gebhart/patrepeval huggingface dataset:
Arabidopsis mutants deficient in polyunsaturated fatty acid synthesis. Biochemical and genetic characterization of a plant oleoyl-phosphatidylcholine desaturase. (1992)

The overall fatty acid composition of leaf lipids in a mutant of Arabidopsis thaliana was characterized by reduced levels of polyunsaturated 18-carbon fatty acids and an increased proportion of oleate as a consequence of a single recessive nuclear mutation. Quantitative analysis of the fatty acid composition of individual lipids demonstrated that all the major phospholipids of the extrachloroplast membranes are affected by the mutation, whereas the chlorplast lipids show fatty acid compositions only slightly different from those of wild type plants. These results are consistent with the parallel operation of two pathways of lipid synthesis in plant leaf cells (the prokaryotic pathway in the chloroplast and the eukaryotic pathway in the endoplasmic reticulum) and with genetic evidence (Browse, J., Kunst, L., Anderson, S., Hugly, S., and Somerville, C.R. (1989) Plant Physiol 90, 522-529) that an independent 18:1/16:1 desaturase operates on chloroplast membrane lipids. Direct enzyme assays confirmed that the mutant plants are deficient in the activity of a microsomal oleoyl-phosphatidycholine desaturase and demonstrated that this desaturase is the major enzyme responsible for the synthesis of polyunsaturated phospholipids. Despite this deficiency in 18:1-desaturase activity, mutant plants contained relatively high levels of 18:3 in their leaf phospholipids. This finding is interpreted as additional evidence that considerable two-way exchange of lipid occurs between the chloroplast and endoplasmic reticulum and that this exchange allows the chloroplast desaturases to provide lipids containing 18:3 to the extrachloroplast compartment, thus partially alleviating the deficiency in 18:1 desaturase activity.
Computational complexity of Volterra based nonlinearcompensators (1996)

The Volterra series can be used to represent a wide class of nonlinear systems with memory. A Volterra inverse can be used to apply post (or pre)-distortion for the purpose of nonlinear compensation. The authors determine and compare the computational complexity of two such compensators: one based on the analytical pth order Volterra inverse, the other on the adaptive Volterra inverse.
The sequence of a 6·3 kb segment of yeast chromosome III reveals an open reading frame coding for a putative mismatch binding protein (1991)

We report the sequence of a 6.3 kb segment of DNA mapping near the end of the right arm of chromosome III of Saccharomyces cerevisiae. The sequence reveals a major open reading frame coding for a putative protein of 1047 amino acids with a striking similarity to the bacterial proteins involved in recognition of mismatched DNA base pairs. This is particularly interesting as the existence of a yeast mismatch repair system similar to that of bacteria has been postulated for some years, but a yeast protein homologous to the bacterial mismatch binding protein had not been identified. The results of a comparison of the putative yeast mismatch binding protein with the bacterial mismatch binding proteins and with two cognate mammalian sequences, support the idea that a similar mismatch repair system may be present also in mammalian cells. The possibility that all of these proteins may have evolved from a common ancestral gene is also discussed.
Surface resonant states and superlensing in acoustic metamaterials (2007)

We report that the negative material responses of acoustic metamaterials can lead to a plethora of surface resonant states. We determine that negative effective-mass density is the necessary condition for the existence of surface states on acoustic metamaterials. We offer the microscopic picture of these unique surface states; in addition, we find that these surface excitations enhance the transmission of evanescent pressure fields across the metamaterial. The evanescent pressure fields scattered from an object can be resonantly coupled and enhanced at the surface of the acoustic metamaterial, resulting in an image with resolution below the diffraction limit. This concept of acoustic superlens opens exciting opportunities to design acoustic metamaterials for ultrasonic imaging.
Nursing clinical education: a partnership with health information management professionals. (1992)

