43 results match your criteria faithfully matching


A novel decoding method for motor imagery tasks with 4D data representation and 3D convolutional neural networks.

J Neural Eng 2021 Apr 9. Epub 2021 Apr 9.

Beijing University of Technology, 100 Pingyuan, Beijing University of Technology, Chaoyang District, Beijing, Beijing, 100022, CHINA.

Objective: Motor imagery electroencephalography (MI-EEG) produces one of the most commonly used biosignals in intelligent rehabilitation systems. The newly developed 3-dimensional convolutional neural network (3DCNN) is gaining increasing attention for its ability to recognize MI tasks. The key to successful identification of movement intention is dependent on whether the data representation can faithfully reflect the cortical activity induced by MI. Read More

View Article and Full-Text PDF

NF-YA Overexpression in Lung Cancer: LUAD.

Genes (Basel) 2020 02 14;11(2). Epub 2020 Feb 14.

Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.

The trimeric transcription factor (TF) NF-Y regulates the CCAAT box, a DNA element enriched in promoters of genes overexpressed in many types of cancer. The regulatory NF-YA is present in two major isoforms, NF-YAl ("long") and NF-YAs ("short"). There is growing indication that NF-YA levels are increased in tumors. Read More

View Article and Full-Text PDF
February 2020

Fabrication of 3D scaffolds reproducing intestinal epithelium topography by high-resolution 3D stereolithography.

Biomaterials 2019 11 5;221:119404. Epub 2019 Aug 5.

LAAS-CNRS, Université de Toulouse, CNRS, F-31400, Toulouse, France. Electronic address:

The small intestine is a complex tissue with a crypt/villus architecture and high tissue polarity. Maintenance of tissue integrity and function is supported by a constant renewal of the epithelium, with proliferative cells located in the crypts and differentiated cells migrating upward to the top of villi. So far, most in vitro studies have been limited to 2D surfaces or 3D organoid cultures that do not fully recapitulate the tissue 3D architecture, microenvironment and cell compartmentalization found in vivo. Read More

View Article and Full-Text PDF
November 2019

Transversely isotropic and isotropic material considerations in determining the mechanical response of geometrically accurate bovine tibia bone.

Med Biol Eng Comput 2019 Oct 3;57(10):2159-2178. Epub 2019 Aug 3.

Mechanical Engineering Department, American University of Beirut, P.O. Box 11-0236, Riad El-Solh, Beirut, 1107 2020, Lebanon.

In finite element method (FEM) simulations of the mechanical response of bones, proper selection of stiffness versus density (E-ρ) formulae for bone constituents is necessary for obtaining accurate results. A considerable number of such formulae can be found in the biomechanics' literature covering both cortical and cancellous constituents. For determining the first and second modal frequencies (in both cranial-caudal and medial-lateral planes) of bovine tibia bone, this work assembled and numerically tested 22 isotropic and 21 orthotropic stiffness-density formulae combinations (cases). Read More

View Article and Full-Text PDF
October 2019

FluoEM, virtual labeling of axons in three-dimensional electron microscopy data for long-range connectomics.

Elife 2018 08 14;7. Epub 2018 Aug 14.

Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany.

The labeling and identification of long-range axonal inputs from multiple sources within densely reconstructed electron microscopy (EM) datasets from mammalian brains has been notoriously difficult because of the limited color label space of EM. Here, we report FluoEM for the identification of multi-color fluorescently labeled axons in dense EM data without the need for artificial fiducial marks or chemical label conversion. The approach is based on correlated tissue imaging and computational matching of neurite reconstructions, amounting to a virtual color labeling of axons in dense EM circuit data. Read More

View Article and Full-Text PDF

Quantum Transduction with Adaptive Control.

Phys Rev Lett 2018 Jan;120(2):020502

Departments of Applied Physics and Physics, Yale University, New Haven, Connecticut 06520, USA.

Quantum transducers play a crucial role in hybrid quantum networks. A good quantum transducer can faithfully convert quantum signals from one mode to another with minimum decoherence. Most investigations of quantum transduction are based on the protocol of direct mode conversion. Read More

View Article and Full-Text PDF
January 2018

Photonic quantum state transfer between a cold atomic gas and a crystal.

Nature 2017 11;551(7681):485-488

ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain.

