gebhart/patrepeval huggingface dataset:
Inheritance and genetic mapping of fruit sucrose accumulation in <i>Lycopersicon chmielewskii</i> (1993)

Fruit of the domestic tomato ( Lycopersicon esculentum Mill.) accumulate soluble sugars primarily in the form of the hexoses, glucose and fructose. In contrast, the predominant sugar in fruit of the wild tomato relative, L. chmielewskii , is sucrose. In the present study, the inheritance and linkage relations of sucrose accumulation were examined in interspecific L. esculentum x L. chmielewskii populations. In backcrosses to either the wild or domestic tomato, segregation for sucrose accumulation permitted qualitative analysis of the trait and indicated monogenic recessive control, although deviations from Mendelian inheritance were observed in some populations. This major gene, designated sucr , was mapped in F 2 , F 3 , and BC 1 F 2 populations using a set of 95 informative RFLP and isozyme markers covering the tomato genome. A map location near the centromere of chromosome 3 was established, with tight linkage to the genomic clone TG102. Association of sucrose accumulation with yellow fruit, encoded by an allele of the r gene, permitted alignment with the classical map, thereby confirming the map location of sucr . A linkage map of the region surrounding sucr was obtained by monitoring recombination between flanking markers in the back‐crosses to tomato. A cDNA clone of tomato fruit acid invertase, TIV1, was mapped to TG102 and sucr , with no recombination between the two RFLP markers observed in over 1700 meiotic products. Despite the tight linkage, TG102 and TIV1 hybridize to distinct restriction fragments, hence do not represent the same gene. The genetic data strongly suggest that sucr is an allele of the invertase gene and thus support previous biochemical studies that demonstrated low invertase activity in sucrose‐accumulating fruit. L. hisutum , another low‐invertase, sucrose‐accumulating species, was hybridized with L. chmielewskii and the resulting F 1 plants accumulated sucrose, indicating that genetic control of soluble sugar composition is conserved in these two species.
Random projections based item authentication (2009)

In this paper, we consider an item authentication using unclonable forensic features of item surface microstructure images (a.k.a. fingerprints). The advocated authentication approach is based on the source coding jointly with the random projections. The source coding ensures the source reconstruction at the decoder based on the authentication data. The random projections are used to cope with the security, privacy, robustness and complexity issues. Finally, the authentication is accomplished as a binary hypothesis testing for both direct and random projections domains. The asymptotic performance approximation is derived and compared with the exact solutions.
The SMS3D photovoltaic concentrator (2008)

A novel photovoltaic concentrator is presented. The goal is to achieve high concentration design with high efficiency and high acceptance angle that in the same time is compact and convenient for thermal and mechanical management [1]. This photovoltaic system is based on 1 cm<sup>2</sup> multi-junction tandem solar cells and an XR concentrator. The XR concentrator in this system is an SMS 3D design formed by one reflective (X) and one refractive (R) free-form surfaces (i.e., without rotational or linear symmetry) and has been chosen for its excellent aspect ratio and for its ability to perform near the thermodynamic limit. It is a mirror-lens device that has no shadowing elements and has square entry aperture (the whole system aperture area is used for collecting light). This large acceptance angle relaxes the manufacturing tolerances of all the optical and mechanical components of the system included the concentrator itself and is one of the keys to get a cost competitive photovoltaic generator. For the geometrical concentration of 1000x the simulation results show the acceptance angle of ±1.8 deg. The irradiance distribution on the cell is achieved with ultra-short homogenizing prism, whose size is optimised to keep the maximum values under the ones that the cell can accept. The application of the XR optics to high-concentration is being developed in a consortium leaded by The Boeing Company, which has been awarded a project by US DOE in the framework of the Solar America Initiative.
Gabor Cube Selection Based Multitask Joint Sparse Representation for Hyperspectral Image Classification (2016)

