gebhart/patrepeval huggingface dataset:
Knowledge Discovery from Layered Neural Networks Based on Non-negative Task Matrix Decomposition (2020)

Interpretability has become an important issue in the machine learning field, along with the success of layered neural networks in various practical tasks. Since a trained layered neural network consists of a complex nonlinear relationship between large number of parameters, we failed to understand how they could achieve input-output mappings with a given data set. In this paper, we propose the non-negative task matrix decomposition method, which applies non-negative matrix factorization to a trained layered neural network. This enables us to decompose the inference mechanism of a trained layered neural network into multiple principal tasks of input-output mapping, and reveal the roles of hidden units in terms of their contribution to each principal task.
On-line Oxygen Storage Capacity Estimation of a Catalyst (2003)

&lt;div class="htmlview paragraph"&gt;Presented in this paper is an on-line method for estimating the oxygen storage capacity contained within a catalyst. The oxygen storage capacity of a catalyst changes over time due to catalyst brick temperatures, poisoned catalyst sites, and thermal aging. Information regarding the current oxygen storage capacity of a catalyst is advantageous in the development of robust emission control strategies and on-board diagnostics. The method of collecting the oxygen storage capacity information is extremely important for measurement accuracy and repeatability. Furthermore, the information must be obtained in such a way that it is transparent to the operator and may be implemented on-line during normal drive cycles. This on-line method for estimation of oxygen storage capacity of a catalyst has been demonstrated on a Ford F150 platform with an underbody catalyst.&lt;/div&gt;
Optimizing Spatial Biopsy Sampling for the Detection of Prostate Cancer (2021)

A RTB approach can maintain state-of-the-art detection rates while requiring fewer retrieved cores. This result informs decision making about biopsy site selection and total retrieved core count.
Modeling of nitrogen fixation and polymer production in the heterotrophic diazotroph Azotobacter vinelandii DJ (2020)

Nitrogen fixation is an important metabolic process carried out by microorganisms, which converts molecular nitrogen into inorganic nitrogenous compounds such as ammonia (NH<sub>3</sub>). These nitrogenous compounds are crucial for biogeochemical cycles and for the synthesis of essential biomolecules, i.e. nucleic acids, amino acids and proteins. <i>Azotobacter vinelandii</i> is a bacterial non-photosynthetic model organism to study aerobic nitrogen fixation (diazotrophy) and hydrogen production. Moreover, the diazotroph can produce biopolymers like alginate and polyhydroxybutyrate (PHB) that have important industrial applications. However, many metabolic processes such as partitioning of carbon and nitrogen metabolism in <i>A. vinelandii</i> remain unknown to date. Genome-scale metabolic models (M-models) represent reliable tools to unravel and optimize metabolic functions at genome-scale. M-models are mathematical representations that contain information about genes, reactions, metabolites and their associations. M-models can simulate optimal reaction fluxes under a wide variety of conditions using experimentally determined constraints. Here we report on the development of a M-model of the wild type bacterium <i>A. vinelandii</i> DJ (<i>i</i>DT1278) which consists of 2,003 metabolites, 2,469 reactions, and 1,278 genes. We validated the model using high-throughput phenotypic and physiological data, testing 180 carbon sources and 95 nitrogen sources. <i>i</i>DT1278 was able to achieve an accuracy of 89% and 91% for growth with carbon sources and nitrogen source, respectively. This comprehensive M-model will help to comprehend metabolic processes associated with nitrogen fixation, ammonium assimilation, and production of organic nitrogen in an environmentally important microorganism.
Imaging through an opaque material (2011)

We introduce a method to measure the transmission matrix of a complex medium in optics, thanks to a spatial light modulator. Using this matrix, we demonstrate experimentally light focusing and imaging through an opaque medium.
Graphical reduction of reaction networks by linear elimination of\n species (2015)

