gebhart/patrepeval huggingface dataset:
Novel Localization of a Na+/H+ Exchanger in a Late Endosomal Compartment of Yeast (1998)

Na+/H+ exchangers catalyze the electrically silent countertransport of Na+ and H+, controlling the transmembrane movement of salt, water, and acid-base equivalents, and are therefore critical for Na+ tolerance, cell volume control, and pH regulation. In contrast to numerous well studied plasma membrane isoforms (NHE1-4), much less is known about intracellular Na+/H+ exchangers, and thus far no vertebrate isoform has been shown to have an exclusively endosomal distribution. In this context, we show that the yeast NHE homologue, Nhx1 (Nass, R., Cunningham, K. W., and Rao, R. (1997) J. Biol. Chem. 272, 26145-26152), localizes uniquely to prevacuolar compartments, equivalent to late endosomes of animal cells. In living yeast, we show that these compartments closely abut the vacuolar membrane in a striking bipolar distribution, suggesting that vacuole biogenesis occurs at distinct sites. Nhx1 is the founding member of a newly emergent cluster of exchanger homologues, from yeasts, worms, and humans that may share a common intracellular localization. By compartmentalizing Na+, intracellular exchangers play an important role in halotolerance; furthermore, we hypothesize that salt and water movement into vesicles may regulate vesicle volume and pH and thus contribute to vacuole biogenesis.
ANALYSIS AND DESIGN OF NUMERICAL SCHEMES FOR GAS DYNAMICS, 1: ARTIFICIAL DIFFUSION, UPWIND BIASING, LIMITERS AND THEIR EFFECT ON ACCURACY AND MULTIGRID CONVERGENCE (1995)

SUMMARY The theory of non-oscillatory scalar schemes is developed in this paper in terms of the local extremum diminishing (LED) principle that maxima should not increase and minima should not decrease. This principle can be used for multi-dimensional problems on both structured and unstructured meshes, while it is equivalent to the total variation diminishing (TVD) principle for one-dimensional problems. A new formulation of symmetric limned positive (SLIP) schemes is presented, which can be generalized to produce schemes with arbitrary high order of accuracy in regions where the solution contains no extrema, and which can also be implemented on multi-dimensional unstructured meshes. Systems of equations lead to waves travelling with distinct speeds and possibly in opposite directions. Alternative treatments using characteristic splitting and scalar diffusive fluxes are examined, together with a modification of the scalar diffusion through the addition of pressure differences to the momentum equations to produce full upwinding in supersonic flow. This convective upwind and split pressure (CUSP) scheme exhibits very rapid convergence in multigrid calculations of transonic flow, and provides excellent shock resolution at very Mach numbers.
Will molecular dynamics simulations of proteins ever reach equilibrium? (2012)

We show that conformational entropies calculated for five proteins and protein-ligand complexes with dihedral-distribution histogramming, the von Mises approach, or quasi-harmonic analysis do not converge to any useful precision even if molecular dynamics (MD) simulations of 380-500 ns length are employed (the uncertainty is 12-89 kJ mol(-1)). To explain this, we suggest a simple protein model involving dihedrals with effective barriers forming a uniform distribution and show that for such a model, the entropy increases logarithmically with time until all significantly populated dihedral states have been sampled, in agreement with the simulations (during the simulations, 52-70% of the available dihedral phase space has been visited). This is also confirmed by the analysis of the trajectories of a 1 ms simulation of bovine pancreatic trypsin inhibitor (31 kJ mol(-1) difference in the entropy between the first and second part of the simulation). Strictly speaking, this means that it is practically impossible to equilibrate MD simulations of proteins. We discuss the implications of such a lack of strict equilibration of protein MD simulations and show that ligand-binding free energies estimated with the MM/GBSA method (molecular mechanics with generalised Born and surface-area solvation) vary by 3-15 kJ mol(-1) during a 500 ns simulation (the higher estimate is caused by rare conformational changes), although they involve a questionable but well-converged normal-mode entropy estimate, whereas free energies estimated by free-energy perturbation vary by less than 0.6 kJ mol(-1) for the same simulation.
Knowing When to Look: Adaptive Attention via a Visual Sentinel for Image Captioning (2017)

