gebhart/patrepeval huggingface dataset:
A new methodology of extraction, optimization and application of crisp and fuzzy logical rules (2001)

A new methodology of extraction, optimization, and application of sets of logical rules is described. Neural networks are used for initial rule extraction, local or global minimization procedures for optimization, and Gaussian uncertainties of measurements are assumed during application of logical rules. Algorithms for extraction of logical rules from data with real-valued features require determination of linguistic variables or membership functions. Contest-dependent membership functions for crisp and fuzzy linguistic variables are introduced and methods of their determination described. Several neural and machine learning methods of logical rule extraction generating initial rules are described, based on constrained multilayer perceptron, networks with localized transfer functions or on separability criteria for determination of linguistic variables. A tradeoff between accuracy/simplicity is explored at the rule extraction stage and between rejection/error level at the optimization stage. Gaussian uncertainties of measurements are assumed during application of crisp logical rules, leading to "soft trapezoidal" membership functions and allowing to optimize the linguistic variables using gradient procedures. Numerous applications of this methodology to benchmark and real-life problems are reported and very simple crisp logical rules for many datasets provided.
Recognition and retrieval of sound events using sparse coding convolutional neural network (2017)

This paper proposes a novel deep convolutional neural network (CNN), called sparse coding convolutional neural network (SC-CNN), to address the problem of sound event recognition and retrieval task. Unlike the general framework of a CNN, in which feature learning process is performed hierarchically, the proposed framework models the whole memorizing procedures in the human brain, including encoding, storage, and recollection. Sound data from the RWCP sound scene dataset with added noise from NOISEX-92 noise dataset are used to compare the performance of the proposed system with the state-of-the-art baselines. The experimental results indicated that the proposed SC-CNN outperformed the state-of-the-art systems in sound event recognition and retrieval. In the sound event recognition task, the proposed system achieved an accuracy of 94.6%, 100% and 100% under 0db, 10db and clean noise conditions, respectively. In the retrieval task, the proposed system improves the mAP rate of the general CNN by approximately 6%.
Insight into Binding of Phosphodiesterase-9A Selective Inhibitors by Crystal Structures and Mutagenesis (2010)

PDE9 inhibitors have been studied as therapeutics for treatment of cardiovascular diseases, diabetes, and neurodegenerative disorders. To illustrate the inhibitor selectivity, the crystal structures of the PDE9A catalytic domain in complex with the enantiomers of PDE9 inhibitor 1-(2-chlorophenyl)-6-(3,3,3-trifluoro-2-methylpropyl)-1H-pyrazolo[3,4-d]pyrimidine-4(5H)-one ((R)-BAY73-6691 or (S)-BAY73-6691, 1r or 1s) were determined and mutagenesis was performed. The structures showed that the fluoromethyl groups of 1r and 1s had different orientations while the other parts of the inhibitors commonly interacted with PDE9A. These differences may explain the slightly different affinity of 1r (IC(50) = 22 nM) and 1s (IC(50) = 88 nM). The mutagenesis experiments revealed that contribution of the binding residues to the inhibitor sensitivity varies dramatically, from few-fold to 3 orders of magnitude. On the basis of the crystal structures, a hypothesized compound that simulates the recently published PDE9 inhibitors was modeled to provide insight into the inhibitor selectivity.
Computer simulation of pressure-induced structural transitions in MgO [001] tilt grain boundaries (1999)

Atomistic simulations using lattice and molecular dynamics were carried out on the {210}, {310}, and {410} tilt grain boundaries of MgO as a function of pressure up to 100 GPa at a single temperature of 600 K. The calculations show a significant change in the structure of the tilt grain boundaries as pressure increases. The results show that, beyond the previously identified reversible pressure induced collapse of the channel structure, an irreversible shear was identified that forms a mirror grain boundary, which does not possess well-defined dislocation cores and is consequently denser. These mirror boundaries are energetically more favorable than the symmetric boundaries at elevated pressures. As applied pressure approaches 100 GPa a reversible structural transition occurs causing the boundaries to shear perpendicular to the boundary plane forming highly dense structures that contained seven coordinate ions at the boundary and the presence of an edge dislocation-like structure. We suggest that differences between the boundary structures seen in the HREM studies with those predicted by simulations may result from stresses upon the crystal during preparation causing irreversible shearing.
Rab7B/42 Is Functionally Involved in Protein Degradation on Melanosomes in Keratinocytes (2020)

