gebhart/patrepeval huggingface dataset:
HIV-1 gp120 and chemokine activation of Pyk2 and mitogen-activated protein kinases in primary macrophages mediated by calcium-dependent, pertussis toxin–insensitive chemokine receptor signaling (2001)

Human immunodeficiency virus type 1 (HIV-1) uses the chemokine receptors CCR5 and CXCR4 as coreceptors for entry. It was recently demonstrated that HIV-1 glycoprotein 120 (gp120) elevated calcium and activated several ionic signaling responses in primary human macrophages, which are important targets for HIV-1 in vivo. This study shows that chemokine receptor engagement by both CCR5-dependent (R5) and CXCR4-dependent (X4) gp120 led to rapid phosphorylation of the focal adhesion-related tyrosine kinase Pyk2 in macrophages. Pyk2 phosphorylation was also induced by macrophage inflammatory protein-1beta (MIP-1beta) and stromal cell-derived factor-1alpha, chemokine ligands for CCR5 and CXCR4. Activation was blocked by EGTA and by a potent blocker of calcium release-activated Ca++ (CRAC) channels, but was insensitive to pertussis toxin (PTX), implicating CRAC-mediated extracellular Ca++ influx but not Galpha(i) protein-dependent mechanisms. Coreceptor engagement by gp120 and chemokines also activated 2 members of the mitogen-activated protein kinase (MAPK) superfamily, c-Jun amino-terminal kinase/stress-activated protein kinase and p38 MAPK. Furthermore, gp120-stimulated macrophages secreted the chemokines monocyte chemotactic protein-1 and MIP-1beta in a manner that was dependent on MAPK activation. Thus, the gp120 signaling cascade in macrophages includes coreceptor binding, PTX-insensitive signal transduction, ionic signaling including Ca++ influx, and activation of Pyk2 and MAPK pathways, and leads to secretion of inflammatory mediators. HIV-1 Env signaling through these pathways may contribute to dysregulation of uninfected macrophage functions, new target cell recruitment, or modulation of macrophage infection.
Not your granddad's disinfection by‐product problems and solutions (2014)

Emerging DBP problems and the control challenges they pose promise to keep environmental engineers and scientists occupied for years to come.
Design, Manufacturing and Validation of a Resolver for Industrial Permanent Magnet Servomotors (2020)

Resolvers are feedback elements that have been used in the control of electric motors for many years. They are highly preferred in many parts of industry, especially in defense. One of the most important reasons for using resolvers is that their mechanical strength is higher than other electronic feedback elements in harsh environments requiring shock resistance or high vibration. At the same time, its ability to work at high temperatures makes them preferred in demanding and harsh applications. Therefore, this study focuses on the design and production of a resolver for which we cannot have a domestic product, although its use has increased in recent years. Initial design and finite element analysis of the resolver is performed, prototype manufacturing is completed and a resolver design is accomplished after the validation. The design process of this resolver is also clarified in this study.
A humanoid robot pushing model inspired by human motion (2012)

This thesis explores an observed method used by humans when pushing a large object of unknown mass. Body motion and reaction forces are analyzed for feet-apart pushing with varying stance length. It is found that, via articulation of the waist, a human will push their static zero-moment point (ZMP) as far forward as possible prior to pushing. Along with an extended back leg, this provides a larger support region in which the ZMP can move before stability is lost. Using this motion, the subject can produce a larger force than if the waist is constrained. Further, in this stance the subject is stable without object contact and can exert a range of forces by controlling mass distribution at the feet. For this increases in force exertion and stability, a linearized double inverted pendulum model with a feet-apart stance is proposed for use in the humanoid robot pushing of an unknown mass. Using the human pushing data and our humanoid, HUBO+, the advantage of this model and the added degree of freedom is shown against the commonly used single inverted pendulum model for humanoid robot pushing.%%%%M.S., Mechanical Engineering and Mechanics  – Drexel University, 2012
Integration of Formal Methods and Testing for Model-Based Security Engineering (2014)

