gebhart/patrepeval huggingface dataset:
Tissue Organization by Cadherin Adhesion Molecules: Dynamic Molecular and Cellular Mechanisms of Morphogenetic Regulation (2011)

This review addresses the cellular and molecular mechanisms of cadherin-based tissue morphogenesis. Tissue physiology is profoundly influenced by the distinctive organizations of cells in organs and tissues. In metazoa, adhesion receptors of the classical cadherin family play important roles in establishing and maintaining such tissue organization. Indeed, it is apparent that cadherins participate in a range of morphogenetic events that range from support of tissue integrity to dynamic cellular rearrangements. A comprehensive understanding of cadherin-based morphogenesis must then define the molecular and cellular mechanisms that support these distinct cadherin biologies. Here we focus on four key mechanistic elements: the molecular basis for adhesion through cadherin ectodomains, the regulation of cadherin expression at the cell surface, cooperation between cadherins and the actin cytoskeleton, and regulation by cell signaling. We discuss current progress and outline issues for further research in these fields.
High-Q on-chip inductors using thin-film wafer level packaging technology demonstrated on a 90 nm RF-CMOS 5 GHz VCO (2005)

High-Q inductors are important for the realization of high-performance, low-power RF-circuits. In this work, on-chip inductors with Q-factors above 40 have been realized above the passivation of a 90 nm RF-CMOS process using wafer-level packaging (WLP) techniques. The influence of a patterned polysilicon and metal ground shield on the inductor-Q is compared and the influence of highly doped active area underneath the inductors is shown. A 5-15 GHz WLP balun has been realized. The technology is demonstrated by a low-power 5GHz 90nm RF-CMOS VCO with a core current consumption of only 430 /spl mu/A from a 1.2 V supply, a phase noise of -112dBc/Hz at 1MHz offset and a tuning range of 530MHz.
Tennis Space: An Interactive and Immersive Environment for Tennis Simulation (2009)

This paper reports the design and implementation of an interactive and immersive environment (IIE) for tennis simulation. The presented design layout, named Tennis Space, provides the necessary immersive experience without overly restricting the player. To address the instability problem of real-time tracking of fast moving objects, a hybrid tracking solution integrating optical tracking and ultrasound-inertial tracking technologies is developed. An L-shaped IIE has been implemented for tennis simulation and has received positive feedback from users.
Correction: Fungal Cell Gigantism during Mammalian Infection (2010)

The interaction between fungal pathogens with the host frequently results in morphological changes, such as hyphae formation. The encapsulated pathogenic fungus Cryptococcus neoformans is not considered a dimorphic fungus, and is predominantly found in host tissues as round yeast cells. However, there is a specific morphological change associated with cryptococcal infection that involves an increase in capsule volume. We now report another morphological change whereby gigantic cells are formed in tissue. The paper reports the phenotypic characterization of giant cells isolated from infected mice and the cellular changes associated with giant cell formation. C. neoformans infection in mice resulted in the appearance of giant cells with cell bodies up to 30 mm in diameter and capsules resistant to stripping with c-radiation and organic solvents. The proportion of giant cells ranged from 10 to 80% of the total lung fungal burden, depending on infection time, individual mice, and correlated with the type of immune response. When placed on agar, giant cells budded to produce small daughter cells that traversed the capsule of the mother cell at the speed of 20-50 m/h. Giant cells with dimensions that approximated those in vivo were observed in vitro after prolonged culture in minimal media, and were the oldest in the culture, suggesting that giant cell formation is an aging-dependent phenomenon. Giant cells recovered from mice displayed polyploidy, suggesting a mechanism by which gigantism results from cell cycle progression without cell fission. Giant cell formation was dependent on cAMP, but not on Ras1. Real-time imaging showed that giant cells were engaged, but not engulfed by phagocytic cells. We describe a remarkable new strategy for C. neoformans to evade the immune response by enlarging cell size, and suggest that gigantism results from replication without fission, a phenomenon that may also occur with other fungal pathogens.
Assembly and compositional analysis of human genomic data (2002)