Today's HIM professional can be a positive and an integral component in providing nursing clinical education. Creativity is the key. HIM professionals can share expertise in the documentation and quality assessment process as well as in the transition to the computerized patient record. By providing HIM information through nursing clinical education, a collaborative partnership can emerge.
Checkpoint Ensembles: Ensemble Methods from a Single Training Process (2017)

We present the checkpoint ensembles method that can learn ensemble models on a single training process. Although checkpoint ensembles can be applied to any parametric iterative learning technique, here we focus on neural networks. Neural networks' composable and simple neurons make it possible to capture many individual and interaction effects among features. However, small sample sizes and sampling noise may result in patterns in the training data that are not representative of the true relationship between the features and the outcome. As a solution, regularization during training is often used (e.g. dropout). However, regularization is no panacea -- it does not perfectly address overfitting. Even with methods like dropout, two methodologies are commonly used in practice. First is to utilize a validation set independent to the training set as a way to decide when to stop training. Second is to use ensemble methods to further reduce overfitting and take advantage of local optima (i.e. averaging over the predictions of several models). In this paper, we explore checkpoint ensembles -- a simple technique that combines these two ideas in one training process. Checkpoint ensembles improve performance by averaging the predictions from "checkpoints" of the best models within single training process. We use three real-world data sets -- text, image, and electronic health record data -- using three prediction models: a vanilla neural network, a convolutional neural network, and a long short term memory network to show that checkpoint ensembles outperform existing methods: a method that selects a model by minimum validation score, and two methods that average models by weights. Our results also show that checkpoint ensembles capture a portion of the performance gains that traditional ensembles provide.
Digitalis metabolism and human liver alcohol dehydrogenase. (1980)

Human liver alcohol dehydrogenase (alcohol: NAD" oxidoreductase, EC 1.1.1.1) catalyzes the oxidation of the 3 beta-OH group of digitoxigenin, digoxigenin, and gitoxigenin to their 3-keto derivatives, which have been characterized by high performance liquid chromatography and mass spectrometry. These studies have identified human liver alcohol dehydrogenase as the unknown NAD(H)-dependent liver enzyme specific for the free hydroxyl group at C3 of the cardiac genins; this hydroxyl is the critical site of the genins' enzymatic oxidation and concomitant pharmacological inactivation in humans. Several kinetic approaches have demonstrated that ethanol and the pharmacologically active components of the digitalis glycosides are oxidized with closely similar kcat/Km values at the same site on human liver alcohol dehydrogenase, for which they compete. Human liver alcohol dehydrogenase thereby becomes an important biochemical link in the metabolism, pharmacology, and toxicology of ethanol and these glycosides, structurally unrelated agents that are both used widely. Both the competition of ethanol with these cardiac sterols and the narrow margin of safety in the therapeutic use of digitalis derivatives would seem to place at increased risk those individuals who receive digitalis and simultaneously consume large amounts of ethanol or whose alcohol dehydrogenase function is impaired.
jModelTest: Phylogenetic Model Averaging (2008)

jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.). It implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion," the "Bayesian information criterion," and a "decision-theoretic performance-based" approach. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment installed. The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es.
Camera calibration with one-dimensional objects (2004)

Camera calibration has been studied extensively in computer vision and photogrammetry and the proposed techniques in the literature include those using 3D apparatus (two or three planes orthogonal to each other or a plane undergoing a pure translation, etc.), 2D objects (planar patterns undergoing unknown motions), and 0D features (self-calibration using unknown scene points). Yet, this paper proposes a new calibration technique using 1D objects (points aligned on a line), thus filling the missing dimension in calibration. In particular, we show that camera calibration is not possible with free-moving 1D objects, but can be solved if one point is fixed. A closed-form solution is developed if six or more observations of such a 1D object are made. For higher accuracy, a nonlinear technique based on the maximum likelihood criterion is then used to refine the estimate. Singularities have also been studied. Besides the theoretical aspect, the proposed technique is also important in practice especially when calibrating multiple cameras mounted apart from each other, where the calibration objects are required to be visible simultaneously.
Collision induced decomposition of peptides. Choice of collision parameters (1996)