The large amount of spectral and spatial information contained in hyperspectral imagery has provided great opportunity to effectively characterize and identify the surface materials of interest. As a novel feature extraction technique, a series of Gabor wavelet filters with different scales and frequencies was applied on hyperspectral data to extract spectral-spatial-combined features, which produced impressive performance on pixel-oriented classification. However, the incredibly large number of Gabor features could cause too much burden for onboard computation, limiting the efficiency of the method. To make matters worse, due to the nonhomogeneous spatial distribution of materials as well as the different characteristics of the constructed Gabor filters, some Gabor features could have a smaller or even negative impact on material representation, deteriorating the classification accuracy eventually. In this paper, a Gabor cube selection based multitask joint sparse representation approach, abbreviated as GS-MTJSRC, was proposed for hyperspectral image classification. First, based on the Fisher discrimination criterion, the most representative Gabor cubes for each class were picked out. Next, under multitask joint sparse representation framework, a coefficient vector could be obtained for each test sample with the selected Gabor cube features, which could be directly used for the following residual-based classification. Experimental results on three real hyperspectral data sets with different characteristics and spatial resolutions demonstrated the feasibility and efficiency of the proposed method.
Supraphysiologic control over HIV-1 replication mediated by CD8 T cells expressing a re-engineered CD4-based chimeric antigen receptor (2017)

HIV is adept at avoiding naturally generated T cell responses; therefore, there is a need to develop HIV-specific T cells with greater potency for use in HIV cure strategies. Starting with a CD4-based chimeric antigen receptor (CAR) that was previously used without toxicity in clinical trials, we optimized the vector backbone, promoter, HIV targeting moiety, and transmembrane and signaling domains to determine which components augmented the ability of T cells to control HIV replication. This re-engineered CAR was at least 50-fold more potent in vitro at controlling HIV replication than the original CD4 CAR, or a TCR-based approach, and substantially better than broadly neutralizing antibody-based CARs. A humanized mouse model of HIV infection demonstrated that T cells expressing optimized CARs were superior at expanding in response to antigen, protecting CD4 T cells from infection, and reducing viral loads compared to T cells expressing the original, clinical trial CAR. Moreover, in a humanized mouse model of HIV treatment, CD4 CAR T cells containing the 4-1BB costimulatory domain controlled HIV spread after ART removal better than analogous CAR T cells containing the CD28 costimulatory domain. Together, these data indicate that potent HIV-specific T cells can be generated using improved CAR design and that CAR T cells could be important components of an HIV cure strategy.
Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community (2014)

This study characterized in detail twenty-one cellulose-degrading enzymes derived from a thermophilic microbial community and found that 70% of them were [C2mim][OAc]-tolerant. A comparison of optimum temperature and [C2mim][OAc]-tolerance demonstrates that a positive correlation exists between these properties for those enzymes with a optimum temperature >70°C, further strengthening the link between thermotolerance and IL-tolerance for lignocelluolytic glycoside hydrolases.
Holography: The Usefulness of Digital Holographic Microscopy for Clinical Diagnostics (2017)

Digital holographic (DH) microscopy is a digital high-resolution holographic imaging technique with the capacity of quantification of cellular conditions without any staining or labeling of cells. The unique measurable parameters are the cell number, cell area, thickness, and volume, which can be coupled to proliferation, migration, cell cycle analysis, viability, and cell death. The technique is cell friendly, fast and simple to use and has unique imaging capabilities for time-lapse investigations on both the single cell and the cell-population levels. The interest for analyzing specifically cell volume changes with DH microscopy, resulting from cytotoxic treatments, drug response, or apoptosis events has recently increased in popularity. We and others have used DH microscopy showing that the technique has the sensitivity to distinguish between different cells and treatments. Recently, DH microscopy has been used for cellular diagnosis in the clinic, providing support for using the concept of DH, e.g., screening of malaria infection of red blood cells (RBC), cervix cancer screening, and sperm quality. Because of its quick and label-free sample handling, DH microscopy will be an important tool in the future for personalized medicine investigations, determining the optimal therapeutic concentration for both different cancer types and individual treatments.
Pregel (2010)

