gebhart/patrepeval huggingface dataset:
Abstract B24: New views on microRNAs involvement in melanoma (2012)

Abstract MicroRNAs (miRNAs) are small non-coding RNAs with regulatory roles, which are involved in a broad spectrum of physiological and pathological processes, including cancer. Most published data is focused on miRNAs that are differentially expressed between melanocytes and melanoma cells. These experiments lead to the discovery of a plurality of new miRNA-based mechanisms. However, this widely common approach fails to address at least two important issues: a) the effect of genomic mutations on target gene regulation by miRNAs; b) the role of miRNAs in shaping the phenotypic heterogeneous nature of metastatic disease. Here we address these issues to provide new insights on the pathogenesis of melanoma and facilitate the development of innovative diagnostic and therapeutic implementations. Melanoma cells acquire tens of thousands of genomic mutations, most of which are defined as “passengers” and few as “drivers”. We analyzed a fully sequenced genome of melanoma tumor and found that &gt;200 mutations hit the 3′UTR of genes, the main target area of miRNAs (out of 499 that hit transcribed genes). Three different computational algorithms (PITA, miRanda and our in-house tool, MirHB) concur and predict that these somatic mutations globally reduce the binding of miRNAs to the mutated 3′UTRs. This phenomenon is not genome-specific and proved to reflects the nature of the characteristic UV-induced mutation, C-to-T. Accordingly, mutation patterns in other malignancies, which are not primarily induced by UV-radiation, such as lung cancer and AML, do not yield similar predictions. This indicates that miRNA-based regulation can progressively perturb even with no apparent alterations in the expression of miRNAs. We define these mutations as “dormant drivers”, as each mutation is expected to have a moderate effect, but the cumulative effect is significant. We next identified miRNAs that regulate the aggressive phenotype of established melanoma cells. For that purpose, we tested two isogenic human melanoma cell lines (derived from the same patient) that dramatically differ in net proliferation, invasion, tube formation and tumorigenicity in vivo. Comparative screening revealed a large cohort of differentially expressed miRNAs. Molecular manipulation of highly ranked miRNAs (miR-31, -34a, -184, -185 and -204 and miR-17-5p) resulted in significant changes of the aggressive phenotype in vitro and in vivo. Remarkably, none of these miRNAs has been studied in cutaneous melanoma before. In conclusion, this study might lead to the development of novel lines of therapy. Citation Format: Eyal Greenberg, Eran Eyal, Gideon Rechavi, Noam Shomron, Jacob Schachter, Gal Markel, Yael Nemlich, Steven Hajdu, Orit Itzhaki, Liat Edry, Oz Solomon, Ninette Amariglio, Michal J. Besser, Yona Keisari. New views on microRNAs involvement in melanoma [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr B24.
Simultaneous OPC and decomposition for double exposure lithography (2011)

Double exposure techniques are an economically viable method for extending the life of the current 193nm wavelength immersion lithography techniques into future generations of semiconductor scaling. One popular example of double exposure is the use of double dipole illumination, where the X and Y dipoles are separately optimized for vertical and horizontal features respectively. The primary challenge in such double exposure techniques lies in the process of target layout decomposition into patterns that can be optimally printed using their respective source. Current approaches for decomposition are rule-based. They suffer from the drawbacks of scalability, rule count explosion and inability to guarantee sufficient yield in the presence of process variation. Further, rules are characterized specific to sources and are relatively easy to develop for dipoles, but far more difficult to develop for more complex sources such as used in source mask optimization (SMO). Decomposed target layouts have to further undergo optical proximity correction (OPC) in order to be converted to a mask for use in manufacturing. In this paper, we propose a novel approach which integrates the processes of decomposition and optical proximity correction. We preclude the intermediate target decomposition stage. Instead, we directly optimize the masks for both exposures simultaneously in order to obtain a wafer image that both closely matches the target layout and is also robust to process variation. For this purpose, we define a lithographic cost function that is a weighted sum of intensity error and intensity slope. We develop methods to analytically predict the change in this cost function due to movement of fragments on each mask. We then utilize a gradient-descent algorithm for fragment movement to minimize the cost function. Since our methodology is based on the knowledge of the SOCS decomposition kernels, it is not restricted to dipoles alone, but can be utilized for any complex sources for which such kernels are known. Our experiments on 1x metal (M1) show significant improvement in layout process window compared to traditional rule-based decomposition methods.
Scintillators for PET and SPECT (2017)

