gebhart/patrepeval huggingface dataset:
Diffusionsgewichtete MRT der Prostata: Vorteile einer gezoomten EPI mit paralleler Sendetechnik (2015)

Die diffusionsgewichtete MRT (DWI) der Prostata ist häufig durch Verzerrungsartefakte belastet. Ziel der Studie war die Evaluation einer FOV-reduzierten DW-EPI (zoomed EPI, z-EPI) mit 2D-selektiver paralleler Sendetechnik im Vergleich zu einer konventionellen single-shot-EPI (k-EPI).
Lipoxygenase Inhibiting Steroidal Glycosides and Naphthene Derivatives from Haloxylon salicornicum (2005)

Allostigmasterol glycosides 1 and 2 and monocyclic naphthene derivatives 3 and 4 have been isolated from methanolic extract of Haloxylon salicornicum and their structures elucidated through spectroscopy. Triacontanoic acid 5, ergosterol peroxide 6 and lupeol 7 were also obtained for the first time from this species. Both 1 and 2 showed moderate lipoxygenase inhibiting activity.
Intracoronary Infusion of Catecholamines Causes Focal Arrhythmias in Pigs (2008)

Regional elevation of a catecholamine, which is one of the alterations produced by acute ischemia, can by itself cause tachyarrhythmias. These arrhythmias are closely associated with a shortened refractory period and a large gradient of the spatial distribution of refractoriness but not with a steep restitution curve.
Synthesis and opioid activity of dermorphin tetrapeptides bearing D-methionine S-oxide at position 2 (1986)

Eight new dermorphin tetrapeptides, X-Tyr-D-MetO-Phe-aa-Y (X = H, H2N = C(NH); aa = Gly, 2-aminoethanol, sarcosine; Y = NH2, NH-alkyl), were prepared and tested for opioid activity. They show dose-related naloxone-reversible opioid effects in vitro and in vivo. H-Tyr-D-MetO-Phe-Gly-NH2 (I) (guinea pig ileum IC50 = 13.6 nM; tail-flick ED50 = 1.97 pmol/mouse, icv, and 0.65 mumol/kg, sc), though less effective in the periphery, has central activities higher than those of dermorphin H-Tyr-D-Ala-Phe-Gly-Tyr-Pro-Ser-NH2. Following intracerebroventricular or subcutaneous administrations in mice, I is about respectively 1500 and 17 times as potent an analgesic as morphine.
MultiSDGAN: Translation of OCT Images to Superresolved Segmentation Labels Using Multi-Discriminators in Multi-Stages (2021)

Optical coherence tomography (OCT) has been identified as a non-invasive and inexpensive imaging modality to discover potential biomarkers for Alzheimer's diagnosis and progress determination. Current hypotheses presume the thickness of the retinal layers, which are analyzable within OCT scans, as an effective biomarker for the presence of Alzheimer's. As a logical first step, this work concentrates on the accurate segmentation of retinal layers to isolate the layers for further analysis. This paper proposes a generative adversarial network (GAN) that concurrently learns to increase the image resolution for higher clarity and then segment the retinal layers. We propose a multi-stage and multi-discriminatory generative adversarial network (MultiSDGAN) specifically for superresolution and segmentation of OCT scans of the retinal layer. The resulting generator is adversarially trained against multiple discriminator networks at multiple stages. We aim to avoid early saturation of generator model training leading to poor segmentation accuracies and enhance the process of OCT domain translation by satisfying all the discriminators in multiple scales. We also investigated incorporating the Dice loss and Structured Similarity Index Measure (SSIM) as additional loss functions to specifically target and improve our proposed GAN architecture's segmentation and superresolution performance, respectively. The ablation study results conducted on our data set suggest that the proposed MultiSDGAN with ten-fold cross-validation (10-CV) provides a reduced equal error rate with 44.24% and 34.09% relative improvements, respectively (p-values of the improvement level tests .01). Furthermore, our experimental results also demonstrate that the addition of the new terms to the loss function improves the segmentation results significantly by relative improvements of 31.33% (p-value .01).
Small Molecule CXCR4 Chemokine Receptor Antagonists: Developing Drug Candidates (2007)

