gebhart/patrepeval huggingface dataset:
Abstract 5603: Response of human prostate cancer xenografts to IGF-IR inhibition correlates with PTEN and androgen receptor splice variant status (2012)

Abstract Clinical studies with agents targeting the insulin-like growth factor receptor (IGF-IR) in prostate cancer have shown promise but as with most single agent trials only a portion of patients that enter into a targeted agent trial respond, e.g. activating mutations in the EGF-receptor in patients with lung cancer. We have shown in human tumor xenografts that the combination of IGF-IR inhibition with the human mab IMC-A12 in combination with androgen deprivation (ADT) was more efficacious than ADT alone. In a subsequent neoadjuvant study with IMC-A12, responses were at least as efficacious in hi-grade disease (Gleason 7 (4+3), 8, and 9) when compared to ADT alone. In order to determine predictors of response to IMC-A12 plus ADT (surgical castration) in human prostate cancer, we examined the response of 21 human prostate cancer xenografts (LuCaP series) grown in SCID mice for responses to castration, IMC-A12 40mg/kg ip 3x a week for four weeks, or castration followed by four weeks of IMC-A12. At the end of the IMC-A12 treatment animals were followed until tumor recurrence. When all animals were completed tumor growth was analyzed. The main differences in growth rates, as expected based on previous studies, occurred in mice receiving IMC-A12 plus castration compared to castration alone. Responses were segregated into three groups: Major Response - slope of tumor growth was negative in the IMC-A12 + Castration group compared to castration alone; Moderate Response - slope of combined treatment is flat and castration alone is positive; No-response - no differences in slope between castration and castration plus IMC-A12. We then examined the association of response to IMC-A12 to potential effectors of IGF-IR expression and signaling in the prostate including AR and AR splice variants and PTEN status. Tumor transcript profiles were generated on all xenografts prior to treatment and gene sets predictive of response determined. None of the PTEN null tumors showed a strong response to IMC-A12 and all PTEN null tumors expressed the AR-splice variant ARv567es. Of the 3 xenografts with one copy of PTEN, non- or partial responders either expressed no AR (neuroendocrine tumor) or expressed ARv567es. Of xenografts with 2 or more copies of PTEN, non- or moderate responders expressed AR-variants. Finally, transcript profiles provided a gene signature that was highly predictive of response to IMC-A12. These data indicate that PTEN insufficiency or the presence of an AR-splice variant that cannot increase IGF-IR via non-genomic activity are associated with resistance to IMC-A12. Further, a gene signature has been developed from the 21 xenografts that is predictive of response to IMC-A12 and castration. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5603. doi:1538-7445.AM2012-5603
Feline bordetellosis: challenge and vaccine studies (1993)

Four eight-week-old cats, shown to be free from feline calicivirus, feline herpesvirus and Chlamydia psittaci were challenged with an aerosol of Bordetella bronchiseptica. Within five days the cats developed signs of respiratory disease, characterised by nasal discharge, sneezing, spontaneous or induced coughing and dry or wet rales at auscultation. These signs were present for about 10 days, after which they began to resolve. To test the protective capacity of an experimental fimbrial antigen-based subunit vaccine, 10 kittens were vaccinated twice, with two weeks between the vaccinations, and five kittens were left unvaccinated. Two weeks after the booster the 15 kittens were challenged with an aerosol of B bronchiseptica as the sole pathogen. On the day of challenge the vaccinated kittens had a mean bordetella antibody titre of 2(9.5) whereas the control cats remained seronegative (titre < 2(2)). The control cats developed signs of respiratory disease after challenge, whereas the vaccinated cats were almost completely protected. The degrees of protection against rhinitis, sneezing, spontaneous or induced coughing, and dry or wet rales at auscultation were 100 per cent, 95 per cent, 95 per cent and 100 per cent, respectively. Furthermore, the vaccinated kittens cleared the challenge bacteria more quickly than the controls, resulting in a reduction of 80 per cent on days 15 and 18 after challenge and a reduction of 99 per cent on days 22 and 29 after challenge. The results show that B bronchiseptica can act as a primary pathogen in cats and that a vaccine containing the fimbrial antigen induces a protective immune response.
Disparity search range estimation: Enforcing temporal consistency (2010)

