gebhart/patrepeval huggingface dataset:
The diagnostic and molecular characteristics of malignant mesothelioma and ovarian/peritoneal serous carcinoma (2010)

Malignant mesothelioma and ovarian/peritoneal serous carcinoma are two of the most common tumours affecting the serosal cavities. Unlike other malignant tumours diagnosed at this anatomical site, such as lung and breast carcinoma, malignant mesothelioma and serous carcinoma share a common histogenesis, may be difficult to differentiate morphologically, and co-express many of the diagnostic markers used by cytopathologists in effusion diagnosis. Selected markers have nevertheless shown sufficient sensitivity and specificity to differentiate serous carcinoma from malignant mesothelioma effectively. Recently, our group applied high throughput technology to the identification of new markers that may aid in differentiating these two cancer types and validated several of these markers in follow-up studies. This review will present current data regarding the diagnostic and biological aspects of malignant mesothelioma and ovarian/peritoneal serous carcinoma.
A Study of Force and Position Tracking Control for Robot Contact with an Arbitrarily Inclined Plane (2013)

This paper proposes an adaptive impedance control method for a robot's end-effector while it slides steadily on an arbitrarily inclined panel; it concentrates on robot force position tracking control for the inclined plane with an unknown normal direction and varying environmental damping and stiffness. The proposed control strategy uses the Recursive Least Squares (RLS) algorithm to estimate environmental damping and stiffness parameters during the impact-contact process between the robot and the environment. It achieves the expected posture adjustment of the robot's end-effector based on the measured contact torques and, during the robot's end-effector's sliding on the inclined plane, a fuzzy control is developed to adjust the robot impedance model parameters on-line and adaptively for changes in environmental damping and stiffness. The designed robot force position control method is robust to the changes of the environmental parameters but the implementation of the proposed control algorithms is simple. Finally, experiments demonstrate the effectiveness of the proposed method.
First-principles equation of state and phase stability for the<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mi mathvariant="normal">Ni</mml:mi><mml:mtext>−</mml:mtext><mml:mi mathvariant="normal">Al</mml:mi></mml:mrow></mml:math>system under high pressures (2004)

The equation of state (EOS) of alloys at high pressures is generalized with the cluster expansion method. It is shown that this provides a more accurate description. The low temperature EOSs of $\mathrm{Ni}\text{\ensuremath{-}}\mathrm{Al}$ alloys on FCC and BCC lattices are obtained with density functional calculations, and the results are in good agreement with experiments. The merits of the generalized EOS model are confirmed by comparison with the mixing model. In addition, the FCC phase diagram of the $\mathrm{Ni}\text{\ensuremath{-}}\mathrm{Al}$ system is calculated by the cluster variation method (CVM) with both spin-polarized and nonspin-polarized effective cluster interactions (ECI). The influence of magnetic energy on the phase stability is analyzed. A long-standing discrepancy between ab initio formation enthalpies and experimental data is addressed by defining a better reference state. This aids both evaluation of an ab initio phase diagram and understanding the thermodynamic behaviors of alloys and compounds. For the first time the high-pressure behavior of order-disorder transition is investigated by ab initio calculations. It is found that order-disorder temperatures follow the Simon melting equation. This may be instructive for experimental and theoretical research on the effect of an order-disorder transition on shock Hugoniots.
Automatic property generation for formal verification applied to HDL-based design of an on-board computer for space applications (2013)

The flexibility of Commercial-Off-The-Shelf (COTS) SRAM based FPGAs is an attractive option for the design of artificial satellites, however, the functional verification of HDL-based designs is required and is of fundamental importance. Formal verification using model checking represents a system as formal model that are automatically generated by synthesis tools. On the other hand, the properties are represented by temporal logic expressions and are traditionally manually elaborated, which is susceptible to human errors increasing the costs and time of the verification. This work presents a new method for automatic property generation for formal verification of Hardware Description Language (HDL) based systems. The industrial case study is a communication subsystem of an artificial satellite, which was developed in cooperation with the Brazilian Institute of Space Research (INPE).
Serial rebinding of ligands to clustered receptors as exemplified by bacterial chemotaxis (2005)

Serial ligation is the repeated reversible binding of a ligand to one receptor after another. It is a widespread phenomenon throughout biochemical systems, occurring anytime receptors are clustered together and ligand binding is reversible. Computer simulations are used in this work to investigate a representative example, which is the serial ligation of an extracellular aspartate molecule to the membrane-bound chemotaxis receptors of an Escherichia coli bacterium. It is found that the initial binding site of a ligand to a cluster of receptors is more likely to be near the edge of the cluster than near the middle, although there is no overall bias when all rebindings are considered. Serial ligation does not lead directly to signal amplification or attenuation but instead causes binding events to be correlated in both space and time: a ligand is likely to bind many times in rapid succession in a small region of the receptor cluster, but there can also be long intervals between bindings. This leads to an increased level of noise in the received signal but may allow a single ligand to be sensed above a uniform level of background noise. The focus of this paper is on the interpretation of simulation results so they can be generalized to a wide variety of other systems and to allow the identification of systems in which serial ligation is likely to be important. In the process, several characteristic times are identified, as are scaling laws for the spatial and temporal dynamics.
The Silver Lining—Utilizing Cloud Computing in Broadcast Applications (2011)