Keratinocytes uptake melanosomes from melanocytes and retain them in the perinuclear region, where they form melanin caps. Although these processes are crucial to protecting nuclear DNA against ultraviolet injury, the molecular basis of melanosome uptake and decomposition in keratinocytes is poorly understood. One of the major reasons for its being poorly understood is the lack of a specific marker protein that can be used to visualize or monitor melanosomes (or melanosome-containing compartments) that have been incorporated into keratinocytes. In this study, we performed a comprehensive localization screening for mammalian Rab family small GTPases (Rab1-45) and succeeded in identifying 11 Rabs that were enriched around melanosomes that had been incorporated into keratinocytes. We also established a new assay by using a recently developed melanosome probe (called M-INK) as a means of quantitatively assessing the degradation of proteins on incorporated melanosomes in control and each of a series of Rab-knockdown keratinocytes. The results showed that knockdown or CRISPR/Cas9-mediated knockout of Rab7B (also identified as Rab42) in keratinocytes caused strong inhibition of protein degradation on melanosomes. Our findings indicated that Rab7B/42 is recruited to melanosome-containing compartments and that it promotes protein degradation on melanosomes in keratinocytes.Key words: degradation, keratinocytes, melanocytes, melanosome, Rab small GTPase.
4-Phenylbutyric Acid Reduces Endoplasmic Reticulum Stress, Trypsin Activation, and Acinar Cell Apoptosis While Increasing Secretion in Rat Pancreatic Acini (2012)

By incubation with 4-PBA, beneficial in urea cycle deficiency, it was possible to enhance enzyme secretion to suppress trypsin activation, UPR activation, and proapoptotic pathways. The data hint new perspectives for the use of chemical chaperones in pancreatic diseases.
Human phenotypes caused by <i>PIEZO1</i> mutations; one gene, two overlapping phenotypes? (2018)

PIEZO1 is a large mechanosensitive ion channel protein. Diseases associated with PIEZO1 include autosomal recessive generalised lymphatic dysplasia of Fotiou (GLDF) and autosomal dominant dehydrated hereditary stomatocytosis with or without pseudohyperkalemia and/or perinatal oedema (DHS). The two disorders show overlapping features, fetal hydrops/perinatal oedema have been reported in both. Electrophysiological studies suggest opposite mechanisms of action: the mutations identified in GLDF patients cause a loss-of-function mechanism of disease and mutations in DHS patients cause gain of function. This raises the question: Is the pathogenic disease mechanism behind the fetal oedema the same in the two phenotypes? In this Symposium Review, we will discuss the two conditions and highlight key questions that remain to be answered. For instance, the perinatal oedema often resolves soon after birth and we are still at a loss to understand why. Are there any mechanisms which could compensate for the faulty PIEZO1 in these patients? Are there physiological changes at birth that are less reliant on the function of PIEZO1? Thus, there is a clear need for further studies into the two disorders, in order to fully understand the role of PIEZO1 in health and disease.
Solution thermodynamics of some slightly soluble hydrocarbons in water (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolution thermodynamics of some slightly soluble hydrocarbons in waterWillie E. May, Stanley P. Wasik, Michele M. Miller, Yadu B. Tewari, Jeanice M. Brown-Thomas, and Robert N. GoldbergCite this: J. Chem. Eng. Data 1983, 28, 2, 197–200Publication Date (Print):April 1, 1983Publication History Published online1 May 2002Published inissue 1 April 1983https://pubs.acs.org/doi/10.1021/je00032a021https://doi.org/10.1021/je00032a021research-articleACS PublicationsRequest reuse permissionsArticle Views296Altmetric-Citations85LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
No-Snapback Silicon-Controlled Rectifier for Electrostatic Discharge Protection of High-Voltage ICs (2015)

In this letter, we develop a no-snapback silicon-controlled rectifier (NS-SCR) in a 0.35-um BCD technology. This device is constructed by embedding in a typical SCR a p-type/intrinsic/n-type diode as the trigger element and two highly doped extension regions as parts of the bases of the parasitic bipolar transistors. These added features allow for a high electric field to be maintained at the reverse biased n/p junction in the electrostatic discharge (ESD) current path, prevent the onset of strong conductivity modulation, and result in a nosnapback transmission line pulsing I-V characteristic. Stacking the NS-SCR's offers an ESD protection solution that is area-efficient, robust, and latch-up immune. The high temperature effect on the leakage current of NS-SCR is also studied.
Measuring the impact of apnea and obesity on circadian activity patterns using functional linear modeling of actigraphy data (2011)

