gebhart/patrepeval huggingface dataset:
Genetic and Molecular Analysis of Utility of sd1 Alleles in Rice Breeding (2007)

The widespread adoption of the high-yielding semi-dwarf rice variety, IR8, led to the “green revolution” in Asia in the 1960s. The short stature of this variety is due to a loss-of-function of the SD1 gene that encodes a GA20 oxidase-2 (GA20ox-2) which catalyzes late steps of gibberellin biosynthesis. In this study, we investigated how widely sd1 mutations have been employed in the generation of semi-dwarf varieties of rice. Genetic and molecular analyses revealed that the sd1 allele of IR8 has been used in the production of japonica varieties. Sequence analysis of the SD1 locus of 57 semi-dwarf varieties showed that at least 7 sd1 alleles have been used in the breeding of semi-dwarf rice varieties in China, USA and Japan. The utilization of such a high number of different alleles all controlling the same target trait highlights that mutations in GA20ox-2 induce an agronomically advantageous architecture in rice.
A new structure of a switching flux synchronous polyphased machine with hybrid excitation (2007)

The aim of this paper is to present the structure of a new flux switching synchronous machine with hybrid excitation. This machine uses the flux switching principle where all the active parts are located on the stator. The rotor is only a salient passive rotor and can be robust and made with a low cost technology. This new machine can be supplied with electricity by means of a traditional three phase voltage converter or can be associated with a diode rectifier. The hybrid excitation is an association of permanent magnets and a wound exciter.
TH‐EF‐BRA‐02: Patient‐Specific Dose Maps for CT Scans Using a Fast, Deterministic Boltzmann Transport Equation Solver (2015)

Purpose: To develop a rapid and accurate software tool for computing patient‐specific radiation dose maps of dose delivered from kV computed tomography (CT) scans. Methods: Monte Carlo methods currently provide the gold‐standard for calculating patient‐specific dose maps, but require immense computational resources to achieve sufficiently high statistical accuracy. To overcome this limitation, a deterministic method was implemented to solve the same underlying Boltzmann transport equation (BTE) that governs particle interactions and transport. Phase‐space was discretized according to spatial location, energy, and angle, and a deterministic finite element algorithm was applied to compute the object's photon fluence distribution, which does not exhibit stochastic noise. A computationally efficient GPU implementation for a standard workstation was developed, and comparison was made between the performance of the deterministic BTE solver and a standard Monte Carlo algorithm for a cone‐beam projection of a virtual anthropomorphic chest phantom. Results: The BTE solution and Monte Carlo results were in strong agreement with a relative root‐mean square error (RMSE) of 3.47%. Some larger differences existed at high‐contrast boundaries (e.g., air/water) and within the bone, and are under further investigation. Notably, the computation time of the BTE solver was 8 seconds, while to obtain the same level of statistical uncertainty with conventional Monte Carlo required 1200 CPU‐hours. Additionally, unlike Monte Carlo, the BTE computation time is only weakly dependent on the number of sources, making it extremely well‐suited for CT dose calculations. Therefore, the BTE‐based method is expected to offer a >30,000x speed increase compared to Monte Carlo for entire CT scans, even after application of variance reduction techniques and GPU implementation. Conclusion: The novel deterministic BTE solver offers a significantly faster alternative to Monte Carlo‐based methods for computing dose delivered by CT scans, which can enable estimation of patient‐specific organ doses for each CT examination performed. Adam Wang, Alex Maslowski, Todd Wareing, and Josh Star‐Lack are employees of Varian Medical Systems.
Inducing single-cell suspension of BTI-TN5B1-4 insect cells: II. The effect of sulfated polyanions on baculovirus infection (1997)

