal was amplified, cloned into a plasmid vector (pASK75), and expressed in E. coli. Sequence analysis of the cDNA and the corresponding polypeptide indicate that, overall, both share approximately 87% homology with the mouse and human leptin genes and polypeptides. Amino terminal sequencing (30 amino acid residues) of the recombinant bovine leptin (rBL) protein revealed 100% homology with mouse and human leptin. The bovine leptin gene is expressed as a 3,090 nt mRNA which is detected in adipose tissue, but is not found in brain (despite the appreciable fat content and lipid metabolism) or other tissues. Leptin gene expression in several adipose depots (subcutaneous, renal, and omental) was similar (P = .73) in finished cattle.
A Simple and Efficient Large-Scale Synthesis of Metal Salts of Medium-Chain Fatty Acids (2009)

A simple, inexpensive, one-step general procedure was developed for the preparation of medium-chain fatty acid (MCFA) metal salts. This approach offers the advantage of a practical route and is superior to literature methods. Also, it overcomes many of the limitations previously reported for the preparation of fatty acid salts. The potential utility of this method is illustrated by the production of pilot-scale quantities of high-purity (>99.9%) sodium decanoate.
A novel ultra-low loss hollow-core waveguide using subwavelength high-contrast gratings (2009)

We propose a novel ultra-low loss single-mode hollow-core waveguide using subwavelength high-contrast grating (HCG). We analyzed and simulated the propagation loss of the waveguide and show it can be as low as 0.006 dB/m, three orders of magnitude lower than the lowest loss of the state-of-art chip-scale hollow waveguides. This novel HCG hollow-core waveguide design will serve as a basic building block in many chip-scale integrated photonic circuits enabling system-level applications including optical interconnects, optical delay lines, and optical sensors.
Molecular Engineering of Azobenzene-Functionalized Polyimides To Enhance Both Photomechanical Work and Motion (2014)

Photomechanical effects in polymeric materials directly convert input photonic energy into a macroscopic mechanical output. The photoinitiated mechanical output of these materials is typically dominated by classical mechanics, primarily derived from the material stiffness and sample geometry. Accordingly, large magnitude shape change (e.g., motion) is typically traded for large magnitude force generation. Here, we report on the systematic preparation and comparison of photomechanical effects in a set of isomerically varied linear and cross-linked azobenzene-functionalized materials that demonstrate the critical role of segmental mobility (evident in the magnitude of the β-transition) to assimilate the typically exclusive properties of large force generation and large shape change in a single material.
The role of p53 and the CD95 (APO-1/Fas) death system in chemotherapy-induced apoptosis. (1998)

To explore the pathway of p53 dependent cell death, we investigated if p53 dependent apoptosis following DNA damage is mediated by the CD95 (APO-1/Fas) receptor/ligand system. We investigated cell lines of solid human tumors upon treatment with clinically relevant chemotherapeutic drugs known to act via p53 accumulation. Treatment with these cytotoxic drugs led to an upregulation of both, the CD95 receptor (CD95) and the CD95L (CD95L). Induction of the CD95L occurred in p53 wild-type (wt), p53 mutant (mt) and in cell lines lacking p53 altogether (p53-/-). Thus, the regulation of the CD95L in response to chemotherapeutic drugs clearly involves p53 independent mechanisms. Most importantly, upregulation of CD95 occurred only in cell lines with wild-type p53, thereby strongly increasing the responsiveness towards CD95 mediated apoptosis. Thus, upregulation of the CD95 receptor seems to be dependent on intact wild-type p53. Apoptosis was mediated by cleavage of the receptor proximal caspase, caspase-8 (FLICE/MACH). Caspase-8 cleavage was observed, independent of the p53 status of the tumor cells and irrespective whether or not apoptosis was dependent on the CD95 system. Hence, additional effector pathways besides CD95/CD95L signaling are likely to contribute to drug-induced apoptosis.
4D Nanoscale Diffraction Observed by Convergent-Beam Ultrafast Electron Microscopy (2009)

Diffraction with focused electron probes is among the most powerful tools for the study of time-averaged nanoscale structures in condensed matter. Here, we report four-dimensional (4D) nanoscale diffraction, probing specific site dynamics with 10 orders of magnitude improvement in time resolution, in convergent-beam ultrafast electron microscopy (CB-UEM). As an application, we measured the change of diffraction intensities in laser-heated crystalline silicon as a function of time and fluence. The structural dynamics (change in 7.3 +/- 3.5 picoseconds), the temperatures (up to 366 kelvin), and the amplitudes of atomic vibrations (up to 0.084 angstroms) are determined for atoms strictly localized within the confined probe area (10 to 300 nanometers in diameter). We anticipate a broad range of applications for CB-UEM and its variants, especially in the studies of single particles and heterogeneous structures.
Biochemical and Molecular Characterization of Secreted α-Xylosidase from Aspergillus niger (2011)

