gebhart/patrepeval huggingface dataset:
Isolation of caveolae using affinity two-phase partitioning (2004)

The intention of this work was to establish alternative purification methods to obtain highly purified caveolae from various tissues. In order to isolate caveolae, sufficiently pure plasma membranes are needed. A method is presented for the isolation of plasma membranes from lung tissue using a combination of conventional polyethylene glycol/dextran two-phase partitioning and affinity partitioning using the lectin wheat germ agglutinin as affinity ligand. A caveolae-enriched fraction was purified from lung plasma membranes isolated by this procedure. Caveolae were released from the membranes by Triton X-100 treatment or by sonication. Highly purified caveolae were obtained at low buoyant density by sucrose gradient centrifugation. The affinity method is advantageous to other methods for the isolation of plasma membranes and should be useful for other tissues as well. A method to purify caveolae by immunoaffinity partitioning was developed exploiting the interaction between caveolin and anti-caveolin antibodies. A sandwich approach was used where primary antibodies directed against caveolin interacted with biotinylated secondary antibodies and NeutrAvidin coupled to dextran in a polyethylene glycol/dextran two-phase system. Caveolae were directed efficiently into the immunoaffinity bottom phase of the two-phase system by the anti-caveolin antibody. Immunoaffinity two-phase partitioning has wider applications potentially, as this technique should be useful to purify any type of membrane by selecting appropriate antibodies directed against surface components of the membrane of interest. Caveolae were isolated to a high degree of purity from apical and basolateral domains of liver plasma membranes. The caveolae from the two domains were quite homogeneous as studied by immunoaffinity partitioning and electron microscopy. Analysis showed that the caveolae differed in properties in several respects.
Synergistic impact of resection margin and microscopic vascular invasion for patients with HBV-related intrahepatic cholangiocarcinoma (2021)

Combined analysis of RM and MVI can better stratify the risks of postoperative death and recurrence in patients with HBV-related ICC, which may help subsequent adjuvant therapy and closer follow-up.
Adaptive optics two-photon endomicroscopy enables deep-brain imaging at synaptic resolution over large volumes (2020)

Optical deep-brain imaging in vivo at high resolution has remained a great challenge over the decades. Two-photon endomicroscopy provides a minimally invasive approach to image buried brain structures, once it is integrated with a gradient refractive index (GRIN) lens embedded in the brain. However, its imaging resolution and field of view are compromised by the intrinsic aberrations of the GRIN lens. Here, we develop a two-photon endomicroscopy by adding adaptive optics based on direct wavefront sensing, which enables recovery of diffraction-limited resolution in deep-brain imaging. A new precompensation strategy plays a critical role to correct aberrations over large volumes and achieve rapid random-access multiplane imaging. We investigate the neuronal plasticity in the hippocampus, a critical deep brain structure, and reveal the relationship between the somatic and dendritic activity of pyramidal neurons.
Reactions of Complex Ligands, LXXVII. Axial‐Chiral Metal Carbenes: Synthesis and Structure of 1,1‐Binaphthyl‐Derived Carbonyl‐Carbene Complexes of Chromium (1997)

Abstract Axial‐chiral mono‐ and biscarbene complexes of chromium containing the 1,1‐binaphthyl skeleton have been obtained in both racemic and enantiopure forms in a one‐pot reaction starting from lithiated 2,2‐dimethoxy‐1,1‐binaphthyl ( 1 ) and hexacarbonyl chromium via the Fischer route. An X‐ray structure analysis of the biscarbene complex 2 reveals that the biscarbene functionalization significantly increases the dihedral angle defined by the biaryl planes. The enantiopure complexes have been characterized by CD spectroscopy.
Analysis of deficit round robin scheduling for future aeronautical data link (2011)