We present a brief overview of various security testing works that range from applying off-the-shell tools (both dynamic tools as well as static program analysis) to theorem-prover based testing for ensuring the compliance of systems to high-level security policies.Moreover, we report on the process of selecting the most appropriate (security) testing tools during product development derive open research questions based on our experience in developing, introducing, and applying (security) testing tools at SAP SE.
Physangulidine A, a Withanolide from Physalis angulata, Perturbs the Cell Cycle and Induces Cell Death by Apoptosis in Prostate Cancer Cells (2012)

Recently, our group reported the discovery of three new withanolides, physangulidines A-C, from Physalis angulata. In this study, the biological effects of physangulidine A (1), which was the most active and abundant of the three new constituents, are described. It was found that 1 significantly reduces survival in clonogenic assays for two hormone-independent prostate cancer cell lines. Flow cytometry and confocal microscopy studies in DU145 human prostate cancer cells indicated that 1 induces cell cycle arrest in the G(2)/M phase and causes defective mitosis. It was determined also that 1 produces programed cell death by apoptosis, as evidenced by biochemical markers and distinct changes in cell morphology. These results imply that the antimitotic and proapoptotic effects of 1 may contribute significantly to the biological activities and potential medicinal properties of its plant of origin.
A comparison of four algorithms for metal artifact reduction in CT imaging (2011)

Streak artifacts caused by the presence of metal have been a significant problem in CT imaging since its inception in 1972. With the fast evolving medical device industry, the number of metal objects implanted in patients is increasing annually. This correlates directly with an increased likelihood of encountering metal in a patient CT scan, thus necessitating the need for an effective and reproducible metal artifact reduction (MAR) algorithm. Previous comparisons between MAR algorithms have typically only evaluated a small number of patients and a limited range of metal implants. Although the results of many methods are promising, the reproducibility of these results is key to providing more tangible evidence of their effectiveness. This study presents a direct comparison between the performances, assessed by board certified radiologists, of four MAR algorithms: 3 non-iterative and one iterative method, all applied and compared to the original clinical images. The results of the evaluation indicated a negative mean score in almost all uses for two of the non-iterative methods, signifying an overall decrease in the diagnostic quality of the images, generally due to perceived loss of detail. One non-iterative algorithm showed a slight improvement. The iterative algorithm was superior in all studies by producing a considerable improvement in all uses.
Impact of Base Station Cooperation on Cell Planning (2010)

Base station cooperation (BSC) has been identified as a key radio access technology for next-generation cellular networks such as LTE-Advanced. BSC impacts cell planning, which is the methodical selection of base station (BS) sites, and BS equipment configuration for cost-effective cellular networks. In this paper, the impact of BSC on cell plan parameters (coverage, traffic, handover, and cost), as well as additional cell planning steps required for BSC are discussed. Results show that BSC maximizes its gains over noncooperation (NC) in a network wherein interference from cooperating BSs is the main limitation. Locations exist where NC may produce higher throughputs, therefore dynamic or semistatic switching between BSC and NC, called fractional BSC, is recommended. Because of interference from noncooperating BSs, the gains of BSC over NC are upper bounded, and diminishes at greater intersite distances because of noise. This encourages smaller cell sizes, higher transmit powers, and dynamic clustering of cooperative BSs.
Wavelength selection and measurement error theoretical analysis on ground-based coherent differential absorption lidar using 1.53  µm wavelength for simultaneous vertical profiling of water vapor density and wind speed: publisher’s note (2020)

This publisher's note amends the title in Appl. Opt.59, 2238 (2020).APOPAI0003-693510.1364/AO.384675.
Reliability Challenges with Materials for Analog Computing (2019)

Specialized hardware for deep learning using analog memory devices has the potential to outperform conventional GPUs by a large margin. At the core of such hardware are arrays of non-volatile-memory (NVM) devices that can perform the simple matrix operations needed for deep learning in parallel and in constant time. Several implementations can be found in the literature that use different materials as memory elements, including phase-change-memory (PCM), resistive-random-access-memory (RRAM), electrochemical-random-access-memory (ECRAM), and ferroelectric devices. While the current focus is to demonstrate functionality, there is an increasing concern about the reliability margins of this emerging technology. In this paper we will briefly describe operation and device requirements, and then focus on possible reliability exposure in terms of variability, stability and drift, retention and durability.
Formation of functional centromeric chromatin is specified epigenetically in Candida albicans (2006)