This paper presents a new approach for estimating the disparity search range in stereo video that enforces temporal consistency. Reliable search range estimation is very important since an incorrect estimate causes most stereo matching methods to get trapped in local minima or produce unstable results over time. In this work, the search range is estimated based on a disparity histogram that is generated with sparse feature matching algorithms such as SURF. To achieve more stable results over time, we further propose to enforce temporal consistency by calculating a weighted sum of temporally-neighboring histograms, where the weights are determined by the similarity of depth distribution between frames. Experimental results show that this proposed method yields accurate disparity search ranges for several challenging stereo videos and is robust to various forms of noise, scene complexity and camera configurations.
Recognition of the SARS-CoV-2 nucleoprotein by VHHs and development of a sandwich immunoassay (2021)

Coronaviruses are enveloped viruses with a positive-sense RNA genome and with a nucleocapsid of helical symmetry. Coronavirus nucleoproteins (N) localize to the cytoplasm and the nucleolus and is required for viral RNA synthesis. During virion assembly, N protein binds to the viral RNA and leads to a helical nucleocapsid formation. The current situation of the Covid-19 pandemic shows the importance of obtaining reliable solutions for the rapid detection of SARS-CoV-2 and the determination of the immunity of the population for the virus. Several solutions have been developed in record time for diagnosis. Regarding diagnosis, the reference method remains the RT-PCR (Reverse Transcriptase Polymerase Chain Reaction) which allows to detect the RNA of the SARS-Cov-2. This is an expensive method, requiring the transport of the sample to well-equipped laboratory and qualified personnel to carry out the analyzes. It is therefore necessary for diagnostic tests to be widely available and accessible highlighting the importance to develop an antibody-based assay. Nucleocapsid is the most abundant coronavirus protein and it is of upmost importance to develop specific antibodies to detect this protein in a diagnostic test. We immunized one alpaca with the recombinantNprotein of SARS-CoV2. After phage display selection, we identified 6 VHHs recognizing the C terminal domain (CTD) and 2 VHHs the N terminal domain. All VHHs have an affinity in the nanomolar range and can bind on ELISA the N extracted from infected cells. These VHHs are also able to recognize SARS-CoV-2 virus in infected cells or on infected hamster tissues. An ELISA sandwich assay has been set up using one anti NTD and one anti-CTD VHHs to detect the nucleoprotein in solution. This assay has allowed us to detect as little as 20 ng/ml of N.
Highly prevalent TERT promoter mutations in aggressive thyroid cancers (2013)

Mutations 1 295 228 C>T and 1 295 250 C>T (termed C228T and C250T respectively), corresponding to -124 C>T and -146 C>T from the translation start site in the promoter of the telomerase reverse transcriptase (TERT) gene, have recently been reported in human cancers, but not in thyroid cancers yet. We explored these mutations in thyroid cancers by genomic sequencing of a large number of primary tumor samples. We found the C228T mutation in 0 of 85 (0.0%) benign thyroid tumors, 30 of 257 (11.7%) papillary thyroid cancers (PTC), 9 of 79 (11.4%) follicular thyroid cancers (FTC), 3 of 8 (37.5%) poorly differentiated thyroid cancers (PDTC), 23 of 54 (42.6%) anaplastic thyroid cancers (ATC), and 8 of 12 (66.7%) thyroid cancer cell lines. The C250T mutation was uncommon, but mutually exclusive with the C228T mutation, and the two mutations were collectively found in 11 of 79 (13.9%) FTC, 25 of 54 (46.3%) ATC, and 11 of 12 (91.7%) thyroid cancer cell lines. Among PTC variants, the C228T mutation was found in 4 of 13 (30.8%) tall-cell PTC (TCPTC), 23 of 187 (12.3%) conventional PTC, and 2 of 56 (3.6%) follicular variant PTC samples. No TERT mutation was found in 16 medullary thyroid cancer samples. The C228T mutation was associated with the BRAF V600E mutation in PTC, being present in 19 of 104 (18.3%) BRAF mutation-positive PTC vs 11 of 153 (7.2%) the BRAF mutation-negative PTC samples (P=0.0094). Conversely, BRAF mutation was found in 19 of 30 (63.3%) C228T mutation-positive PTC vs 85 of 227 (37.4%) C228T mutation-negative PTC samples (P=0.0094). We thus for the first time, to our knowledge, demonstrate TERT promoter mutations in thyroid cancers, that are particularly prevalent in the aggressive thyroid cancers TCPTC, PDTC, ATC and BRAF mutation-positive PTC, revealing a novel genetic background for thyroid cancers.
Determining The Acoustic Resistance of Small Sound Holes for MEMS Microphones (2011)