A scintillator is a material with the ability to absorb ionizing radiation, such as x-rays or gamma rays, and 
to convert a fraction of the absorbed energy into visible or ultraviolet (UV) photons. The conversion process 
typically takes place on a timescale of nanoseconds to microseconds, thus producing a brief pulse of photons 
corresponding to each gamma ray or x-ray that interacts with the scintillator material [1]. The light pulse, 
the intensity of which is approximately proportional to the energy deposited in the scintillator, is sensed by a 
photodetector and converted into an electrical signal.
Emulsifier Developed from Waste Vegetable Oil for Application in Invert-Emulsion Oil based Mud (2018)

Abstract Emulsifiers are a class of chemicals derived from fatty acids or their derivatives and used in water-in-oil based mud (OBM) in other words invert emulsion oil based mud. The role of an emulsifier in invert emulsion OBM is to lower the interfacial tension between water and oil to allow the formation of stable emulsion which is an essential quality of oil based mud. These emulsifiers surround the water droplets like an encapsulation with the fatty acid components extend into the oil phase and acts like a small osmatic cell allowing only water to pass through but not salts. Most of the commercially available emulsifiers are derived from Tall oil fatty acid (TOFA) which shows excellent emulsion stability even at harsh conditions. Our objective in this study is to make use of the huge quantity of used cooking/vegetable oil available in the kingdom and convert to an emulsifier suitable for the application in invert-emulsion OBM as vegetable oil contains a wide range of different fatty acids in the form triglycerides. A comparative study has been carried out by formulating invert-emulsion OBM using commercially available emulsifier and the emulsifier derived from used cooking/vegetable oil. Emulsifier (Arc-Eco-Mul) from used or waste vegetable oil has been synthesized by an in-house developed process. A series of different invert-emulsion OBM have been formulated with varying density using in-house developed product Arc-Eco-Mul as primary emulsifier. For comparison, a mud is formulated using commercial primary emulsifier. Mud properties such as density, rheology, API and HPHT filtration control tests have been conducted for fresh mud and for muds hot-rolled at 300degF and 500psi for 16h. It is observed from the laboratory experiments that the mud samples formulated using 12-ppb of Arc-Eco-Mul have similar rheological properties and better filtration control properties compared to the mud samples formulated using 12-ppb of commercial emulsifier. Most importantly, there is no phase separation in the filtrate collected from HPHT filtration control experiment, which showed a very stable emulsion formed by in-house developed Arc-Eco-Mul. Concentration screening experiments showed that only 6-ppb loading of Arc-Eco-Mul is required to achieve a mud with very good rheological and filtration control properties with high emulsion stability. The in-house developed Arc-Eco-Mul from used cooking/vegetable oil has similar properties as commercial additives that are currently used in the industry. This will open an avenue for recycling used cooking oil for oil and gas industry applications.
Electro-optic polymers for visible light (2022)

We developed a high-performance EO polymer for visible light by adopting figures of merit (FOMs) including wavelength factors to compare the performance of EO polymers over a wide wavelength range. We found EO polymers whose FOMs at 640 nm are larger than those at 1550 nm of the C-band EO polymer. A modulator using the EO polymer for visible light gives that the modulator’s figure of merit, VpiL is as small as 0.65 V·cm, which is smaller than the typical value of C-band EO polymer modulators.
Enhanced capacity and coverage by Wi-Fi LTE integration (2015)

