gebhart/patrepeval huggingface dataset:
A Novel Implementation Framework of Digital Twins for Intelligent Manufacturing Based on Container Technology and Cloud Manufacturing Services (2022)

Many core technologies of Industry 4.0 have gained substantial advancement in recent years. Digital Twin (DT) has become the key technology and tool for manufacturing industries to realize intelligent cyber-physical integration and digital transformation by leveraging these technologies. Although there have been many DT-related works, there is no standard definition, unified framework, and implementation approach of DT until now. Widely developing DTs for the manufacturing industry is still challenging. Thus, this paper proposes a novel implementation framework of digital twins for intelligent manufacturing, denoted as IF-DTiM, which possesses several distinct merits to distinguish itself from previous works. First, IF-DTiM fully utilizes new-generation container technology so that DT-related applications and services can be packaged in a self-contained way, rapidly deployed, and robustly operated with the capabilities of failover, autoscaling, and load balancing. Second, it leverages existing intelligent cloud manufacturing services to realize the intelligence for DT externally in a scalable and plug-and-play manner instead of using traditional approaches to embed intelligence in DT. Third, IF-DTiM contains Product DT for products, Equipment DT (i.e., EQ DT) for equipment, and Process DT for production lines, which can generically fulfill the demands and scenarios to achieve intelligent manufacturing for various manufacturing industries. Testing results show that IF-DTiM can achieve remarkable performance in rapid deployment and real-time data exchanges of DT-related applications. Finally, we develop an example DTiM system for CNC machining based on IF-DTiM to demonstrate its efficacy and applicability in facilitating the manufacturing industry to build their DT systems. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Note to Practitioners</i> —Developing Digital Twin (DT) systems to realize intelligent manufacturing is challenging. The proposed IF-DTiM (Implementation Framework of Digital Twins for Intelligent Manufacturing) provides a novel container-technology and cloud-manufacturing-service-based systematic methodology for building DTiM. In this paper, we present the system architecture and several operational scenarios (e.g., how to create and use DTs) of IF-DTiM, together with the design of its core functional mechanisms (e.g., rapid deployment scheme for DT, real-time data exchange for DT, DT interface pattern, and general workflow architecture for DT). Also, an example DTiM system for CNC machining based on IF-DTiM is presented to facilitate the practitioners to adopt the designs and niches in IF-DTiM to build their desired DTiM systems.
On-line knowledge embedding for an interactive EC-based montage system (2003)

Proposes an online knowledge embedding method for interactive evolutionary computation (EC) to reduce human fatigue. Online knowledge embedding is a method in which a user explicitly uses search hints that he obtains during an interactive EC operation for the next search. To evaluate this method, we developed two interactive EC-based montage systems. Our montage systems generate images of a face by combining six different part-images. The first system embeds the user's intention in an EC search and the second does not. The results of subjective tests and other evaluation measurements have shown that the proposed method realizes a faster convergence than ordinary interactive EC searches do.
Recombinant Immunotoxin Containing a Disulfide-Stabilized Fv Directed at erbB2 That Does Not Require Proteolytic Activation (1996)

PE35/e23(dsFv)KDEL is a recombinant immunotoxin composed of a recombinant form of Pseudomonas exotoxin that does not need proteolytic activation and a disulfide-stabilized Fv fragment of the anti-erbB2 monoclonal antibody e23. In this molecule, the variable heavy (V H) domain is inserted near the carboxyl terminus of PE at position 607 and the variable light (V L) domain is connected to the V H domain by a disulfide bond engineered into the framework region. The disulfide bond forms between cysteines introduced at position 44 of V H and position 99 of V L [Reiter et al. (1994) J. Biol. Chem. 269, 18327-18331]. In contrast to other PE-derived Fv fusion proteins, this type of recombinant toxin does not need proteolytic activation of the toxin domain. PE35/e23(dsFv)KDEL is very cytotoxic toward erbB2 antigen-expressing N87 cells (IC50 = 0.8 ng/mL) despite the fact that it binds to the erbB2 protein only 25% as well as e23(dsFv)PE38KDEL, in which the dsFv moiety is located at the amino terminus of the toxin. The lower binding affinity is probably due to interference by domain III of PE with the amino terminus of e23(V H), possibly where the antigen binding sites are located. Nevertheless, the specificity of immunotoxin is still retained, and it is very stable at 37 degrees C. Because of its small size, stability, and activity without proteolytic processing, this immunotoxin may be advantageous for tumor treatment. PE35/e23(dsFv)KDEL was also used to gain information about whether reduction of the disulfide bonds connecting V H and V L occur in the endoplasmic reticulum (ER) or in a proximal compartment. To do this, we switched the ER retention sequence KDEL from the toxin--V H subunit to the V L subunit. Our results suggest that reduction of the disulfide bond connecting the dsFv heterodimer occurs before the immunotoxin reaches the ER, where translocation to the cytosol appears to occur.
The Evolution of Mammalian Gene Families (2006)

