gebhart/patrepeval huggingface dataset:
Early Steps in Proanthocyanidin Biosynthesis in the Model Legume <i>Medicago truncatula</i>  (2007)

Oligomeric proanthocyanidins (PAs) composed primarily of epicatechin units accumulate in the seed coats of the model legume Medicago truncatula, reaching maximal levels at around 20 d after pollination. Genes encoding the single Medicago anthocyanidin synthase (ANS; EC 1.14.11.19) and leucoanthocyanidin reductase (LAR; EC 1.17.1.3) were cloned and the corresponding enzymes functionally identified. Recombinant MtANS converted leucocyanidin to cyanidin, and, more efficiently, dihydroquercetin to the flavonol quercetin. Levels of transcripts encoding dihydroflavonol reductase, ANS, and anthocyanidin reductase (ANR), the enzyme responsible for conversion of anthocyanidin to (-)-epicatechin, paralleled the accumulation of PAs in developing seeds, whereas LAR transcripts appeared to be more transiently expressed. LAR, ANS, and ANR proteins were localized to the cytosol in transfected tobacco (Nicotiana tabacum) leaves. Antisense down-regulation of ANS in M. truncatula resulted in reduced anthocyanin and PA levels, but had no impact on flavonol levels. Transgenic tobacco plants constitutively overexpressing MtLAR showed reduced anthocyanin content, but no catechin or increased levels of PAs were detected either in leaves or in flowers. Our results confirm previously ascribed in vivo functions for ANS and ANR. However, the apparent lack of catechin in M. truncatula PAs, the poor correlation between LAR expression and PA accumulation, and the lack of production of catechin monomers or oligomers in transgenic plants overexpressing MtLAR question the role of MtLAR in PA biosynthesis in Medicago.
MSTAR: an absolute metrology system with submicrometer accuracy (2004)

Laser metrology systems are a key component of stellar interferometers, used to monitor path lengths and dimensions internal to the instrument. Most interferometers use 'relative' metrology, in which the integer number of wavelengths along the path is unknown, and the measurement of length is ambiguous. Changes in the path length can be measured relative to an initial calibration point, but interruption of the metrology beam at any time requires a re-calibration of the system. The MSTAR sensor (Modulation Sideband Technology for Absolute Ranging) is a new system for measuring absolute distance, capable of resolving the integer cycle ambiguity of standard interferometers, and making it possible to measure distance with sub-nanometer accuracy. We describe the design of the system, show results for target distances up to 1 meter, and demonstrate how the system can be scaled to kilometer-scale distances. In recent experiments, we have used white light interferometry to augment the 'truth' measurements and validate the zero-point of the system. MSTAR is a general-purpose tool for conveniently measuring length with much greater accuracy than was previously possible, and has a wide range of possible applications.
Rearrangement of Cyclic Ethynylcarbinols. III. A Few Supplementary Reaction with Monocyclic and Bicyclic Terpenoids. (1961)

1) Although 3-ethynylmenthol and 2-ethynylcarbomenthol, among monocyclic compounds of camphor system, have been reported as undergoing Meyer-Schuster rearrangement in the main, the present series of experiments have clarified that the Rupe reaction also progresses in these compounds, same as in 1-ethynylcyclohexanol. 2) 2-Ethynyl-1, 3, 3-trimethyl-2-norborneol undergoes Meyer-Schuster rearrangement by treatment with hydrochloric acid and formic acid, but only the Rupe reaction takes place, accompanied by the Wagner rearrangement, by treatment with sulfuric acid. 3) 1-Methyl-2-ethynylnorborneol undergoes both Meyer-Schuster rearrangement and Rupe reaction, irrespective of the catalyst used. This compound is similar to monocyclic compounds in that it undergoes endocyclic dehydration during the Rupe reaction. 4) 2-Ethynylnorborneol dose not undergo the Meyer-Schuster rearrangement and only the Rupe reaction takes place, similar to monocyclic compounds in general.
KidsArm &#x2014; An image-guided pediatric anastomosis robot (2013)

