gebhart/patrepeval huggingface dataset:
Function of Multiple Heme c Moieties in Intramolecular Electron Transport and Ubiquinone Reduction in the Quinohemoprotein Alcohol Dehydrogenase-Cytochrome c Complex of Gluconobacter suboxydans (1996)

Alcohol dehydrogenase (ADH) of acetic acid bacteria functions as the primary dehydrogenase of the ethanol oxidase respiratory chain, where it donates electrons to ubiquinone. ADH is a membrane-bound quinohemoprotein-cytochrome c complex which consists of subunits I (78 kDa), II (48 kDa), and III (14 kDa) and contains several hemes c as well as pyrroloquinoline quinone as prosthetic groups. To understand the role of the heme c moieties in the intramolecular electron transport and the ubiquinone reduction, the ADH complex of Gluconobacter suboxydans was separated into a subunit I/III complex and subunit II, then reconstituted into the complex. The subunit I/III complex, probably subunit I, contained 1 mol each of pyrroloquinoline quinone and heme c and exhibited significant ferricyanide reductase, but no Q1 reductase activities. Subunit II was a triheme cytochrome c and had no enzyme activity, but it enabled the subunit I/III complex to reproduce the Q1 and ferricyanide reductase activities. Hybrid ADH consisting of the subunit I/III complex of G. suboxydans ADH and subunit II of Acetobacter aceti ADH was constructed and it had showed a significant Q1 reductase activity, indicating that subunit II has a ubiquinone-binding site. Inactive ADH from G. suboxydans exhibiting only 10% of the Q1 and ferricyanide reductase activities of the active enzyme has been isolated separately from active ADH (Matsushita, K., Yakushi, T., Takaki, Y., Toyama, H., and Adachi, O (1995) J. Bacteriol. 177, 6552-6559). Using these active and inactive ADHs and also isolated subunit I/III complex, we performed kinetic studies which suggested that ADH contains four ferricyanide-reacting sites, one of which was detected in subunit I and the others in subunit II. One of the three ferricyanide-reacting sites in subunit II was defective in inactive ADH. The ferricyanide-reacting site remained inactive even after alkali treatment of inactive ADH and also after reconstituting the ADH complex from the subunits, in contrast to the restoration of Q1 reductase activity and the other ferricyanide reductase activities. Thus, the data suggested that the heme c in subunit I and two of the three heme c moieties in subunit II are involved in the intramolecular electron transport of ADH into ubiquinone, where one of the two heme c sites may work at, or close to, the ubiquinone-reacting site and another between that and the heme c site in subunit I. The remaining heme c moiety in subunit II may have a function other than the electron transfer from ethanol to ubiquinone in ADH.
Advances in heat and mass transfer in biotechnology, 1997 : presented at the 1997 ASME International Mechanical Engineering Congress and Exposition, November 16-21, 1997, Dallas, Texas (1997)

In this compilation by Clegg (Duke U.) of 32 of the conference technical papers prefaced by section introductions, the major foci are on: heat and mass transfer in cells and biomolecules; bioheat mass transfer under microgravity conditions; bioprocessing of cells for gene therapy and tissue engineer
Quantification of Escherichia coli by kinetic 5'-nuclease polymerase chain reaction (real-time PCR) oriented to sfmD gene (2005)

In connection to an appropriate sample preparation technique, the method is suitable for food safety and technological hygiene applications.
Varicella-Zoster Virus ORF63 Inhibits Apoptosis of Primary Human Neurons (2005)

Virus-encoded modulation of apoptosis may serve as a mechanism to enhance cell survival and virus persistence. The impact of productive varicella-zoster virus (VZV) infection on apoptosis appears to be cell type specific, as infected human sensory neurons are resistant to apoptosis, yet human fibroblasts readily become apoptotic. We sought to identify the viral gene product(s) responsible for this antiapoptotic phenotype in primary human sensory neurons. Treatment with phosphonoacetic acid to inhibit viral DNA replication and late-phase gene expression did not alter the antiapoptotic phenotype, implicating immediate-early (IE) or early genes or a virion component. Compared to the parental VZV strain (rOKA), a recombinant virus unable to express one copy of the diploid IE gene ORF63 (rOka deltaORF63) demonstrated a significant induction of apoptosis in infected neurons, as determined by three methods: annexin V staining, deoxynucleotidyltransferase-mediated dUTP-biotin nick end label staining, and transmission electron microscopy. Furthermore, neurons transfected with a plasmid expressing ORF63 resisted apoptosis induced by nerve growth factor withdrawal. These results show that ORF63 can suppress apoptosis of neurons and provide the first identification of a VZV gene encoding an antiapoptotic function. As ORF63 is expressed in neurons during both productive and latent infection, it may play a significant role in viral pathogenesis by promoting neuron survival during primary and reactivated infections.
Standard methods for research on<i>Apis mellifera</i>gut symbionts (2013)