Gene families are groups of homologous genes that are likely to have highly similar functions. Differences in family size due to lineage-specific gene duplication and gene loss may provide clues to the evolutionary forces that have shaped mammalian genomes. Here we analyze the gene families contained within the whole genomes of human, chimpanzee, mouse, rat, and dog. In total we find that more than half of the 9,990 families present in the mammalian common ancestor have either expanded or contracted along at least one lineage. Additionally, we find that a large number of families are completely lost from one or more mammalian genomes, and a similar number of gene families have arisen subsequent to the mammalian common ancestor. Along the lineage leading to modern humans we infer the gain of 689 genes and the loss of 86 genes since the split from chimpanzees, including changes likely driven by adaptive natural selection. Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes) in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences. This genomic "revolving door" of gene gain and loss represents a large number of genetic differences separating humans from our closest relatives.
Efficient dilation, erosion, opening, and closing algorithms (2002)

We propose an efficient and deterministic algorithm for computing the one-dimensional dilation and erosion (max and min) sliding window filters. For a p-element sliding window, our algorithm computes the 1D filter using 1.5 + o(1) comparisons per sample point. Our algorithm constitutes a deterministic improvement over the best previously known such algorithm, independently developed by van Herk (1992) and by Gil and Werman (1993) (the HGW algorithm). Also, the results presented in this paper constitute an improvement over the Gevorkian et al. (1997) (GAA) variant of the HGW algorithm. The improvement over the GAA variant is also in the computation model. The GAA algorithm makes the assumption that the input is independently and identically distributed (the i.i.d. assumption), whereas our main result is deterministic. We also deal with the problem of computing the dilation and erosion filters simultaneously, as required, e.g., for computing the unbiased morphological edge. In the case of i.i.d. inputs, we show that this simultaneous computation can be done more efficiently then separately computing each. We then turn to the opening filter, defined as the application of the min filter to the max filter and give an efficient algorithm for its computation. Specifically, this algorithm is only slightly slower than the computation of just the max filter. The improved algorithms are readily generalized to two dimensions (for a rectangular window), as well as to any higher finite dimension (for a hyperbox window), with the number of comparisons per window remaining constant. For the sake of concreteness, we also make a few comments on implementation considerations in a contemporary programming language.
A 167-processor 65 nm computational platform with per-processor dynamic supply voltage and dynamic clock frequency scaling (2008)

A 167-processor 65 nm computational platform well suited for DSP, communication, and multimedia workloads contains 164 programmable processors with dynamic supply voltage and dynamic clock frequency circuits, three algorithm-specific processors, and three 16 KB shared memories, all clocked by independent oscillators and connected by configurable long-distance-capable links.
Genome map of Campylobacter fetus subsp. fetus ATCC 27374 (1995)

