gebhart/patrepeval huggingface dataset:
Abstract PR07: Transcriptome meta-analysis identifies new 5-gene classifier for early detection of pancreatic cancer (2015)

Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) is a truly devastating disease, primarily due to late diagnosis when curative resection is no longer possible and the lack of accurate early detection biomarkers. Therefore, increasing PDAC survival depends heavily on improving the accuracy and effectiveness of early PDAC detection. Methods:Key PDAC biomarkers were identified through an optimized meta-analysis strategy of raw data in 4 PDAC transcriptome datasets (training sets). Application of identical normalization and statistical testing procedures for each dataset generated a list of differentially expressed genes by empirical Bayes moderated t-statistic. The top ranking PDAC-specific genes from this list that were consistently differentially expressed in these training sets were used for developing a classifier for PDAC. The biomarker panel with the highest sensitivity and specificity in the training sets was validated for diagnostic performance in nine independent validation datasets. A subset of genes in the panel were evaluated by immunohistochemistry (IHC) in human PDAC tissue sections. Cell based assays assessed the effect of two genes on PDAC migration and invasion. Results and Conclusions: A 5-gene classifier panel was identified that disntinguished between PDAC and normal pancreas with high sensitivity, specificity and accuracy in the four training sets. Validation of this 5-gene predictor in 9 independent test sets confirmed the diagnostic accuracy to not only discriminate accurately between PDAC and healthy controls, but also between pancreatitis and PDAC. IHC analysis of two of the proteins encoded by the panel confirmed enhanced expression in PDAC cells. Cell-based experiments demonstrated that both proteins enhance migration and invasion of PDAC cells as well as soft agar growth, suggesting a causal link to PDAC development and progression. The immediate clinical utility upon further prospective validation of this PDAC biomarker panel will be accurate PDAC diagnosis in patients with pancreatic abnormalities on imaging, risk stratification and evaluation of the risk of malignancy in pancreatic cysts. This abstract is also presented as Poster B26. Citation Format: Manoj Bhasin, Octavian Bucur, Ken Ndebele, Jessica Plati, Andrea Bullock, Xuesong Gu, Eduardo Castan, Robert Najarian, Jen Jen Yeh, Channing Der, Jon Cody Haines, Karl Ruping, Rebecca Miksad, Roya Khosravi-Far, Towia Aron Libermann. Transcriptome meta-analysis identifies new 5-gene classifier for early detection of pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Innovations in Research and Treatment; May 18-21, 2014; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2015;75(13 Suppl):Abstract nr PR07.
Steroid-binding G-protein-coupled receptors: new drug discovery targets for old ligands (2006)

Steroid-binding receptors have long been a successful target class for the pharmaceutical industry. Clinical applications for steroids range from contraception and hormone replacement therapy to immune regulation and cancer therapy. With the recent demonstration that the orphan GPCR, GPR30 binds and is activated by estrogen, as well as the identification of a GPR30-selective agonist, it is likely that GPR30 represents a novel drug target with many potential clinical applications. This review discusses the role of GPR30 in mediating the effects of estrogen, as well as recent efforts to isolate GPR30-specific ligands using a combination of virtual and biomolecular screening. Finally, comments are made on the future directions regarding GPCRs, steroids and drug discovery.
Pattern Collapse-Free Drying with Sacrificial Gap Fill Polymers (2018)

This work discusses pattern collapse-free drying by application of a sacrificial polymer during the semiconductor wafer cleaning process. The sacrificial polymer is dispensed onto the wafer, displacing the rinse liquid and subsequently dried to form a solid polymer fill within the patterned structure, providing both mechanical support and a means for dry polymer removal by either plasma or thermal exposure. Polymer film thickness, gap fill capability and removal rate are explored for plasma ashable and thermally removable polymer families.
Multiple hit read-out of a microchannel plate detector with a three-layer delay-line anode (2005)

We have developed a delay-line read-out technique for microchannel plate detectors with an increased acceptance for multiple hit events compared to standard two-layer delay-line anodes. This technique allows unambiguous determination of arrival time and position of at least four simultaneously detected particles, and/or to detect an even larger number of particles in a shower, as long as any two particles do not arrive both at the same time and at the same position within certain limits. We demonstrate and discuss the abilities and limitations of this technique and the relevance for certain experimental tasks.
Screen printed MWCNT/PDMS based dry electrode sensor for electrocardiogram (ECG) measurements (2015)

This paper reports on the development of a novel printed and flexible dry electrode sensor consisting of multi-walled carbon nanotube (MWCNT)/ polydimethylsiloxane (PDMS) composite for electrocardiogram (ECG) measurements. The sensor was screen printed using silver (Ag) flake ink on flexible polyethylene terephthalate (PET) substrate. MWCNT/PDMS was then bar coated on the screen printed electrode. The capability of the printed sensor, which is conformal enough to have a better electrode-skin contact without the use of wet gel and skin preparation, was demonstrated. The response of the flexible dry electrode sensor is analyzed and presented in this paper.
Aqueous extraction—An alternative oilseed milling process (1974)