Attention-based neural encoder-decoder frameworks have been widely adopted for image captioning. Most methods force visual attention to be active for every generated word. However, the decoder likely requires little to no visual information from the image to predict non-visual words such as the and of. Other words that may seem visual can often be predicted reliably just from the language model e.g., sign after behind a red stop or phone following talking on a cell. In this paper, we propose a novel adaptive attention model with a visual sentinel. At each time step, our model decides whether to attend to the image (and if so, to which regions) or to the visual sentinel. The model decides whether to attend to the image and where, in order to extract meaningful information for sequential word generation. We test our method on the COCO image captioning 2015 challenge dataset and Flickr30K. Our approach sets the new state-of-the-art by a significant margin.
CFC-12 to HCFC-22 plant conversion : OORG production sector case study (1994)

During the course of the Ozone Operations Resource Group's (OORG) Fifth regular meeting on February 17, 1994, at World Bank headquarters in Washington, DC, Dr. Michael Harris, the Chairman of the OORG Production Woriking Group, updated participants on the status of ozone depleting substance (ODS) production around the world. Of particular note, he stated that halon production in India is expanding while three new CFC production plants are presently coming on stream in China. Meanwhile Russia, a major non-Article 5 country, is making additional expansions in its CFC production capacity as well. As a partial consequence, Montreal Protocol guidelines are still required on how to evaluate non-ODS alternatives production projects in countries still subject to planned increased production of ODS chemicals. Production plant by-product emission reduction is, in general, the most cost-effective intervention in production plant technology by far. The unit abatement costs in such cases are often negative. Furthermore, HCFC-22 conversions of CFC-11/12 plants have relatively low unit abatement costs. Nonethelss, substantial heterogeneity in project contexts will make a case by case anaysis necessary. This is especially true due to the critical role played by the specific character of plant construction materials and their impact upon both performance and cost of plants.
Stable Rotating Waves in Two-Dimensional Discrete Active Media (1994)

The existence and stability of stable rotating solutions (spiral waves) in a discrete system of coupled phase models is proven. Monotone methods are used to obtain existence and qualitative features of the solutions. An application of Fenichel's results for singular perturbation implies the existence for a one variable model for excitability. Numerical comparisons with the phase model and a realistic membrane model are made. A numerically computed Hopf bifurcation shows the existence of the “wobbling core” observed in spatially continuous models.
Diterpene Synthases and Their Responsible Cyclic Natural Products (2014)

This review provides an overview of diterpene synthases which were initially identified via genetic and/or biochemical means, traversing all organisms researched to date.
Major Role for FeoB in Campylobacter jejuni Ferrous Iron Acquisition, Gut Colonization, and Intracellular Survival (2006)

To assess the importance of ferrous iron acquisition in Campylobacter physiology and pathogenesis, we disrupted and characterized the Fe2+ iron transporter, FeoB, in Campylobacter jejuni NCTC 11168, 81-176, and ATCC 43431. The feoB mutant was significantly affected in its ability to transport 55Fe2+. It accumulated half the amount of iron than the wild-type strain during growth in an iron-containing medium. The intracellular iron of the feoB mutant was localized in the periplasmic space versus the cytoplasm for the wild-type strain. These results indicate that the feoB gene of C. jejuni encodes a functional ferrous iron transport system. Reverse transcriptase PCR analysis revealed the cotranscription of feoB and Cj1397, which encodes a homolog of Escherichia coli feoA. C. jejuni 81-176 feoB mutants exhibited reduced ability to persist in human INT-407 embryonic intestinal cells and porcine IPEC-1 small intestinal epithelial cells compared to the wild type. C. jejuni NCTC 11168 feoB mutant was outcompeted by the wild type for colonization and/or survival in the rabbit ileal loop. The feoB mutants of the three C. jejuni strains were significantly affected in their ability to colonize the chick cecum. And finally, the three feoB mutants were outcompeted by their respective wild-type strains for infection of the intestinal tracts of colostrum-deprived piglets. Taken together, these results demonstrate that FeoB-mediated ferrous iron acquisition contributes significantly to colonization of the gastrointestinal tract during both commensal and infectious relationship, and thus it plays an important role in Campylobacter pathogenesis.
Functional Characteristics of an Endophyte Community Colonizing Rice Roots as Revealed by Metagenomic Analysis (2011)