Sulfated polyanions can be used to rapidly induce and maintain single-cell suspensions of BTI-TN5B1-4 insect cells, a cell line which clumps in suspension. Elimination of cell clumping results in a significant increase in volumetric yield of the baculovirus expression vector system. Sulfated polyanions, however, inhibited baculovirus infection of BTI-TN5B1-4. Data from binding studies and fusion assays suggest that the inhibition of infection was not due to the observed reduction in viral attachment rate but to inhibition of viral membrane fusion in the endosome.The three most effective polyanions for inducing single cells are dextran sulfate, pentosan sulfate, and polyvinyl sulfate. At concentrations required for single-cell formation, dextran sulfate and pentosan sulfate did not affect viral infection at multiplicities of infection greater than one plaque forming unit per cell. In contrast, polyvinyl sulfate blocked viral infection even at a high multiplicity of infection of 20 plaque-forming units per cell. To bypass this inhibition, polyvinyl sulfate can be removed by resuspending the cells in fresh medium before virus addition, and then added back to the cell suspension after a substantial amount of virus has been internalized. Alternatively, polyvinyl sulfate can be neutralized with a polycation before virus addition, and an equivalent amount of polyvinyl sulfate added back after most of the virus has been internalized. We present a simple mathematical model of the attachment and entry of baculovirus in BTI-TN5B1-4, which can be used to design appropriate infection regimens.
Efficient flow-sensitive interprocedural computation of pointer-induced aliases and side effects (1993)

We present practical approximation methods for computing interprocedural aliases and side effects for a program written in a language that includes pointers, reference parameters and recursion. We present the following results: 1) An algorithm for flow-sensitive interprocedural alias analysis which is more precise and efficient than the best interprocedural method known. 2) An extension of traditional flow-insensitive alias analysis which accommodates pointers and provides a framework for a family of algorithms which trade off precision for efficiency. 3) An algorithm which correctly computes side effects in the presence of pointers. Pointers cannot be correctly handled by conventional methods for side effect analysis. 4) An alias naming technique which handles dynamically allocated objects and guarantees the correctness of data-flow analysis. 5) A compact representation based on transitive reduction which does not result in a loss of precision and improves precision in some case. 6) A method for intraprocedural alias analysis which is based on a sparse representation.
Multi-stream spectral representation for statistical parametric speech synthesis (2016)

In statistical parametric speech synthesis such as Hidden Markov Model (HMM) based synthesis, one of the problems is in the over-smoothing of parameters, which leads to a muffled sensation in the synthesised output. In this paper, we propose an approach in which the high frequency spectrum is modelled separately from the low frequency spectrum. The high frequency band, which does not carry much linguistic information, is clustered using a very large decision tree so as to generate parameters as close as possible to natural speech samples. The boundary frequency can be adjusted at synthesis time for each state. Subjective listening tests show that the proposed approach is significantly preferred over the conventional approach using a single spectrum stream. Samples synthesised using the proposed approach sound less muffled and more natural.
High Performance Simplified LDPC Decoder without Knowledge of Multi-path Rayleigh Channel (2006)

This paper presents a high performance simplified LDPC decoder which doesn't need knowledge of multi-path channels and is robust over level mismatches between demodulator and decoder. This decoder also has the benefit of avoiding a high error floor caused by the approximation in the max-log domain known as the min-sum algorithm in categorized Tanner graphs. To overcome error floor and to get the robustness, we apply some individual coefficients to LLR values in every category. Simulation results in AWGN and multi-path fading channels show that even though categorized low profile and approximations are used, good performance is achieved, which can not be achieved by ordinary single coefficient methods (e.g., normalized BP algorithm). Unlike the recently developed simplified algorithms which use the noise variance of the channel estimate, simulation results show that the proposed multi-coefficient method which doesn't use the noise variance is robust over varying fading conditions
Platinum-Coated Palladium Nanotubes as Oxygen Reduction Reaction Electrocatalysts (2012)