Abstract Oil can be removed from oilseed materials by a process which consists of an aqueous extraction of the comminuted seed, followed by a centrifugal separation which divides the aqueous extract into oil, solid, and aqueous phases. The protein may be recovered in the solids or aqueous phase, depending upon the conditions selected. Unit operations of this process are grinding, solid‐liquid separation, centrifugation, demulsification, and drying of products. Aqueous extraction has been applied, to date, to coconuts and peanuts. For coconuts, a procedure has been developed to recover 93% of the oil and 91% of the protein. The major protein product is 25% protein and, when reconstituted in water, forms an acceptable beverage. The estimated production cost of this product is $.24/1b. For peanuts, the recovery of oil was 89% and protein 92% for the concentrate procedure, whereas the corresponding values for the isolate procedure were 86% and 89%, respectively. The costs of production were estimated as $.17/1b of concentrate (67% protein) and $.28/1b of isolate (89% protein). Aqueous extraction offers several advantages over conventional solvent extraction‐less initial capital investments, safer operation, capability of discontinuous operation, and production of a variety of products. Another advantage of aqueous processing is the capability for utilization of certain chemicals to remove or inactivate undesirable substances. In the case of peanuts, hydrogen peroxide and sodium hypoehlorite have proven to be effective for destruetion of aflatoxins. Aqueous processing has the potential for application to a variety of other oilseeds.
Type-I cascaded quadratic soliton compression in lithium niobate: Compressing femtosecond pulses from high-power fiber lasers (2010)

The output pulses of a commercial high-power femtosecond fiber laser or amplifier are typically around 300--500 fs with wavelengths of approximately 1030 nm and tens of microjoules of pulse energy. Here, we present a numerical study of cascaded quadratic soliton compression of such pulses in ${\mathrm{LiNbO}}_{3}$ using second-harmonic generation in a type-I phase-matching configuration. We find that because of competing cubic material nonlinearities, compression can only occur in the nonstationary regime, where group-velocity-mismatch--induced Raman-like nonlocal effects prevent compression to less than 100 fs. However, the strong group-velocity dispersion implies that the pulses can achieve moderate compression to durations of less than 130 fs in available crystal lengths. Most of the pulse energy is conserved because the compression is moderate. The effects of diffraction and spatial walk-off are addressed, and in particular the latter could become an issue when compressing such long crystals (around 10 cm long). We finally show that the second harmonic contains a short pulse locked to the pump and a long multi-picosecond red-shifted detrimental component. The latter is caused by the nonlocal effects in the nonstationary regime, but because it is strongly red-shifted to a position that can be predicted, we show that it can be removed using a bandpass filter, leaving a visible component of less than 100 fs at $\ensuremath{\lambda}=515$ nm with excellent pulse quality.
Estimation of Mineralizable Nitrogen from 15N-Labelled Crop Residues using Alkaline-Hydrolyzable Nitrogen Methods (2015)

Crop residues play a significant role in soil N cycling. The type of residue, C/N ratio, tillage, and soil moisture influence potentially mineralizable soil-N. This study was established to estimate the N mineralization potential of various crop residues using Direct Steam Distillation (DSD) and the Illinois Soil Nitrogen Test (ISNT). Corn (Zea mays L.), soybean (Glycine max L.), wheat (Triticum aestivum L.), rice (Oryza sativa L.), and grain sorghum (Sorghum bicolor L.) residues were grown in a greenhouse and labeled with 15N using 10 atom% 15N labeled-urea. To assess the N mineralization potential of various crop residues, 0.2 g of residue was subjected to both the DSD and ISNT. Hydrolyzed-N was captured and analyzed for atom% 15N to compare fertilizer atom% 15N to that of the original residue. Total N was quantified to establish recovery percentage. For percentage of N recovery there was a significant residue by method interaction (p < 0.0001) indicating that the two methods recovered varying amounts of N based on the type of residue. Atom% 15N recovered from the soybean residue as alkaline hydrolyzable-N (AH-N) was significantly lower than what was quantified in the plant tissue using TN. Conversely, atom% 15N recovered from the rice residue as AH-N was significantly greater than that which was quantified in the original plant tissue using TN. Comparison of atom% 15N in the residue and recovered AH-N suggested that certain crop species partition fertilizer N differently. Specific estimation of N mineralization potential of crop residues could aid producers in determining fertilizer N needs and encourage the development and implementation of soil-based N tests.
1|A Kalman filter-based algorithm for IMU-camera calibration (2007)