The quasi-steady state approximation and time-scale separation are commonly\napplied methods to simplify models of biochemical reaction networks based on\nordinary differential equations (ODEs). The concentrations of the "fast"\nspecies are assumed effectively to be at steady state with respect to the\n"slow" species. Under this assumption the steady state equations can be used to\neliminate the "fast" variables and a new ODE system with only the slow species\ncan be obtained.\n We interpret a reduced system obtained by time-scale separation as the ODE\nsystem arising from a unique reaction network, by identification of a set of\nreactions and the corresponding rate functions. The procedure is graphically\nbased and can easily be worked out by hand for small networks. For larger\nnetworks, we provide a pseudo-algorithm. We study properties of the reduced\nnetwork, its kinetics and conservation laws, and show that the kinetics of the\nreduced network fulfil realistic assumptions, provided the original network\ndoes. We illustrate our results using biological examples such as substrate\nmechanisms, post-translational modification systems and networks with\nintermediates (transient) steps.\n
Study of PAG Material Design for ArF Immersion Photoresist (2008)

One of some critical issues for ArF immersion lithography was leaching of resist components to water fluid. To decrease the leaching amount, increase hydrophobicity of Photo Acid Generator (PAG) was one of the most effective methods. The hydrophobicity of PAG was detected by simulating Log-P value and measuring Retention Time (RT) on reversed phase chromatography. However, simple high hydrophobic PAG indicated high defect number. The improvement of this issue was achieved by introducing acid cleavable group into PAG cation frame. It may suggest that PAG material proposed on this study showed low leaching amount and low defect risk as new concept for ArF immersion resist.
High-Temperature Deformation Behavior of Polycrystalline Yttrium Aluminum Garnet (YAG) (2008)

The high-temperature deformation behavior of polycrystalline yttrium aluminum garnet (YAG) has been investigated using constant displacement rate compression tests conducted in vacuum. The behavior in the strain rate regime of 10−5-10−3/S in the temperature range of 1400°-1610°C was studied and compared with available data on polycrystalline alumina and mullite. Polycrystalline YAG was found to behave in a manner similar to alumina but with a slightly better creep resistance. Mullite was significantly better at 1400°C and marginally superior at 1500°C.
Ogden material calibration via magnetic resonance cartography, parameter sensitivity and variational system identification (2022)

Contemporary material characterization techniques that leverage deformation fields and the weak form of the equilibrium equations face challenges in the numerical solution procedure of the inverse characterization problem. As material models and descriptions differ, so too must the approaches for identifying parameters and their corresponding mechanisms. The widely used Ogden material model can be comprised of a chosen number of terms of the same mathematical form, which presents challenges of parsimonious representation, interpretability and stability. Robust techniques for system identification of any material model are important to assess and improve experimental design, in addition to their centrality to forward computations. Using fully three-dimensional displacement fields acquired in silicone elastomers with our recently developed magnetic resonance cartography (MR-<i><b>u</b></i>) technique on the order of greater than [Formula: see text], we leverage partial differential equation-constrained optimization as the basis of variational system identification of our material parameters. We incorporate the statistical <i>F</i>-test to maintain parsimony of representation. Using a new, local deformation decomposition locally into mixtures of biaxial and uniaxial tensile states, we evaluate experiments based on an analytical sensitivity metric and discuss the implications for experimental design. This article is part of the theme issue 'The Ogden model of rubber mechanics: Fifty years of impact on nonlinear elasticity'.
Toll-like receptor 3 downregulation is an escape mechanism from apoptosis during hepatocarcinogenesis (2019)

Hepatocellular carcinoma (HCC) is a heterogeneous disease associated with a poor prognosis. In patients with HCC, TLR3 downregulation is associated with reduced survival. Herein, we show that the absence of TLR3 is associated with a lower rate of apoptosis, and subsequently more rapid hepatocarcinogenesis, without any change to the immune infiltrate in the liver. Therefore, the poor prognosis associated with low TLR3 expression in HCC is likely linked to tumors ability to escape apoptosis. TLR3 may become a promising therapeutic target in TLR3-positive HCC.
JGOG2033: Randomized phase III trial of whole pelvic radiotherapy vs cisplatin-based chemotherapy in patients with intermediate risk endometrial carcinoma (2005)