In the pathogenic yeast Candida albicans, the 3-kb centromeric DNA regions (CEN) of each of the eight chromosomes have different and unique DNA sequences. The centromeric histone CaCse4p (CENP-A homolog) occurs only within these 3-kb CEN regions to form specialized centromeric chromatin. Centromere activity was maintained on small chromosome fragments derived in vivo by homologous recombination of a native chromosome with linear DNA fragments containing a telomere and a selectable marker. An in vivo derived 85-kb truncated chromosome containing the 3-kb CEN7 locus on 69 kb of chromosome 7 DNA was stably and autonomously maintained in mitosis, indicating that preexisting active CEN chromatin remains functional through many generations. This same 85-kb chromosome fragment, isolated as naked DNA (devoid of chromatin proteins) from C. albicans and reintroduced back into C. albicans cells by standard DNA transformation techniques, was unable to reform functional CEN chromatin and was mitotically unstable. Comparison of active and inactive CEN chromatin digested with micrococcal nuclease revealed that periodic nucleosome arrays are disrupted at active centromeres. Chromatin immunoprecipitation with antibodies against CaCse4p confirmed that CEN7 introduced into C. albicans cells as naked DNA did not recruit CaCse4p or induce its spread to a duplicate region only 7 kb away from active CEN7 chromatin. These results indicate that CaCse4p recruitment and centromere activation are epigenetically specified and maintained in C. albicans.
Time-reversal waves and super resolution (2008)

Time-reversal mirrors (TRMs) refocus an incident acoustic field to the position of the original source regardless of the complexity of the propagation medium. TRM's have now been implemented in a variety of physical scenarios from MHz ultrasonics with order centimeter aperture size to hundreds/thousands of Hz in ocean acoustics with order hundred meter aperture size. Common to this broad range of scales is a remarkable robustness exemplified by observations at all scales that the more complex the medium between the probe source and the TRM, the sharper the focus. The relation between the medium complexity and the size of the focal spot is studied in this paper. It is certainly the most exciting property of TRM compared to standard focusing devices. A TRM acts as an antenna that uses complex environments to appears wider than it is, resulting for a broadband pulse in a refocusing quality that does not depend of the TRM aperture.
Characterization of time-resolved laser differential phase using 3D complementary cumulative distribution functions (2012)

An experimental method for characterizing the time-resolved phase noise of a fast switching tunable laser is discussed. The method experimentally determines a complementary cumulative distribution function of the laser's differential phase as a function of time after a switching event. A time resolved bit error rate of differential quadrature phase shift keying formatted data, calculated using the phase noise measurements, was fitted to an experimental time-resolved bit error rate measurement using a field programmable gate array, finding a good agreement between the time-resolved bit error rates.
A method of extracting construction areas using Gaofen-1 remote sensing images (2018)

The precisely extraction of construction areas in remote sensing images can play an important role in territorial planning, land use management, urban environments and disaster reduction. In this article, we propose a method for extracting construction areas using Gaofen-1 panchromatic remote sensing images by adopting the improved Pantex<sup>[1]</sup> (a procedure for the calculation of texture-derived built-up presence index) and unsupervised classification. First of all, texture cooccurrence measures of 10 different directions and displacements are calculated. In this step, we improve the built-up presence index that we use the windows size of 21*21 to calculate the GLCM contrast measure instead of 9*9 according to the spatial resolution of Gaofen-1 panchromatic image. Then we use the intersection operator “MIN” to combine the 10 different anisotropic GLCM contrast measure to generate the final built-up presence index result. At last, we use the unsupervised classification method to classify the Pantex result into two classes and the one with larger cluster center is the construction area class. Confusion matrix of Beijing-Tianjin-Hebei region experiment shows that this method can effectively and accurately extract the construction areas in Gaofen-1 panchromatic images with the overall accuracy of more than 92%.
Vehicle-sharing: Technological infrastructure, vehicles, and user-side devices - Technological review (2013)