Minimally invasive surgery (MIS) revolutionized surgery by drastically reducing patient recovery times by allowing surgeons to perform procedures through a series of small incisions. However, MIS has also increased the complexity of the tasks as tools did not have the same degrees of freedom and dexterity compared to open procedures. In particular, pediatric patients pose a unique challenge as they have smaller volumes and different tissue properties. Our group designed KidsArm, an image-guided pediatric surgical robot, to automate anastomosis. KidsArm is single port anastomosis tool that uses a pair of stereo cameras to generate a 3D point cloud to guide the tool tip and apply a series of sutures. The system was designed to be minimally invasive and constrained by standard pediatric trocar sizes while also being automated. An image processing system was created to extract and track surface features on the simulated tissue samples while providing feedback to the robot controller. The system was tested on two scenarios: side-to-side and end-to-end silicone samples. KidsArm successfully applied 3 sutures autonomously on the side-to-side scenario however the end-to-end scenario proved to be more difficult due to greater deformation and workspace restrictions. However, KidsArm demonstrates that it is feasible for a robot to autonomously perform anastomosis. More work will be required to accelerate the process and characterize the behavior with tissue samples.
Characterization of Interleukin-1 Receptor-associated Kinase in Normal and Endotoxin-tolerant Cells (2000)

Interleukin-1 receptor-associated kinase (IRAK), a signal transducer for interleukin-1, has also been suggested to participate in the Toll-like receptor-mediated innate immune response to bacterial endotoxin lipopolysaccharide (LPS). Using the human promonocytic THP-1 cell line, we demonstrated that the endogenous IRAK is quickly activated in response to bacterial LPS stimulation, as measured by its in vitro kinase activity toward myelin basic protein. LPS also triggers the association of IRAK with MyD88, the adaptor protein linking IRAK to the Toll-like receptor/interleukin-1beta receptor intracellular domain. Macrophage cells with prolonged LPS treatment become tolerant to additional dose of LPS and no longer express inflammatory cytokines. Endotoxin tolerance is a common phenomenon observed in blood from sepsis patients. We observed for the first time that the quantity of IRAK is greatly reduced in LPS-tolerant THP-1 cells, and its activity no longer responds to further LPS challenge. In addition, IRAK does not associate with MyD88 in the tolerant cells. Furthermore, application of AG126, a putative tyrosine kinase inhibitor, can substantially alleviate the LPS-induced cytokine gene expression and can also decrease IRAK level and activity. Our study indicates that IRAK is essential for LPS-mediated signaling and that cells may develop endotoxin tolerance by down-regulating IRAK.
<i>sgk1</i>, a member of an RNA cluster associated with cell death in a model of Parkinson's disease (2005)

In an effort to gain deeper insight into the molecular processes underlying neurodegeneration in Parkinson's disease, we performed gene expression profiling at several early time points after MPTP-injection into old (1-year) mice. We used a PCR-based gene expression profiling method, digital expression pattern display (DEPD), a method of very high sensitivity and reproducibility, which displays almost all transcripts of a tissue. To identify cell death-associated genes, we defined clusters of differentially expressed transcripts with expression behaviour that correlated with the temporal profile of cell death progression and characterized one of these cell death clusters further. We selected one of the strongest regulated genes, the serum and glucocorticoid-regulated kinase 1 (sgk1), and validated its differential expression by Northern blot analysis, semiquantitative PCR and in situ hybridization. Up-regulation of sgk1 (i) coincides with the onset of dopaminergic cell death in both the 8-week acute and 1-year subacute MPTP models, (ii) spans the entire brain, (iii) is attenuated by the l-deprenyl-mediated inhibition of the MPTP conversion to its active metabolite MPP+ and (iv) is not induced by dehydration. This study demonstrated that the combination of the DEPD technology, clustering analysis and a detailed histopathology is a useful tool for elucidating molecular pathways in neurodegenerative diseases.
Type-based alias analysis (1998)

