gebhart/patrepeval huggingface dataset:
Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp. (2015)

High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.
On Speed Estimation from Incremental Encoders with Tunable Error Bounds (2021)

In many mechatronics applications, the knowledge of the rotational velocity of a shaft is a key feature and it may result into a fundamental measurement for control and safety. To this aim, encoders are now the leading speed sensing technology, because of their simple rationale and the reduced cost. To overcome the intrinsic limitations of such a technology, sophisticated techniques have been developed, which can enhance the speed estimation accuracy. As a drawback, significant computational burden is needed. In this paper, we propose a novel switching technique that guarantees both the boundedness of the velocity estimation error and the practical implementation on commercial devices. Experimental results are additionally provided to demonstrate the estimation improvement of the proposed approach with respect to other available techniques.
Integrative proteomic and gene expression analysis identify potential biomarkers for adjuvant trastuzumab resistance: analysis from the Fin-her phase III randomized trial (2015)

Trastuzumab is a remarkably effective therapy for patients with human epidermal growth factor receptor 2 (HER2)--positive breast cancer (BC). However, not all women with high levels of HER2 benefit from trastuzumab. By integrating mRNA and protein expression data from Reverse-Phase Protein Array Analysis (RPPA) in HER2-positive BC, we developed gene expression metagenes that reflect pathway activation levels. Next we assessed the ability of these metagenes to predict resistance to adjuvant trastuzumab using gene expression data from two independent datasets.10 metagenes passed external validation (false discovery rate [fdr] < 0.05) and showed biological relevance with their pathway of origin. These metagenes were further screened for their association with trastuzumab resistance. An association with trastuzumab resistance was observed and validated only for the AnnexinA1 metagene (ANXA1). In the randomised phase III Fin-her study, tumours with low levels of the ANXA1 metagene showed a benefit from trastuzumab (multivariate: hazard ratio [HR] for distant recurrence = 0.16[95%CI 0.05-0.5]; p = 0.002; fdr = 0.03), while high expression levels of the ANXA1 metagene were associated with a lack of benefit to trastuzmab (HR = 1.29[95%CI 0.55-3.02]; p = 0.56). The association of ANXA1 with trastuzumab resistance was successfully validated in an independent series of subjects who had received trastuzumab with chemotherapy (Log Rank; p = 0.01).In conclusion, in HER2-positive BC, some proteins are associated with distinct gene expression profiles. Our findings identify the ANXA1metagene as a novel biomarker for trastuzumab resistance.
A Personal Tribute to Frank A. Gotch and Lee W. Henderson, Giants in Dialysis and in Life (2017)

FIGURE 2. Thouarella brucei Thomson and Ritchie, 1906, lectotype (NMS.Z.1921.143.1298): A, whole colony; B, detail of a branchlet.
Practical Attacks Against Privacy and Availability in 4G/LTE Mobile\n Communication Systems (2015)

Mobile communication systems now constitute an essential part of life\nthroughout the world. Fourth generation "Long Term Evolution" (LTE) mobile\ncommunication networks are being deployed. The LTE suite of specifications is\nconsidered to be significantly better than its predecessors not only in terms\nof functionality but also with respect to security and privacy for subscribers.\n We carefully analyzed LTE access network protocol specifications and\nuncovered several vulnerabilities. Using commercial LTE mobile devices in real\nLTE networks, we demonstrate inexpensive, and practical attacks exploiting\nthese vulnerabilities. Our first class of attacks consists of three different\nways of making an LTE device leak its location: A semi-passive attacker can\nlocate an LTE device within a 2 sq.km area within a city whereas an active\nattacker can precisely locate an LTE device using GPS co-ordinates or\ntrilateration via cell-tower signal strength information. Our second class of\nattacks can persistently deny some or all services to a target LTE device. To\nthe best of our knowledge, our work constitutes the first publicly reported\npractical attacks against LTE access network protocols.\n We present several countermeasures to resist our specific attacks. We also\ndiscuss possible trade-offs that may explain why these vulnerabilities exist\nand recommend that safety margins introduced into future specifications to\naddress such trade-offs should incorporate greater agility to accommodate\nsubsequent changes in the trade-off equilibrium.\n
Functional characterization and development of novel human kinase insert domain receptor chimeric antigen receptor T-cells for immunotherapy of non-small cell lung cancer (2022)