A physical map of the chromosome of Cu7zp~Mx~frr ,&ms subsp. ,&us was constructed by using pulsed-field gel electrophoresis of restriction fragments generated by SuIl, Snlul and NorI. Digestion of the type strain ATCC 27374 with these restriction endonucleases resulted in generating 4-14 fragments. The order of the fragments was deduced from hybridization of these restriction fragments to Southern blots of pulsed-field gel electrophoresis gels generated by the other two enzymes. The estimated genome size was I I60 kb. The position of several homologous and heterologous genes was determined on the circular map. These included the 2.8.kb sapA gene, encoding the 97-kDa surface array protein. Three copies of ribosomal RNA genes for which the IhS, 2% and 5S rRNA appeared to be located in close proximity in each of the three regions. The RNA polymerase genes rpoA. rpoB, and rpoD were mapped and appeared to be situated close together in one region. The flagellin genes (,flclAB) of C. jqjL[ni and the gyrase genes ,gyA and gyB of C. prt$?ngrm and Bacillus .suhti/is, respectively. were used to identify the locations of ,flaAB. the gw-A and the g!rB genes on the ATCC 27374 chromosome.
Histological evaluation of the effect of trichloroacetic acid and mineral trioxide aggregate on human teeth pulp (2017)

Objective: The objective of this study was to compare between the effects of two medicaments [trichloroacetic acid (TCA) and mineral trioxide aggregate (MTA)] on the remaining pulp tissue of the young permanent teeth after pulpotomy.Materials and methods: The present study comprised 30 premolars. Pulpotomy procedure was performed. The radicular pulp was capped with MTA in premolar in one side and with TCA in those of the other side. Premolars were reviewed after successive periods (1 week, 1, and 3 months). Teeth were extracted after examination periods. Sections was then stained by standard hematoxylin and eosin stain.Results and conclusion: Bridge formation was seen in TCA group after 3 months which is a desirable finding in pulpotomy procedures, whereas MTA is superior to TCA in treating pulps in human teeth.
RecQ helicase, in concert with RecA and SSB proteins, initiates and disrupts DNA recombination (1998)

RecQ helicase is important to homologous recombination and DNA repair in Escherichia coli. We demonstrate that RecQ helicase, in conjunction with RecA and SSB proteins, can initiate recombination events in vitro. In addition, RecQ protein is capable of unwinding a wide variety of DNA substrates, including joint molecules formed by RecA protein. These data are consistent with RecQ helicase assuming two roles in the cell; it can be (1) an initiator of homologous recombination, or (2) a disrupter of joint molecules formed by aberrant recombination. These findings also shed light on the function of the eukaryotic homologs of RecQ helicase, the Sgs1, Blm, and Wrn helicases.
Identification of a nitrate‐responsive <i>cis</i> ‐element in the Arabidopsis <i>NIR1</i> promoter defines the presence of multiple <i>cis</i> ‐regulatory elements for nitrogen response (2010)

Nitrate is a major nitrogen source for land plants and also acts as a signaling molecule that induces changes in growth and gene expression. To identify the cis-acting DNA element involved in nitrate-responsive gene expression, we analyzed the promoter of the Arabidopsis gene encoding nitrite reductase (NIR1). A region from positions -188 to -1, relative to the translation start site, was found to contain at least one cis-element necessary for the nitrate-dependent activation of the promoter, in which the activity of nitrate transporter NRT2.1 and/or NRT2.2 plays a critical role. To define this nitrate-responsive cis-element (NRE), we compared the sequences of several nitrite reductase gene promoters from various higher plants and identified a conserved sequence motif as the putative NRE. A synthetic promoter in which the four copies of a 43-bp sequence containing the motif were fused to the 35S minimal promoter was found to direct nitrate-responsive transcription. Furthermore, mutations within this conserved motif in the native NIR1 promoter markedly reduced the nitrate-responsive activity of the promoter, indicating that the 43-bp sequence is an NRE that is both necessary and sufficient for nitrate-responsive transcription. We also show that both the native NIR1 promoter and the synthetic promoter display a similar level of sensitivity to nitrate, but respond differentially to exogenously supplied glutamine, indicating independent modulation of NIR1 expression by NRE-mediated nitrate induction and feedback repression mediated by other cis-element(s). These findings thus define the presence of multiple cis-elements involved in the nitrogen response in Arabidopsis.
Transfer learning through deep learning (2018)