Collision-induced dissociation product ion spectra of a series of doubly charged tryptic peptide ions produced by electrospray ionization were obtained by triple-quadrupole tandem mass spectrometry. The sequence information content of the product ion spectra was explored as a function of collision energy and collision-cell gas pressure for parent ions with molecular masses ranging from 300 to 2000 u. The energy range (at a given pressure) in which the degree of fragmentation is acceptable was found to be narrow for parent ions of a given mass, and the optimal collision energy was observed to exhibit a strong linear correlation with parent ion mass. This observed correlation opens the way for on-line software-controled selection of optimal mass spectrometric conditions in the enzymatic digestion-liquid chromatography-tandem mass spectrometric strategy of amino acid sequencing of proteins.
Effect of collagen crosslinking on the rate of resorption of implanted collagen tubing in rabbits (1977)

Collagen tubes were tanned with glutaraldehyde for different periods of time. Some were oxidized with periodate and sterilized with either 60Co (1.5 Mrad) or propylene oxide. The tubes were coated with polyfilamentous polyester fabric, filled with x-ray contrast material, and implanted subcutaneously in rats and rabbits. Rate of resorption was ascertained by x-ray procedure of progressive leakage of contrast material. A close relation between tanning time of the collagen fabric-combined prostheses and rate of their resorption in subcutis was found in both rats and rabbits. In rabbits, however, the implants were resorbed at a significantly faster rate than in rats. No effect of oxidation of collagen on the resorption was observed. Collagen tubes tanned for shorter time periods and sterilized with propylene oxide were more resistant to degradation than those sterilized with irradiation. This difference was absent, however, with material tanned for longer times. The mechanism of resorption of implanted collagen tubes was studied by morphological methods. The role of inflammatory cells in resorption is documented. The paper indicates the advantages as well as limits of the x-ray method of studying the resorption rate of biodegradable materials.
Corticothalamic Projections from the Rat Primary Somatosensory Cortex (2003)

To study the cells of origin of corticothalamic inputs to the ventral posterior and posterior medial nuclei of the somatosensory thalamus in rats, we injected small aliquots of tracer into each nucleus and analyzed the pattern of retrograde labeling in the posteromedial barrel subfield of primary somatosensory cortex, which can be divided into barrel and nonbarrel zones. The ventral posterior nucleus is innervated by neurons in layer VIa of both zones, whereas the posterior medial nucleus is innervated by neurons in layers Vb and VIb of both zones with additional innervation from layer VIa of nonbarrel cortex. Thus, only the posterior medial nucleus receives a layer Vb input. Because the layer Vb input is interpreted as the initiation of a feedforward cortico-thalamocortical pathway, this implies that the target of the posterior medial nucleus, which includes the nonbarrel cortex, is a higher-order cortical area. We thus suggest that this cortical zone, which is classically considered part of the primary somatosensory cortex, should be reclassified as higher-order cortex.
Magnetoresistive sensors for nondestructive evaluation (Invited Paper) (2005)

New high-sensitivity solid-state magnetoresistive (MR) sensor technologies offer significant advantages in nondestructive evaluation (NDE) systems. A key advantage of MR sensors is a flat frequency response extending from dc to hundreds of MHz, making them particularly attractive for low-frequency and multi-frequency eddy current detection for deep-flaw detection and depth profiling. MR sensors are mass produced by thin film processing techniques similar to integrated circuit manufacturing, dramatically reducing the cost per sensor. The fabrication process is compatible with silicon circuit technology, allowing integration of sensors with on-chip signal processing. MR sensors can easily be produced in dense arrays for rapid, single-pass scanning of large areas. The small size and low power consumption of these solid-state magnetic sensors enable the assembly of compact arrays of sensors on a variety of substrates as well as on-chip sensor arrays. Arrays have been fabricated with sensor spacing as small as 5 &#956;m. This paper presents a review of the state of the art in MR sensors and applications in NDE. The physical principles, manufacturing process, and performance characteristics of the three main types of MR devices, anisotropic magnetoresistance (AMR), giant magnetoresistance (GMR) and tunneling magnetoresistance (TMR) are discussed. Their performance is compared to other magnetic sensor technologies for NDE applications. Finally, we provide a comprehensive review of the literature on NDE applications of MR sensors.
A “Core−Shell” Approach to Producing 3D Polymer Nanocomposites (1999)