Interfacing fundamentally different quantum systems is key to building future hybrid quantum networks. Such heterogeneous networks offer capabilities superior to those of their homogeneous counterparts, as they merge the individual advantages of disparate quantum nodes in a single network architecture. However, few investigations of optical hybrid interconnections have been carried out, owing to fundamental and technological challenges such as wavelength and bandwidth matching of the interfacing photons. Read More

View Article and Full-Text PDF
November 2017

Patient-derived xenografts effectively capture responses to oncology therapy in a heterogeneous cohort of patients with solid tumors.

Ann Oncol 2017 Oct;28(10):2595-2605

Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, R&D, Baltimore. Electronic address:

Background: While patient-derived xenografts (PDXs) offer a powerful modality for translational cancer research, a precise evaluation of how accurately patient responses correlate with matching PDXs in a large, heterogeneous population is needed for assessing the utility of this platform for preclinical drug-testing and personalized patient cancer treatment.

Patients And Methods: Tumors obtained from surgical or biopsy procedures from 237 cancer patients with a variety of solid tumors were implanted into immunodeficient mice and whole-exome sequencing was carried out. For 92 patients, responses to anticancer therapies were compared with that of their corresponding PDX models. Read More

View Article and Full-Text PDF
October 2017

Measurement of Dynamic Joint Stiffness from Multiple Short Data Segments.

IEEE Trans Neural Syst Rehabil Eng 2017 07 2;25(7):925-934. Epub 2017 Mar 2.

This paper presents our new method, Short Segment-Structural Decomposition SubSpace (SS-SDSS), for the estimation of dynamic joint stiffness from short data segments. The main application is for data sets that are only piecewise stationary. Our approach is to: 1) derive a data-driven, mathematical model for dynamic stiffness for short data segments; 2) bin the non-stationary data into a number of short, stationary data segments; and 3) estimate the model parameters from subsets of segments with the same properties. Read More

View Article and Full-Text PDF

The paleoclimate context and future trajectory of extreme summer hydroclimate in eastern Australia.

J Geophys Res Atmos 2016 Nov 31;121(21):12820-12838. Epub 2016 Oct 31.

School of Ecosystem and Forest Sciences, University of Melbourne, Richmond, Victoria, Australia.

Eastern Australia recently experienced an intense drought (Millennium Drought, 2003-2009) and record-breaking rainfall and flooding (austral summer 2010-2011). There is some limited evidence for a climate change contribution to these events, but such analyses are hampered by the paucity of information on long-term natural variability. Analyzing a new reconstruction of summer (December-January-February) Palmer Drought Severity Index (the Australia-New Zealand Drought Atlas; ANZDA, 1500-2012 CE), we find moisture deficits during the Millennium Drought fall within the range of the last 500 years of natural hydroclimate variability. Read More

View Article and Full-Text PDF
November 2016

"Sticky"-Ends-Guided Creation of Functional Hollow Nanopores for Guest Encapsulation and Water Transport.

Acc Chem Res 2016 05 13;49(5):922-30. Epub 2016 Apr 13.

Institute of Bioengineering and Nanotechnology , 31 Biopolis Way, The Nanos, Singapore 138669.

Commercial uses of water-transporting aquaporins for seawater desalination and wastewater reclamation/reuse are being investigated in both academia and the industry. Presently, structural complexity, stability, scalability, and activity reconstitution of these costly channel proteins still present substantial challenges to scientists and engineers. An attractive strategy is to develop robust synthetic water channels able to mimic the water-transporting function of aquaporins for utility in the making of next generation of water channel-based biomimetic porous membranes for various water purification applications. Read More

View Article and Full-Text PDF

Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation.

Cell Rep 2016 Feb 11;14(7):1787-1799. Epub 2016 Feb 11.

Howard Hughes Medical Institute; Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical challenges can confound its analysis. Here, we use improved methods to obtain ribosome-footprint profiles and mRNA abundances that more faithfully reflect gene expression in Saccharomyces cerevisiae. Our results support proposals that both the beginning of coding regions and codons matching rare tRNAs are more slowly translated. Read More

View Article and Full-Text PDF
February 2016

In Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology.

J Mol Biol 2016 Jan 9;428(2 Pt A):332-343. Epub 2015 Oct 9.

Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. Electronic address:

Cryo-electron tomography is a powerful technique that can faithfully image the native cellular environment at nanometer resolution. Unlike many other imaging approaches, cryo-electron tomography provides a label-free method of detecting biological structures, relying on the intrinsic contrast of frozen cellular material for direct identification of macromolecules. Recent advances in sample preparation, detector technology, and phase plate imaging have enabled the structural characterization of protein complexes within intact cells. Read More

View Article and Full-Text PDF
January 2016

Faithful Completion of Images of Scenic Landmarks Using Internet Images.

IEEE Trans Vis Comput Graph 2016 08 18;22(8):1945-58. Epub 2015 Sep 18.

Previous works on image completion typically aim to produce visually plausible results rather than factually correct ones. In this paper, we propose an approach to faithfully complete the missing regions of an image. We assume that the input image is taken at a well-known landmark, so similar images taken at the same location can be easily found on the Internet. Read More

View Article and Full-Text PDF

Not looking yourself: The cost of self-selecting photographs for identity verification.

Br J Psychol 2016 May 23;107(2):359-73. Epub 2015 Jun 23.

School of Psychology, University of New South Wales, Kensington, Sydney, New South Wales, Australia.

Photo-identification is based on the premise that photographs are representative of facial appearance. However, previous studies show that ratings of likeness vary across different photographs of the same face, suggesting that some images capture identity better than others. Two experiments were designed to examine the relationship between likeness judgments and face matching accuracy. Read More

View Article and Full-Text PDF

Establishment of patient-derived xenograft models and cell lines for malignancies of the upper gastrointestinal tract.

J Transl Med 2015 Apr 11;13:115. Epub 2015 Apr 11.

Laboratory for Experimental Oncology and Radiobiology, Academic Medical Center, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands.

Background: The upper gastrointestinal tract is home to some of most notorious cancers like esophagogastric and pancreatic cancer. Several factors contribute to the lethality of these tumors, but one that stands out for both tumor types is the strong inter- as well as intratumor heterogeneity. Unfortunately, genetic tumor models do not match this heterogeneity, and for esophageal cancer no adequate genetic models exist. Read More

View Article and Full-Text PDF

Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models.

J Phys Chem B 2015 Jul 27;119(29):9029-37. Epub 2014 Oct 27.

‡Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States.

We develop a systematic procedure for obtaining rate and transition matrices that optimally describe the dynamics of aggregated superstates formed by combining (clustering or lumping) microstates. These reduced dynamical models are constructed by matching the time-dependent occupancy-number correlation functions of the superstates in the full and aggregated systems. Identical results are obtained by using a projection operator formalism. Read More

View Article and Full-Text PDF

Temporal and spatial patterning of transgene expression by near-infrared irradiation.

Biomaterials 2014 Sep 21;35(28):8134-8143. Epub 2014 Jun 21.

Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain.

We investigated whether near-infrared (NIR) light could be employed for patterning transgene expression in plasmonic cell constructs. Hollow gold nanoparticles with a plasmon surface band absorption peaking at ∼750 nm, a wavelength within the so called "tissue optical window", were used as fillers in fibrin-based hydrogels. These composites, which efficiently transduce NIR photon energy into heat, were loaded with genetically-modified cells that harbor a heat-activated and ligand-dependent gene switch for regulating transgene expression. Read More

View Article and Full-Text PDF
September 2014

Vertical-plane sound localization with distorted spectral cues.

Hear Res 2013 Dec 27;306:76-92. Epub 2013 Sep 27.

Kresge Hearing Research Institute, University of Michigan Medical School, 1150 W. Medical Center Drive, Ann Arbor, MI 48109-5616, USA; National Centre for Audiology, Western University, 1201 Western Road, London, Ontario, Canada N6G 1H1. Electronic address:

For human listeners, the primary cues for localization in the vertical plane are provided by the direction-dependent filtering of the pinnae, head, and upper body. Vertical-plane localization generally is accurate for broadband sounds, but when such sounds are presented at near-threshold levels or at high levels with short durations (<20 ms), the apparent location is biased toward the horizontal plane (i.e. Read More

View Article and Full-Text PDF
December 2013

Hyperconjugative interactions in permethylated siloxanes and ethers: the nature of the SiO bond.