In this work a review of the technological aspects of Vehicle Sharing Systems is given. First a definition of Vehicle Sharing System is provided; then the main problems related to these kind of systems are introduced by comparing different solutions both presented in literature and currently used by Vehicle Sharing Systems companies. System infrastructure, fleet management and user interaction aspects are discussed in detail. Finally, a bunch of Vehicle Sharing Systems initiatives are introduced and synthetically compared.
Application of Flow Cytometry in the Analysis and Sterile Sorting of Cell Populations Based on Integrin Expression (2003)

Flow cytometry is the rapid analysis of populations of cells on a cell-by-cell basis by passing them individually through a beam of laser light, and the measurement of light emitted from the cells by scatter or fluorescence (1,2). Integrins have been studied by flow cytometry since the mid-1980s when immunologists started examining CD11 (integrins αM, αX, and αL) as markers of T-cell differentiation in mixed cell populations (3,4). These analyses highlight many of the advantages and utility of flow cytometry over other forms of integrin analysis. With the appropriate antibody, flow cytometry can identify individual cells in a mixed cell population. Cell-surface expression of integrins can be differentiated from intracellular pools by flow cytometry analysis, unlike Western blotting or immunoprecipitation. Multicolor analysis can simultaneously measure the levels of two or three different integrins, enabling the researcher to determine that both an α and β subunits are present on the plasma membrane. Lastly, flow cytometry can sterilely sort viable cells on the basis of their cell-surface integrin expression and retain their viability for further growth and analysis.
Valganciclovir for cytomegalovirus prevention and treatment (2005)

Cytomegalovirus (CMV) continues to be an important cause of significant disease in various groups of immunocompromised hosts, including organ and hematopoietic stem cell transplant recipients and AIDS patients. Therapeutic and preventative strategies have been used in these patients to improve overall outcomes. Ganciclovir has traditionally been the first-line drug for the treatment and prevention of CMV. Valganciclovir is a prodrug of ganciclovir with enhanced oral bioavailability. Studies have shown that it is effective for the prevention of CMV disease in high-risk (donor seropositive/recipient seronegative) solid-organ transplant recipients. It is also as effective as intravenous ganciclovir for the treatment of CMV retinitis in AIDS patients. The side-effect profile is similar to ganciclovir. Treatment studies in solid-organ transplant recipients, evaluation in pediatric patients, and prevention studies in stem cell recipients are ongoing and will help define the full role of valganciclovir in immuno...
Utilizing high resolution and reconfigurable patterns in combination with inkjet printing to produce high performance circuits (2014)

Inkjet printing on pre-fabricated high-resolution substrate is developed to improve the operational speed of printed organic transistors. The high-resolution features are designed to define transistor critical dimensions, while maintaining the flexibility to incorporate different circuit constructions. Logic gate and ring oscillator circuits fabricated by inkjet printing on the high-resolution substrate are demonstrated, to show that the same high resolution pattern can be adapted for constructing different electronic circuits.
Biomechanical Contribution of the Rib Cage to Thoracic Stability (2011)

Because of testing methodology, the rib cage accounted for a greater percentage of thoracic stability than previously estimated. Different rib cage structures resisted motion in different loading planes.
Ozone flow visualization techniques (1981)

Flow visualization techniques using ozone for tracing gas flows are proposed whereby ozone is detected through its strong absorption of ultraviolet light, which is easily made visible with fluorescent materials, or through its reaction with nitric oxide to form excited nitrogen dioxide, which in relaxing emits detectable light. It is shown that response speeds in the kHz range are possible with an ultraviolet detection system for initial ozone concentrations of about 1%.
The Kaneohe acoustic thermometry experiment and rays (1994)