In 1990, the United States Human Genome Project was initiated as a fifteen-year endeavor to sequence the approximately three billion bases making up the human genome (Vaughan, 1996). As of December 31, 2001, the public sequencing efforts have sequenced a total of 2.01 billion finished bases representing 63.0% of the human genome (http://www.ncbi.nlm.nih.gov/genome/seq/page.cgi?F=HsProgress.shtml&&ORG=Hs) to a Bermuda quality error rate of 1/10000 (Smith and Carrano, 1996). In addition, 1.11 billion bases representing 34.8% of the human genome has been sequenced to a rough-draft level. Efforts such as UCSC's GoldenPath (Kent and Haussler, 2001) and NCBI's contig assembly (Jang et al., 1999) attempt to assemble the human genome by incorporating both finished and rough-draft sequence. The availability of the human genome data allows us to ask questions concerning the maintenance of specific regions of the human genome. We consider two hypotheses for maintenance of high G+C regions: the presence of specific repetitive elements and compositional mutation biases. Our results rule out the possibility of the G+C content of repetitive elements determining regions of high and low G+C regions in the human genome. We determine that there is a compositional bias for mutation rates. However, these biases are not responsible for the maintenance of high G+C regions. In addition, we show that regions of the human under less selective pressure will mutate towards a higher A+T composition, regardless of the surrounding G+C composition. We also analyze sequence organization and show that previous studies of isochore regions (Bernardi, 1993) cannot be generalized within the human genome. In addition, we propose a method to assemble only those parts of the human genome that are finished into larger contigs. Analysis of the contigs can lead to the mining of meaningful biological data that can give insights into genetic variation and evolution. I suggest a method to help aid in single nucleotide polymorphism (SNP) detection, which can help to determine differences within a population. I also discuss a dynamic-programming based approach to sequence assembly validation and detection of large-scale polymorphisms within a population that is made possible through the availability of large human sequence contigs.
Time-lapse monitoring of CO2 sequestration: A site investigation through integration of reservoir properties, seismic imaging, and borehole and surface gravity data (2015)

ABSTRACT We have developed a feasibility study on the application of time-lapse gravity as a monitoring tool for a proposed CO2 sequestration test site. The results are a component of a larger geotechnical suitability study to evaluate a specific field’s potential for CO2 storage and to evaluate viable techniques for effective monitoring there. The reservoir model for this study was constructed from detailed reservoir data available through separate reservoir characterization studies of the field. The gravity inversion used was a highly constrained binary approach that incorporated reservoir geometry from seismic data and the internal 3D distributions of density change predicted from the reservoir engineering database. Incorporating borehole data for joint surface/borehole monitoring further improved the potential of time-lapse gravity to define CO2 movement during sequestration. In this paper, we present a subset of the entire study. Our results indicate that the site likely has a favorable combination of geometry, depth, thickness, and predicted density change from CO2 movement to be effectively monitored with surface time-lapse gravity.
A study of the preparation of epitaxy-ready polished surfaces of (100) Gallium Antimonide substrates demonstrating ultra-low surface defects for MBE growth (2016)

Gallium Antimonide (GaSb) is an important Group III-V compound semiconductor which is suitable for use in the manufacture of a wide variety of optoelectronic devices such as infra-red (IR) focal plane detectors. A significant issue for the commercialisation of these products is the production of epitaxy ready GaSb, which remains a challenge for the substrate manufacturer, as the stringent demands of the MBE process, requires a high quality starting wafer. In this work large diameter GaSb crystals were grown by the Czochralski (Cz) method and wafers prepared for chemo-mechanical polishing (CMP). Innovative epi-ready treatments and novel post polish cleaning methodologies were applied. The effect of these modified finishing chemistries on substrate surface quality and the performance of epitaxially grown MBE GaSb IR detector structures were investigated. Improvements in the lowering of surface defectivity, maintaining of the surface roughness and optimisation of all flatness parameters is confirmed both pre and post MBE growth. In this paper we also discuss the influence of bulk GaSb quality on substrate surface performance through the characterisation of epitaxial structures grown on near zero etch pit density (EPD) crystals. In summary progression and development of current substrate polishing techniques has been demonstrated to deliver a consistent improved surface on GaSb wafers with a readily desorbed oxide for epitaxial growth.
The third type of chaos in a system of two adaptively coupled phase oscillators (2020)