Platinum (Pt) coated palladium (Pd) nanotubes (Pt/PdNTs) with a wall thickness of 6 nm, outer diameter of 60 nm, and length of 5–20 μm are synthesized via the partial galvanic displacement of Pd nanotubes. Pt coatings are controlled to a loading of 9 (PtPd 9), 14 (PtPd 14), and 18 (PtPd 18) wt % and estimated to have a thickness of 1.1, 1.7, and 2.2 Pt atoms, respectively, if a uniform and continuous coating is assumed. Oxygen reduction experiments have been used to evaluate Pt/PdNTs, Pt nanotubes, Pd nanotubes, and supported Pt nanoparticle activity for proton exchange membrane fuel cell cathodes. The dollar and area (specific surface area) normalized ORR activities of Pt/PdNTs exceed the United States Department of Energy (DOE) targets. PtPd 9, PtPd 14, and PtPd 18 produce dollar activities of 10.4, 9.4, and 8.7 A$–1, respectively; PtPd 9 exceeds the DOE dollar activity target (9.7 A$–1) by 7%. Pt/PdNTs further exceed the DOE area activity target by 40–43%.
Acousto-elastic measurements and baseline-free assessment of bolted joints using guided waves in space structures (2010)

Integrity of bolted joints is critical for successful deployment and operation of space structures. Conventional structural qualification tests span weeks if not months and inhibit rapid launch of space systems. Recent developments in the embedded ultrasonic acousto-elastic method offer fast diagnosis of bolted joints and opportunities for locating the fault. However, in current acousto-elastic measurement procedures, a baseline representing the healthy condition of the joint is necessary. To mitigate a requirement of the baseline, a new methodology based on relative amplitude and phase measurements is developed. The approach has been validated on laboratory specimens, and modifications were suggested for applications in realistic structures. The paper discusses principles of the baseline-free acoustoelastic method, its practical realization, and respective advantages and disadvantages. Comparison of baseline and baseline-free approaches is presented showing the utility of the recently proposed methodology. Fundamentals of the acousto-elastic response were studied in experiments involving guided wave propagation in a thin plate under tension. The results indicate a difference between acousto-elastic responses collected using sensors oriented parallel and perpendicular to the applied stress. It is suggested that this effect may be used to infer stress orientation in the sample. Practical issues related to acousto-elastic measurements in realistic complex structures are discussed, damage diagnosis algorithms are presented, and potential extensions of the acousto-elastic technique are proposed.
Laser speckle micro-rheology for biomechanical evaluation of breast tumors(Conference Presentation) (2016)

The stiffness of the extra cellular matrix (ECM) is recognized as a key regulator of cancer cell proliferation, migration and invasion. Therefore technologies that quantify ECM stiffness with micro-scale scale resolution will likely provide important insights into neoplastic progression. Laser Speckle Micro-Rheology (LSM) is a novel optical tool for measuring tissue viscoelastic properties with micro-scale resolution. In LSM, speckle images are collected through an objective lens by a high-speed camera. Spatio-temporal correlation analysis of speckle frames yields the intensity autocorrelation function, g2(t), for each pixel, and subsequently a 2D map of viscoelastic modulus, G*(ω) is reconstructed. Here, we investigate the utility of LSM for micro-mechanical evaluation of the ECM in human breast lesions. Specimens collected 18 women undergoing lumpectomy or mastectomy were evaluated with LSM. Because collagen is the key protein associated with ECM stiffness, G*(ω) maps obtained from LSM were compared with collagen content measured by second harmonic generation (SHG) microscopy. Regions of low G*(ω), identified by LSM, corresponded to low-intensity SHG signal and adipose tissue. Likewise, regions with high G*(ω) in LSM images matched high intensity SHG signal caused by desmoplastic collagen accumulation. Quantitative regression analysis demonstrated a strong, statistically significant correlation between G*(ω) and SHG signal intensity (R=0.66 p< 0.01). These findings highlight the capability of LSM for quantifying the ECM micro-mechanics, potentially providing important insights into the biomechanical regulators of breast cancer progression.
Identification of Purine-Scaffold Small-Molecule Inhibitors of Stat3 Activation by QSAR Studies (2010)