The aviation community is currently working on the standardization of data communication systems for the future air traffic management. In this context, the International Civil Aviation Organization (ICAO) has initiated a work on standardization of an IPv6-based aeronautical telecommunications network and on future radio access technologies, respectively. In this paper, we integrate L-Band Digital Aeronautical Communications System Option 1 (L-DACS 1), which is one candidate for future radio access technologies, with realistic IPv6-based network layer functionality and analyze Deficit Round Robin (DRR) with fragmentation algorithm for the forward and return link in L-DACS 1. Our analysis mainly covers two application domains: file transfer and real-time services. We show that DRR with fragmentation scheduler provides good performance results in terms of throughput, delay, and bandwidth fairness.
Prognostic molecular markers in early breast cancer (2004)

A multitude of molecules involved in breast cancer biology have been studied as potential prognostic markers. In the present review we discuss the role of established molecular markers, as well as potential applications of emerging new technologies. Those molecules used routinely to make treatment decisions in patients with early-stage breast cancer include markers of proliferation (e.g. Ki-67), hormone receptors, and the human epidermal growth factor receptor 2. Tumor markers shown to have prognostic value but not used routinely include cyclin D1 and cyclin E, urokinase-like plasminogen activator/plasminogen activator inhibitor, and cathepsin D. The level of evidence for other molecular markers is lower, in part because most studies were retrospective and not adequately powered, making their findings unsuitable for choosing treatments for individual patients. Gene microarrays have been successfully used to classify breast cancers into subtypes with specific gene expression profiles and to evaluate prognosis. RT-PCR has also been used to evaluate expression of multiple genes in archival tissue. Proteomics technologies are in development.
Evolution of optical access network technologies in radio systems (2009)

Radio system architecture has drastically changed thanks to the evolution of optical fibre technologies. This paper describes optical access technologies that contribute to the efficient construction of radio systems including mobile communication and terrestrial digital media broadcasting.
Intestinal IL-17R signaling modulates commensal microbiota by regulating expression of Nox1 and Pigr (2016)

Abstract Despite recent advances in understanding the role of IL-17 in host immunity, its role in regulating enteric immune responses as well as its impact on the commensal microbiome has not been well studied. To further understand this, we have generated intestinal epithelial cell specific IL-17R knockout mice. Our data shows that global and intestinal epithelial cell specific Il17r−/− mice have overgrowth of segmented filamentous bacteria (SFB), suggesting a critical role of IL-17 signaling in SFB colonization. Higher SFB colonization in Il17ra fl/fl ;x villin cre+ mice resulted in expansion of IL-17A and IL-22 producing Th17 cells. The expansion of SFB was also confirmed by 16S rRNA. Furthermore this analysis also showed higher abundance of S24-7 and the Clostridiales family in Il17ra fl/fl ;x villin cre+ mice. RNA sequencing data from the distal small intestine of SFB-colonized Il17ra−/− and Il17ra fl/fl ;x villin cre+ mice revealed substantial reduction of Nox1 (an apical NADPH oxidase) and Pigr genes. Mouse and human primary intestinal organoid culture further confirmed a direct role of IL-17 in regulating Nox1 and Pigr expression. Reduced Nox1 expression correlated with significant reduction in H202 levels in the terminal ileum of Il17rc fl/fl ;x villin cre+ mice. Furthermore, Nox1−/− and IgA−/− mice showed a higher degree of SFB colonization in the feces and terminal ileum as compared to cohoused control WT mice. We have evidence that Il17ra fl/fl ;x villin cre+ mice are more susceptible to autoimmune inflammation. Collectively, our data indicate IL-17R-dependent intestinal signaling controls commensal bacteria by regulating the expression of Nox1 and Pigr which regulates lumenal H202 and sIgA concentrations respectively.
Audio fingerprinting in UbiComp environments &#x2014; performance measurements and applications (2008)

We propose an audio-based mechanism for device authentication. The method is feasible with low-end microphones and can be extended to further UbiComp application domains as improved location estimation of sensor nodes or alarming. Measurement results obtained in a preparatory study demonstrate the performance of the approach.
Bonded anchors in concrete structures suffering from ASR damage (2016)