Capacitive MEMS microphones are now widely used for mobile phones and headsets. The frequency response of MEMS microphones is influenced by the package geometry. This can be applied to tune the performance of the microphone in the system. Packages with small sound inlet holes are acoustic low-pass filters. The cut-off frequency is determined by the diameter of the holes. In previous work we did not find sufficient agreement between a lumped element simulation and the measured frequency response of the microphones. Now we measured the acoustic resistance of small sound inlet holes directly. The measured resistances agree well with calculated values. The frequency response of MEMS microphones was measured for different sound hole diameters and lengths. The results are in good agreement with calculated transfer functions of the package.
A complete characterization of path delay faults through stuck-at faults (1999)

A complete one-to-one characterization of path delay fault testability for a combinational circuit is presented in terms of testability of stuck-at faults in an equivalent unfolded circuit. The unfolded circuit is obtained simply by replicating the cone feeding each internal fanout stem line, thereby making it internally fanout free. Unfolding preserves both functional, and structural characteristics of the original circuit. Earlier results describing correlation of path delay and stuck-at faults are either incomplete, or use a complex model of equivalent circuit based on timing parameters. We show that a path delay fault (rising or falling) is testable if certain single or multiple stuck-at fault in the equivalent circuit is testable. Thus, all aspects of path delay faults related to testability under various classification schemes are interpreted using the stuck-at fault model alone in the unfolded circuit. The results unify most of the existing concepts, provide a better understanding of path delay faults in logic circuits, and have potential applications in identification of false paths.
Design of optimal lattice space-time codes (2006)

In this paper we propose a systematic procedure for designing optimal lattice (space-time) codes. By employing stochastic optimization techniques we design lattice codes with minimum error rates when lattice decoders are employed at the receiver. Our design methodology can be tailored to obtain optimal lattice (space-time) codes for any fading statistics and SNR of interest. Further, we obtain fundamental lower bounds on the error probabilities yielded by lattice decoders and characterize their asymptotic behavior
Dynamic renegotiation of UPC parameters for arbitrary traffic sources in ATM networks (2002)

In networks based on the asynchronous transfer mode (ATM), traffic sources are subjected to a usage parameter control (UPC) function which employs a deterministic algorithm to control or shape the emitted cell stream. The UPC parameters constitute a traffic descriptor which is part of a traffic contract that is negotiated with the network provider at the connection set-up time. The network makes connection admission control (CAC) decisions based on the negotiated UPC-based traffic descriptor. However the source traffic characteristics may change dramatically on a slow time-scale making the initially negotiated UPC descriptor inappropriate for the entire traffic stream. Allowing the source to dynamically renegotiate UPC parameters over time is a viable means of accommodating sources with slow time-scale variations. This paper develops a methodology for estimating and dynamically renegotiating UPC parameters for an arbitrary source in an ATM network environment. The methodology makes no specific modeling assumptions on the user cell stream, is robust for a wide class of traffic streams, and permits trade-offs to be made in the choice of the UPC parameters according to the constraints imposed by the source.
High-resolution three-dimensional mapping of individual grains in polycrystals by topotomography (2007)