In recent years, there have been significant changes to the way audiences store and consume video content and how broadcasters successfully monetize that content. There have been successes and failures, but ultimately with each new advance in technology there has been a struggle between the content providers and the content consumers. Content providers, desperate to retain their ability to monetize expensive rights-based assets, are suspicious of new open platform technologies. Consumers are wary of closed technologies, having been hurt in the past by countless format wars and technology races. Looking to the music industry, we can see just how badly things can go wrong when the business model does not keep pace with advances in technology. This paper examines recent developments in disruptive cloud computing platform, including the foundation technologies that have made this possible, such as hypervisors, virtualization, hardware abstraction, and data center automation. From these foundation technologies, platforms such as Amazon's Elastic Computing Cloud (EC2), and Microsoft Azure have evolved; current status and likely future developments are examined. Building from this analysis, how current broadcast products that are already utilizing these cloud platforms in isolation is discussed. The way in which next-generation system integration, at the software level, can bring these products together into a coherent solution for broadcasters with the capability to reduce costs and improve time-to-market for new channels and services is also examined. The paper concludes with an assessment of the market opportunity for this new technology and an identification of current gap technologies and services in this new sector.
Study of Expression of Ku70 and NHEJ in CML Cells (2008)

Abstract Objective FThe DNA double strand breaks (DSB) in mammalian cells are predominantly repaired by a process called non-homologous DNA end joining (NHEJ). Ku70 played a pivotal role in NHEJ pathway. As a common hematological malignant disease with unique chromosomal translocation t (9;22), chronic myeloid leukemia (CML) can be considered as a paradigm for neoplasias that evolve through a multi-step process. As we reported before, protein Ku70 expressed significantly higher in CML than in normal BM cells. Meanwhile, its expression level in blast phase was markedly higher than that in chronic phase. The present study furthermore aims to investigate the expression of the gene Ku70 in CML cells at different clinical stage and reveal the correlation among the expression of the gene Ku70, the protein Ku70 and BCR-ABL in cells of CML. The NHEJ efficiency to repair DSB in CML was also investigated. Methods: Bone marrow cells were collected from 24 cases of normal adults and 27 cases of de novo diagnosed CML patients. 15 CML patients were in chronic phase and 12 in blast phase. The expression of gene Ku70 was detected by RT-PCR and RQ-RT-PCR. The fusion gene BCR-ABL was detected by TaqMan probe Real Time PCR, using ABL as the internal control. Nucleic extracted proteins were used to determine NHEJ efficiency by an in vitro end-ligation system. Results: The mean level of NHEJ activity of normal BM cells and CML cells were 18.6±13.1% vs 24.8±14.9%, .024. The gene Ku 70 expression in normal BM cells and CML cells were 31.08±8.41 vs 544.63±1185.71 copies/10,000 β-Actin copies, P=0.039. gene Ku 70 expressed significantly higher in blast phase (1103.31±1645.62 copies/10,000 β-Actin copies, P&lt;0.01). There were positive correlations of BCR-ABL when compared with the expression of the gene Ku70 (r=0.573 P=0.002) and with the protein Ku70 (r=0.705 P&lt;0.001) in CML cells. There was also significantly correlations between the expression of the gene Ku70 and the protein Ku70 (r=0. 808, P&lt;0.001). Conclusions: The gene and protein of Ku70 were expressed significantly higher in CML than in normal BM cells with NHEJ activity was also enhanced in CML cells. Meanwhile, Ku70 expression level in acute phase was markedly higher than that in chronic phase. There were significantly correlations among the expression of fusion gene BCR-ABL, the gene Ku70 and the protein Ku70 in cells of CML This Study illustrates DNA instability in CML cells which was mainly damaged by DSB, and this kind of DNA damage was repaired by NHEJ pathway predominantly. NHEJ pathway plays an important role in disease progression of CML.
Criteria for one-dimensional transport in split-gate field-effect transistors (2002)

The authors have fabricated AlGaAs-GaAs split-gate field-effect transistors with different lengths and widths in order to establish geometric design criteria for one-dimensional (1D) transport. The experiments show a more negative 1D threshold voltage for zero length split-gate devices (constrictions) than for finite length split-gate devices for the same given width. The experiments reveal the existence of a critical width between the gates below which a 1D regime cannot be supported in split-gate FETs longer than 0.5 mu m.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Shared and Unique Proteins in Human, Mouse and Rat Saliva Proteomes: Footprints of Functional Adaptation (2013)