To facilitate the discovery of clinically useful Stat3 inhibitors, computational analysis of the binding to Stat3 of the existing Stat3 dimerization disruptors and quantitative structure-activity relationships (QSAR) were pursued, by which a pharmacophore model was derived for predicting optimized Stat3 dimerization inhibitors. The 2,6,9-trisubstituted-purine scaffold was functionalized in order to access the three subpockets of the Stat3 SH2 domain surface and to derive potent Stat3-binding inhibitors. Select purine scaffolds showed good affinities (K(D), 0.8-12 μM) for purified, nonphosphorylated Stat3 and inhibited Stat3 DNA-binding activity in vitro and intracellular phosphorylation at 20-60 μM. Furthermore, agents selectively suppressed viability of human prostate, breast and pancreatic cancer cells, and v-Src-transformed mouse fibroblasts that harbor aberrant Stat3 activity. Studies herein identified novel small-molecule trisubstituted purines as effective inhibitors of constitutively active Stat3 and of the viability of Stat3-dependent tumor cells, and are the first to validate the use of purine bases as templates for building novel Stat3 inhibitors.
Scanning optical microscope (1980)

The scanning optical microscope uses a laser spot to examine a specimen. This technique improves on the resolution and contrast of the conventional microscope, and so has particular advantages for the study of semiconductor materials and devices and living biological specimens
An mHealth Tool Suite for Mobility Assessment (2016)

The assessment of mobility and functional impairments in the elderly is important for early detection and prevention of fall conditions. Falls create serious threats to health by causing disabling fractures that reduce independence in the elderly. Moreover, they exert heavy economic burdens on society due to high treatment costs. Modern smartphones enable the development of innovative mobile health (mHealth) applications by integrating a growing number of inertial and environmental sensors along with the ever-increasing data processing and communication capabilities. Mobility assessment is one of the promising mHealth application domains. In this paper, we introduce a suite of smartphone applications for assessing mobility in the elderly population. The suite currently includes smartphone applications that automate and quantify the following standardized medical tests for assessing mobility: Timed Up and Go (TUG), 30-Second Chair Stand Test (30SCS), and 4-Stage Balance Test (4SBT). For each application, we describe its functionality and a list of parameters extracted by processing signals from smartphone’s inertial sensors. The paper shows the results from studies conducted on geriatric patients for TUG tests and from experiments conducted in the laboratory on healthy subjects for 30SCS and 4SBT tests.
An information-theoretic, vector-space-model approach to cross-language information retrieval (2011)

Abstract In this article, we demonstrate several novel ways in which insights from information theory (IT) and computational linguistics (CL) can be woven into a vector-space-model (VSM) approach to information retrieval (IR). Our proposals focus, essentially, on three areas: pre-processing (morphological analysis), term weighting, and alternative geometrical models to the widely used term-by-document matrix. The latter include (1) PARAFAC2 decomposition of a term-by-document-by-language tensor, and (2) eigenvalue decomposition of a term-by-term matrix (inspired by Statistical Machine Translation). We evaluate all proposals, comparing them to a ‘standard’ approach based on Latent Semantic Analysis, on a multilingual document clustering task. The evidence suggests that proper consideration of IT within IR is indeed called for: in all cases, our best results are achieved using the information-theoretic variations upon the standard approach. Furthermore, we show that different information-theoretic options can be combined for still better results. A key function of language is to encode and convey information, and contributions of IT to the field of CL can be traced back a number of decades. We think that our proposals help bring IR and CL more into line with one another. In our conclusion, we suggest that the fact that our proposals yield empirical improvements is not coincidental given that they increase the theoretical transparency of VSM approaches to IR; on the contrary, they help shed light on why aspects of these approaches work as they do.
Abstract 3523: A high-throughput screening strategy for the identification of novel lymphoproliferative elements (2019)