J Am Chem Soc 2013 Apr 9;135(15):5762-7. Epub 2013 Apr 9.

Department of Chemistry, University of Wisconsin, Madison Wisconsin 53706, USA.

The paradoxically low basicity (despite high anionicity) of oxygen in the characteristic Si-O-Si linkages of silicone polymers is investigated with hybrid density functional and natural bond orbital (NBO) computational methods, extending a previous study of idealized disiloxane and dimethyl ether parent species to fully methylated derivatives that more faithfully model the silicone polymers of industrial and environmental importance. Despite the complicating distortions of the sterically crowded di-t-butyl ether "analog", the physical picture of enhanced hyperconjugative (resonance-type) delocalization in Si-O vs C-O bonding is essentially preserved (and indeed accentuated) in permethylated species. NBO-based orbital overlap diagrams are employed in conjunction with structural, hybridization, and polarity descriptors to illustrate the subtle phase-matching relationships that confer superior enthalpic and entropic stability (and low basicity) on permethylated Si-O-Si linkages. Read More

View Article and Full-Text PDF

Recognition criteria vary with fluctuating uncertainty.

J Vis 2012 Aug 6;12(8). Epub 2012 Aug 6.

Optometry Division, Applied Vision Research Centre, City University London, UK.

In distinct experiments we examined memories for orientation and size. After viewing a randomly oriented Gabor patch (or a plain white disk of random size), observers were given unlimited time to reproduce as faithfully as possible the orientation (or size) of that standard stimulus with an adjustable Gabor patch (or disk). Then, with this match stimulus still in view, a recognition probe was presented. Read More

View Article and Full-Text PDF

Robust web image/video super-resolution.

IEEE Trans Image Process 2010 Aug 15;19(8):2017-28. Epub 2010 Mar 15.

Microsoft Research Asia, Beijing, 100081, China.

This paper proposes a robust single-image super-resolution method for enlarging low quality web image/video degraded by downsampling and compression. To simultaneously improve the resolution and perceptual quality of such web image/video, we bring forward a practical solution which combines adaptive regularization and learning-based super-resolution. The contribution of this work is twofold. Read More

View Article and Full-Text PDF

A statistical validation of the individuality and repeatability of striated tool marks: screwdrivers and tongue and groove pliers.

J Forensic Sci 2010 Mar 5;55(2):348-57. Epub 2010 Feb 5.

Intelligent Automation, Inc., 15400 Calhoun Drive, Suite 400, Rockville, MD 20855, USA.

Tool mark identification relies on the premise that microscopic imperfections on a tool's working surface are sufficiently unique and faithfully transferred to enable a one-to-one association between a tool and the tool marks it creates. This paper presents a study undertaken to assess the validity of this premise. As part of this study sets of striated tool marks were created under different conditions and on different media. Read More

View Article and Full-Text PDF

Establishment of a strain inheriting a sex-linked SNP marker in Patagonian pejerrey (Odontesthes hatcheri), a species with both genotypic and temperature-dependent sex determination.

Anim Genet 2010 Feb 15;41(1):81-4. Epub 2009 Sep 15.

Department of Aquatic Biosciences, Tokyo University of Marine Science and Technology, Konan, Minato, Japan.

The Patagonian pejerrey Odontesthes hatcheri is an atherinopsid species presenting genotypic sex determination (GSD) at intermediate temperatures and temperature-dependent sex determination at the low and high ranges of thermal tolerance. A recent study revealed the presence of a sex-linked SNP marker in some males of this species, but a strain which inherits the marker faithfully has not been established. This research was conducted to develop such a strain, for use as a tool to study the molecular mechanisms of gonadal sex differentiation and sexual dimorphism, and to obtain basic information on the GSD mode in this species. Read More

View Article and Full-Text PDF
February 2010

Clinical utility of five dimensional systems for personality diagnosis: a "consumer preference" study.

J Nerv Ment Dis 2008 May;196(5):356-74

Department of Psychiatry, Columbia University, New York State Psychiatric Institute, New York, New York 10032, USA.