By orienting a crystal grain with its diffraction vector along the sample rotation axis, it is possible to use powerful tomographic and topographic imaging techniques to reconstruct the three-dimensional grain shape inside a polycrystalline sample. The acquisition and reconstruction can be performed from projection images with the detector positioned either in the diffracted-beam or in the direct-beam position. In the first case, the projection data consist of a series of integrated, monochromatic beam X-ray diffraction topographs of the grain under investigation. In the second case, the corresponding diffraction contrast in the transmitted beam may be interpreted as an additional contribution to the X-ray attenuation coefficient of the material. This latter variant is restricted to grains with small orientation spread but offers the possibility to characterize simultaneously the three-dimensional grain shape and the absorption microstructure of the surrounding sample material. The contrast mechanism is sensitive to local strain fields and can, in certain cases, reveal details of the grain microstructure, such as the presence of second-phase inclusions. The methodology is successfully demonstrated on an aluminium polycrystal, with a resulting three-dimensional mapping accuracy better than 7 µm. The possibilities and limitations of the technique are listed and its performance relative to other three-dimensional mapping techniques is discussed.
Design and Development of 256x256 Linear Mode Low-Noise Avalanche Photodiode Arrays (2011)

A larger format photodiode array is always desirable for many LADAR imaging applications. However, as the array format increases, the laser power or the lens aperture has to increase to maintain the same flux per pixel thus increasing the size, weight and power of the imaging system. In order to avoid this negative impact, it is essential to improve the pixel sensitivity. The sensitivity of a short wavelength infrared linear-mode avalanche photodiode (APD) is a delicate balance of quantum efficiency, usable gain, excess noise factor, capacitance, and dark current of APD as well as the input equivalent noise of the amplifier. By using InA1As as a multiplication layer in an InP-based APD, the ionization coefficient ratio, k, is reduced from 0.40 (lnP) to 0.22, and the excess noise is reduced by about 50%. An additional improvement in excess noise of 25% was achieved by employing an impact-ionization-engineering structure with a k value of 0.15. Compared with the traditional InP structure, about 30% reduction in the noise-equivalent power with the following amplifier can be achieved. Spectrolab demonstrated 30-um mesa APD pixels with a dark current less than 10 nA and a capacitance of 60 fF at gain of 10. APD gain uninformity determines the usable gain of most pixels in an array, which is critical to focal plane array sensitivity. By fine tuning the material growth and device process, a break-down-voltage standard deviation of 0.1 V and gain of 30 on individual pixels were demonstrated in our 256x256 linear-mode APD arrays.
Use of ligase chain reaction for enhanced detection of<i>Phytophthora infestans</i> (2002)

Sequences of the internal transcribed spacer region 2 (ITS 2) of ribosomal DNA from 10 different species of Phytophthora were aligned, and regions of dissimilarity were used to construct ligase chain reaction (LCR) primers for detecting the late blight pathogen, Phytophthora infestans. Ligase chain reaction primers allow differentiation of species down to a single base pair difference. The primers have greater specificity than previously described polymerase chain reaction (PCR) primers and allow differentiation of P. infestans, Phytophthora mirabilis, and Phytophthora phaseoli, which contain identical ITS sequences, from many other Phytophthora species. Ligase chain reaction was coupled with PCR to increase sensitivity of P. infestans detection and can serve as an enhancement to existing PCR protocols. By labeling LCR primers with biotin and digoxigenin, the LCR was combined with an ELISA-based detection system to improve sensitivity and ease of application.
Giant nonlinear processes in plasmonic metasurfaces (2015)

Nonlinear metasurfaces based on coupling locally-enhanced plasmonic response to intersubband transitions of multi-quantum-wells have recently provided second-order susceptibilities several orders of magnitude larger than any other non-linear flat structure measured so far. Here, we demonstrate that a proper design of the plasmonic metasurface inclusions can dramatically enhance the overall non-linear response of the structure. The optimized metasurfaces are then applied to achieve efficient second-harmonic generation (SHG) and differential frequency generation (DFG) in the infrared and terahertz frequency bands, respectively. In case of low-power impinging beams (≈1W), our simulations predict large conversion efficiencies of around 0.8% and 0.01% for SHG and DFG, outperforming previously reported efficiencies in 1–2 orders magnitude and confirming the suitability of this type of plasmonic metasurfaces as a highly-efficient flat platform for non-linear photonics.
Plasmon-polariton waves guided by thin lossy metal films of finite width: Bound modes of asymmetric structures (2001)