Vision-aided Inertial Navigation Systems (V-INS) can provide precise state estimates for the 3D motion of a vehicle when no external references (e.g., GPS) are available. This is achieved by combining inertial measurements from an IMU with visual observations from a camera under the assumption that the rigid transformation between the two sensors is known. Errors in the IMU-camera calibration process causes biases that reduce the accuracy of the estimation process and can even lead to divergence. In this paper, we present a Kalman filter-based algorithm for precisely determining the unknown transformation between a camera and an IMU. Contrary to previous approaches, we explicitly account for the time correlations of the IMU measurements and provide a figure of merit (covariance) for the estimated transformation. The proposed method does not require any special hardware (such as spin table or 3D laser scanner) except a calibration target. Simulation and experimental results are presented that validate the proposed method and quantify its accuracy.
Distributed Cyclic Delay Diversity Systems With Spatially Distributed Interferers (2019)

In this paper, a cooperative single carrier system comprising multiple cooperating remote radio heads and spatially distributed interferers is investigated. Due to the random location of the interferers within the communication range, a mixture of line-of-sight (LoS) and non-line-of-sight (nLoS) paths is considered in the channel model. Under a frequency selective fading channel with a mixture of the LoS and nLoS paths, the distributed cyclic delay diversity is employed to achieve the maximum transmit diversity gain without the exact knowledge of the channel state information at the transmitter side. It is shown that the operating signal-to-noise regions are divided into two regions, i.e., noise-limited and interference-limited. In this paper, the main focus is on the interference-limited region, in which diversity gain is not achieved due to performance limits determined by the system and channel parameters. The existence of these limits on the performance metrics, such as the outage probability and ergodic capacity, is derived analytically and then verified by link-level simulations.
Human Immunodeficiency Virus Type 1 Vif Functionally Interacts with Diverse APOBEC3 Cytidine Deaminases and Moves with Them between Cytoplasmic Sites of mRNA Metabolism (2007)

Vif(IIIB), which has been a standard model for the viral infectivity factor of human immunodeficiency virus type 1 (HIV-1), binds the cytidine deaminase APOBEC3G (A3G) and induces its degradation, thereby precluding its lethal incorporation into assembling virions. Additionally, Vif(IIIB) less efficiently degrades A3F, another potent anti-HIV-1 cytidine deaminase. Although the APOBEC3 paralogs A3A, A3B, and A3C have weaker anti-HIV-1 activities and are only partially degraded by Vif(IIIB), we found that Vif(IIIB) induces their emigration from the nucleus to the cytosol and thereby causes net increases in the cytosolic concentrations and anti-HIV-1 activities of A3A and A3B. In contrast, some other Vifs, exemplified by Vif(HXB2) and Vif(ELI-1), much more efficiently degrade and thereby neutralize all APOBEC3s. Studies focused mainly on A3F imply that it occurs associated with mRNA-PABP1 in translationally active polysomes and to a lesser extent in mRNA processing bodies (P-bodies). A3F appears to stabilize the P-bodies with which it is associated. A correspondingly small proportion of Vif(IIIB) also localizes in P-bodies in an A3F-dependent manner. Stress causes A3A, A3B, A3C, and A3F to colocalize efficiently with Vif(IIIB) and mRNA-PABP1 complexes in stress granules in a manner that is prevented by cycloheximide, an inhibitor of translational elongation. Coimmunoprecipitation studies suggest that Vifs from different HIV-1 isolates associate with all tested APOBEC3s. Thus, Vifs interact closely with structurally diverse APOBEC3s, with effects on their subcellular localization, degradation rates, and antiviral activities. Cytosolic APOBEC3-Vif complexes are predominantly bound to mRNAs that dynamically move between translationally active and storage or processing pools.
Nodal Analysis for Unconventional Reservoirs—Principles and Application (2015)

Summary Nodal analysis is the standard technique used to evaluate the performance of integrated production systems. Two curves represent the capacities of the inflow and of the outflow, and the intersection of the two curves gives the solution operating point. Limitations of traditional nodal analysis include: Results are offered only at a snapshot, not as a function of time. Inflow-performance-relationship (IPR) models are limited, with none available for shale gas wells. Analysis is performed on a well-by-well basis, with no account of multiwell interference. We propose a new nodal-analysis method that enables the study of transient production systems, such as unconventional reservoirs, with IPR models generated from a high-speed semianalytical reservoir simulator and outflow curves generated from a steady-state pipeline simulator. The use of analytical reservoir simulation allows accurate, reliable modeling of the real inflow system. The new approach studies the time-lapse behavior of the system, with consideration of production history and neighboring-well interference. This new method enables the study of transient deliverability at the wellhead, where the measurement is usually available, and shows the time-lapse relationship between wellhead pressure and production rate. We provide examples of wellhead deliverability and choke management and explain advantages of the method with case studies involving tight and shale wells. The method is also applied to design and optimize artificial lift in unconventional wells and to study the method's validity over time. In addition, we discuss an example of operational well dynamics with time-lapse nodal analysis. Furthermore, this new method generates discussion about some concepts that are often taken for granted—What should be the definition of IPR in a transient production system? On the IPR curve, is the zero-rate-pressure the reservoir pressure? Can IPR curves at two different timesteps cross each other? Finding the answers to these questions will help us better understand production systems. The commonly used productivity-index (PI) method is reviewed and compared with the new method. Results show that one should not use the PI method when well operational conditions change.
One order of magnitude faster phase change at reduced power in Ti-Sb-Te (2014)