Chemokine receptors are a target of growing interest for new therapeutic drugs, as their role in multiple disease states has been demonstrated. The CXCR4/ CXCL12 pairing has been implicated in HIV and cancer, as well as chronic inflammatory diseases, including asthma and rheumatoid arthritis. HIV uses CXCR4 or CCR5 receptors in the key binding step of the infection process, leading to the idea that drugs could be developed to block this interaction. Cancer metastasis has also been linked to cellular communication via the chemokine pathways and hence, receptor antagonists could potentially inhibit this important pathway of disease progression. A wealth of data concerning small molecule CXCR4 receptor antagonists has been generated over the last few years, as a variety of these small molecules have been tested, and the understanding of structure activity relationships has improved. Here, we review the developing area of small molecule CXCR4 antagonists and the rapidly increasing amount of data from biological studies. Both peptidic and non-peptidic compounds have been investigated. In particular, we focus on AMD3100 and bismacrocyclic analogues, the most extensively studied class of CXCR4 antagonists, and the recent developments in this area.
Experimentally-Tuned Mathematical Model for Drillstring Vibrations (2007)

Field experience manifests that drillstring vibration is one of the major causes for a deteriorated drilling performance. It is crucial to understand the complex vibrational mechanisms experienced by a drilling system in order to better control its functional operation and improve its performance. Experimental studies of drillstring dynamics are essential to complement the theoretical studies, and to alleviate the complexity of such dynamic models. This paper presents an experimental investigation using a specially designed drilling test rig. The test rig can simulate the drillstring vibrational response due to various excitation mechanisms, which include stick-slip, well-borehole contact, and drilling fluid interaction. The test rig is driven by a variable speed motor which allows for testing different drilling speeds, while a magnetic tension brake is used to simulated stick-slip. In addition, a shaker is employed to excite the drillstring axially in order to simulate the weight-on-bit (WOB). The drillstring is instrumented for vibration measurements. The experimentally identified parameters are used to refine the finite element multibody model of the drillstring, which was derived earlier by the investigators [1]. Comparisons with published data demonstrate the reliability of the developed scheme for prediction of drillstring vibrations.
Analysis of evolutionary algorithms using multi-objective parameter tuning (2014)

Evolutionary Algorithms (EAs) and other metaheuristics are greatly affected by the choice of their parameters, not only as regards the precision of the solutions found, but also for repeatability, robustness, speed of convergence, and other properties. Most of these performance criteria are often conflicting with one another. In our work, we see the problem of EAs' parameter selection and tuning as a multi-objective optimization problem, in which the criteria to be optimized are precision and speed of convergence. We propose EMOPaT (Evolutionary Multi-Objective Parameter Tuning), a method that uses a well-known multi-objective optimization algorithm (NSGA-II) to find a front of non-dominated parameter sets which produce good results according to these two metrics.
InAlGaAs/InGaAs MQW modulators operating at 1.06 μm on GaAs substrate for opto-electronic computing (1992)

Strain-relaxed InAlGaAs/InGaAs MQW device arrays with an exciton absorption peak at 1.06 μm are reported. The array will be used in flip-chip bonded Si/GaAs smart pixels operating at the wavelength corresponding to the emission of diode pumped solid state Nd-YAG lasers. The MQW devices are designed for both electro-optic modulation and detection in the pixels, while the logic functions are implemented by Si CMOS circuits. MQW modulators operating below the GaAs band edge have been demonstrated with strained GaAs/InGaAs MQWs on GaAs substrates. However, the indium content required for operation at 1.06 μm is about 25%, which results in a 2% lattice mismatch between InGaAs and GaAs. In this work, MQW structures are constructed by lattice-matched InAlGaAs/InGaAs multi-layers of the same indium content in both quaternary and ternary materials. The misfit strain from GaAs substrate was accommodated by a compositionally step-graded InAlGaAs buffer with each 0.3 to 0.5 μm thick step representing a less than 10% change in the indium composition. The band gap of each InAlGaAs layer was adjusted to be the same as that of GaAs by controlling the aluminum content. The preliminary results show an electro-absorption of 2500/ cm at 1.06 μm with an applied field of 3 × 105 V/cm.
Clinical disability in posterior cruciate ligament deficient patients does not relate to knee laxity, but relates to dynamic knee function during stair descending (2006)