Wi-Fi provides cost-effective data capacity at hotspots in conjunction with broadband cellular networks. The hotspots are required to capture a large number of users and provide high data rates. Data rates, over the Wi-Fi interface, are influenced by the media access protocol, which loses throughput due to contention based protocol delays and unintended collisions when a large number of users are active. The hotspot range that determines the number of users that can associate is limited by the lower power of the client rather than the access point. By diverting the traffic destined to the access point via another access network, both range and efficiency can be improved. This uplink redirection or diversion is achieved by simultaneous use of the Wi-Fi and LTE radio interfaces. Three options, loose, tight, and hybrid integration, are presented to providing enhanced capacity and coverage.
Moisture Determination in IC Packages by Conductance Technique (1986)

An a.c. conductance technique using a lock-in-amplifier (LIA) is described. The conductance technique is a non-destructive technique and uses the die as a sensor. Our experiments and theoretical calculations revealed that the moisture-induced conductance variation is 10 to 400% whereas the moisture-induced capacitance variation is 0 to 20%. Hence, even though capacitance and conductance values were measured, only conductance variations are reported. A circuit model has been developed to explain the observed experimental behavior. This technique is thus superior to capacitance technique in deterining the low levels of moisture (<5000ppmu) in IC packages. The selective condensation problem experienced in the Harris or Al2O3 sensors is non existent in the conductance technique. Since the applied voltage in the conductance method is ~l00mV, there is no dissociation of water into hydrogen and oxygen, as is possible in the case of Harris sensors. Further, the moisture content determined by this non-destructive technique correlates well with the residual gas analysis (RGA) by the mass spectrometer. This technique is non-destructive, reliable, rapid and suitable for in-line testing.
Blue protein with red fluorescence (2016)

The walleye (Sander vitreus) is a golden yellow fish that inhabits the Northern American lakes. The recent sightings of the blue walleye and the correlation of its sighting to possible increased UV radiation have been proposed earlier. The underlying molecular basis of its adaptation to increased UV radiation is the presence of a protein (Sandercyanin)-ligand complex in the mucus of walleyes. Degradation of heme by UV radiation results in the formation of Biliverdin IXα (BLA), the chromophore bound to Sandercyanin. We show that Sandercyanin is a monomeric protein that forms stable homotetramers on addition of BLA to the protein. A structure of the Sandercyanin-BLA complex, purified from the fish mucus, reveals a glycosylated protein with a lipocalin fold. This protein-ligand complex absorbs light in the UV region (λ<sub>max</sub> of 375 nm) and upon excitation at this wavelength emits in the red region (λ<sub>max</sub> of 675 nm). Unlike all other known biliverdin-bound fluorescent proteins, the chromophore is noncovalently bound to the protein. We provide here a molecular rationale for the observed spectral properties of Sandercyanin.
Wyner-Ziv Successive Refinement of Video and Rate Distortion Analysis (2007)

In Wyner-Ziv video coding system, motion estimation efficiency is much lower than that in conventional video coding system because current frame is not available when doing motion estimation. In this paper, we propose a successive resolution refinement algorithm to improve motion estimation efficiency. Based on our rate distortion analysis, we derive optimal down-sample ratio for two-stage successive resolution refinement system. We also analyze the performance of multistage case, and find that it approaches the performance of ideal motion compensated Wyner-Ziv video coding system, with at most 2.17 dB loss in PSNR. Experimental results demonstrate the correctness of the analysis and show that the proposed method out-performs original bit-plane refinement scheme up to 2.5 dB, with much lower complexity.
Stability assessment and emergency control method using trajectory sensitivities (2004)

Very stressed power systems often lack ability to withstand certain disturbances, what might result in serious consequences. Therefore the tools mitigating such a situation have a crucial significance. This work presents a method for real-time emergency control of power systems based on the trajectory sensitivities. Out of the present conditions a nominal trajectory and its sensitivities is precalculated. If an incipient instability is detected, necessary stabilizing control measures are determined. A short review of trajectory sensitivities and model predictive control is included. A principal description of the method together with a theoretical foundation and examples with simulation results is provided.
High-efficiency coupling structure for a single-line-defect photonic-crystal waveguide (2002)