Roots are the primary site of interaction between plants and microorganisms. To meet food demands in changing climates, improved yields and stress resistance are increasingly important, stimulating efforts to identify factors that affect plant productivity. The role of bacterial endophytes that reside inside plants remains largely unexplored, because analysis of their specific functions is impeded by difficulties in cultivating most prokaryotes. Here, we present the first metagenomic approach to analyze an endophytic bacterial community resident inside roots of rice, one of the most important staple foods. Metagenome sequences were obtained from endophyte cells extracted from roots of field-grown plants. Putative functions were deduced from protein domains or similarity analyses of protein-encoding gene fragments, and allowed insights into the capacities of endophyte cells. This allowed us to predict traits and metabolic processes important for the endophytic lifestyle, suggesting that the endorhizosphere is an exclusive microhabitat requiring numerous adaptations. Prominent features included flagella, plant-polymer-degrading enzymes, protein secretion systems, iron acquisition and storage, quorum sensing, and detoxification of reactive oxygen species. Surprisingly, endophytes might be involved in the entire nitrogen cycle, as protein domains involved in N(2)-fixation, denitrification, and nitrification were detected and selected genes expressed. Our data suggest a high potential of the endophyte community for plant-growth promotion, improvement of plant stress resistance, biocontrol against pathogens, and bioremediation, regardless of their culturability.
Powered ankle-foot prosthesis (2008)

The minimum level of series compliance that adequately protects the transmission from damage during foot collision fails to satisfy bandwidth requirements. As a resolution to this difficulty, parallel motor elasticity is used to lower the forces borne by the SEA, enhancing system force bandwidth. To minimize prosthesis cost of transport (COT) and motor or transmission size, we select a parallel stiffness that supplies the necessary ankle stiffness during early stance period dorsiflexion, eliminating the need for SEA during that gait phase. In future investigations, we hope to apply the ankle-foot design to robotic, orthotic, and exoskeletal applications. In the design of biomimetic ankle-foot systems, we feel both series and parallel motor elasticity are of paramount importance.
Effect of NT‐4 and BDNF delivery to damaged sciatic nerves on phenotypic recovery of fast and slow muscles fibres (2003)

We investigated whether neurotrophin-4 (NT-4) and brain-derived neurotrophic factor (BDNF) affected the reinnervation of slow and fast motor units. Neurotrophin-impregnated or plain fibronectin (FN) conduits were inserted into a sciatic nerve gap. Fast extensor digitorum longus (EDL) and slow soleus muscles were collected 4 months postsurgery. Muscles were weighed and fibre type proportion and mean fibre diameters were derived from muscle cross-sections. All fibre types in muscles from FN animals were severely atrophied and this correlated well with type 1 fibre loss and atrophy in soleus and type 2b loss and atrophy in EDL. Treatment with NT-4 reversed soleus but not EDL mass loss above the FN group by significantly restoring type 1 muscle fibre proportion and diameters towards those of normal unoperated animals. BDNF did not increase muscle mass but did have minor effects on fibre type and diameter. Thus, NT-4 significantly improved slow motor unit recovery, and provides a basis for therapies intended to aid the functional recovery of muscles after denervating injury.
The klystron: A microwave source of surprising range and endurance (1998)

This year marks the 60th anniversary of the birth of the klystron at Stanford University. The tube was the first practical source of microwaves and its invention initiated a search for increasingly more powerful sources, which continues to this day. This paper reviews the scientific uses of the klystron and outlines its operating principles. The history of the device is traced from its scientific beginnings to its role in WWII and the Cold War, its subsequent decline in use for military systems, and to its current resurgence as the key component in a major accelerator project. Finally, the paper describes the development of a modular klystron, which may someday power future accelerators at millimeter wavelengths.
Positive newborn screen for methylmalonic aciduria identifies the first mutation in TCblR/CD320, the gene for cellular uptake of transcobalamin-bound vitamin B12 (2010)