We study a new type of attractor, the so-called reversible core, which is a mathematical image of mixed dynamics, in a strongly dissipative time-irreversible system of two adaptively coupled phase oscillators. The existence of mixed dynamics in this system was proved in our previous article [A. A. Emelianova and V. I. Nekorkin, Chaos 29, 111102 (2019)]. In this paper, we attempt to identify the dynamic mechanisms underlying the existence of mixed dynamics. We give the region of the existence of mixed dynamics on the parameter plane and demonstrate in what way, when a type of attractor changes, its main characteristics, such as its fractal dimension and the sum of Lyapunov exponents, transform. We demonstrate that when mixed dynamics appear in the system, the average frequencies of the oscillations in forward and reverse time begin to almost coincide, and its spectra gradually approach each other with an increase in the parameter responsible for the presence of mixed dynamics.
Discovery of an iridacycle catalyst with improved reactivity and enantioselectivity in the hydrogenation of dialkyl ketimines (2013)

Catalytically active iridacycles are formed by cyclometalation of acetophenone imines with Ir–PHOX complexes under hydrogen atmosphere. These complexes show unusually high reactivity and enantioselectivity in the hydrogenation of alkyl methyl ketimines. The structure of the cyclometalated imine has a strong effect on the conversion and enantiomeric excess.
Pre-speech diagnosis in hearing-impaired infants: How auditory experience affects early vocal development (2013)

Using frequent recordings of spontaneous vocalizations from cooing to word production and applying signal analysis methods, we aimed to objectively determine the developmental pre-speech profiles of young hearing-impaired infants with regard to the duration of auditory deprivation and the benefit accrued from hearing aids. The assessment of the benefit from amplification of the hearing level in infants is limited to subjective observation. In this pilot study, we aimed to demonstrate the advantage of an objective fine-grained analysis in three representative infants with similar audiological findings but different early auditory experience. The infants were born with profound hearing loss and aided at different ages within 6 months after birth. Spectral analysis and formant analysis of more than 11 000 vocalizations were performed. This allowed for a reliable identification of the time points at which each infant reached the early vocal stages. The analysis demonstrated that individual developmental courses from cooing to word production varied depending on the duration of early auditory deprivation. The findings suggest that inadequate auditory input affects infants’ vocal development long before the stage of first speech-like vocalizations (canonical babbling). Pre-speech diagnosis as introduced here may offer an additional objective tool in the diagnosis of hearing impairment in pre-lexical infants and in the assessment of the benefit of amplification.
Tachikawa project for prevention of posttraumatic stress disorder with polyunsaturated fatty acid (TPOP): study protocol for a randomized controlled trial (2013)

ClinicalTrials.gov Identifier NCT00671099.
Development of polyaniline–multiwalled carbon nanotube (PANI–MWCNT) nanocomposite for optical pH sensor (2012)

A highly transparent and water soluble nanocomposite of a conducting polymer, polyaniline (PANI) plus multiwalled carbon nanotubes (MWCNTs), was prepared by in situ chemical polymerisation method using sulphonic acid as a dopant. Initially, MWCNTs were functionalised by acid treatment and then dispersed in the monomer, aniline and the resultant MWCNTs coated aniline was polymerised using ammonium per sulphate as an oxidising agent to form PANI–MWCNT nanocomposite. The synthesised nanocomposite was characterised by using spectroscopic (ultraviolet–visible and Fourier transform infrared spectroscopy), field emission scanning electron microscopy and thermal analyses. The ultraviolet–visible spectrum of the salt phase (dark green) of the PANI–MWCNT nanocomposite shows a free carrier tail with increasing absorption at higher wavelength, which confirms the presence of conducting emeraldine salt phase of the PANI; whereas, the base form (deep blue) of the nanocomposite shows a sharp peak at 600 nm representing insulating pernigraniline phase of the polymer. The synthesised nanocomposite was then demonstrated for optical pH sensing.
Powder Synthesis and Hot‐Pressing of a LiTaO 3 Ceramic (2012)

The LiTaO 3 powders with uniformly sized primary particles have been successfully synthesized using a solid state reaction method. The calcined powders were hot‐pressed at 1250°C to form the densest ceramics yet reported of undoped LiTaO 3 . Neutron and electron backscatter diffraction ( EBSD ) analysis confirmed a random distribution of grain orientations in the hot‐pressed body. Neutron, X ‐ray, and EBSD studies all indicated the presence of significant residual stresses in the dense ceramic, likely resulting from the large crystallographic anisotropy in thermal expansion of LiTaO 3 . In addition, EBSD images revealed several unusual microstructural features, presumably related to exaggerated grain growth.
Genotyping of clinicalSerratia marcescensisolates: a comparison of PCR-based methods (2001)