Compared with analysis using summary measures (e.g., average activity over 24 hours, total sleep time), Functional Data Analysis (FDA) is a novel statistical framework that more efficiently analyzes information from actigraphy data. FDA has the potential to reposition the focus of actigraphy data from general sleep assessment to rigorous analyses of circadian activity rhythms.
Protective effects of paeoniflorin against FasL-induced apoptosis of intervertebral disc annulus fibrosus cells via Fas-FasL signalling pathway (2015)

In the present study, we demonstrate that the degeneration of intervertebral discs is caused by ageing and apoptosis of matrix cells. Apoptosis is as essential as the function of proteoglycan synthesis in assessing the possible degeneration of intervertebral discs; paeoniflorin (PF) induces cytoprotective effects on various types of cells. In this study, the function of PF in inhibiting Fas ligand (FasL)-induced apoptosis in annulus fibrosus cells was assessed, and the correlation between apoptosis and the Fas-FasL pathway was determined. Annulus fibrosus cells were derived from the intervertebral discs of 1-month-old Sprague Dawley rats; the cells were characterised by toluidine blue staining and subjected to apoptosis with FasL. PF was diluted to various concentrations and added to annulus fibrosus cells at various times. The impact of PF and FasL on cell apoptosis of annulus fibrosus cells was determined by flow cytometry. Western blot analysis was performed to determine the protein expression levels of Fas and caspase-3. The percentages of apoptotic annulus fibrosus cells as well as the expression levels of caspase-3 and Fas were significantly reduced following treatment with 208, 20.8 or 2.08 µM PF. PF inhibits the activation of the Fas-FasL signal pathway and decreases FasL-induced apoptosis of annulus fibrosus cells.
Adaptive Pipeline Parallelism for Image Feature Extraction Algorithms (2012)

Currently, multimedia data has become one of the major data types processed and transferred on the Internet. With the rapid growth of multimedia data, it is vitally important to find an efficient way to extract useful information from a large amount of data. SIFT and SURF, as the most popular multimedia feature extraction algorithms, have been widely used in many applications. However, the limited processing speed~(about 1.8 and 2.6 images or frames per second for SIFT and SURF respectively on an ordinary CPU) makes it impossible to apply them in many real-world applications with real-time requirements. Therefore, it has become one of the major challenges that how to improve the processing speed of these multimedia feature extraction algorithms. The popularity of multi-core architecture and the increase of computation resources on different platforms provide a new opportunity to accelerate the processing speed of these image feature extraction algorithms. In this paper, we first systematically analyze the major parallel constraints in SIFT and SURF, such as imbalanced workload and indeterminate time distribution. Then, based on these analysis, we design and implement an adaptive pipeline parallel scheme (AD-PIPE) for both SIFT and SURF to alleviate these limitations. In our scheme, we dynamically check the workload in different pipeline stages and adjust the thread number in different stages to achieve a balanced partition. Experimental results show that our approach is efficient and scalable. It can achieve a speedup of 16.88X and 20.33X respectively for SIFT and SURF on a 16-core machine and a real time processing speed with about 27 and 52 images or frames per second.
Production and playback of human figure motion for 3D virtual environments (2002)

We describe a system for off-line production and real-time playback of motion for articulated human figures in 3D virtual environments. The key notions are (1) the logical storage of full-body motion in posture graphs, which provides a simple motion access method for playback and (2) mapping the motions of higher DOF figures to lower DOF figures using slaving to provide human models at several levels of detail, both to geometry and articulation, for later playback. We present our system in the context of a simple problem: animating human figures in a distributed simulation, using DIS protocols for communicating the human state information. We also discuss several related techniques for real-time animation of articulated figures in visual simulation.
Synthesis of an Extremely Bent Acyclic Allene (A “Carbodicarbene”): A Strong Donor Ligand (2008)

Pushed to the limit: Pushing CC π bonds to the breaking point by using a push–push substitution pattern forces allenes to bend (see structure; C light blue, N dark blue). An acyclic allene featuring a CCC bond angle of 134.8° has been isolated in which the typically sp-hybridized central carbon atom approaches a configuration that has two lone pairs of electrons, and acts as a very strong η1-donor ligand for transition metals.
Emergency Administration of Abciximab for Treatment of Patients With Acute Ischemic Stroke: Results of an International Phase III Trial (2007)

This trial did not demonstrate either safety or efficacy of intravenous administration of abciximab for the treatment of patients with acute ischemic stroke regardless of end point or population studied. There was an increased rate of symptomatic or fatal intracranial hemorrhage in the primary and wake-up cohorts.
Toward evaluating lighting design interface paradigms for novice users (2009)