Elevated methylmalonic acid in five asymptomatic newborns whose fibroblasts showed decreased uptake of transcobalamin-bound cobalamin (holo-TC), suggested a defect in the cellular uptake of cobalamin. Analysis of TCblR/CD320, the gene for the receptor for cellular uptake of holo-TC, identified a homozygous single codon deletion, c.262_264GAG (p.E88del), resulting in the loss of a glutamic acid residue in the low-density lipoprotein receptor type A-like domain. Inserting the codon by site-directed mutagenesis fully restored TCblR function.
Radiative cooling computed for model atmospheres (1982)

Calculations of spectral radiance are reported from several model atmospheres appropriate to different climatic conditions by use of the LOWTRAN 5 computer code. From these data we evaluate the radiative cooling power and the temperature drop below ambient temperature for horizontal surfaces that radiate toward the sky. The surfaces are ideal blackbodies or have ideal infrared-selective properties with zero reflectance in the 8-13-microm range and unity reflectance elsewhere. For freely radiating surfaces, the cooling power at ambient temperature lies between 58 Wm(-2) and 113 Wm(-2) for the different surfaces and model atmospheres. The maximum temperature difference for a device with a nonradiative heat transfer coefficient of 1 Wm(-2) K(-1) is between 11 and 21 degrees C for a blackbody and between 18 and 33 degrees C for an infrared-selective surface. For radiators arranged so that they intercept only the atmospheric zenith radiance, the cooling powers and temperature differences are higher than for freely radiating surfaces, the increase being largest for humid atmospheres. The influence of altered contents of water vapor was found to affect strongly the radiative cooling, whereas changes in ozone and aerosol abundance were less important. The significance of these results to different cooling applications is briefly discussed.
Characteristics of fetal anticonvulsant syndrome associated autistic disorder (2005)

The aim of this study was to evaluate the clinical features and frequency of autistic disorder or Asperger syndrome (AS; according to Diagnostic and Statistical Manual of Mental Disorders, 4th edition [DSM-IV] criteria) in children exposed to anticonvulsant medication in utero. During a 20-year study period, 626 children were born in Aberdeen to mothers taking antiepileptic drugs (AEDs). The study examined long-term effects of prenatal exposure to AEDs in 260 children (122 males, 138 females). Of these, 26 (16 males) were reported by parents to have social or behavioural difficulties. Eleven children (6 males, 5 females) fulfilled the DSM-IV criteria for autistic disorder and one (female) fulfilled the DSM-IV criteria for AS. These children comprised 4.6% of the exposed children studied, and 1.9% of all exposed children born during the study period. Mean age of these children at diagnosis was 5 years 4 months (SD 2y 11mo) and 9 years 10 months (SD 3y 10mo) at the time of this study. Other children from the group of 26 had difficulties in areas of speech and language development and social communication but did not meet the criteria for an autism spectrum disorder (ASD). Sodium valproate was the drug most commonly associated with autistic disorder, five of 56 (8.9%) of the study children exposed to sodium valproate alone had either autistic disorder or AS. It was concluded that prenatal exposure to anticonvulsant medication is a risk factor for the development of an ASD. Fetal anticonvulsant syndrome associated autistic disorder is characterized by an even sex ratio, absence of regression or skill loss, and language delay in the absence of global delay.
Efficacy of Fish Oil on Serum of TNFα, IL-1β, and IL-6 Oxidative Stress Markers in Multiple Sclerosis Treated with Interferon Beta-1b (2013)

Fish oil supplementation is highly effective in reducing the levels of cytokines and nitric oxide catabolites in patients with relapsing-remitting MS.
Use of Polymerase Chain Reaction-Amplified Ribosomal Intergenic Sequences for the Diagnosis ofVerticillium tricorpus (1994)