This paper evaluates three alias analyses based on programming language types. The first analysis uses type compatibility to determine aliases. The second extends the first by using additional high-level information such as field names. The third extends the second with a flow-insensitive analysis. Although other researchers suggests using types to disambiguate memory references, none evaluates its effectiveness. We perform both static and dynamic evaluations of type-based alias analyses for Modula-3, a statically-typed type-safe language. The static analysis reveals that type compatibility alone yields a very imprecise alias analysis, but the other two analyses significantly improve alias precision. We use redundant load elimination (RLE) to demonstrate the effectiveness of the three alias algorithms in terms of the opportunities for optimization, the impact on simulated execution times, and to compute an upper bound on what a perfect alias analysis would yield. We show modest dynamic improvements for (RLE), and more surprisingly, that on average our alias analysis is within 2.5% of a perfect alias analysis with respect to RLE on 8 Modula-3 programs. These results illustrate that to explore thoroughly the effectiveness of alias analyses, researchers need static, dynamic, and upper-bound analysis. In addition, we show that for type-safe languages like Modula-3 and Java, a fast and simple alias analysis may be sufficient for many applications.
Infrared spectroscopy of human tissue. V. Infrared spectroscopic studies of myeloid leukemia (ML‐1) cells at different phases of the cell cycle (1999)

Infrared spectra of myeloid leukemia (ML-1) cells are reported for cells derived from an asynchronous, exponentially growing culture, as well as for cells that were fractionated according to their stage within the cell division cycle.The observed results suggest that the cells' DNA is detectable by infrared spectroscopy mainly when the cell is in the S phase, during the replication of DNA.In the G1 and G2 phases, the DNA is so tightly packed in the nucleus that it appears opaque to infrared radiation.Consequently, the nucleic acid spectral contributions in the G1 and G2 phases would be mostly that of cytoplasmic RNA.These results suggest that infrared spectral changes observed earlier between normal and abnormal cells may have been due to different distributions of cells within the stages of the cell division cycle.
INFLUENCE OF DIFFUSE GLASS ON THE GROWTH AND PRODUCTION OF TOMATO (2012)

There is a great deal of interest for diffuse glass in Dutch horticulture ever since higher light transmission values and the diffusing characteristics of diffuse glass have increased production for some crops. Thus an experiment was designed to examine the effects of a variation in haze factors and light transmissions for diffuse glass or a diffuse coating on the growth and production of tomato. The influence of diffuse glass with a haze factor of 45, 62 and 71% and light transmission equal to or greater than that of standard glass, as well as standard glass with a commercial coating with a haze factor of 50% and 6% less light transmission than that of standard glass was compared to that of standard glass. The crops were planted mid-December 2010 and grown to the middle of November 2011. The influence of diffuse light on light interception, crop morphology, photosynthesis and growth was measured and analysed. Light penetrated deeper into the crop resulting in a higher photosynthetic capacity in the lower canopy, but only in winter. Tomato grown under diffuse glass was more generative, transferring more into fruit production than vegetative growth, in comparison to standard glass or coated glass. The production under the three diffuse glass coverings showed a 7-9% increase in June relative to that under standard glass, and retained this increased production to the end of the year, ending with 8-11% more production. The most important reason for the increased production was an increase in individual fruit weight by 5-8 g. Plants grown under diffuse glass or coating were less susceptible to Botrytis spp. during the last months of the crop, possibly due to a higher dry matter content. The coating was applied in the beginning of May and the treatment continued through August when the global radiation diminished and more light was necessary in the crop and the coating was removed. The overall production under the coating was 5% higher than that under standard glass. An estimation of the benefits and consequences of diffuse light characteristics on the growth, development and production of tomato under Dutch conditions are discussed, along with recommendations for the optimal characteristics for diffuse glass.
Improving the crack resistance of bulk molding compounds and sheet molding compounds (1978)