A new strategy to producing three-dimensional (3D) ordered polymer nanocomposites is proposed that employs a core−shell latex morphology. We synthesized core−shell latex particles in which a core-forming polymer had a glass transition temperature significantly higher than that of a shell-forming polymer. Particles were assembled in a 3D close-packed structure and annealed in such a way that latex cores remained intact while latex shells deformed and flew. As a result, a continuous matrix was formed that contained an organized 3D array of monodisperse “core” particles. A possibility to control the functionality of the “core” beads was demonstrated by labeling the core-forming polymer with a fluorescent dye. We discuss conditions in which an ordered, void-free polymer nanocomposite can be obtained.
Use of 2-acetamidophenanthrene and 2-acetamidofluorene in investigations of mechanisms of hepatocarcinogenesis (1983)

Comparison studies have been undertaken on the hepatocarcinogen 2-acetamidofluorene (AAF) and its nonhepatocarcinogenic analog 2-acetamidophenanthrene (AAP). Previous studies have shown that amount of compound acutely and persistently bound to rat liver DNA is comparable for the two compounds following single injections into adult Fischer rats, but that AAP fails to initiate tumors in weanling Sprague-Dawley rats. In this work we show that the amount of bound adduct from AAF and AAP is also comparable after three weeks of feeding compound to weanling Sprague-Dawley male rats. Three of the adducts found in RNA of AAP-treated rats cochromatographed on Sephadex LH-20 with two adenosine adducts and one guanosine adduct prepared by reaction of the nucleosides with N-acetoxy-N-trifluoroacetyl-2-aminophenanthrene at neutrality. Because of the lack of initiating ability of AAP in liver, we have also investigated early biochemical alterations in liver after various regimens. Feeding of either AAF or AAP to male weanling rats, followed by three weeks of DDT feeding produced no alteration in either histochemically detected gamma-glutamyltranspeptidase or in ganglioside complement in total liver homogenate. Partial hepatectomy after feeding of either AAF or AAP resulted in the appearance of new fucoganglioside and alteration in the distribution of the major gangliosides. DDT feeding after partial hepatectomy resulted in foci of elevated gamma-glutamyltranspeptidase in AAF-fed rats but not in AAP-fed rats. These results support a previous proposal that AAP may initiate tumorigenesis in rat liver, but that the promoting regimens now in use lack the ability to cause further progression of the initiated cells. The data also suggests that ganglioside synthesis may be a more sensitive marker for early stages in carcinogenesis than are the various histochemical stains now in use.
Electron tunnel sensor technology (1991)

Researchers designed and constructed a novel electron tunnel sensor which takes advantage of the mechanical properties of micro-machined silicon. For the first time, electrostatic forces are used to control the tunnel electrode separation, thereby avoiding the thermal drift and noise problems associated with piezoelectric actuators. The entire structure is composed of micro-machined silicon single crystals, including a folded cantilever spring and a tip. The application of this sensor to the development of a sensitive accelerometer is described.
Hardware and software techniques for controlling DRAM power modes (2001)