The overall goal of our study was to compare the proteins found in the saliva proteomes of three mammals: human, mouse and rat. Our first objective was to compare two human proteomes with very different analysis depths. The 89 shared proteins in this comparison apparently represent a core of highly-expressed human salivary proteins. Of the proteins unique to each proteome, one-half to 2/3 lack signal peptides and probably are contaminants instead of less highly-represented salivary proteins. We recently published the first rodent saliva proteomes with salivas collected from the genome mouse (C57BL/6) and the genome rat (BN/SsNHsd/Mcwi). Our second objective was to compare the proteins in the human proteome with those we identified in the genome mouse and rat to determine those common to all three mammals as well as the specialized rodent subset. We also identified proteins unique to each of the three mammals because differences in the secreted protein constitutions can provide clues to differences in the evolutionary adaptation of the secretions in the three different mammals.
A Parallel Computing Framework for Cloud Services (2020)

In recent years, the field of big data processing has increasingly demanded computer performance for data processing. In order to enable users to use the big data processing platform conveniently and quickly, and put more attention on the writing of parallel computing algorithms, this paper focuses on cloud services, parallel computing, IronPython and virtualization as the main research content, and uses Python for the client, Service node and computing node module design, using the reflexive and self-observing capabilities of Python, calling library functions to achieve functions that cannot be achieved in other languages. The parallel computing framework based on Python designed in this paper can be easily implemented on the virtual machine of the cloud computing platform, and can efficiently and intelligently distribute computing requests.
(WIP) IoT Context Descriptor: Situation Detection and Action Invocation Model for Real-Time High-Volume Transactions (2018)

In our previous work, a runtime-specific rule was introduced that described how to detect situations and invoke actions of connected vehicles in the surrounding context. However, rule developers were required to check carefully whether each rule was consistent to the other rules or not. Our next challenge is how to simplify the validation of the application logics when the number of rules is increasing. In this paper, we propose IoT Context Descriptor, a context model for situation detection and action invocation for IoT that is aiming at accelerating easy development of situation detection and action invocation while securing the processing of real-time high-volume transactions.
The Epithelial Mitogen Keratinocyte Growth Factor Binds to Collagens via the Consensus Sequence Glycine-Proline-Hydroxyproline (2002)

The binding of certain growth factors and cytokines to components of the extracellular matrix can regulate their local availability and modulate their biological activities. We show that mesenchymal cell-derived keratinocyte growth factor (KGF), a key stimulator of epithelial cell proliferation during wound healing, preferentially binds to collagens I, III, and VI. Binding is inhibited in a dose-dependent manner by denatured single collagen chains and collagen cyanogen bromide peptides. This interaction is saturable with dissociation constants of approximately 10(-8) to 10(-9) m and estimated molar ratios of up to three molecules of KGF bound to one molecule of triple helical collagen. Furthermore, collagen-bound KGF stimulated the proliferation of transformed keratinocyte or HaCaT cells. Ligand blotting of collagen-derived peptides points to a limited set of collagenous consensus sequences that bind KGF. By using synthetic collagen peptides, we defined the consensus sequence (Gly-Pro-Hyp)(n) as the collagen binding motif. We conclude that the preferential binding of KGF to the abundant collagens leads to a spatial pattern of bioavailable KGF that is dictated by the local organization of the collagenous extracellular matrix. The defined collagenous consensus peptide or its analogue may be useful in wound healing by increasing KGF bioactivity and thus modulating local epithelial remodeling and regeneration.
Enzymatic Detachment of <i>Staphylococcus epidermidis</i> Biofilms (2004)

The gram-positive bacterium Staphylococcus epidermidis is the most common cause of infections associated with catheters and other indwelling medical devices. S. epidermidis produces an extracellular slime that enables it to form adherent biofilms on plastic surfaces. We found that a biofilm-releasing enzyme produced by the gram-negative periodontal pathogen Actinobacillus actinomycetemcomitans rapidly and efficiently removed S. epidermidis biofilms from plastic surfaces. The enzyme worked by releasing extracellular slime from S. epidermidis cells. Precoating surfaces with the enzyme prevented S. epidermidis biofilm formation. Our findings demonstrate that biofilm-releasing enzymes can exhibit broad-spectrum activity and that these enzymes may be useful as antibiofilm agents.
The Theory of Probabilistic Databases (1987)