CAR-T cell therapy, in which T cells are transfected or transduced with a chimeric antigen receptor (CAR), is a transformative type of cancer immunotherapy. Despite outstanding success in hematological malignancies, their efficacy against solid tumors has been limited. Here, we aimed to explore whether T cells modified by a CAR targeting the vascular endothelial growth factor 2 receptor/ kinase insert domain receptor (KDR) could destroy tumors and their vasculature. A second-generation KDR-CAR was constructed and transfected into T cells using lentivirus. The 3D structure of the CAR construct and target antigen was predicted. Moreover, in silico analysis, including molecular docking and molecular dynamics (MD) simulation, were used to evaluate the minimum energy of interaction and stability of the complex. The anti-cancer effect of KDR-specific CAR-T cells was tested with KDR-expressing and KDR overexpressing A549 cell line. The in-silico study suggested that this CAR construct could be effective for lung cancer therapy. We evaluated this using both in vitro and in vivo experiments. The KDR-CAR-T cells targeted and killed KDR-A549 with high efficiency by expressing IFN-γ and releasing granzyme B. The in vivo study showed that KDR-CAR-T cells dramatically inhibited the growth of lung cancer KDR-A549 xenografts in BALB/c-nu mice at day 10. The characterization of T cells modified by KDR-CAR by computational biology and wet-lab experiments suggested its applicability as a new treatment strategy for lung cancer and, potentially, for other vascularized solid tumors.
Discriminative training of n-gram classifiers for speech and text routing (2003)

We present a method for conditional maximum likelihood estimation of N-gram models used for text or speech utterance classification. The method employs a well known technique relying on a generalization of the Baum-Eagon inequality from polynomials to rational functions. The best performance is achieved for the 1-gram classifier where conditional maximum likelihood training reduces the class error rate over a maximum likelihood classifier by 45% relative.
Characterization of Infrared Matrix-Assisted Laser Desorption Ionization Samples by Fourier Transform Infrared Attenuated TotalReflection Spectroscopy (2004)

Fourier transform infrared attenuated total reflection (FT-IR ATR) spectroscopy was used to characterize thin films of succinic acid, a matrix compound commonly used with infrared matrix-assisted laser desorption ionization (IR-MALDI) mass spectrometry. IR spectra of succinic acid thin films deposited alone and in combination with the analyte biomolecules insulin and cytochrome c were obtained by FT-IR ATR spectroscopy. Spectra of analyte and matrix alone were similar to those obtained previously from KBr pellets, Nujol mull, or thin-film absorption, although the ATR spectra have significantly lower background interferences. Thin films deposited from mixtures of water and methanol have additional peaks compared to films deposited from a methanol solution. These additional peaks are attributed to carboxylate groups stabilized by residual water molecules. No evidence was found to suggest that residual water absorption contributes to absorption at wavelengths typically used for IR-MALDI. Absorption of energy by analyte vibrational modes with rapid energy transfer to the matrix is suggested as a contributor to desorption and ionization consistent with the FT-IR ATR results.
Organic electroluminescent devices using europium complex‐doped poly(N‐vinylcarbazole) (2004)

Abstract Electroluminescence (EL) properties of europium (Eu) complex‐doped poly( N ‐vinylcarbazole) (PVK) were investigated. A device structure of glass substrate/indium‐tin oxide/hole‐injection layer/Eu complex‐doped PVK/hole‐blocking layer/electron transport layer/electron‐injection layer/Al was employed. Red emission originating from Eu complex was observed. Relatively high luminance of 50 cd/m 2 and an efficiency of 0.2% were obtained. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Spreading of a Herschel-Bulkley fluid using lubrication approximation (2014)

In this work the flow of 1.5% Carbopol-940 solution was studied as it was transported through a wedge-like system at different angles, entrance heights, exit heights, and velocities. The high-speed video recordings of the flow were processed by tracking air bubbles entrapped in the solution. This data was used to find the velocity field of the solution beneath the wedge. Also, the force imposed by the solution on the inclined top plate of the wedge was measured. The theoretical description in the framework of the lubrication approximation for Newtonian fluids was used for comparison to the experimental results. It was found that Herschel-Bulkley fluids exhibit qualitatively similar behavior to the Newtonian fluid, such as the reverse flow near the top of the wedge. Overall, this work proves that the lubrication approximation can be effectively used to characterize the flow field of non-Newtonian Herschel-Bulkley fluids at the wedge angles at least up to 20 degrees.
Thermally Stable N2-Intercalated WO3 Photoanodes for Water Oxidation (2012)

We describe stable intercalation compounds of the composition xN(2)·WO(3) (x = 0.034-0.039), formed by trapping N(2) in WO(3). The incorporation of N(2) significantly reduced the absorption threshold of WO(3); notably, 0.039N(2)·WO(3) anodes exhibited photocurrent under illumination at wavelengths ≤640 nm with a faradaic efficiency for O(2) evolution in 1.0 M HClO(4)(aq) of nearly unity. Spectroscopic and computational results indicated that deformation of the WO(3) host lattice, as well as weak electronic interactions between trapped N(2) and the WO(3) matrix, contributed to the observed red shift in optical absorption. Noble-gas-intercalated WO(3) materials similar to xN(2)·WO(3) are predicted to function as photoanodes that are responsive to visible light.
Multiplexed analysis of a single EV (MASEV) reveals unique biomarker composition with diagnostic impact (2022)