Many practical computing problems concern large graphs. Standard examples include the Web graph and various social networks. The scale of these graphs - in some cases billions of vertices, trillions of edges - poses challenges to their efficient processing. In this paper we present a computational model suitable for this task. Programs are expressed as a sequence of iterations, in each of which a vertex can receive messages sent in the previous iteration, send messages to other vertices, and modify its own state and that of its outgoing edges or mutate graph topology. This vertex-centric approach is flexible enough to express a broad set of algorithms. The model has been designed for efficient, scalable and fault-tolerant implementation on clusters of thousands of commodity computers, and its implied synchronicity makes reasoning about programs easier. Distribution-related details are hidden behind an abstract API. The result is a framework for processing large graphs that is expressive and easy to program.
Association of BRCA1/2defects with genomic scores predictive of DNA damage repair deficiency among breast cancer subtypes (2014)

The HRD scores showed strong correlation with BRCA1/2 deficiency regardless of breast cancer subtype. The frequency of elevated scores suggests that a significant proportion of all breast tumor subtypes may carry defects in the homologous recombination DNA repair pathway. The HRD scores can be combined to produce a more robust predictor of HRD. The combination of a robust score, and the FFPE compatible assay described in this study, may facilitate use of agents targeting homologous recombination DNA repair in the clinical setting.
Stereoselective cobalt-catalysed [2 + 2 + 2] cross-addition of norbornadiene and norbornene (1978)

A cobalt complex, formed by reducing [Co(acac)3](Hacac = acetylacetone) with diethyl-aluminium chloride in the presence of the bidentate ligand bis(1,2-diphenylphosphino)ethane, is an active catalyst for the stereoselective [2 + 2 + 2] cycloaddition of norbornene to norbornadiene.
Sleep disordered breathing detection using heart rate variability and R-peak envelope spectrogram (2009)

We report that combining the interbeat heart rate as measured by the RR interval (RR) and R-peak envelope (RPE) derived from R-peak of ECG waveform may significantly improve the detection of sleep disordered breathing (SDB) from single lead ECG recording. The method uses textural features extracted from normalized gray-level cooccurrence matrices of the time frequency plots of HRV or RPE sequences. An optimum subset of textural features is selected for classification of the records. A multi-layer perceptron (MLP) serves as a classifier. To evaluate the performance of the proposed method, single Lead ECG recordings from 7 normal subjects and 7 obstructive sleep apnea patients were used. With 500 randomized Monte-Carlo simulations, the average training sensitivity, specificity and accuracy were 100.0%, 99.9%, and 99.9%, respectively. The mean testing sensitivity, specificity and accuracy were 99.0%, 96.7%, and 97.8%, respectively.
Segmentation for mixed raster contents with multiple extracted constant color areas (2005)

Mixed Raster Contents (MRC) is a powerful image representation concept in achieving high compression ratios while maintaining high reconstructed image quality. The Multiple Extracted Constant Color Areas (MECCA) model, which is composed of one contone background layer and multiple constant color foreground layers has the advantages of its ease of decomposition and inherent text enhancement and noise reduction features. This paper presents a segmentation algorithm that extracts uniform text and other uniform color objects that carry detail information. The algorithm consists of four steps. First the test and objects are extracted from the image. Next, they are tested for color constancy and other features to decide if they should be represented by the MRC foreground layers. The objects that are chosen are then clustered in color space. The image is finally segmented such that each foreground layer codes the objects from the same color cluster.
PRISC: programmable reduced instruction set computers (1994)