ABS!l’RACT A theory of probabilistic databases is outlined. This theory is one component of an integrated approach to data-modelling that accomodates both probabilistic and relational data. In fact, many of the results presented here were developed in the context of a framework for structural modelling of systems. Much that is fundamental to relational database theory was also developed in this context, and previous to the introduction by Codd of the relational model of data. Probabilistic databases can store types of information that cannot be represented using the relational model. Probabilistic databases may also be viewed as generalisations of relational databases; any relational database can be represented without loss of information by a probabilistic database. A number of relational database concepts are shown to have probabilistic counterparts. In many cases, it is preferable to deal with the probabilistic formulation of a concept even when applying it to a relational database. For example, we define a new project-join mapping for relational databases that is based on transf orming a relational to a probabilistic database. This mapping is shown to have more fmed points than the standard one.
Proposed pathway for the biosynthesis of serovar-specific glycopeptidolipids in Mycobacterium avium serovar 2 (2003)

Members of the Mycobacterium avium complex are distinguished by the presence of highly antigenic surface molecules called glycopeptidolipids (GPLs) and the oligosaccharide portion of the serovar-specific GPL defines the 28 serovars. Previously, the genomic region (ser2) encoding the enzymes responsible for the glycosylation of the lipopeptide core to generate the serovar-2-specific GPLs has been described. In this work, the ser2 gene clusters of M. avium serovar 2 strains 2151 and TMC 724 were fully sequenced and compared to the homologous regions of M. avium serovar 1 strain 104, M. avium subsp. paratuberculosis and M. avium subsp. silvaticum. It was also determined that 104Rg, a mutant of strain 104 that produces truncated GPLs, lost several GPL biosynthesis genes by deletion. This comparison, together with analysis of protein similarities, supports a biosynthetic model in which serovar-2-specific GPLs are synthesized from a serovar-1-specific GPL intermediate that is derived from a non-specific GPL precursor. We also identified a gene encoding an enzyme that is necessary for the biosynthesis of serovar-3- and 9-specific GPLs, but not serovar-2-specific GPLs, suggesting that the different serovars may have evolved from the acquisition or loss of genetic information. In addition, a subcluster of genes for the biosynthesis and transfer of fucose, which are needed to make serovar-specific GPLs such as those of serovar 2, is found in the non-GPL-producing M. avium subspecies paratuberculosis and silvaticum.
An Improved Indoor Positioning System Using RGB-D Cameras and Wireless Networks for Use in Complex Environments (2017)

This work presents an <i>Indoor Positioning System</i> to estimate the location of people navigating in complex indoor environments. The developed technique combines <i>WiFi Positioning Systems</i> and <i>depth maps</i>, delivering promising results in complex inhabited environments, consisting of various connected rooms, where people are freely moving. This is a non-intrusive system in which personal information about subjects is not needed and, although RGB-D cameras are installed in the sensing area, users are only required to carry their smart-phones. In this article, the methods developed to combine the above-mentioned technologies and the experiments performed to test the system are detailed. The obtained results show a significant improvement in terms of accuracy and performance with respect to previous WiFi-based solutions as well as an extension in the range of operation.
Superwideband extension of g.718 and g.729.1 speech codecs (2010)

This communication presents the recently standardized superwideband (SWB) extensions of ITU-T G.718 and G.729.1. These extensions were standardized as G.718 annex B and G.729.1 annex E. The SWB functionality is implemented using embedded scalable layers on top of the wideband (WB) core codecs, and it extends the bit rate of the codecs to 48 and 64 kbit/s for the G.718 and G.729.1, respectively. The main technology is a two-mode SWB coding method of the high frequencies. In addition, the G.729.1 SWB extension enhances the lower frequency range. The codec performance is illustrated with some listening test results extracted from the ITU-T Characterization phase.
Self-driven soft imaging in liquid by means of photothermal excitation (2011)

The use of a laser to induce oscillations of an atomic force microscopy cantilever provides a way to excite the dynamics of the system in a very controlled manner. This excitation scheme has been used to obtain reliable self-sustained oscillations, in air and in liquid environments, and to implement an additional control loop leading to a soft, low-interaction, working mode. The dynamics of the oscillating cantilever has been characterized, both theoretically and experimentally, and the effectiveness of the approach has been verified on a test sample.
Person counting using stereo (2002)

Stores and shopping malls would like to keep track of shopper volume by employing automatic techniques for counting shoppers. Existing approaches instrument doors with infrared beams and count beam interruptions, but this approach cannot resolve groups of people well. We are applying a vision-based approach that detects and tracks people from a stereo camera mounted above a door and pointing down. After applying real-time stereo vision and 3D image reconstruction, the system segments the scene by selecting stereo pixels falling inside a 3D volume of interest, which is placed to capture the heads and torsos of adult shoppers. The main novelties of our approach include (1) remapping the stereo disparities to an orthographic "occupancy map", which simplifies person modeling, and (2) tracking people using a Gaussian mixture model. On a test set of 900 enter/exit events in four hours of video, our system has achieved a net counting error rate of just 1.4%.