α-Linked xylose is a major component of xyloglucans in the cell walls of higher plants. An α-xylosidase (AxlA) was purified from a commercial enzyme preparation from Aspergillus niger, and the encoding gene was identified. The protein is a member of glycosyl hydrolase family 31. It was active on p-nitrophenyl-α-d-xyloside, isoprimeverose, xyloglucan heptasaccharide (XXXG), and tamarind xyloglucan. When expressed in Pichia pastoris, AxlA had activity comparable to the native enzyme on pNPαX and IP despite apparent hyperglycosylation. The pH optimum of AxlA was between 3.0 and 4.0. AxlA together with β-glucosidase depolymerized xyloglucan heptasaccharide. A combination of AxlA, β-glucosidase, xyloglucanase, and β-galactosidase in the optimal proportions of 51:5:19:25 or 59:5:11:25 could completely depolymerize tamarind XG to free Glc or Xyl, respectively. To the best of our knowledge, this is the first characterization of a secreted microbial α-xylosidase. Secreted α-xylosidases appear to be rare in nature, being absent from other tested commercial enzyme mixtures and from the genomes of most filamentous fungi.
Koi herpesvirus represents a third cyprinid herpesvirus (CyHV-3) in the family Herpesviridae (2005)

The sequences of four complete genes were analysed in order to determine the relatedness of koi herpesvirus (KHV) to three fish viruses in the family Herpesviridae: carp pox herpesvirus (Cyprinid herpesvirus 1, CyHV-1), haematopoietic necrosis herpesvirus of goldfish (Cyprinid herpesvirus 2, CyHV-2) and channel catfish virus (Ictalurid herpesvirus 1, IcHV-1). The genes were predicted to encode a helicase, an intercapsomeric triplex protein, the DNA polymerase and the major capsid protein. The results showed that KHV is related closely to CyHV-1 and CyHV-2, and that the three cyprinid viruses are related, albeit more distantly, to IcHV-1. Twelve KHV isolates from four diverse geographical areas yielded identical sequences for a region of the DNA polymerase gene. These findings, with previously published morphological and biological data, indicate that KHV should join the group of related lower-vertebrate viruses in the family Herpesviridae under the formal designation Cyprinid herpesvirus 3 (CyHV-3).
Options Extending the Applicability of High-Temperature Irradiation-Resistant Thermocouples (2009)

Several options have been identified that could further enhance the reliability and extend the applicability of high-temperature irradiation-resistant thermocouples (HTIR-TCs) developed by the Idaho National Laboratory (INL) for in-pile testing, allowing their use in temperature applications as high as 1800%C.The INL and the University of Idaho (UI) investigated these options with the ultimate objective of providing recommendations for alternate thermocouple designs that are optimized for various applications. This paper reports results from INL/UI investigations. Results are reported from tests completed to evaluate the ductility, resolution, transient response, and stability of thermocouples made from specially formulated alloys of molybdenum and niobium,not considered in initial HTIR-TC development. In addition, this paper reports insights gained by comparing the performance of HTIR-TCs fabricated with various heat Ntreatments and alternate geometries.
Exploiting dynamical symmetry in coupled nonlinear elements for efficient frequency down-conversion (2007)

The rich dynamical behavior stemming from unidirectional coupling in a single array of overdamped nonlinear elements has, recently, been extensively studied. By adjusting control parameters, one obtains regimes of oscillations with a frequency that scales in a characteristic way with the control parameter. With an external time-sinusoidal driving signal, a richness of synchronized (to the drive frequency or its subharmonics depending on the control parameter) dynamical behavior ensues. Including M > or = 2 arrays with a suitably chosen cross coupling has also been shown to lead to multifrequency patterns in the emergent dynamics. Here, we consider this arrangement and demonstrate that, under the appropriate conditions, the oscillation frequency of each successive array decreases by a rational factor with increasing M . This frequency down-conversion, obtainable without a heterodyning signal, affords the promise of very efficient signal processing in a variety of applications wherein, currently, the frequency down-conversion stage typically involves multistep processes with complicated and (often) noisy circuitry.
Virtual Electrophysiological Study of Atrial Fibrillation in Fibrotic Remodeling (2015)

Research has indicated that atrial fibrillation (AF) ablation failure is related to the presence of atrial fibrosis. However it remains unclear whether this information can be successfully used in predicting the optimal ablation targets for AF termination. We aimed to provide a proof-of-concept that patient-specific virtual electrophysiological study that combines i) atrial structure and fibrosis distribution from clinical MRI and ii) modeling of atrial electrophysiology, could be used to predict: (1) how fibrosis distribution determines the locations from which paced beats degrade into AF; (2) the dynamic behavior of persistent AF rotors; and (3) the optimal ablation targets in each patient. Four MRI-based patient-specific models of fibrotic left atria were generated, ranging in fibrosis amount. Virtual electrophysiological studies were performed in these models, and where AF was inducible, the dynamics of AF were used to determine the ablation locations that render AF non-inducible. In 2 of the 4 models patient-specific models AF was induced; in these models the distance between a given pacing location and the closest fibrotic region determined whether AF was inducible from that particular location, with only the mid-range distances resulting in arrhythmia. Phase singularities of persistent rotors were found to move within restricted regions of tissue, which were independent of the pacing location from which AF was induced. Electrophysiological sensitivity analysis demonstrated that these regions changed little with variations in electrophysiological parameters. Patient-specific distribution of fibrosis was thus found to be a critical component of AF initiation and maintenance. When the restricted regions encompassing the meander of the persistent phase singularities were modeled as ablation lesions, AF could no longer be induced. The study demonstrates that a patient-specific modeling approach to identify non-invasively AF ablation targets prior to the clinical procedure is feasible.