Deep learning method, convolutional neural network (CNN) outperforms conventional machine learning method in the famous 1000-class large scale image recognition challenge held in 2012. Since then, state-of-art CNN model is getting deeper and its capacity is getting larger. Multiple regularization techniques have been proposed to overcome overfitting, which results in exceeding human’s level. However, every machine learning method is very domain-dependent, an efficient way to increase its ability to generalize well to the real-world domain is still an open research issue. The common scenario where training dataset is small, latency of prediction is critical, or memory resource is constrained would impact the applicability of deep learning. Transfer learning is used to address these restraints. This project focuses on experiment with multiple transfer learning methods through deep learning on a very noisy dataset, namely WebVision Database. In this report, I discuss the current state of deep learning and transfer learning. Then, I review multiple significant transfer learning methods and suggest how we can combine the use of them. I experiment with a baseline transfer method and another adaptation-transfer method on WebVision Database. I find that this dataset is hard-to-transfer and baseline method still convincingly works. I also report on the implementation in detail and evaluate the result obtained. Finally, I explore the potential of further experiment could be done and conclude the project.
Phylogenetic signal in plant pathogen–host range (2007)

What determines which plant species are susceptible to a given plant pathogen is poorly understood. Experimental inoculations with fungal pathogens of plant leaves in a tropical rain forest show that most fungal pathogens are polyphagous but that most plant species in a local community are resistant to any given pathogen. The likelihood that a pathogen can infect two plant species decreases continuously with phylogenetic distance between the plants, even to ancient evolutionary distances. This phylogenetic signal in host range allows us to predict the likely host range of plant pathogens in a local community, providing an important tool for plant ecology, design of agronomic systems, quarantine regulations in international trade, and risk analysis of biological control agents. In particular, the results suggest that the rate of spread and ecological impacts of a disease through a natural plant community will depend strongly on the phylogenetic structure of the community itself and that current regulatory approaches strongly underestimate the local risks of global movement of plant pathogens or their hosts.
PVRED: A Position-Velocity Recurrent Encoder-Decoder for Human Motion Prediction (2019)

Human motion prediction, which aims to predict future human poses given past poses, has recently seen increased interest. Many recent approaches are based on Recurrent Neural Networks (RNN) which model human poses with exponential maps. These approaches neglect the pose velocity as well as temporal relation of different poses, and tend to converge to the mean pose or fail to generate natural-looking poses. We therefore propose a novel Position-Velocity Recurrent Encoder-Decoder (PVRED) for human motion prediction, which makes full use of pose velocities and temporal positional information. A temporal position embedding method is presented and a Position-Velocity RNN (PVRNN) is proposed. We also emphasize the benefits of quaternion parameterization of poses and design a novel trainable Quaternion Transformation (QT) layer, which is combined with a robust loss function during training. We provide quantitative results for both short-term prediction in the future 0.5 seconds and long-term prediction in the future 0.5 to 1 seconds. Experiments on several benchmarks show that our approach considerably outperforms the state-of-the-art methods. In addition, qualitative visualizations in the future 4 seconds show that our approach could predict future human-like and meaningful poses in very long time horizons. Code is publicly available on GitHub: \textcolor{red}{https://github.com/hongsong-wang/PVRNN}.
Formulation and evaluation of matrix-type transdermal delivery system of ondansetron hydrochloride using solvent casting technique (2011)

The purpose of this research was to develop a matrix-type transdermal therapeutic system containing drug Ondansetron hydrochloride (OSH) with different ratios of hydrophilic and hydrophobic polymeric systems by the solvent evaporation technique by using 25 % w/w of di-butyl phthalate to the polymer weight, incorporated as plasticizer. 5% menthol was used to enhance the Transdermal permeation of OSH. Formulated transdermal patches were physically evaluated with regard to thickness, weight variation, drug content, flatness, folding endurance, percentage of moisture content and water vapour transmission rate. All prepared formulations indicated good physical stability. Ex vivo permeation studies of formulations were performed by using Franz diffusion cells. Formulation prepared with combination of hydrophilic polymers containing permeation enhancer showed best ex vivo skin permeation through rat skin (Wistar albino rat) as compared to all other formulations. The release profile of OSH followed zero-order kinetics in all formulations. However, the release profile of the optimized formulation F17 (r2 = 0.999 for Higuchi) indicated that the permeation of the drug from the patches was governed by a diffusion mechanism. Formulation F showed highest flux among all the formulations in drug permeation. These results indicate that the formulations containing menthol as the penetration enhancer (5%) giving better penetration of OSH through rat skin were considered as suitable for large scale manufacturing with a backing layer and a suitable adhesive membrane.
Selective loss of cone function in mice lacking the cyclic nucleotide-gated channel CNG3 (1999)