5002 Background: Optimal adjuvant therapy for intermediate risk endometrial cancer patients is poorly defined. Methods: A Japan Gynecologic Oncology Group (JGOG) conducted a multi-center randomized Phase III trial of whole pelvic irradiation (WPI) vs. cyclophosphamide-doxorubicin-CDDP (CAP) chemotherapy in women with endometrial carcinoma with deeper than 50% myometrial invasion postoperatively. 425 pts were entered from 1/1994 to 12/2000. Of the 385 evaluable endometrioid adenocarcinoma, 193 were to receive WPI and 192, CAP. WPI arm employed at least 40 Gray (Gy) in 20 fractions. CAP arm consisted of cyclophosphamide (333 mg/m2), doxorubicin (40 mg/m2) and cisplatin (50 mg/m2) every 4 weeks for 3 or more courses. Results: Pt Characteristics: The treatment arms were well balanced in terms of patient and tumor characteristic, with G1 55%, G2 30%, and G3 15%. Median follow-up was 1825 days (range 65–1825). Response and Survival: There were no statistically significant differences in progression-free survival (PFS) and overall survival (OS) between the 2 regimens for all pts. The PFS of WPI and CAP arms was 84.0% and 82.1%, and the OS of WPI and CAP arms was 85.9% and 87.1%, respectively. Especially, among 229 pts with intermediate risk as stage pTIc, the PFS of WPI and CAP arms was 89.6% and 87.2%, and the OS of WPI and CAP arms was 88.9 and 88.9, respectively. Recurrence in each WPI and CAP arm was 15.1%, 16.5%, respectively, with 30% pelvic and 70% extrapelvic recurrent sites. Toxicity: Adverse effects were not significantly increased in the CAP arm, compared to WPI arm. Conclusions: Adjuvant cisplatin-based combined chemotherapy might have potential as an alternative to radiotherapy for intermediate risk endometrial cancer, such as only deeper than 50% myometrial invasion. No significant financial relationships to disclose.
Mobility versus Alignment of a Semiconducting π-Extended Discotic Liquid-Crystalline Triindole (2016)

The p-type semiconducting properties of a triphenylene-fused triindole mesogen, have been studied by applying two complementary methods which have different alignment requirements. The attachment of only three flexible alkyl chains to the nitrogen atoms of this π-extended core is sufficient to induce columnar mesomorphism. High hole mobility values (0.65 cm<sup>2</sup> V<sup>-1</sup> s<sup>-1</sup>) have been estimated by space-charge limited current (SCLC) measurements in a diode-like structure which are easily prepared from the melt, rendering this material a good candidate for OPVs and OLEDs devices. The mobility predicted theoretically via a hole-hopping mechanism is in very good agreement with the experimental values determined at the SCLC regime. On the other hand the hole mobility determined on solution processed thin film transistors (OFETs) is significantly lower, which can be rationalized by the high tendency of these large molecules to align on surfaces with their extended π-conjugated core parallel to the substrate as demonstrated by SERS. Despite the differences obtained with the two methods, the acceptable performance found on OFETs fabricated by simple drop-casting processing of such an enlarged aromatic core is remarkable and suggests facile hopping between neighboring molecular columns owing to the large conducting/isolating ratio found in this discotic compound.
Base resolution maps reveal the importance of 5-hydroxymethylcytosine in a human glioblastoma (2017)

Aberrant genetic and epigenetic variations drive malignant transformation and are hallmarks of cancer. Using PCR-free sample preparation we achieved the first in-depth whole genome (hydroxyl)-methylcytosine, single-base-resolution maps from a glioblastoma tumour/margin sample of a patient. Our data provide new insights into how genetic and epigenetic variations are interrelated. In the tumour, global hypermethylation with a depletion of 5-hydroxymethylcytosine was observed. The majority of single nucleotide variations were identified as cytosine-to-thymine deamination products within CpG context, where cytosine was preferentially methylated in the margin. Notably, we observe that cells neighbouring tumour cells display epigenetic alterations characteristic of the tumour itself although genetically they appear "normal". This shows the potential transfer of epigenetic information between cells that contributes to the intratumour heterogeneity of glioblastoma. Together, our reference (epi)-genome provides a human model system for future studies that aim to explore the link between genetic and epigenetic variations in cancer progression.
Effective design and simulation of surface-based lattice structures featuring volume fraction and cell type grading (2018)