Abstract Exosomes and extracellular vesicles (EV) are increasingly being explored as circulating biomarkers, but their heterogenous composition will likely mandate the development of single EV technologies. Highly multiplexed analyses of single EVs have been challenging to implement beyond a few colors during spectral sensing. We use a multiplexed analysis of the single EV technique (MASEV) to interrogate thousands of individual EVs during 5 cycles of multi-channel fluorescence staining for 15 EV biomarkers. Contrary to the common belief, we show that i) several “ubiquitous” markers are much less common than believed; ii) that multiple biomarkers concur in single vesicles but only in small fractions, iii) that affinity purification can lead to loss of rare EV subtypes, and iv) that deep profiling allows detailed analysis of EV potentially improving the diagnostic content. These findings establish the potential of MASEV for uncovering fundamental EV biology and heterogeneity and increasing diagnostic specificity. Abstract Figure Graphical abstract Multiplexed analysis of single EV (MASEV) allows robust protein profiling at the single EV level, a prerequisite for early cancer detection or organ of origin determination.
An Exact Expression for Lommel's Diffraction Integral (1974)

A number of authors have obtained diffraction corrections for a circular piston source by numerical or graphical integration of an approximate expression for the piston field attributable to E. Lommel [Abhandl. Bayer. Akad. Wiss. 15, 233 (1886)]. Lommel's expression gives the piston field in terms of trigonometric functions and Lommel functions of two variables, the latter being defined as infinite sums involving cylindrical Bessel functions. It is shown here that the required integral of Lommel's expression can be evaluated analytically to obtain a simple closed form expression for the diffraction correction. The extrema of this expression are obtained as roots of simple transcendental equations. It is also shown that the same expression can be obtained by taking the limit as ka → ∞ (where k is the wavenumber and a is the piston radius) of Williams's exact integral expression for the diffraction correction [J. Acoust. Soc. Am. 23, 1 (1951)]. Finally, it is shown both analytically and by numerical integration of Williams's exact expression that the simple closed form expression is a good approximation for all distances from the source provided that (ka)12 ≫ l.
Observation of the Stimulated Quantum Cherenkov Effect (2020)

We present the first observation of the quantum nature of the Cherenkov effect, by phasematching light &amp; electron waves. Interacting coherently along hundreds of microns, each electron simultaneously absorbs and emits hundreds of photon quanta.
Interfacial impedance based electrochemical detection of carbon dioxide using RTIL (2016)

Current challenges in CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> gas sensors include stable signal to noise ratio (SNR), drifting sensor performance due to environmental factors, selectivity of sensing element in varying test matrices. We performed an evaluation of materials and sensor element design to address these challenges. We report effective utilization of room temperature ionic liquids (RTILs) in developing electrochemical CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> sensors offering unique value for commodity applications. In this study, we have characterized RTILs with different anionic groups for varying concentrations of CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> from 400 ppm to 1000 ppm using gold electrodes and carbon paste electrodes (CPE) on printed circuit board (PCB) substrates. This analysis was carried out using electrochemical impedance spectroscopy (EIS) and helped in identification of robust performing combination of RTIL and electrode material for environmental CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> sensing.
Oxygen adsorption on aNbC0.9(111) surface: Angle-resolved photoemission study (1991)

Angle-resolved photoemission spectroscopy utilizing synchrotron radiation has been used to study the adsorption of oxygen on a NbC(111) surface at 80 K. Oxygen is adsorbed dissociatively forming a (1\ifmmode\times\else\texttimes\fi{}1) overlayer on the NbC(111) surface. The O 2p--derived states are found at 1.0 and 2.6 eV below the Fermi level in normal-emission spectra. From polarization-dependent measurements, these states are assigned to the 2${\mathit{p}}_{\mathit{z}}$- and 2${\mathit{p}}_{\mathit{x},}$y-derived states, respectively. Two-dimensional band dispersions in the \ensuremath{\Gamma}\ifmmode\bar\else\textasciimacron\fi{}--M\ifmmode\bar\else\textasciimacron\fi{} direction of these states are determined from the off-normal-emission measurements. The experimentally determined dispersive features of the 2${\mathit{p}}_{\mathit{z}}$- and 2${\mathit{p}}_{\mathit{x},}$y-derived states can be understood in terms of a simple tight-binding picture.
Immunotherapy of glioblastoma multiforme (2003)