Abstract We investigated the factors which influence clinical subjective symptoms during activities in Posterior cruciate ligament (PCL) deficient patients by evaluating knee laxity, muscle strength and knee mechanics during level walking, stair ascent and descent. Twenty‐two subjects with isolated PCL deficient knees and 20 healthy volunteers were involved. The PCL deficient patients were divided into two subgroups based on previous history of experiencing giving‐way during stair descent; a giving‐way group (10 subjects) and a nongiving‐way group (12 subjects). Giving‐way during activities of daily living is a key symptom in isolated PCL deficient patients. No statistically significant differences in the knee laxity, muscle strength and knee mechanics during level walking and were observed between the giving‐way group and the nongiving‐way group. However, we found significant differences in the knee mechanics during stair ascent and descent between the two groups, and these differences were more remarkable during stair descent. Peak values of knee flexion angle, external knee flexion moment and posterior knee force during early stance phase were significantly lower in the giving‐way group than in the nongiving‐way group. This study indicated that the symptom of giving‐way during stair descent was related to knee mechanics during stair descent, unlike other quantitative evaluations such as KT‐2000 or Biodex.
SwarmControl: An Automated Distributed Control Framework for Self-Optimizing Drone Networks (2020)

Networks of Unmanned Aerial Vehicles (UAVs), composed of hundreds, possibly thousands of highly mobile and wirelessly connected flying drones will play a vital role in future Internet of Things (IoT) and 5G networks. However, how to control UAV networks in an automated and scalable fashion in distributed, interference-prone, and potentially adversarial environments is still an open research problem. This article introduces SwarmControl, a new software-defined control framework for UAV wireless networks based on distributed optimization principles. In essence, SwarmControl provides the Network Operator (NO) with a unified centralized abstraction of the networking and flight control functionalities. High-level control directives are then automatically decomposed and converted into distributed network control actions that are executed through programmable software-radio protocol stacks. SwarmControl (i) constructs a network control problem representation of the directives of the NO; (ii) decomposes it into a set of distributed sub-problems; and (iii) automatically generates numerical solution algorithms to be executed at individual UAVs.We present a prototype of an SDR-based, fully reconfigurable UAV network platform that implements the proposed control framework, based on which we assess the effectiveness and flexibility of SwarmControl with extensive flight experiments. Results indicate that the SwarmControl framework enables swift reconfiguration of the network control functionalities, and it can achieve an average throughput gain of 159% compared to the state-of-the-art solutions.
Ezh2 restricts the smooth muscle lineage during mouse lung mesothelial development (2016)

During development, the lung mesoderm generates a variety of cell lineages, including airway and vascular smooth muscle. Epigenetic changes in adult lung mesodermal lineages are thought to contribute towards diseases such as idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease, although the factors that regulate early lung mesoderm development are unknown. We show in mouse that the PRC2 component Ezh2 is required to restrict smooth muscle differentiation in the developing lung mesothelium. Mesodermal loss of Ezh2 leads to the formation of ectopic smooth muscle in the submesothelial region of the developing lung mesoderm. Loss of Ezh2 specifically in the developing mesothelium reveals a mesothelial cell-autonomous role for Ezh2 in repression of the smooth muscle differentiation program. Loss of Ezh2 derepresses expression of myocardin and Tbx18, which are important regulators of smooth muscle differentiation from the mesothelium and related cell lineages. Together, these findings uncover an Ezh2-dependent mechanism to restrict the smooth muscle gene expression program in the developing mesothelium and allow appropriate cell fate decisions to occur in this multipotent mesoderm lineage.
Structural elucidation of rokitamycin, midecamycin and erythromycin metabolites formed by pathogenic Nocardia (1995)

Abstract Pathogenic Nocardia spp. converted rokitamycin, midecamycin and erythromycin into inactive metabolites, the structures of which were determined from NMR and mass spectral data. Depending on the species of Nocardia , these macrolides underwent phosphorylation at 2′‐OH, hydrolysis of the 4″‐O‐acyl group, glycosylation at 2′‐OH and/or reduction of the 18‐formyl group. Full 1 H and 13 C assignments are presented and some solvent effects are described.
Tumor mutation burden assessment on FFPE samples using a targeted next-generation sequencing assay (2018)