Fastening elements play a crucial role in the construction industry. They allow the connection of load bearing structural members with each other, and with appliances during initial construction. In course of the structural life-time post-installed anchors are key elements in all types of rehabilitation and restoration efforts. In recent years the deterioration of concrete structures due to alkali silica reaction (ASR) has become a concern in many fields of structural engineering ranging from bridges to nuclear containment. In this contribution we present a systematic investigation of how the long-term load carrying capacity of bonded anchors under tension is affected by (a) pre-existing ASR induced damage, or (b) by ongoing ASR after installation of the anchor. In particular, we will present a full experimental characterization of a standard concrete in reference conditions as well as after different durations of accelerated testing in alkaline rich solution. For each scenario pull-out tests according to the RILEM recommendation are performed on two typical postinstalled chemical anchor systems as well as the reference case of a standard cast-in rebar. Additionally, for all scenarios pull-out tests with wide support are performed prompting concrete cone failure. The results of the experimental investigation will be presented and serve for the calibration as well as validation of multi-phase multi-scale numerical simulations. The latter are performed to study in detail the relevant mechanisms and extrapolate the observed behavior to life-times far beyond those of laboratory tests and alternative geometrical configurations. A model parameter sensitivity analysis completes the study.
Photochemical reactions of c i s- and t r a n s-1,2-dichloroethene adsorbed on Pd(111) and Pt(111) (1988)

The photochemical behaviors of cis- and trans-1,2-dichloroethene (DCE) adsorbed on Pd(111) and Pt(111) surfaces have been studied using electron energy loss spectroscopy (EELS). For multilayer coverage on either metal surface, irradiation of physisorbed DCE at 110 K with broad band irradiation (λ&amp;gt;200 nm) results in photoisomerization, cis–trans. For monolayer coverage on Pt(111) at 110 K, photolysis of chemisorbed DCE causes loss of the two chlorine atoms to form a single hydrocarbon product, chemisorbed acetylene. Apparently, for λ&amp;gt;237 nm, the chlorine atoms remain bound to the platinum surface whereas for shorter wavelengths, λ&amp;gt;200 nm, the chlorine atoms leave the surface. These results are interpretable in terms of singlet excitation of the chemisorbed alkane followed by chlorine elimination on an excited singlet reaction surface. This study indicates that photochemistry of molecules chemisorbed on a metal surface is possible despite the proximity of the conducting surface. It shows that energy relaxation processes connected with this proximity are not prohibitively fast.
Interlayer couplings, Moiré patterns, and 2D electronic superlattices in MoS 2 /WSe 2 hetero-bilayers (2017)

By using direct growth, we create a rotationally aligned MoS<sub>2</sub>/WSe<sub>2</sub> hetero-bilayer as a designer van der Waals heterostructure. With rotational alignment, the lattice mismatch leads to a periodic variation of atomic registry between individual van der Waals layers, exhibiting a Moiré pattern with a well-defined periodicity. By combining scanning tunneling microscopy/spectroscopy, transmission electron microscopy, and first-principles calculations, we investigate interlayer coupling as a function of atomic registry. We quantitatively determine the influence of interlayer coupling on the electronic structure of the hetero-bilayer at different critical points. We show that the direct gap semiconductor concept is retained in the bilayer although the valence and conduction band edges are located at different layers. We further show that the local bandgap is periodically modulated in the <i>X</i>-<i>Y</i> direction with an amplitude of ~0.15 eV, leading to the formation of a two-dimensional electronic superlattice.
Butyrate induced changes in Wnt-signaling specific gene expression in colorectal cancer cells (2014)

We have identified, for the first time, in CRC cells, the total array of direct and indirect Wnt-target genes whose expression is modulated by butyrate. Knowledge of the molecular mechanisms determining the response of CRC cells to butyrate in vitro may assist in determining more effective preventive and therapeutic strategies against CRC.
The stage analysis and countermeasures of coal spontaneous combustion based on “five stages” division (2018)