In this paper we present a numerical investigation into surface-based lattice structures with the aim of facilitating their design for additive manufacturing. We give the surface equations for these structures and show how they can be used to tailor their volume fractions. Finite element analysis is used to investigate the effect of cell type, orientation and volume fraction on the elastic moduli of the lattice structures, giving rise to a valuable set of numerical parameters which can be used to design a lattice to provide a specified stiffness. We find the I-WP lattice in the [001] orientation provides the highest stiffness along a single loading direction, but the diamond lattice may be more suitable for cases where lower mechanical anisotropy is important. Our stiffness models enable the construction of a powerful numerical tool for predicting the performance of graded structures. We highlight a particular problem which can arise when two lattice types are hybridised; an aberration leading to structural weakening and high stress concentrations. We put forward a novel solution to this problem and demonstrate its usage. The methods and results detailed in this paper enable the efficient design of lattice structures functionally graded by volume fraction and cell type.
Autophagy in protists (2011)

Autophagy is the degradative process by which eukaryotic cells digest their own components using acid hydrolases within the lysosome. Originally thought to function almost exclusively in providing starving cells with nutrients taken from their own cellular constituents, autophagy is in fact involved in numerous cellular events including differentiation, turnover of macromolecules and organelles, and defense against parasitic invaders. During the last 10-20 years, molecular components of the autophagic machinery have been discovered, revealing a complex interactome of proteins and lipids, which, in a concerted way, induce membrane formation to engulf cellular material and target it for lysosomal degradation. Here, our emphasis is autophagy in protists. We discuss experimental and genomic data indicating that the canonical autophagy machinery characterized in animals and fungi appeared prior to the radiation of major eukaryotic lineages. Moreover, we describe how comparative bioinformatics revealed that this canonical machinery has been subject to moderation, outright loss or elaboration on multiple occasions in protist lineages, most probably as a consequence of diverse lifestyle adaptations. We also review experimental studies illustrating how several pathogenic protists either utilize autophagy mechanisms or manipulate host-cell autophagy in order to establish or maintain infection within a host. The essentiality of autophagy for the pathogenicity of many parasites, and the unique features of some of the autophagy-related proteins involved, suggest possible new targets for drug discovery. Further studies of the molecular details of autophagy in protists will undoubtedly enhance our understanding of the diversity and complexity of this cellular phenomenon and the opportunities it offers as a drug target.
Mechanisms of human neutrophil elastase-catalysed inactivation of factor VIII(a) (2011)

Summary Mechanisms of inflammation and coagulation are linked through various pathways. Human neutrophil elastase (HNE), can bind to activated platelets, might be localised on platelet membranes that provide negatively-charged phospholipid essential for the optimum function of tenase complex. In this study, we examined the effect of HNE on factor (F)VIII. FVIII activity was rapidly diminished in the presence of HNE and was undetectable within 10 minutes. The inactivation rate waŝ8-fold greater than that of activated protein C (APC). This time-dependent inactivation was moderately affected by von Willebrand factor. HNE proteolysed the heavy chain (HCh) of FVIII into two terminal products, A11–358 and A2375–708, by limited proteolysis at Val358, Val374, and Val708. Cleavage at Val708 was much slower than that at Val358 in the &gt;90-kDa A1-A2-B compared to the 90-kDa A1-A2. The 80-kDa light chain (LCh) was proteolysed to 75-kDa product by cleavage at Val1670. HNE-cata- lysed FVIIIa inactivation was markedly slower than that of native FVIII (by ~25-fold), due to delayed cleavage at Val708 in FVIIIa. The inactivation rate mediated by HNE was ~8-fold lower than that by APC. Cleavages at Val358 and Val708 were regulated by the presence of LCh and HCh, respectively. In conclusion, HNE-catalysed FVIII inactivation was associated with the limited-proteolysis that led to A11–358, A2375–708, and A3-C1-C21671–2332, and subsequently to critical cleavage at Val708. HNE-related FVIII(a) reaction might play a role in inactivation of HNE-induced coagulation process, and appeared to depend on the amounts of inactivated FVIII and active FVIIIa which is predominantly resistant to HNE inactivation. Note: An account of this work was presented at the 51st annual meeting of the American Society of Hematology, December 10, 2009, New Orleans, LA, USA.
Evaluation of an Ebb and Flow Nutrient Delivery Technique Applicable to Growing Plants in Microgravity (2002)