Abstract Fiber‐reinforced plastics exhibit two types of mechanical failure: gross fracture and microcracking. Gross fracture involves both matrix and fiber failures. Principal resistance to crack propagation derives from partial decoupling of fibers and then stressing, remove finite volumes of them to fracture. Classical concepts of fracture mechanics can be applied to such composites, though modifications of methodology to treat anisotropy and other special effects are required. Microcracking occurs principally in the matrix phase and usually accompanies cyclic fatigue, drop impact, bending, or rapid cooling from molding temperatures. It lowers composite stiffness, environmental resistance and may reduce strength. Matrix resins require high fracture toughness to minimize or eliminate microcracking. This paper discusses cracking in bulk molding compounds and sheet molding compounds, complex materials containing high percentages of glass fibers and calcium carbonate filler. Microcracking can be greatly reduced by tire addition of small amounts of a rubber to the polyester matrix. Various tests such as impact, bending, acoustic emission and crack propagation demonstrate the improved toughness properties which result. No sacrifice of original strength characteristics occurs, and markedly improved resistance to damage has been noted with rubber modified epoxy and polyester matrix resins.
Robust fat suppression at 3T in high‐resolution diffusion‐weighted single‐shot echo‐planar imaging of human brain (2011)

Single-shot echo-planar imaging is the most common acquisition technique for whole-brain diffusion tensor imaging (DTI) studies in vivo. Higher field MRI systems are readily available and advantageous for acquiring DTI due to increased signal. One of the practical issues for DTI with single-shot echo-planar imaging at high-field is incomplete fat suppression resulting in a chemically shifted fat artifact within the brain image. Unsuppressed fat is especially detrimental in DTI because the diffusion coefficient of fat is two orders of magnitude lower than that of parenchyma, producing brighter appearing fat artifacts with greater diffusion weighting. In this work, several fat suppression techniques were tested alone and in combination with the goal of finding a method that provides robust fat suppression and can be used in high-resolution single-shot echo-planar imaging DTI studies. Combination of chemical shift saturation with slice-select gradient reversal within a dual-spin-echo diffusion preparation period was found to provide robust fat suppression at 3 T.
Palytoxin: A New Marine Toxin from a Coelenterate (1971)

Palytoxin has been isolated from the zoanthids "limu-make-o-Hana" (Tentatively identified as Palythoa sp.) as a noncrystalline, chromatographically pure entity. Apart from polypeptide and protein toxins, it is the most highly toxic substance known, with a lethal dose (LD(59)) in mice of 0.15 microgram per kilogram by intravenous injection. Unlike the potent toxins batrachotoxin, saxitoxin, and tetrodotoxin which have molecular weights of 500 or less, palytoxin has an estimated molecular weight of 3300 and contains no repetitive amino acid or sugar units.
<i>Bacillus cereus</i>, a Volatile Human Pathogen (2010)

Bacillus cereus is a Gram-positive aerobic or facultatively anaerobic, motile, spore-forming, rod-shaped bacterium that is widely distributed environmentally. While B. cereus is associated mainly with food poisoning, it is being increasingly reported to be a cause of serious and potentially fatal non-gastrointestinal-tract infections. The pathogenicity of B. cereus, whether intestinal or nonintestinal, is intimately associated with the production of tissue-destructive exoenzymes. Among these secreted toxins are four hemolysins, three distinct phospholipases, an emesis-inducing toxin, and proteases. The major hurdle in evaluating B. cereus when isolated from a clinical specimen is overcoming its stigma as an insignificant contaminant. Outside its notoriety in association with food poisoning and severe eye infections, this bacterium has been incriminated in a multitude of other clinical conditions such as anthrax-like progressive pneumonia, fulminant sepsis, and devastating central nervous system infections, particularly in immunosuppressed individuals, intravenous drug abusers, and neonates. Its role in nosocomial acquired bacteremia and wound infections in postsurgical patients has also been well defined, especially when intravascular devices such as catheters are inserted. Primary cutaneous infections mimicking clostridial gas gangrene induced subsequent to trauma have also been well documented. B. cereus produces a potent beta-lactamase conferring marked resistance to beta-lactam antibiotics. Antimicrobials noted to be effective in the empirical management of a B. cereus infection while awaiting antimicrobial susceptibility results for the isolate include ciprofloxacin and vancomycin.
Self-reconstruction of mesh-arrays with 1 1/2 -track switches by digital neural circuits (2002)