This thesis introduces Programmable Reduced Instruction Set Computers (PRISC) as a new class of general-purpose computers. PRISC use RISC techniques as a base, but in addition to the conventional RISC instruction resources, PRISC offer hardware programmable resources which can be configured based on the needs of a particular application. This thesis presents the architecture, operating system, and programming language compilation techniques which are needed to successfully build PRISC. Performance results are provided for the simplest form of PRISC -- a RISC microprocessor with a set of programmable functional units consisting of only combinational functions. Results for the SPECint92 benchmark suite indicate that an augmented compiler can provide a performance improvement of 22% over the underlying RISC computer with a hardware area investment less than that needed for a 2 kilobyte SRAM. In addition, active manipulation of the source code leads to significantly higher local performance gains (250%-500%) for general abstract data types such as short-set vectors, hash tables, and finite state machines. Results on end-user applications that utilize these data types indicate a performance gain from 32%-213%.
Optical Negative-Index Materials Based on Pairs of Metal Nanorods (2005)

Pairs of gold nanorods exhibit “-0.3” effective refractive index near 1.3 um. This type of artificially designed materials can be used for obtaining negative-index materials and applying them for super-lenses in the visible and near-infrared.
Low-Coherence, Wavelength-Encoded Addressing for Integrated Long-Gauge Length Fiber Optic Strain Sensing (1997)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text R. Posey, A. D. Kersey, M. LeBlanc, and M. Davis, "Low-Coherence, Wavelength-Encoded Addressing for Integrated Long-Gauge Length Fiber Optic Strain Sensing," in 12th International Conference on Optical Fiber Sensors, Vol. 16 of 1997 OSA Technical Digest Series (Optica Publishing Group, 1997), paper OThD3. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Optical resolution of racemic <i>S</i>‐(Carboxymethyl)cysteine (1982)

Abstract Racemic S ‐(carboxymethyl)cysteine [( R, S )‐2] obtained from racemic cysteine is resolved via its ammonium salt ( R, S )‐3 by preferential crystallization procedure. Furthermore, ( R, S )‐2 forms with optically active amines separable, diastereomeric salts. Thus, (1 R ,2 S )‐2‐amino‐1‐phenyl‐1‐propanol ( 4 ) affords optically pure ( R )‐ S ‐(carboxymethyl)cysteine [( R )‐2] in 93% yield. The resolution of ( R, S )‐2 is also possible with ( R )‐1‐phenylethylamine ( 5 ).
Convergent Synthesis of Thioether Containing Peptides (2020)

Thioether containing peptides were obtained following three synthetic routes. In route A, halo acids esterified on 2-chlorotrityl(Cltr) resin were reacted with <i>N</i>-fluorenylmethoxycarbonyl (Fmoc) aminothiols. These were either cleaved from the resin to the corresponding (Fmoc-aminothiol)carboxylic acids, which were used as key building blocks in solid phase peptide synthesis (SPPS), or the <i>N</i>-Fmoc group was deprotected and peptide chains were elongated by standard SPPS. The obtained <i>N</i>-Fmoc protected thioether containing peptides were then condensed either in solution, or on solid support, with the appropriate amino components of peptides. In route B, the thioether containing peptides were obtained by the reaction of <i>N</i>-Fmoc aminothiols with bromoacetylated peptides, which were synthesized on Cltr-resin, followed by removal of the <i>N</i>-Fmoc group and subsequent peptide elongation by standard SPPS. In route C, the thioether containing peptides were obtained by the condensation of a haloacylated peptide synthesized on Cltr-resin and a thiol-peptide synthesized either on 4-methoxytrityl(Mmt) or trityl(Trt) resin.
Antioxidant and Astroprotective Effects of a<i>Pulicaria incisa</i>Infusion (2012)

Oxidative stress is involved in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's diseases. Astrocytes, the most abundant glial cells in the brain, protect neurons from reactive oxygen species (ROS) and provide them with trophic support, such as glial-derived neurotrophic factor (GDNF). Thus, any damage to astrocytes will affect neuronal survival. In the present study, an infusion prepared from the desert plant Pulicaria incisa (Pi) was tested for its protective and antioxidant effects on astrocytes subjected to oxidative stress. The Pi infusion attenuated the intracellular accumulation of ROS following treatment with hydrogen peroxide and zinc and prevented the H(2)O(2)-induced death of astrocytes. The Pi infusion also exhibited an antioxidant effect in vitro and induced GDNF transcription in astrocytes. It is proposed that this Pi infusion be further evaluated for use as a functional beverage for the prevention and/or treatment of brain injuries and neurodegenerative diseases in which oxidative stress plays a role.
First chronic results from a flexible sieve electrode to interface nerves without the need for guidance channels (2002)