This study compares the clinical relevance and utility of five dimensional diagnostic systems for personality disorders that have been proposed for the forthcoming edition of DSM (DSM-V): (1) a criteria counting model based on current DSM-IV diagnostic criteria; (2) a prototype matching model based on current DSM-IV diagnostic criteria; (3) a prototype matching model based on the Shedler-Westen Assessment Procedure (SWAP); (4) the Five Factor Model; and (5) Cloninger's Psychobiological Model. A random national sample of psychiatrists and psychologists applied all 5 diagnostic systems to a patient in their care and rated the clinical utility of each system. The SWAP Prototype Matching and DSM-IV Prototype Matching models were judged most clinically useful and relevant. Read More

View Article and Full-Text PDF

Imitating the neighbours: vocal dialect matching in a mimic-model system.

Biol Lett 2006 Sep;2(3):367-70

School of Integrative Biology, The University of Queensland, St Lucia, Qld 4072, Australia.

Vocal mimicry provides a unique system for investigating song learning and cultural evolution in birds. Male lyrebirds produce complex vocal displays that include extensive and accurate mimicry of many other bird species. We recorded and analysed the songs of the Albert's lyrebird (Menura alberti) and its most commonly imitated model species, the satin bowerbird (Ptilonorhynchus violaceus), at six sites in southeast Queensland, Australia. Read More

View Article and Full-Text PDF
September 2006

An accurate and simple quantum model for liquid water.

J Chem Phys 2006 Nov;125(18):184507

Center for Biophysical Modeling and Simulation, University of Utah, Salt Lake City, Utah 84112, USA.

The path-integral molecular dynamics and centroid molecular dynamics methods have been applied to investigate the behavior of liquid water at ambient conditions starting from a recently developed simple point charge/flexible (SPC/Fw) model. Several quantum structural, thermodynamic, and dynamical properties have been computed and compared to the corresponding classical values, as well as to the available experimental data. The path-integral molecular dynamics simulations show that the inclusion of quantum effects results in a less structured liquid with a reduced amount of hydrogen bonding in comparison to its classical analog. Read More

View Article and Full-Text PDF
November 2006

Development of complex classical force fields through force matching to ab initio data: application to a room-temperature ionic liquid.

J Phys Chem B 2006 Mar;110(11):5697-707

Atomistic Simulation Centre, School of Physics, Queen's University, Belfast BT7 1NN, UK.

Recent experimental neutron diffraction data and ab initio molecular dynamics simulation of the ionic liquid dimethylimidazolium chloride ([dmim]Cl) have provided a structural description of the system at the molecular level. However, partial radial distribution functions calculated from the latter, when compared to previous classical simulation results, highlight some limitations in the structural description offered by force field-based simulations. With the availability of ab initio data it is possible to improve the classical description of [dmim]Cl by using the force matching approach, and the strategy for fitting complex force fields in their original functional form is discussed. Read More

View Article and Full-Text PDF

Structure and function of SNARE and SNARE-interacting proteins.

Authors:
Axel T Brunger

Q Rev Biophys 2005 Feb 9;38(1):1-47. Epub 2005 Dec 9.

Howard Hughes Medical Institute, Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.

This review focuses on the so-called SNARE (soluble N-ethyl maleimide sensitive factor attachment protein receptor) proteins that are involved in exocytosis at the pre-synpatic plasma membrane. SNAREs play a role in docking and fusion of synaptic vesicles to the active zone, as well as in the Ca2+-triggering step itself, most likely in combination with the Ca2+ sensor synaptotagmin. Different SNARE domains are involved in different processes, such as regulation, docking, and fusion. Read More

View Article and Full-Text PDF
February 2005

Extensive genomic and functional polymorphism of the complement control proteins.

Immunogenetics 2005 Dec 11;57(11):805-15. Epub 2005 Nov 11.

CY O'Connor ERADE Village, Canning Vale, Western Australia.

Using combinations of genomic markers, we describe more than 20 distinct ancestral haplotypes (AH) of complement control proteins (CCPs), located within the regulators of complement activation (RCA) alpha block at 1q32. This extensive polymorphism, including functional sites, is important because CCPs are involved in the regulation of complement activation whilst also serving as self and viral receptors. To identify haplotypes, we used the genomic matching technique (GMT) based on the pragmatic observation that extreme nucleotide polymorphism is packaged with duplicated sequences as polymorphic frozen blocks (PFB). Read More

View Article and Full-Text PDF
December 2005