The polymerase chain reaction (PCR)-based procedures of randomly amplified polymorphic DNA (RAPD) and repetitive element (RE)-based PCR were used to amplify total DNA prepared from each of 62 clinical Serratia marcescens isolates. Three different random primers, designated 1060, 1254 and 1283, were used individually in RAPD-PCR. Primers representing enterobacterial repetitive intergenic consensus (ERIC) sequences, extragenic palindromic (REP) elements, and polymorphic GC-rich repetitive sequences (PGRS) constituted the repetitive element-PCR. We were able to generate 40, 40 and 58 genotypic groupings using the 1060, 1254 and 1283 RAPD primers, respectively. Using the ERIC, REP and PGRS primers, 19, 54 and 60 unique genotypic profiles were yielded, respectively. The PGRS primers, which were developed to amplify GC-rich repetitive sequences in the genome of Mycobacteria, were the most discriminatory. These data indicate that both of these PCR-based approaches are a valid means of discriminating strain differences among isolates of S. marcescens and the amount of differentiation depends on the primer used. These techniques should prove useful for routine surveillance or in examining outbreaks of S. marcescens in clinical settings.
Architectural design and implementation of the Singapore high-speed ATM-testbed (2002)

This paper covers some technical planning and design issues of the Singapore national ATM network testbed. The network architecture and current implementation are discussed. We elaborate on a reference model that is aimed at effectively addressing the challenge of supporting multiple multimedia services over a broadband network with quality of service (QOS) guarantees and exhibits scalability and manageability properties. The model separates user information transport from control, and management. It applies QOS abstractions to simplify resource allocation for multimedia connections, and suggests a service abstraction for supporting service level control and management. Finally, the current implementation status of the testbed is presented.
Pressure Control Based on PWM Command of On-Off Switching Valves (2022)

International audience
Phase space analysis of quantum transport in electronic nanodevices (2020)

Abstract Electronic transport in nanodevices is commonly studied theoretically and numerically within the Landauer-Büttiker formalism: a device is characterized by its scattering properties to and from reservoirs connected by perfect semi-infinite leads, and transport quantities are derived from the scattering matrix. In some respects, however, the device becomes a ‘black box’ as one only analyses what goes in and out. Here we use the Husimi function as a complementary tool for quantitatively understanding transport in graphene nanodevices. It is a phase space representation of the scattering wavefunctions that allows to link the scattering matrix to a more semiclassical and intuitive description and gain additional insight in to the transport process. In this article we use the Husimi function to analyze some of the fascinating electronic transport properties of graphene, Klein tunneling and intervalley scattering , in two exemplary graphene nanodevices. By this we demonstrate the usefulness of the Husimi function in electronic nanodevices and present novel results e.g. on Klein tunneling outside the Dirac regime and intervalley scattering at a pn-junction and a tilted graphene edge.
The AC133+CD38−, but not the rhodamine-low, phenotype tracks LTC-IC and SRC function in human cord blood ex vivo expansion cultures (2009)

Phenotypic markers associated with human hematopoietic stem cells (HSCs) were developed and validated using uncultured cells. Because phenotype and function can be dissociated during culture, better markers to prospectively track and isolate HSCs in ex vivo cultures could be instrumental in advancing HSC-based therapies. Using an expansion system previously shown to increase hematopoietic progenitors and SCID-repopulating cells (SRCs), we demonstrated that the rhodamine-low phenotype was lost, whereas AC133 expression was retained throughout culture. Furthermore, the AC133(+)CD38(-) subpopulation was significantly enriched in long-term culture-initiating cells (LTC-IC) and SRCs after culture. Preculture and postculture analysis of total nucleated cell and LTC-IC number, and limiting dilution analysis in NOD/SCID mice, showed a 43-fold expansion of the AC133(+)CD38(-) subpopulation that corresponded to a 7.3-fold and 4.4-fold expansion of LTC-ICs and SRCs in this subpopulation, respectively. Thus, AC133(+)CD38(-) is an improved marker that tracks and enriches for LTC-IC and SRC in ex vivo cultures.
Defined Meridic and Holidic Diets and Aseptic Feeding Procedures for Artificially Rearing the Ectoparasitoid Exeristes roborator (Fabricius)1 (1975)