The "three stages" division of coal spontaneous combustion is fuzzy and lacks adequate risk and warning levels corresponding to its divisions; additionally, the targeted prevention measures for each stage have not been described. To address the shortcomings of the "three stages" division, the "five stages" division was proposed to more clearly analyze the stage changes of the spontaneous combustion of coal. The "five stages" method divides the process of the spontaneous combustion of coal into five stages, including: the latent stage, heat accumulating stage, evaporation stage, active stage, and hypoxic stage. The critical point of each stage was determined using adiabatic oxidation experiments and programmed heat experiments. As the critical point of the latent stage, the temperature of zero activation energy is approximately 55-70°C. In the heat accumulating stage, the critical point is the temperature (approximately 90°C) where the external moisture of coal evaporates violently while the internal moisture of coal has not yet fully evaporated. During the evaporation stage, the temperature (approximately 105°C) where the internal moisture has evaporated completely represents the end of this stage and the start of the active stage (105-170°C). When the oxygen concentration drops to 5%, the spontaneous combustion of coal enters the hypoxic stage. Thus, an oxygen concentration of 5% represents the critical point of the start of the hypoxic stage (above 170°C). After the analysis of each stage, risk and warning levels were determined. Considering the major prevention measures of the spontaneous combustion of coal, a staged warning and disposal table was created.
The CRISPR road: from bench to bedside on an RNA-guided path. (2015)

The development of next-generation sequencing has greatly expanded our understanding of genomic alterations in cancer. This has furthered a need for new research strategies, particularly the generation of animal models for novel genetic alterations such as insertions, deletions or chromosomal rearrangements. As sequencing technology has increased its efficiency and resolution in recent years, the classic generation of genetically engineered mouse models cannot keep up with the pace of new discoveries. Gene editing in embryonic stem cells using homologous recombination has provided excellent mouse models to study alterations in tumor suppressor genes and oncogenes, however this approach is time-consuming and costly. Another significant limitation to these models is that germline mutations are constitutively present throughout all tissues in the mouse, limiting their relevance to the organ-specific somatic mutations that produce most human cancers. cDNA-based over-expression and RNA interference-mediated knockdown have also allowed scientists to study particular genes or changes in expression of key drivers, but these models are far from physiological. Ideally, a successful model system would overcome these key limitations, and would also be able to adapt quickly to accommodate the plethora of new targets and growing diversity of genomic changes that have been implicated in cancer development.
Extracellular Recordings of Patterned Human Pluripotent Stem Cell‐Derived Cardiomyocytes on Aligned Fibers (2016)

Human induced pluripotent stem cell (hiPSC) derived cardiomyocytes (CMs) hold high potential for use in drug assessment and myocardial regeneration. To create tissue-like constructs of CMs for extracellular monitoring, we placed aligned fibers (AFs) on the surface of a microelectrode array and then seeded hiPSC-CMs for subsequent monitoring for 14 days. As expected, the CMs organized into anisotropic and matured tissue and the extracellular recordings showed reduced premature beating higher signal amplitude and a higher probability of T-wave detection as compared to the culture without fibers. The CMs on the aligned fibers samples also exhibited anisotropic propagation of the field potential. These results therefore suggest that the hiPSC-CMs cultured on AFs can be used more reliably for cell based assays.
Acutely damaged axons are remyelinated in multiple sclerosis and experimental models of demyelination (2017)

Remyelination is in the center of new therapies for the treatment of multiple sclerosis to resolve and improve disease symptoms and protect axons from further damage. Although remyelination is considered beneficial in the long term, it is not known, whether this is also the case early in lesion formation. Additionally, the precise timing of acute axonal damage and remyelination has not been assessed so far. To shed light onto the interrelation between axons and the myelin sheath during de- and remyelination, we employed cuprizone- and focal lysolecithin-induced demyelination and performed time course experiments assessing the evolution of early and late stage remyelination and axonal damage. We observed damaged axons with signs of remyelination after cuprizone diet cessation and lysolecithin injection. Similar observations were made in early multiple sclerosis lesions. To assess the correlation of remyelination and axonal damage in multiple sclerosis lesions, we took advantage of a cohort of patients with early and late stage remyelinated lesions and assessed the number of APP- and SMI32- positive damaged axons and the density of SMI31-positive and silver impregnated preserved axons. Early de- and remyelinating lesions did not differ with respect to axonal density and axonal damage, but we observed a lower axonal density in late stage demyelinated multiple sclerosis lesions than in remyelinated multiple sclerosis lesions. Our findings suggest that remyelination may not only be protective over a long period of time, but may play an important role in the immediate axonal recuperation after a demyelinating insult.
GLOBAL MODELLING OF THE FIRST THREE TORSIONAL STATES OF METHANOL ($v_t$ = 0, 1, 2, $J_{max}$ = 30): CH$_{3}$OH AND CH$_3^{18}$OH (2007)