SummaryGut microbes can play an important role in digestion, disease resistance, and the general health of animals, but little is known about the biology of gut symbionts in Apis mellifera. As part of the BEEBOOK series describing honey bee research methods, we provide standard protocols for studying gut symbionts. We describe non-culture-based approaches based on Next Generation Sequencing (NGS), methodology that has greatly improved our ability to identify the microbial communities associated with honey bees. We also describe Fluorescent In Situ Hybridization (FISH) microscopy, which allows a visual examination of the microenvironments where particular microbes occur. Culturing methods are also described, as they allow the researcher to isolate particular bacteria of interest for further study or gene identification, and enable the assignment of particular functions to particular gut community members. We hope these methods will help others advance the state of knowledge regarding bee gut symbionts and the role they play in honey bee health.
An efficient FPGA overlay for portable custom instruction set extensions (2013)

Custom instruction set extensions can substantially boost performance of reconfigurable softcore CPUs. While this approach is commonly tailored to one specific FPGA system, we are presenting a fine-grained FPGA-like overlay architecture which can be implemented in the user logic of various FPGA families from different vendors. This allows the execution of a portable application consisting of a program binary and an overlay configuration in a completely heterogeneous environment. Furthermore, we are presenting different optimizations for dramatically reducing the implementation cost of the proposed overlay architecture. In particular, this includes the mapping of the overlay interconnection network directly into the switch fabric of the hosting FPGA. Our case study demonstrates an overhead reduction of an order of magnitude as compared to related approaches.
A luminescence lifetime assisted ratiometric fluorimeter for biological applications (2009)

In general, the most difficult task in developing devices for fluorescence ratiometric sensing is the isolation of signals from overlapping emission wavelengths. Wavelength discrimination can be achieved by using monochromators or bandpass filters, which often lead to decreased signal intensities. The result is a device that is both complex and expensive. Here we present an alternative system--a low-cost standalone optical fluorimeter based on luminescence lifetime assisted ratiometric sensing (LARS). This paper describes the principle of this technique and the overall design of the sensor device. The most significant innovation of LARS is the ability to discriminate between two overlapping luminescence signals based on differences in their luminescence decay rates. Thus, minimal filtering is required and the two signals can be isolated despite significant overlap of luminescence spectra. The result is a device that is both simple and inexpensive. The electronic circuit employs the lock-in amplification technique for the signal processing and the system is controlled by an onboard microcontroller. In addition, the system is designed to communicate with external devices via Bluetooth.
Timing estimation for a filtered Poisson process in Gaussian noise (1991)

The problem of estimation of time shift of an inhomogeneous casually filtered Poisson process in the presence of additive Gaussian noise is discussed. Approximate expressions for the likelihood function, the MAP estimator, and the MMSE estimator that becomes increasingly accurate as the per-unit-time density of superimposed filter responses becomes small are obtained. The optimal MAP estimator takes the form of a cascade of linear and memoryless nonlinear components. For smooth point process intensities, the performance of the MAP estimator is studied via local bias and local variance. A rate distortion type lower bound on the MSE of any estimator of time delay is then derived by identification of a communications channel that accounts for the mapping from time delay to observation process. Results of numerical studies of estimator performance are presented. Based on the examples considered it is concluded: (1) the small-error MSE of the nonlinear MAP estimator can be significantly better than the small-error MSE of the optimal linear estimator: (2) the rate distortion lower bound can be significantly tighter than the Poisson limited bounds determined in previous studies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Novel presenilin-1 mutation with widespread cortical amyloid deposition but limited cerebral amyloid angiopathy (2000)

The N405S mutation of PS1 is a major determinant of cortical Abeta deposition but not cerebral amyloid angiopathy in Alzheimer's disease.
Left-ventricular geometry and risk of sudden cardiac arrest in patients with preserved or moderately reduced left-ventricular ejection fraction (2016)

Concentric and eccentric LV hypertrophy, but also concentric remodelling without hypertrophy, are associated with increased risk of SCA. These novel findings suggest the potential utility of evaluating LV geometry as a potential risk stratification tool in patients with preserved or moderately reduced LVEF.
Ultrastructural studies on the cells in vivo, in vitro of ameloblastoma. (1986)

Ameloblastoma in the maxilla is relatively rare even though this tumor is most frequently seen among odontogenic tumors.We had a chance to treat a case of ameloblastoma (follicular type) in the maxilla which seemed to be clinically at first a malignant tumor and took primary culture cells from the tumor tissue.Ultrastructural observation of the cells in vivo and in vitro were performed.In the cells in vitro, nucleus was round and nucleolonema in the nucleoli were recognized. In the cytoplasm, many lysosomes were found and the number of rough endoplasmic reticulum was not so large as in vivo.The cells in vitro resembled columnar epithelial cells in vivo.As compared with the active cells in vivo, the cells in vitro had few organella.
Device for continuous extracorporeal blood purification using target-specific metal nanomagnets (2011)