To date, slow Set operation speed and high Reset operation power remain to be important limitations for substituting dynamic random access memory by phase change memory. Here, we demonstrate phase change memory cell based on Ti0.4Sb2Te3 alloy, showing one order of magnitude faster Set operation speed and as low as one-fifth Reset operation power, compared with Ge2Sb2Te5-based phase change memory cell at the same size. The enhancements may be rooted in the common presence of titanium-centred octahedral motifs in both amorphous and crystalline Ti0.4Sb2Te3 phases. The essentially unchanged local structures around the titanium atoms may be responsible for the significantly improved performance, as these structures could act as nucleation centres to facilitate a swift, low-energy order-disorder transition for the rest of the Sb-centred octahedrons. Our study may provide an alternative to the development of high-speed, low-power dynamic random access memory-like phase change memory technology.
A simple, scalable and provably stable explicit rate computation scheme for flow control in communication networks (2001)

Abstract This paper describes fast rate computation (FASTRAC), an explicit rate flow control algorithm for available bit rate (ABR) traffic. Using digital control theory, we develop a simple rate controller for the ABR flow control process. We prove that the controller is stable, fair to all participating sources and configurable with respect to responsiveness. The analysis presented shows that stability of the flow control process depends primarily on two factors, the control update rate and the feedback delay. The implementation of the proposed algorithm is much simpler than other fair rate allocation algorithms. The proposed algorithm demonstrates the ability to scale with speed, distance, different feedback delays, number of users, and number of nodes while remaining robust, efficient, and fair under stressing and dynamic traffic conditions. Copyright © 2001 John Wiley & Sons, Ltd.
Complementary beamforming: new approaches (2006)

Smart antenna technology can greatly improve the coverage radius of wireless systems by focusing the transmitted signal (beam) toward desired users. However, beamforming has an important side effect as it creates a region, herein referred to as the complementary region, where some users in the network cannot sense the directional signals (beams). We have referred to this as the hidden beam problem in Tarokh et al.. From a physical layer perspective, beamforming reduces cochannel interference (CCI). However, in systems that use medium access-control techniques such as the carrier-sense multiple access (CSMA) protocol in wireless local area networks, during a busy period of the channel, the users in the complementary region may wrongly decide that the medium is idle and transmit packets. This may cause CCI, unnecessary retransmissions, subsequent backoff, and increased network latency. We introduced the concept of complementary beamforming (CBF) to address this issue in Tarokh et al.. In this paper, we propose two new methods, called "subspace complementary beamforming " (SCBF) and "complementary superposition beamforming" (CSBF). The SCBF uses dummy data to ensure a controlled level of received energy in all directions of eigenvectors unused by downlink beamforming. The technique works in multipath fading channels. The approach achieves similar results to those reported in Tarokh et al.. However, it enables the second technique (CSBF) which can also send data content in the complementary beam. This allows passive nodes in the network to receive "broadcast" information, while the active nodes are engaged in the exchange of user-specific data. It is shown that CBF effects can be achieved simply by increasing the transmit power of only one of antenna elements when space-division multiple access is not applied. Simulations are provided in order to quantify overall network performance improvements when using CBF, confirming significant throughput and delay performance enhancements.
Photonic Crystals: Theory, Applications and Fabrication (2009)

The Only Source You Need for Understanding the Design and Applications of Photonic Crystal-Based Devices This book presents in detail the fundamental theoretical background necessary to understand the unique optical phenomena arising from the crystalline nature of photonic-crystal structures and their application across a range of disciplines. Organized to take readers from basic concepts to more advanced topics, the book covers: Preliminary concepts of electromagnetic waves and periodic media Numerical methods for analyzing photonic-crystal structures Devices and applications based on photonic bandgaps Engineering photonic-crystal dispersion properties Fabrication of two- and three-dimensional photonic crystals The authors assume an elementary knowledge of electromagnetism, vector calculus, Fourier analysis, and complex number analysis. Therefore, the book is appropriate for advanced undergraduate students in physics, applied physics, optics, electronics, and chemical and electrical engineering, as well as graduate students and researchers in these fields.