&lt;div class="htmlview paragraph"&gt;A promising approach for the watering and aeration of substrates in space-based plant root modules is to use a periodic watering/evacuation through a porous membrane or an Ebb/Flow Nutrient Delivery System (EFNDS). Wheat (&lt;i&gt;Triticum aestivum&lt;/i&gt; cv Yecora rojo) grown utilizing the EFNDS approach achieved productivities equivalent to controls employing a traditional direct flow approach. When the EFNDS approach is used in conjunction with a fibrous ion-exchange resin substrate (FIERS), the ebb cycle effectively vented 50-55% of the FIERS pores by volume (resupplying oxygen), and freed the substrate of unwanted root exudates. Several advantages of the EFNDS approach can be crucial during plant cultivation in microgravity.&lt;/div&gt;
ChemInform Abstract: CHEMICAL CONSEQUENCES OF ORBITAL INTERACTIONS PART 2, ETHYLENE AND BUTADIENE BRIDGED POLYCYCLIC HYDROCARBONS CONTAINING THREE‐ AND FOUR‐MEMBERED RINGS (1975)

Abstract Es werden die π‐Orbital‐Wechselwirkungen zwischen den kleinen Ringen und den Äthylen‐ bzw. Butadienbrücken z.B. für Dewarbenzol und Benzvalen bzw. für 2,3‐Dimethylen‐bicyclo[2.
A MIMO radar for Sense and Avoid function: A fully static solution for UAV (2010)

Up to now, UAV are employed in crisis or war times. For training purposes, some areas are especially attributed for UAV deployment in a limited space area and in a limited time slot. In the future, both for emerging civilian applications and for training purpose, these limitations will no longer be acceptable and UAV will have to be inserted in the general air traffic. Thus, “Sense and Avoid” systems will be mandatory. The radar is the most pertinent non-cooperative “all-weather” sensor because it provides, by essence, accurate ranging, direction and closing speed. In this paper, we propose a low cost radar solution based on the coherent “MIMO” principles. This design allows the implementation of the radar within the UAV airframe without any moving part.
PAPR Reduction Method for Digital Predistortion Linearizer Compensating for Frequency Dependent IMD Components (2018)

This paper proposes a method for reducing the peak-to-average power ratio (PAPR) at the output signal of a digital predistortion linearizer (DPDL) that compensates for frequency dependent intermodulation distortion (IMD) components. The proposed method controls the amplitude and phase values of the frequency components corresponding to the transmission bandwidth of the output signal. A DPDL employing the proposed method simultaneously provides IMD component cancellation of out-of-band components and PAPR reduction at the output signal. This paper identifies the amplitude and phase conditions to minimize the PAPR. Experimental results based on a 2-GHz band 1-W class power amplifier show that the proposed method improves the drain efficiency of the power amplifier when degradation is allowed in the error vector magnitude. To the best knowledge of the authors, this is the first PAPR reduction method for DPDL that reduces the PAPR while simultaneously compensating for IMD components.
Vehicle Powertrain Thermal Management System Using Model Predictive Control (2016)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;An advanced powertrain cooling system with appropriate control strategy and active actuators allows greater flexibility in managing engine temperatures and operating near constraints. An organized controls development process is necessary to allow comparison of multiple configurations to select the best way forward. In this work, we formulate, calibrate and validate a Model Predictive Controller (MPC) for temperature regulation and constraint handling in an advanced cooling system. A model-based development process was followed; where the system model was used to develop and calibrate a gain scheduled linear MPC. The implementation of MPC for continuous systems and the modification related to implementing switching systems has been described.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Multiple hardware configurations were compared with their corresponding control system in simulations. The system level requirements were translated into MPC calibration parameters for consistent comparison between multiple configurations. Some of the configurations were then evaluated via hardware in the loop testing prior to evaluation in a vehicle. The paper works through key steps related to the development of MPC for system level evaluation of actuators for powertrain thermal management.&lt;/div&gt;&lt;/div&gt;