Background: Tumor mutation burden (TMB) predicts durable benefit from immune checkpoint blockade in several cancer types. We demonstrate the ability of a targeted panel with fast turn-around time and low input needs to estimate TMB from research samples. Methods: We developed a single sample analysis workflow to estimate mutation burden (TMB; nonsynonymous mutations/Mb) from FFPE and fresh frozen tumor research samples. The assay utilizes a PCR-based targeted panel that covers 409 genes and 1.7 Mb of genomic regions. The workflow requires only 10 ng of input DNA and enables a 2.5-day turn-around time from sample to the final report. Sequencing is performed on high throughput semiconductor sequencing platform to achieve sufficient depth (∼500x coverage) and accuracy. The workflow is tumor sample only, with no matched normal sample required; germ-line variants, along with background noise, are removed through filters based on population databases. The assay is research use only, not for diagnostic procedures. Results: A comparison with whole exome sequencing (WES) on 12 FFPE tumors, where WES was performed on tumors and their matched normal using Agilent’s exome enrichment kit (∼150x coverage for tumor; ∼100x coverage for normal) on illumina platform and our assay ran on tumors only, showed high correlation (r2=0.83) between TMB estimates by our assay with that from WES. To assess reproducibility, we compared raw somatic mutations/Mb in library replicates for a cohort of 21 FFPE research samples (19 CRC, 2 Melanoma) and observed high correlation (r2=0.97). Our pipeline identifies mutation signatures consistent with specific mechanisms such as UV and tobacco damage, as well as substitutions from FFPE processing. Conclusions: A simple workflow has been developed on the Ion Torrent sequencing platform with an AmpliSeq panel to estimate TMB from FFPE and fresh frozen tumor research samples. This solution will advance research in immuno-oncology. Legal entity responsible for the study: Thermo Fisher Scientific. Funding: Thermo Fisher Scientific. Disclosure: R. Chaudhary, D. Cyanam, V. Mittal, W. Tom, J. Au-Young, C. Allen, S. Sadis, F. Hyland: Employment: Thermo Fisher Scientific.
Low-barrier heterojunction of epitaxial silicide composed of W-encapsulating Si clusters with n-type Si (2012)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Naoya Okada, Noriyuki Uchida, Toshihiko Kanayama; Low-barrier heterojunction of epitaxial silicide composed of W-encapsulating Si clusters with n-type Si. Appl. Phys. Lett. 19 November 2012; 101 (21): 212103. https://doi.org/10.1063/1.4767136 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioApplied Physics Letters Search Advanced Search |Citation Search
Probabilistic Inference of Hand Motion from Neural Activity in Motor Cortex (2002)

Statistical learning and probabilistic inference techniques are used to infer the hand position of a subject from multi-electrode recordings of neural activity in motor cortex. First, an array of electrodes provides training data of neural firing conditioned on hand kinematics. We learn a nonparametric representation of this firing activity using a Bayesian model and rigorously compare it with previous models using cross-validation. Second, we infer a posterior probability distribution over hand motion conditioned on a sequence of neural test data using Bayesian inference. The learned firing models of multiple cells are used to define a non-Gaussian likelihood term which is combined with a prior probability for the kinematics. A particle filtering method is used to represent, update, and propagate the posterior distribution over time. The approach is compared with traditional linear filtering methods; the results suggest that it may be appropriate for neural prosthetic applications.
Different interfaces to crystalline ZnO nanorods and their applications (2009)

Abstract In this paper we will demonstrate the growth of crystalline ZnO nanorods on different substrates including some of crystalline as well as amorphous nature. The application of these ZnO nanorods to optoelectronics and to bioelectronics will be highlighted. We demonstrate the fabrication of n‐ZnO nanorods/p‐type substrates and fabricated light emitting diodes (LEDs) based on these structures. Among the presented LEDs, a hybrid configuration based on the integration of p‐type polymers on flexible plastic provides a potential for developing large area white LEDs. Moreover, ZnO nanorods based intracellular measurements using bare and functionalized ZnO surfaces were demonstrated to be a valuable non‐destructive tool for obtaining intracellular measurements paving the way for a wealth of intracellular information. (© 2009 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Expression and purification of the leucine zipper and DNA-binding domains of Fos and Jun: both Fos and Jun contact DNA directly. (1990)