We present the design and fabrication of a planar structure for coupling light from a multimode feed waveguide into a single-line-defect photonic-crystal waveguide. Finite-difference time-domain calculations predict a coupling efficiency of greater than 90%, and preliminary experimental results indicate successful coupling through a single-line-defect photonic-crystal waveguide. Device design, fabrication, and characterization are presented.
Layout Optimization of Shapeable Components With Extended Pattern Search Applied to Transmission Design (2004)

An extended pattern search algorithm is presented for the placement of shapeable components within a product layout. Shapeable octrees are used to evaluate the amount of overlap between pairs of components, extending previous technology that requires fixed-size components. The method is used to conceptualize the layout of the cross-section of an automatic transmission.
The MYB96 Transcription Factor Regulates Cuticular Wax Biosynthesis under Drought Conditions in<i>Arabidopsis</i>  (2011)

Drought stress activates several defense responses in plants, such as stomatal closure, maintenance of root water uptake, and synthesis of osmoprotectants. Accumulating evidence suggests that deposition of cuticular waxes is also associated with plant responses to cellular dehydration. Yet, how cuticular wax biosynthesis is regulated in response to drought is unknown. We have recently reported that an Arabidopsis thaliana abscisic acid (ABA)-responsive R2R3-type MYB transcription factor, MYB96, promotes drought resistance. Here, we show that transcriptional activation of cuticular wax biosynthesis by MYB96 contributes to drought resistance. Microarray assays showed that a group of wax biosynthetic genes is upregulated in the activation-tagged myb96-1D mutant but downregulated in the MYB96-deficient myb96-1 mutant. Cuticular wax accumulation was altered accordingly in the mutants. In addition, activation of cuticular wax biosynthesis by drought and ABA requires MYB96. By contrast, biosynthesis of cutin monomers was only marginally affected in the mutants. Notably, the MYB96 protein acts as a transcriptional activator of genes encoding very-long-chain fatty acid-condensing enzymes involved in cuticular wax biosynthesis by directly binding to conserved sequence motifs present in the gene promoters. These results demonstrate that ABA-mediated MYB96 activation of cuticular wax biosynthesis serves as a drought resistance mechanism.
Ultra-broad-band MIMO array with steerable spotlight beams (2015)

This paper introduces concept of an ultra-broad-band cellular phased array with multiple steerable spotlight beams. The proposed array produces multiple 65-degree coverage beams and multiple steerable “spotlight” beams (HPBW<;14deg) for cellular MIMO coverage with hot-spots or small-cell enhancement. The spotlight beams can be steered electronically both in azimuth and elevation directions to provide mobile cellular services at high-demand “hot-spot” areas where high capacity service is required. These spotlight beams may also be used to fill voids or deficiencies caused by regular coverage beams, or to create a small-cell region within the coverage area. The proposed array uses ultra-broad-band aperture-couple patch providing over 45% frequency bandwidth from 1700 MHz to 2700 MHz, covering both the UMTS and LTE 2.5 bands.
Diode-pumped laser action In a new broadly tunable crystal: Yb 3+ :Sr 3 Y(BO 3 ) 3 (2001)

The first demonstration of laser action under diode-pumping is herein reported with a Yb:Sr3Y (BO3)3 (Yb:SrYBO or Yb:BOYS) double-borate crystal.
Review of Selected Advances in Electrical Capacitance Volume Tomography for Multiphase Flow Monitoring (2022)

Electrical Capacitance Volume Tomography (ECVT) has emerged as an attractive technology for addressing instrumentation requirements in various energy-related multiphase flow systems. ECVT can monitor multiple flow conditions and reconstruct real-time 3D images from capacitance measurements using a large set of electrode plates placed around the processes column enclosing the sensed flow system. ECVT is non-intrusive and allows the measurement of changes in mutual capacitance between all possible plate pair combinations. The objective of this paper is to provide a comprehensive review of recent advances in ECVT, enabling robust monitoring of multiphase flows, especially water-containing multiphase flows.
Performance analysis of turbo decoder for 3GPP standard using the sliding window algorithm (2002)