Journal Article Defined Meridic and Holidic Diets and Aseptic Feeding Procedures for Artificially Rearing the Ectoparasitoid Exeristes roborator (Fabricius) Get access S. N. Thompson S. N. Thompson 2Asst. Prof, of Entomology, Div. of Biological Control, Univ. Calif., Riverside 92502. Search for other works by this author on: Oxford Academic Google Scholar Annals of the Entomological Society of America, Volume 68, Issue 2, 17 March 1975, Pages 220–226, https://doi.org/10.1093/aesa/68.2.220 Published: 17 March 1975 Article history Received: 09 July 1974 Published: 17 March 1975
mechanism design experiments (2010)

Mechanism design is the art of designing institutions that align individual incentives with overall social goals. Mechanism design theory was initiated by Hurwicz (1972) and is surveyed in Groves and Ledyard (1987). To bridge the gap between a theoretical mechanism and an actual economic process that solves fundamental social problems, it is important to observe and evaluate the performance of the mechanism in the context of actual decision problems faced by real people with real incentives. These situations can be created and carefully controlled in a laboratory. A mechanism design experiment takes a theoretical mechanism, recreates it in a simple environment in a laboratory with human subjects as economic agents, observes the behaviour of human subjects under the mechanism, and assesses its performance in relation to what it was created to do and to the theory upon which its creation rests. The laboratory serves as a wind tunnel for new mechanisms, providing evidence which one can use to eliminate fragile ones, and to identify the characteristics of successful ones.
Grain Refinements of Cu<sub>6</sub>Sn<sub>5</sub> in Sn-3wt%Ag-5wt%Cu High Temperature Solder Alloys (2018)

This paper investigated the effect of trace addition of Al and Mg on the grain refinements of Cu 6 Sn 5 in Sn-3wt%Ag-5wt%Cu high temperature solder alloys. Furthermore, the effect of Al and Mg addition on the Sn/Ag 3 Sn eutectic were also investigated. It was found that the addition of both Al and Mg successfully refined the Cu 6 Sn 5 in Sn-3wt%Ag-5wt%Cu solder alloy. In addition, Al suppresses the formation of Ag 3 Sn in the Sn/Ag 3 Sn eutectic; while Mg promotes the formation of fine Sn/Ag 3 Sn eutectic microstructure. The refinement of Cu 6 Sn 5 is believed to be due to heterogeneous nucleation by Al and Mg rich intermetallic particles respectively. Effect of Al and Mg addition on the undercooling of the Sn/Ag 3 Sn eutectic was found to be similar, both reducing undercooling effectively at a low addition rate of 0.025wt%. The addition of Al and Mg have mixed effect on the nucleation temperature of Cu 6 Sn 5 . It is found that the nucleation temperature of Cu 6 Sn 5 is increased with 0.025wt% Al and 0.1wt% Mg addition to the unmodified alloy, while the nucleation temperature slowly decreases again as the trace element addition rate increases.
In situ microfluidic SERS assay for monitoring enzymatic breakdown of organophosphates (2015)

In this paper, we report on a method to probe the breakdown of the organophosphate (OP) simulants o,s-diethyl methyl phosphonothioate (OSDMP) and demeton S by the enzyme organophosphorous hydrolase (OPH) in a microfluidic device by surface enhanced Raman spectroscopy (SERS). SERS hotspots were formed on-demand inside the microfluidic device by laser-induced aggregation of injected Ag NPs suspensions. The Ag NP clusters, covering micron-sized areas, were formed within minutes using a conventional confocal Raman laser microscope. These Ag NP clusters were used to enhance the Raman spectra of the thiol products of OP breakdown in the microfluidic device: ethanethiol (EtSH) and (ethylsulfanyl) ethane-1-thiol (2-EET). When the OPH enzyme and its substrates OSDMP and demeton S were introduced, the thiolated breakdown products were generated, resulting in changes in the SERS spectra. With the ability to analyze reaction volumes as low as 20 nL, our approach demonstrates great potential for miniaturization of SERS analytical protocols.