Author Institution: Department of Physical Sciences and Centre for Laser, Atomic, and; Molecular Sciences, University of New Brunswick, Saint John, NB E2L 4L5,; Canada; Optical Technology Division, National Institute of Standards and Technology,; Gaitherburg, MD 20899-8441; Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA 91109
Unpepp: Bringing Renewable Energy To Redwood National Park (2020)

In summer 2000, the interns, Lonny Grafman and Angi Sorensen, spent twelve weeks monitoring on-site energy use, tracking solar energy availability, and creating preliminary designs for the two systems: a solar thermal water heater and a DC-powered lighting system for the campground restroom at Gold Bluffs Beach and a 2-kilowatt solar electric system
Research on Intuitive Tele-operation Motion Mapping Algorithm for Omnidirectional Mobile Heterogeneous Slave Arm System (2020)

In order to meet the universality of the human-robot interface on the master side and the specialty of the interaction between the slave robot and environment, the teleoperation robotic system usually has a heterogeneous master-slave structure. The characteristics of master-slave heterogeneity will bring a difficulty to the tele-operation robotic system, and this difficulty is prominently manifested in the differences of master-slave movement trajectories and limited working space brought by the restricted slave robot movement. In order to realize motion mapping control of the heterogeneous tele-operation robotic system in accordance with the operator's intuition, this paper proposes a method to achieve the consistency of master-slave motion trajectory via combining the movement of the slave robotic chassis. When the working spaces of the master and slave are coincident, we adopt the methods of position control for the slave wrist and orientation mapping for the end effector. When the movement of the slave robot is limited, we use the movement of the slave robot platform to realize the dead zone avoidance. Through the redundant degrees of freedom caused by the back-and-forth, left-right movement of the slave robot moving platform, the movement trajectory of the master-slave manipulator is consistent and to further realize the tele-operation mapping control according to the intuition of the operator. In this paper, we verify the effectiveness of the proposed algorithm via a robotic system that includes an excavator-type slave arm and Mecanum wheel omnidirectional mobile platform.
Long Short-Term Memory with Gate and State Level Fusion for Light\n Field-Based Face Recognition (2019)

Long Short-Term Memory (LSTM) is a prominent recurrent neural network for\nextracting dependencies from sequential data such as time-series and multi-view\ndata, having achieved impressive results for different visual recognition\ntasks. A conventional LSTM network can learn a model to posteriorly extract\ninformation from one input sequence. However, if two or more dependent\nsequences of data are simultaneously acquired, the conventional LSTM networks\nmay only process those sequences consecutively, not taking benefit of the\ninformation carried out by their mutual dependencies. In this context, this\npaper proposes two novel LSTM cell architectures that are able to jointly learn\nfrom multiple sequences simultaneously acquired, targeting to create richer and\nmore effective models for recognition tasks. The efficacy of the novel LSTM\ncell architectures is assessed by integrating them into deep learning-based\nmethods for face recognition with multi-view, light field images. The new cell\narchitectures jointly learn the scene horizontal and vertical parallaxes\navailable in a light field image, to capture richer spatio-angular information\nfrom both directions. A comprehensive evaluation, with the IST-EURECOM LFFD\ndataset using three challenging evaluation protocols, shows the advantage of\nusing the novel LSTM cell architectures for face recognition over the\nstate-of-the-art light field-based methods. These results highlight the added\nvalue of the novel cell architectures when learning from correlated input\nsequences.\n