We analyze the performance of a fixed-point turbo decoder using two sliding window algorithms for the 3GPP standard. We show that the bit and frame error rate performance of the sliding window scheme strongly depends on the guard window size. Simulation results also indicate that small guard window sizes can significantly decrease the iteration gain for large frames.
Practical fault localization for dynamic web applications (2010)

We leverage combined concrete and symbolic execution and several fault-localization techniques to create a uniquely powerful tool for localizing faults in PHP applications. The tool automatically generates tests that expose failures, and then automatically localizes the faults responsible for those failures, thus overcoming the limitation of previous fault-localization techniques that a test suite be available upfront. The fault-localization techniques we employ combine variations on the Tarantula algorithm with a technique based on maintaining a mapping between statements and the fragments of output they produce. We implemented these techniques in a tool called Apollo, and evaluated them by localizing 75 randomly selected faults that were exposed by automatically generated tests in four PHP applications. Our findings indicate that, using our best technique, 87.7% of the faults under consideration are localized to within 1% of all executed statements, which constitutes an almost five-fold improvement over the Tarantula algorithm.
Example-based facial sketch generation with non-parametric sampling (2002)

In this paper, we present an example-based facial sketch system. Our system automatically generates a sketch from an input image, by learning from example sketches drawn with a particular style by an artist. There are two key elements in our system: a non-parametric sampling method and a flexible sketch model. Given an input image pixel and its neighborhood, the conditional distribution of a sketch point is computed by querying the examples and finding all similar neighborhoods. An "expected sketch image" is then drawn from the distribution to reflect the drawing style. Finally, facial sketches are obtained by incorporating the sketch model. Experimental results demonstrate the effectiveness of our techniques.
A rate control algorithm based on adaptive R-Q model for MPEG-1 to MPEG-4 transcoding in DCT domain (2003)

This paper proposes an adaptive rate control algorithm for MPEG-1 to MPEG-4 transcoder for video transmission over networks of different capacities and characteristics. It is based on an adaptive R-Q model to follow the new target bit-rate of a transcoded bitstream. In R-Q modeling, the R-Q characteristics predicted from a previous picture of the same picture type are used in combination with the R-Q data measured for the current picture. To overcome the quantizer mismatch between MPEG-1 and MPEG-4 syntax, a gradual adaptation function is applied. It is shown that the adaptive R-Q model-based rate control can efficiently control the output bit-rate to match the target bit budget.
Map-matching for low-sampling-rate GPS trajectories (2009)

Map-matching is the process of aligning a sequence of observed user positions with the road network on a digital map. It is a fundamental pre-processing step for many applications, such as moving object management, traffic flow analysis, and driving directions. In practice there exists huge amount of low-sampling-rate (e.g., one point every 2--5 minutes) GPS trajectories. Unfortunately, most current map-matching approaches only deal with high-sampling-rate (typically one point every 10--30s) GPS data, and become less effective for low-sampling-rate points as the uncertainty in data increases. In this paper, we propose a novel global map-matching algorithm called ST-Matching for low-sampling-rate GPS trajectories. ST-Matching considers (1) the spatial geometric and topological structures of the road network and (2) the temporal/speed constraints of the trajectories. Based on spatio-temporal analysis, a candidate graph is constructed from which the best matching path sequence is identified. We compare ST-Matching with the incremental algorithm and Average-Fréchet-Distance (AFD) based global map-matching algorithm. The experiments are performed both on synthetic and real dataset. The results show that our ST-matching algorithm significantly outperform incremental algorithm in terms of matching accuracy for low-sampling trajectories. Meanwhile, when compared with AFD-based global algorithm, ST-Matching also improves accuracy as well as running time.