The purely bound electromagnetic modes of propagation supported by asymmetric waveguide structures, comprised of a thin lossy metal film of finite width on a dielectric substrate and covered by a different dielectric superstrate, have been characterized at optical wavelengths. The dispersion of the modes with film thickness and width has been assessed and the effects caused by varying the difference between the superstrate and substrate dielectric constants on the characteristics of the modes have been determined. The modes are quite different from those supported by corresponding slab structures or similar finite-width symmetric waveguides. Unlike these limiting cases, the dispersion with film thickness can exhibit an unusual oscillatory character which is explained by a switching or swapping of the constituent interface modes. In addition, the four fundamental modes supported can evolve such that none has a diminishing attenuation with diminishing film thickness. This rather complex evolution of modes is unique to asymmetric finite-width structures. Under certain conditions, a long-ranging mode having a field distribution that is suitable to excitation using an end-fire technique can be supported. The long-ranging mode has a cutoff thickness below which it is no longer propagated, and its attenuation near cutoff decreases very rapidly, much more so than the attenuation related to the long-ranging mode in a comparable symmetric waveguide. Furthermore, its cutoff thickness is larger than that of the ${s}_{b}$ mode in the corresponding asymmetric slab waveguide, which implies that decreasing the film width increases the sensitivity of the mode to the asymmetry in the structure. This result is interesting and potentially useful in that the propagation characteristics of the mode can be affected by a smaller change in the dielectric constant of the substrate or superstrate compared with the ${s}_{b}$ mode guided by the corresponding slab structure.
Detection of high energy ionizing radiation using deeply depleted graphene–oxide–semiconductor junctions (2022)

Graphene’s linear band structure and two-dimensional density of states provide an implicit advantage for sensing charge. Here, these advantages are leveraged in a deeply depleted graphene–oxide–semiconductor (D2GOS) junction detector architecture to sense carriers created by ionizing radiation. Specifically, the room temperature response of a silicon-based D2GOS junction is analyzed during irradiation with 20 MeV Si4+ ions. Detection was demonstrated for doses ranging from 12 to 1200 ions with device functionality maintained with no substantive degradation. To understand the device response, D2GOS pixels were characterized post-irradiation via a combination of electrical characterization, Raman spectroscopy, and photocurrent mapping. This combined characterization methodology underscores the lack of discernible damage caused by irradiation to the graphene while highlighting the nature of interactions between the incident ions and the silicon absorber.
Fast bi-partition mode selection for 3D HEVC depth intra coding (2014)

This paper proposes a fast mode decision algorithm for 3D High Efficiency Video Coding (3D-HEVC) depth intra coding. In the current 3D-HEVC design, it is observed that for most of the cases, full Rate-Distortion (RD) cost search of Bi-partition mode could be skipped since most coding units (CUs) of depth map are very flat or smooth while Bi-partition modes are designed for CUs with edge or sharp transition. Using the rough RD cost value calculated by HEVC Rough Mode Decision as a selection threshold, we propose a fast Bi-partition modes selection algorithm to speed up the encoding process. The test result for the proposed fast algorithm reports 34.4% encoding time saving with 0.3% bitrate increasing on synthesized view for All-Intra test case. Moreover, by simply varying the selection threshold, we can make a tradeoff between encoding time saving and bitrate loss based on the requirement of different applications.
The Methanol Economy Project (2014)

The Methanol Economy Project is based on the concept of replacing fossil fuels with methanol generated either from renewable resources or abundant natural (shale) gas. The full methanol cycle was investigated in this project, from production of methanol through bromination of methane, bireforming of methane to syngas, CO2 capture using supported amines, co-electrolysis of CO2 and water to formate and syngas, decomposition of formate to CO2 and H2, and use of formic acid in a direct formic acid fuel cell. Each of these projects achieved milestones and provided new insights into their respective fields.