Two types of photoreceptors, rods and cones, coexist in the vertebrate retina. An in-depth analysis of the retinal circuitry that transmits rod and cone signals has been hampered by the presence of intimate physical and functional connections between rod and cone pathways. By deleting the cyclic nucleotide-gated channel CNG3 we have generated a mouse lacking any cone-mediated photoresponse. In contrast, the rod pathway is completely intact in CNG3-deficient mice. The functional loss of cone function correlates with a progressive degeneration of cone photoreceptors but not of other retinal cell types. CNG3-deficient mice provide an animal model to dissect unequivocally the contribution of rod and cone pathways for normal retinal function.
Design of high-throughput and low-power true random number generator utilizing perpendicularly magnetized voltage-controlled magnetic tunnel junction (2017)

A true random number generator based on perpendicularly magnetized voltage-controlled magnetic tunnel junction devices (MRNG) is presented. Unlike MTJs used in memory applications where a stable bit is needed to store information, in this work, the MTJ is intentionally designed with small perpendicular magnetic anisotropy (PMA). This allows one to take advantage of the thermally activated fluctuations of its free layer as a stochastic noise source. Furthermore, we take advantage of the voltage dependence of anisotropy to temporarily change the MTJ state into an unstable state when a voltage is applied. Since the MTJ has two energetically stable states, the final state is randomly chosen by thermal fluctuation. The voltage controlled magnetic anisotropy (VCMA) effect is used to generate the metastable state of the MTJ by lowering its energy barrier. The proposed MRNG achieves a high throughput (32 Gbps) by implementing a 64×64 MTJ array into CMOS circuits and executing operations in a parallel manner. Furthermore, the circuit consumes very low energy to generate a random bit (31.5 fJ/bit) due to the high energy efficiency of the voltage-controlled MTJ switching.
Skin Inflammation Induced by the Synergistic Action of IL-17A, IL-22, Oncostatin M, IL-1α, and TNF-α Recapitulates Some Features of Psoriasis (2010)

Keratinocytes play a crucial role in the regulation of skin inflammation, responding to environmental and immune cells stimuli. They produce soluble factors that can act in an autocrine or paracrine manner on immune cells or directly on aggressors. A screening of the activities of 36 cytokines on keratinocyte gene expression identified IL-17A, IL-22, oncostatin M, TNF-alpha, and IL-1alpha as potent cytokines in inducing cutaneous inflammation. These five proinflammatory cytokines synergistically increased production of CXCL8 and beta-defensin 2 (BD2). In addition, ex vivo studies on human skin explants demonstrated upregulation of BD2, S100A7, and CXCL8 expression in response to the same combination of cytokines. In vivo intradermal injection of these five cytokines in mouse increased CXCL1, CXCL2, CXCL3, S100A9, and BD3 expression, associated with neutrophil infiltration. We confirmed and extended this synergistic effect using quantitative real-time PCR analysis and observed increased expression of nine chemokines and 12 antimicrobial peptides. Production of CXCL, CXCL5, and CXCL8 by keratinocytes stimulated in the presence of this cytokine combination was associated with increased neutrophil chemotactic activity. Similarly, high production of BD2, BD3, and S100A7 was associated with an increased antimicrobial activity. Finally, the transcriptional profile observed in this in vitro model of inflammatory keratinocytes correlated with the one of lesional psoriatic skin. Our results demonstrate the important potentiating activities of IL-17A, IL-22, oncostatin M, TNF-alpha, and IL-1alpha on keratinocytes. This is particularly interesting in the context of psoriasis where these cytokines are overexpressed and could synergize to play an important role in upregulation of chemokines and antimicrobial peptides production.