Glioblastoma multiforme is immunogenic and several glioblastoma multiforme-related antigens have now been identified. In addition, the immunologic characteristics of the tumor microenvironment that may affect tumor growth are becoming increasingly understood. The type of immune-based approach selected to treat glioblastoma multiforme will depend on the tumor burden. For minimal disease states, active vaccination may be useful for generating adequate protection from relapse. However, for more advanced stage disease states, more rigorous strategies may need to be applied, such as adoptive T-cell therapy, antibody therapy or a combination of different techniques. The immunosuppressive environment observed during advanced malignancy may need to be reversed for improved efficacy of immune-based therapies.
Supplementary Figure Legend from Phase I Trial of Overlapping Long Peptides from a Tumor Self-Antigen and Poly-ICLC Shows Rapid Induction of Integrated Immune Response in Ovarian Cancer Patients (2023)

&lt;p&gt;PDF file - 68K&lt;/p&gt;
GaN blue vertical-cavity surface-emitting lasers using conductive nanoporous distributed Bragg reflectors (2021)

Due to their unique properties, III-nitride vertical -cavity surface-emitting lasers (VCSELs) are expected to enable several applications ranging across communication, sensing and ranging and spectroscopy. Their technological feasibility however has been hindered by the lack of an electrically conductive, easily manufacturable, wide reflection stopband distributed Bragg reflector (DBR) to serve as the bottom reflector. Here we present the first electrically injected III-nitride VCSEL on an electrically conductive DBR using nanoporous (NP) GaN operating at roomtemperature. The measured threshold current density and the maximum light output power were 42 kA/cm<sup>2</sup> and 0.17 mW, respectively, at 434 nm. Due to the electrical conductivity of the bottom NP GaN DBR, vertical injection was demonstrated and compared with intracavity injection. No change in the threshold current density, the slope efficiency or nearfield pattern was observed demonstrating the feasibility of efficient vertical injection in NP GaN VCSELs. Filamentary lasing was observed within the VCSEL aperture and its correlation with the lasing linewidth was studied.
Target variant detection in leukemia using unaligned RNA-Seq reads (2018)

Abstract Mutations identified in each Acute Myeloid Leukemia (AML) patients are useful for prognosis and to select targeted therapies. Detection of such mutations by the analysis of Next-Generation Sequencing (NGS) data requires a computationally intensive read mapping step and application of several variant calling methods. Targeted mutation identification drastically shifts the usual tradeoff between accuracy and performance by concentrating all computations over a small portion of sequence space. Here, we present km, an efficient approach leveraging k-mer decomposition of reads to identify targeted mutations. Our approach is versatile, as it can detect single-base mutations, several types of insertions and deletions, as well as fusions. We used two independent AML cohorts (The Cancer Genome Atlas and Leucegene), to show that mutation detection by km is fast, accurate and mainly limited by sequencing depth. Therefore, km allows to establish fast diagnostics from NGS data, and could be suitable for clinical applications.
Pore Morphologies in Disordered Nanoporous Thin Films (2003)

Materials with nanometer size heterogeneities are commonplace in the chemical and biological sciences (e.g, polymer blends, microemulsions, gels) and often exhibit complex morphologies. Although this morphology has a dramatic effect on the materials' properties, it is often difficult to accurately characterize. We describe a method, using small-angle X-ray scattering data, of generating representative three-dimensional morphologies of isotropic two-phase materials where the morphology is disordered, and we apply this to thin films containing nanometer sized pores with a range of porosities (4-44%). These representations provide a visualization of the pore morphology, give the pore size scale and extent of interconnection, and permit the determination of the transitions from closed pore to interconnected pores to bicontinuous morphology.
Dynamics of a coplanar-electrode plasma display panel. II. Cell optimization (1999)

Plasma display panels (PDPs) are a leading technology for large-area flat panel displays. As a result, there is significant interest in improving their efficiency, luminosity, and lifetime. In this article, results from a two-dimensional model are used to investigate the consequences of operating conditions, gas mixture, cell dimensions, and material properties on the visible light generation capacity (luminosity and efficiency) of a coplanar-electrode PDP cell sustained in He/Ne/Xe gas mixtures. Of the species that dominantly lead to the generation of visible light (Xe*, Xe**, and Xe2*), Xe2* makes the largest contribution for our conditions since its UV radiation is optically thin and Xe2* is efficiently generated from the long-lived xenon metastable. Significant improvements could be made in PDP light generation efficiency by choosing operating conditions that favor production of Xe2*, such as increasing gas pressure to enhance the three-body collision processes that generate Xe2*. Gas mixtures with more Ne (or less He) were found to produce more visible light at higher efficiency since electron transport in Ne is less collisional than He and Xe2* is produced more efficiently in three body collisions with Ne. PDP light emission characteristics are sensitive to the spacing between the dielectrics and there is an optimum spacing where both total visible light output and efficiency are high. It was found that PDP cells do not generate visible light efficiently during the postavalanche discharge phase due to low values of E/N (electric field/total gas density) in the bulk plasma region. Slight improvements can be made in light generation efficiency be choosing conditions for which PDP cell spends less time in the discharge phase in each cycle.