The anticipated explosive growth of pervasive and mobile computing devices that are typically constrained by energy has brought hardware and software techniques for energy conservation into the spotlight. While there have been several studies and proposals for energy conservation for CPUs and peripherals, energy optimization techniques for selective operating mode control of DRAMs have not been fully explored. It has been shown that, for some systems, as much as 90 percent of overall system energy (excluding I/O) is consumed by the DRAM modules, thus, they serve as a good candidate for energy optimizations. Further, DRAM technology has also matured to provide several low energy operating modes (power modes), making it an opportunistic moment to conduct studies exploring the potential benefits of mode control techniques. This paper conducts an in-depth investigation of software and hardware techniques to take advantage of the DRAM mode control capabilities at a module granularity for energy savings. Using a memory system architecture capturing five different energy modes and corresponding resynchronization times, this paper presents several novel compilation techniques to both cluster the data across memory banks as well as to detect module idleness and perform energy mode transitions. In addition, hardware-assisted approaches (called self-monitoring) based on predictions of module interaccess times are proposed. These techniques are extensively evaluated using a set of a dozen benchmarks. It is shown that we get an average of 61 percent savings in DRAM energy using compiler-directed mode control. One of the self-monitored approaches gives as much as 89 percent savings (72 percent on the average), coming as close as 8.8 percent to the optimal energy savings that one can expect with DRAM module mode control. The optimization techniques are demonstrated to be invaluable for energy savings as memory technologies continue to evolve.
Receptor-mediated endocytosis of transferrin and recycling of the transferrin receptor in rat reticulocytes. (1983)

At 4 degrees C transferrin bound to receptors on the reticulocyte plasma membrane, and at 37 degrees C receptor-mediated endocytosis of transferrin occurred. Uptake at 37 degrees C exceeded binding at 4 degrees C by 2.5-fold and saturated after 20-30 min. During uptake at 37 degrees C, bound transferrin was internalized into a trypsin-resistant space. Trypsinization at 4 degrees C destroyed surface receptors, but with subsequent incubation at 37 degrees C, surface receptors rapidly appeared (albeit in reduced numbers), and uptake occurred at a decreased level. After endocytosis, transferrin was released, apparently intact, into the extracellular space. At 37 degrees C colloidal gold-transferrin (AuTf) clustered in coated pits and then appeared inside various intracellular membrane-bounded compartments. Small vesicles and tubules were labeled after short (5-10 min) incubations at 37 degrees C. Larger multivesicular endosomes became heavily labeled after longer (20-35 min) incubations. Multivesicular endosomes apparently fused with the plasma membrane and released their contents by exocytosis. None of these organelles appeared to be lysosomal in nature, and 98% of intracellular AuTf was localized in acid phosphatase-negative compartments. AuTf, like transferrin, was released with subsequent incubation at 37 degrees C. Freeze-dried and freeze-fractured reticulocytes confirmed the distribution of AuTf in reticulocytes and revealed the presence of clathrin-coated patches amidst the spectrin coating the inner surface of the plasma membrane. These data suggest that transferrin is internalized via coated pits and vesicles and demonstrate that transferrin and its receptor are recycled back to the plasma membrane after endocytosis.
Distribution of Neuraminidase in Arthrobacter and Its Purification by Affinity Chromatography1 (1977)

Neuraminidase [sialidase, EC 3.2.1.18] was found to be widely distributed in bacteria belonging to Arthrobacter. Among these bacteria, Arthrobacter ureafaciens, A. oxydans, and A. aurescens produced relatively potent neuraminidase activities. For the production of this enzyme, not only colominic acid, a homopolymer of N-acetylneuraminic acid, but also N-acetylneuraminic acid, the reaction product of this enzyme, are effective as sources of carbon. An affinity adsorbent specific for neuraminidase was prepared by cross-linking colominic acid with soluble starch by means of epichlorohydrin. Neuraminidase from A. ureafaciens could be purified on this affinity column. The purified neuraminidase was shown to be free from protease, N-acetylneuraminic acid aldolase, phospholipase C, and glycosidases. Aminoff's assay procedure for sialic acid was modified to avoid the centrifugation step. The modified procedure gave a higher molecular extinction coefficient.