Nerves has been previously interfaced with micromachined sieve electrodes for recording and stimulation purposes. In most cases, so-called guidance channels have to be assembled on the sieve to adjust and fix the nerve in the vicinity of the microstructure. In this paper, a new approach of a flexible, polyimide-based sieve electrode is presented. Monolithically integrated fixation flaps offer the opportunity to directly fix the sieve implant on a transected nerve without the need for a guidance channel. The sieve has been fabricated with a thickness of 10 /spl mu/m and chronically implanted between the transected ends of the sciatic nerve of rats. First electrophysiological experiments proved a functional reinnervation and a selective and graded stimulation over ring electrodes around single holes of 40 /spl mu/m diameter in the sieve area.
Synthesis of Diamond Nanowires Using Atmospheric-Pressure Chemical Vapor Deposition (2010)

We report diamond nanowires grown in an atmospheric pressure chemical vapor deposition process. These diamond nanowires are straight, thin and long, and uniform in diameter (60-90 nm) over tens of micrometers. Spectroscopic analysis, electron diffraction, and transmission electron microscopy provided confirmation that these nanowires are diamond with high crystallinity and high structural uniformity. They further revealed that these diamond nanowires are encased within multiwalled carbon nanotubes.
Sulfinylated azadecalins act as functional mimics of a pollen germination stimulant in Arabidopsis pistils (2011)

Polarized cell elongation is triggered by small molecule cues during development of diverse organisms. During plant reproduction, pollen interactions with the stigma result in the polar outgrowth of a pollen tube, which delivers sperm cells to the female gametophyte to effect double fertilization. In many plants, pistils stimulate pollen germination. However, in Arabidopsis, the effect of pistils on pollen germination and the pistil factors that stimulate pollen germination remain poorly characterized. Here, we demonstrate that stigma, style, and ovules in Arabidopsis pistils stimulate pollen germination. We isolated an Arabidopsis pistil extract fraction that stimulates Arabidopsis pollen germination, and employed ultra-high resolution electrospray ionization (ESI), Fourier-transform ion cyclotron resonance (FT-ICR) and MS/MS techniques to accurately determine the mass (202.126 Da) of a compound that is specifically present in this pistil extract fraction. Using the molecular formula (C10H19NOS) and tandem mass spectral fragmentation patterns of the m/z (mass to charge ratio) 202.126 ion, we postulated chemical structures, devised protocols, synthesized N-methanesulfinyl 1- and 2-azadecalins that are close structural mimics of the m/z 202.126 ion, and showed that they are sufficient to stimulate Arabidopsis pollen germination in vitro (30 μm stimulated approximately 50% germination) and elicit accession-specific response. Although N-methanesulfinyl 2-azadecalin stimulated pollen germination in three species of Lineage I of Brassicaceae, it did not induce a germination response in Sisymbrium irio (Lineage II of Brassicaceae) and tobacco, indicating that activity of the compound is not random. Our results show that Arabidopsis pistils promote germination by producing azadecalin-like molecules to ensure rapid fertilization by the appropriate pollen.
β-Lactamase inhibitors: a review of the patent literature (2010 – 2013) (2013)

Research in this field has become increasingly diverse, with several non-β-lactam inhibitor classes now assuming importance. The emphasis has been on finding inhibitors of AmpC, the extended-spectrum β-lactamases and class A and D carbapenemases that can demonstrate synergy with antibiotics against resistant Gram-negative pathogens. Progress has been made. Metallo-β-lactamases (MBL)-mediated resistance, however, represents an unmet challenge. The author believes that it will be extremely difficult to generate a selective, commercially viable MBL inhibitor with sufficient activity against NDM-1 and that alternate design strategies will need to be employed.