The protein products of the fos and jun protooncogenes interact cooperatively in the form of a heterodimer with the activator protein 1 (AP-1) regulatory element. To characterize the properties of these proteins, we have expressed polypeptides comprised of the dimerization and DNA-binding domains of Fos and Jun in Escherichia coli. The mini-Fos (wbFos) and the mini-Jun (wbJun) proteins were purified to apparent homogeneity by using a nickel affinity chromatography procedure. Purified wbFos and wbJun associated rapidly in vitro and interacted cooperatively with the human metallothionein IIA AP-1-binding site. However, efficient DNA binding of wbJun and wbFos-wbJun complexes required an additional activity present in nuclear extracts. This activity was sensitive to alkylating agents and could be partially mimicked by the presence of reducing and stabilizing agents. DNase I footprinting experiments demonstrated that Jun homodimeric complexes and Fos-Jun heterodimeric complexes interacted with the same site on the human metallothionein IIA gene. Moreover, UV-crosslinking studies demonstrated that Fos and Jun contact DNA directly and that both proteins interacted equivalently with either strand of the AP-1-binding site.
Modulation of beta-secretase gene expression by action of catalytic nucleic acids (2002)

Two sites of the initial translation sequence of beta-secretase (BACE) mRNA were chosen as targets for endogenously delivered hammerhead ribozymes. Ribozyme cassettes coding a catalytic core, flanked by the 5'-tRNA(Val) and the 3'-CTE (constitutive transport element) sequences, were cloned into a pUC119 plasmid and used for transfection of transformed primary human embryonal kidney (HEK293) cells. The ribozymes express in the test cells and inhibit beta-secretase gene biosynthesis on the level of mRNA (up to 95%) and on the level of protein (up to 90%) and thus may be considered as therapeutic inhibitors of beta-secretase activity.
Spin-orbit interaction: a new way to control light and surface plasmons on the nanoscale (2022)

International audience
Distributed Matrix-Vector Multiplication: A Convolutional Coding Approach (2019)

Distributed computing systems are well-known to suffer from the problem of slow or failed nodes; these are referred to as stragglers. Straggler mitigation (for distributed matrix computations) has recently been investigated from the standpoint of erasure coding in several works. In this work we present a strategy for distributed matrix-vector multiplication based on convolutional coding. Our scheme can be decoded using a lowcomplexity peeling decoder. The recovery process enjoys excellent numerical stability as compared to Reed-Solomon coding based approaches (which exhibit significant problems owing their badly conditioned decoding matrices). Finally, our schemes are better matched to the practically important case of sparse matrix-vector multiplication as compared to many previous schemes. Extensive simulation results corroborate our findings.
Phase‐based masking for quantitative susceptibility mapping of the human brain at 9.4T (2022)

Automatic, phase-based masking founded on the second derivative of the sign of the wrapped phase, including cortical voxels at the brain surface, was able to mitigate artifacts and restore QSM contrast across cortical and subcortical brain regions.
An Online Impedance Processing Method for Fuel Cell EIS Measurements Enabling Degradation Information Extraction (2019)

Effective diagnostic methods are highly needed to help improve durability and lifetime of fuel cell stacks. This paper proposes a new diagnostic method based on impedance processing of electrochemical impedance spectroscopy (EIS) measurements of a fuel cell stack (FCS). A three-dimensional feature extraction method is designed to replace the equivalent circuit model commonly used for modeling the EIS signature. By tracking internal resistance, polarization resistance, and maximum imaginary response features, the method detects a fault and isolates it from the normal degradation of a fuel cell. The proposed method can separate fault conditions from degradation and extract the degradation information effectively. The method successfully detected and isolated flooding and drying on the experimental data. The method is computationally efficient and easy to adopt for online implementations, making it particularly useful in motive applications such as fuel cell vehicles.