Previously, we have proposed the Hopfield-type neural algorithm for reconstructing mesh-connected processor arrays using single-track switches and mentioned that the algorithm could be realized by hardware where the algorithm requires four neurons for each processor element (PE) in order to decide compensation paths for faulty PEs under the constraints. This paper shows how the algorithm can be realized by a digital neural circuit. It consists of subcircuits for finding candidate compensation paths, deciding whether the neural system reaches a stable state and at the time the system energy is minimum, and subcircuits for neurons. The subcircuit for each neuron can only be made with 17 gates and two flip-flops. Since the state transitions are done in parallel, the circuit will be able to find the compensation paths for a fault pattern very quickly within a time less than 1 /spl mu/s.
High solid and low enzyme loading based saccharification of agricultural biomass (2011)

Two agricultural biomass materials, namely wheat straw and sugarcane bagasse, were pretreated with NaOH and then used as substrates for enzymatic saccharification. After the pretreatment, the increase in glucan content and the decrease in lignin content were more than 65%, while less than 20% increase occurred in xylan content. The enzymatic saccharification was initiated with solid loading 9% (w/v), and then 8%, 7% and 6% (w/v) solid was fed at 8, 24, and 48 h, respectively. The final enzyme solid loading was 9.60 FPU/g solid and 30% (w/v), respectively. At 144 h, the produced glucose, xylose, and reducing sugar concentrations for wheat straw were 81.88, 20.30, and 115.25 g/L, respectively, and for sugarcane bagasse they were 125.97, 8.66, and 169.50 g/L, respectively. The final conversions of wheat straw and sugarcane bagasse were 34.57% and 50.85%, respectively. SEM images showed that the surface structure of the two materials changed a lot via alkali-pretreatment and enzymatic hydrolysis. In summary, a high concentration sugar is produced from the two agricultural biomass materials by high solid and low enzyme loading. Compared to wheat straw, sugarcane bagasse is more suitable for use in sugar production.
Diffractometric Detection of Proteins Using Microbead-Based Rolling Circle Amplification (2009)

We present a robust, sensitive, fluorescent- or radiolabel-free self-assembled optical diffraction biosensor that utilizes rolling circle amplification (RCA) and magnetic microbeads as a signal enhancement method. An aptamer-based sandwich assay was performed on microcontact-printed streptavidin arranged in 15 microm wide alternating lines and could specifically capture and detect platelet-derived growth factor B-chain (PDGF-BB). An aptamer served as a template for the ligation of a padlock probe, and the circularized probe could in turn be used as a template for RCA. The concatameric RCA product hybridized to biotinylated oligonuclotides which then captured streptavidin-labeled magnetic beads. In consequence, the signal from the captured PDGF-BB was amplified via the concatameric RCA product, and the diffraction gratings on the printed areas produced varying intensities of diffraction modes. The detected diffraction intensity and the density of the microbeads on the surface varied as a function of PDGF-BB concentration. Our results demonstrate a robust biosensing platform that is easy to construct and use and devoid of fluorescence microscopy. The self-assembled bead patterns allow both a visual analysis of the molecular binding events under an ordinary bright-field microscope and serve as a diffraction grating biosensor.
Dousing the flames (2009)

Subtitle: FedEx is equipping its aircraft with an automatic fire-suppression system--a first for transport category cargo airplanes.
Cervigram image segmentation based on reconstructive sparse representations (2010)

We proposed an approach based on reconstructive sparse representations to segment tissues in optical images of the uterine cervix. Because of large variations in image appearance caused by the changing of the illumination and specular reflection, the color and texture features in optical images often overlap with each other and are not linearly separable. By leveraging sparse representations the data can be transformed to higher dimensions with sparse constraints and become more separated. K-SVD algorithm is employed to find sparse representations and corresponding dictionaries. The data can be reconstructed from its sparse representations and positive and/or negative dictionaries. Classification can be achieved based on comparing the reconstructive errors. In the experiments we applied our method to automatically segment the biomarker AcetoWhite (AW) regions in an archive of 60,000 images of the uterine cervix. Compared with other general methods, our approach showed lower space and time complexity and higher sensitivity.