In the 1980s, the Kaneohe source, on the north shore of Oahu, transmitted sound (133 Hz; 60-ms resolution) from 183-m depth to a U.S. Navy receiver at 3709-km distance near northern California. Despite the fact that sound reflects from the Oahu slope before being trapped in the sound channel, ray theory is shown capable of determining the spatial coordinates of the stable acoustic pulses. Rays that bounce from the bottom are probably chaotic, but the coordinates and travel times of eigenrays are insensitive to initial conditions and ocean fluctuations. The coda of the reception can probably not be explained with a propagation model in which the sound-speed field is smoothed to suppress scales smaller than the mesoscale. Instead, it appears that scattering of sound from smaller scales distributes otherwise axially trapped sound over 1000 m in the vertical, thus limiting the vertical resolution achievable with tomography. [Work supported by Advanced Research Projects Agency and Office of Naval Research.]
Association study of the short tandem repeat in the 5′ upstream region of the cholecystokinin gene with mood disorders in the Japanese population (2002)

We have recently identified a novel polymorphic short tandem repeat (STR) in the 5' upstream region of the cholecystokinin (CCK) gene and reported its association with panic disorder. A linkage study of affective disorder showed a modest linkage signal on the short arm of chromosome 3, the location of the CCK gene. Furthermore, clinical comorbidity of depression and anxiety disorders have been documented. In the present study, we examined a possible association of the CCK STR with mood disorders. We genotyped 165 subjects with mood disorders consisting of unipolar and bipolar disorders and 253 control samples. However, no significant allelic associations were detected between the STR and either the combined mood disorders (P = 0.885), the unipolar group (P = 0.296), or the bipolar group (P = 0.605). These data suggest that the CCK promoter STR is unlikely to have a major genetic effect on the development of mood disorders in the Japanese population.
Bending Terahertz Beams in “Free Space” (2011)

We demonstrate terahertz beam bending in the free-space region created between two metallic plates. This is achieved by realizing a non-uniform distribution of the effective refractive index, causing empty space to mimic an inhomogeneous dielectric.
Publisher’s Note: Diffusion and Reactions of Hydrogen inF2-Laser-IrradiatedSiO2Glass [Phys. Rev. Lett.89, 135507 (2002)] (2002)

Received 23 September 2002DOI:https://doi.org/10.1103/PhysRevLett.89.189901©2002 American Physical Society
Optogenetics and the Circuit Dynamics of Psychiatric Disease (2015)

This Viewpoint discusses the key breakthroughs, reviews some of the resulting insights into pathophysiology of psychiatry-related symptoms, and illustrates the implications of this emerging vision for circuit-guided psychiatry.
TDP-43 proteinopathy alters the ribosome association of multiple mRNAs including the glypican Dally-like protein (Dlp)/GPC6 (2020)

Abstract Amyotrophic lateral sclerosis (ALS) is a genetically heterogeneous neurodegenerative disease in which 97% of patients exhibit cytoplasmic aggregates containing the RNA binding protein TDP-43. Using tagged ribosome affinity purifications in Drosophila models of TDP-43 proteinopathy, we identified TDP-43 dependent translational alterations in motor neurons impacting the spliceosome, pentose phosphate and oxidative phosphorylation pathways. A subset of the mRNAs with altered ribosome association are also enriched in TDP-43 complexes suggesting that they may be direct targets. Among these, dlp mRNA, which encodes the glypican Dally like protein (Dlp)/GPC6, a wingless (Wg/Wnt) signaling regulator is insolubilized both in flies and patient tissues with TDP-43 pathology. While Dlp/GPC6 forms puncta in the Drosophila neuropil and ALS spinal cords, it is reduced at the neuromuscular synapse in flies suggesting compartment specific effects of TDP-43 proteinopathy. These findings together with genetic interaction data show that Dlp/GPC6 is a novel, physiologically relevant target of TDP-43 proteinopathy.
Engineered Surface and Interfacial Materials (2011)

This chapter contains sections titled: Surface Brush Layers Self-Assembled Monolayers Adsorbed Macromolecules on Different Substrates References