Abstract Introduction - Chimeric Antigen Receptor (CAR) T-cell therapy is effective against certain leukemias and lymphomas and shows promise for other incurable malignancies. Considerable challenges remain however to expand this platform technology beyond transplant-oriented hospital care. Centralized manufacturing of genetically modified T cells, lymphodepleting chemotherapy and patient management of current CAR-T therapies are associated with significant costs and treatment complexity. As a first step to reduce this treatment complexity, the present study describes a high throughput combinatorial domain library screening method to identify synthetic lymphoproliferative elements capable of driving in vivo expansion and survival of CAR-T cells in a lymphoreplete host without the homeostatic proliferation signals generated by lymphodepleting chemotherapy. Methods - High-diversity semi-rationally-designed combinatorial libraries of putative lymphoproliferative protein subdomains were DNA barcoded and assembled into a lentiviral vector co-expressing a ROR2-targeted CAR. Human PBMC were transduced with the library and cultured in vitro for several days. Purified cells were injected into mice bearing xenograft tumors modified to express the ROR2 antigen and compared to unmodified xenograft controls. The expansion rate of integrated cells was monitored weekly by quantitative PCR and, after 21 days of exposure, genomic DNA was isolated from blood, spleen and xenograft tumor tissues. Enriched barcodes were amplified using PCR and amplicons were subjected to HiSeq Next-Generation Sequencing. Barcode decoding was achieved using PacBio long read sequencing analysis to align full-length construct sequences with barcode quantitation. Results - Using this approach, putative CAR-T cell driver candidates and common key protein subdomains were identified that support selective in vivo expansion and survival of human lymphocytes in a tumor-bearing mouse model. Conclusion - Taken together, these results demonstrate that a high throughput combinatorial screening strategy with quantitative bioinformatics is a viable method for identifying protein domain combinations capable of selectively driving human CAR-T cells in vivo. These small synthetic combinatorial protein domains may facilitate lymphodepleting chemotherapy-free regimens and lower CAR-T cell doses in the future. Citation Format: Laurence Jadin, Hiba Shaban, Anirban Kundu, Gregory Schreiber, Scooter Willis, Farzad Haerizadeh, James Onuffer, Gregory Frost. A high-throughput screening strategy for the identification of novel lymphoproliferative elements [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3523.
ChemInform Abstract: Solid‐State Cathode Materials for Lithium Batteries: Effect of Synthesis Temperature on the Physical and Electrochemical Properties of Silver Vanadium Oxide. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
State based multiple channel selection in multi-channel wireless networks (2011)

In this paper, we present an innovative scheme to favor the selection of M out of N available high-performing channels in multi-channel wireless networks through the application of states to individual channels. One channel selection scheme is random selection, which can lead to poor network performance when one or more data channels are disadvantaged. This is due to the inability of random selection to discriminate between high performing and disadvantaged channels. The novel proposed channel selection scheme is shown to perform nearly as well as the highest performing of N channels when one or more channels are disadvantaged. We develop a Markov-chain-based theoretical model and then present simulation results validating a significant performance increase of the proposed channel selection scheme.
A novel integrated optimal battery energy management control architecture considering multiple storage functions (2014)

In this paper we proposes a complete battery energy storage management scheme that include three functions of energy storage a) energy arbitrage b) PV smoothing c) voltage regulation. The proposed methodology enhances coordination of ancillary services applications like voltage support with Energy Time Shift (ETS) and Renewables Capacity Firming (RCF) applications and thus provides much higher value for battery energy storage devices. The design is tested on an EMTP simulation platform which indicates that the proposed architecture provides optimal control strategy for grid level storage for various functions proposed.
Neuregulin/ErbB Signaling Regulates Cardiac Subtype Specification in Differentiating Human Embryonic Stem Cells (2010)

NRG-1β/ErbB signaling regulates the ratio of nodal- to working-type cells in differentiating hESC-CM cultures and presumably functions similarly during early human heart development. We speculate that, by manipulating NRG-1β/ErbB signaling, it will be possible to generate preparations of enriched working-type myocytes for infarct repair, or, conversely, nodal cells for potential use in a biological pacemaker.