Verticillium dahliae, V. albo-atrum, and V. tricorpus are common pathogens of potato. Currently, polymerase chain reaction (PCR) assays based on sequence differences in their ribosomal RNA genes are available for the specific diagnosis of the first two species. Using the same principles, we developed an analogous assay to detect V. tricorpus. The 18-28S rDNA intragenic region of V. tricorpus was obtained by PCR amplification of genomic DNA from the fungus. Sequence analyses indicated that the 5.8S rDNA sequences were conserved among all three Verticillium species but the internal transcribed spacer regions of V. tricorpus clearly were divergent. These sequence differences were used to synthesize a specific primer set for the diagnosis of V. tricorpus [...]
Pattern of transcription of the homeo gene Hox-3.1 in the mouse embryo. (1988)

A cDNA from the Hox-3.1 locus, isolated from a 10.5-day postcoitum (p.c.) mouse embryo cDNA library, and the putative encoded protein are described. The spatial distribution of Hox-3.1 gene transcripts from late gastrulation to embryonic day 14.5 p.c. was monitored by in situ hybridization, using a cDNA probe. When first detectable in 8.5-day p.c. embryos, the transcripts are distributed in all the tissues of the posterior end. At later stages, the distribution becomes progressively spatially restricted and tissue specific. By 12.5 days p.c., transcription is localized most intensely in the neural tube region lying above the heart. The early transcription pattern thus appears to be compatible with a regionalizing role for the Hox-3.1 gene.
Fast (Spherical) Light Field Rendering with Per-Pixel Depth (2007)

Abstract — Image-based rendering techniques are a powerful alternative to traditional polygon-based computer graphics. This paper presents a novel light field rendering technique which performs per-pixel depth correction of rays for high-quality reconstruction. Our technique stores combined RGB and depth values in a parabolic 2D texture for every light field sample acquired at discrete positions on a uniformly sampled sphere. Image synthesis is implemented on the GPU as a fragment program which extracts the correct image information from adjacent cameras for each fragment by applying a per-pixel depth correction of rays. We show that the presented image-based rendering technique provides a significant improvement compared to previous approaches. We explain two different rendering implementations which make use of a uniformly sampled parameterisation to minimize disparity problems and ensure full six degrees of freedom for virtual view synthesis. While one rendering algorithm implements a run-time efficient iterative refinement approach for rendering light fields with per pixel depth correction the other approach employs a raycaster for per pixel depth correction and provides superior rendering quality at moderate frame rates. GPU based per-fragment depth correction of rays, used in both implementations, reduces ghosting artefacts to a non noticeable amount and provides a rendering technique that performs without exhaustive pre-processing for 3D object reconstruction or real-time ray-object intersection calculations at rendering time. Index Terms—Image-Based Rendering, Light Field. 1
Focused ion beam induced optical emission spectroscopy (1988)

We describe a focused ion beam system and a spectroscopic technique that utilize photons emitted from electronically excited sputtered neutrals for surface element identification and end-point detection. When a target is bombarded by a focused ion beam, some of the sputtered atoms (as much as 0.2%) leave the surface in electronically excited states and then quickly decay (10−6–10−8 s) by emitting photons of characteristic energies. A sputter-induced optical emission spectrometer and elemental imaging system were constructed using a focused ion beam in conjunction with a wavelength-selectable photon detector. Count rates as high as 104/s have been achieved for Al and Si with a 25-keV, 1.5-nA Ga+ beam. For these materials, an unambiguous elemental identification and/or end point can be determined by spectral analysis of the emitted photons. Details of the system and its performance will be discussed. In addition, the increase in yield of electronically excited neutrals from oxides or oxidized surfaces is discussed and the utility of a small gas jet to provide oxygen to the target surface is described. Effects of redeposition are considered as they relate to end-point detection.
Fast Evaluation of Time–Harmonic Maxwell's Equations Using the Reduced Basis Method (2013)

The reduced basis method (RBM) generates low- order models for the solution of parametrized partial differential equations to allow for efficient evaluation in many-query and real-time contexts. We show the theoretical framework in which the RBM is applied to Maxwell's equations and present numerical results for model reduction in frequency domain. Using rigorous error estimators, the RBM achieves low-order models under variation of material parameters and geometry. The RBM reduces model order by a factor of 50 to 100 and reduces compute time by a factor of 200 and more for numerical experiments using standard circuit elements.