Lighting design is a complex but fundamental task in computer cinematography, involving the adjustment of light parameters to define final scene appearance. Many user interfaces have been proposed to simplify lighting design. They can be generally categorized in three paradigms: direct light parameter manipulation, indirect light feature manipulation (e.g., shadow dragging), and goal-based optimization of lighting through painting. To this date, no formal evaluation of the relative effectiveness of these paradigms has been performed. In this paper, we present a first step toward evaluating the benefits of these three paradigms in the form of a user study with a focus on novice users. 20 subjects participated in the experiment by performing various trials on simple scenes with up to 8 point lights, designed to test two lighting tasks: precise adjustment of lighting and the artistic exploration of lighting configurations. We collected objective and subjective data and found that subjects can light well with direct and indirect interfaces, preferring the latter. Paint-based goal specification was found to be significantly worse than the other paradigms, especially since users tend to sketch rather than accurately paint goal images, an input that painting algorithms were not designed for. We also found that given enough time, novices can perform relatively complex lighting tasks, unhindered by geometry or lighting complexity. Finally, we believe that our study will impact the design of future lighting interfaces and it will serve as the basis for designing additional experiments to reach a comprehensive evaluation of lighting interfaces.
Access Control Agnostic Trust Negotiation Decision Engine (2007)

Dynamic open environments demand trust negotiation systems for unknown entities willing to communicate. A security context have to be negotiated gradually in a fair peer to peer basis. Trust negotiation engines are driven by decision engines that lack of flexibility: they depend on the implementation, policies languages or credentials types to be used. In this paper we present a trust negotiation engine agnostic regarding policies and rules. The engine is based on iterative weighted Multidimensional Scaling to assist a mobile device during a trust negotiation.
The Gaits of Bipedal and Quadrupedal Animals (1984)

The gaits of reptiles, birds, and mammals are reviewed. It is shown that mammals of different sizes tend to move in dy namically similar fashion whenever their Froude numbers u 2 /gh are equal: here u is speed, g is the acceleration of free fall, and h is the height of the hip joint from the ground. The gaits of turtles and people are examined in detail. The gaits of turtles appear to reduce unwanted displacements ( pitch, roll, etc.) to the minimum possible for animals with such slow muscles. The patterns of force exerted in human walking and running minimize the work required of the muscles at each speed. Much of the energy that would otherwise be neededfor running, by people and other large mammals, is saved by tendon elasticity.
Kinetic study of instability of recombinant plasmid pPLc23<i>trpAl</i> in <i>E. coli</i> using two‐stage continuous culture system (1985)

Derepression of the phage lambda p(L) promoter on recombinant plasmid pPLc 23-trpAl caused a rapid increase of plasmid free segregants in the population. In continuous culture, increased production of trpA protein follwing derepression was accompanied by a continuous deceleration of specific growth rate. In the repressed condition, plasmid loss per generation in continuous culture decreased as dilution rate increased from 0.06 to 1.08 h(-1). Over this range, the concentration of plasmid DNA within the cell decreased eightfold corresponding to a decrease in plasmid number from 74 to 32 molecules/cell. The use of a two-stage continuous culture system coupled with a temperature sensitive expression system allows a high trpA productivity from the derepressed plasmid for more than 48 h and also offers a possibility of minimizing the instability problem of high expression recombinants. Such a system also permits the critical study of the effects of fermentation and other regulatory parameters on expression under better controlled conditions than is possible in a batch culture or single-stage continous culture.
Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity (2017)

The precise identification of Human Leukocyte Antigen class I (HLA-I) binding motifs plays a central role in our ability to understand and predict (neo-)antigen presentation in infectious diseases and cancer. Here, by exploiting co-occurrence of HLA-I alleles across ten newly generated as well as forty public HLA peptidomics datasets comprising more than 115,000 unique peptides, we show that we can rapidly and accurately identify many HLA-I binding motifs and map them to their corresponding alleles without any a priori knowledge of HLA-I binding specificity. Our approach recapitulates and refines known motifs for 43 of the most frequent alleles, uncovers new motifs for 9 alleles that up to now had less than five known ligands and provides a scalable framework to incorporate additional HLA peptidomics studies in the future. The refined motifs improve neo-antigen and cancer testis antigen predictions, indicating that unbiased HLA peptidomics data are ideal for in silico predictions of neo-antigens from tumor exome sequencing data. The new motifs further reveal distant modulation of the binding specificity at P2 for some HLA-I alleles by residues in the HLA-I binding site but outside of the B-pocket and we unravel the underlying mechanisms by protein structure analysis, mutagenesis and in vitro binding assays.