Magnetic separation can be successfully implemented into an extracorporeal blood purification device. Simultaneous and specific filtering of high-molecular compounds may offer promising new therapeutic tools for the future treatment of complex diseases, such as sepsis and autoimmune disorders.
Counting people from multiple cameras (2003)

We are interested in the content analysis of video from a collection of spatially distant cameras viewing a single environment. We address the task of counting the number of different people walking through such an environment, which requires that the system can identify which observations from different cameras show the same person. Our system achieves this by combining visual appearance matching with mutual content constraints between the cameras. We present results from a system with four very different camera views that counts people walking through and around a research lab.
Electron emission observations from as-grown and vacuum-coated chemical vapor deposited diamond (2002)

Field emission has been observed from Chemical Vapor Deposited (CVD) diamond grown on Mo and Si substrates. Emission was observed at fields as low as 20 kV/cm. The samples were tested in the as-grown form, and after coating with thin films of Au, CsI and Ni. The emission current was typically maximum at the onset of the applied field, but was unstable, and decreased rapidly with time from the as-grown films. Thin Au layers, /spl sim/15 nm thick, vacuum deposited onto the diamond samples significantly improved the stability of the emission current at values approximately equal to those from uncoated samples at the onset of the applied field. Thin layers of CsI, /spl sim/5 nm thick, were also observed to improve the stability of the emission current but at values less than those from the uncoated samples at the onset of the applied field. While, Au and Csl improved the stability of the emission, Ni was observed to have no effect.
1.9 picosecond optical temporal analyzer using 1.2 picosecond photodetector and gate (1991)

The authors report on a novel photoconductive-type detector with a response time of 1.2 ps. This is the fastest photodetector to date. It is based on low-temperature-grown GaAs and uses interdigitated electrodes of 0.2 mu m spacing to match the carrier transit time to the carrier lifetime. The responsivity is 0.1 A/W. The detector can be driven to an on-state resistance of a few of ohms, with the response time increasing to only 1.5 ps. The photodetector can therefore also function as a picosecond photogate. The two components have been combined to form an all-semiconductor optical temporal analyzer. The system response time is 1.9 ps, with a minimum detectable average power of 500 pW. The technique is jitter-free, permitting long integration times. Ultraweak picosecond fluorescence and scattering experiments, as well as other ultrafast phenomena can be time-resolved using this relatively simple tool.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Quantitative measurement of MLC leaf displacements using an electronic portal image device (2004)

The success of an IMRT treatment relies on the positioning accuracy of the MLC (multileaf collimator) leaves for both step-and-shoot and dynamic deliveries. In practice, however, there exists no effective and quantitative means for routine MLC QA and this has become one of the bottleneck problems in IMRT implementation. In this work we present an electronic portal image device (EPID) based method for fast and accurate measurement of MLC leaf positions at arbitrary locations within the 40 cm x 40 cm radiation field. The new technique utilizes the fact that the integral signal in a small region of interest (ROI) is a sensitive and reliable indicator of the leaf displacement. In this approach, the integral signal at a ROI was expressed as a weighted sum of the contributions from the displacements of the leaf above the point and the adjacent leaves. The weighting factors or linear coefficients of the system equations were determined by fitting the integral signal data for a group of pre-designed MLC leaf sequences to the known leaf displacements that were intentionally introduced during the creation of the leaf sequences. Once the calibration is done, the system can be used for routine MLC leaf positioning QA to detect possible leaf errors. A series of tests was carried out to examine the functionality and accuracy of the technique. Our results show that the proposed technique is potentially superior to the conventional edge-detecting approach in two aspects: (i) it deals with the problem in a systematic approach and allows us to take into account the influence of the adjacent MLC leaves effectively; and (ii) it may improve the signal-to-noise ratio and is thus capable of quantitatively measuring extremely small leaf positional displacements. Our results indicate that the technique can detect a leaf positional error as small as 0.1 mm at an arbitrary point within the field in the absence of EPID set-up error and 0.3 mm when the uncertainty is considered. Given its simplicity, efficiency and accuracy, we believe that the technique is ideally suitable for routine MLC leaf positioning QA.
Heart rate variability is severely impaired among type 2 diabetic patients with hypertension (2013)

Diabetes appears to have a greater effect on autonomic dysfunction compared with hypertension. Patients suffering from both diabetes and hypertension are at the highest risk of reduced heart rate variability. Early assessment of the autonomic nerve function is suggested in diabetic patients with hypertension.
Phosphate removal in real anaerobic supernatants: modelling and performance of a fluidized bed reactor (1998)

Phosphate removal in anaerobic supernatant coming from a centrifugation sludge station of an A2O process is studied. A fluidized bed reactor is employed to crystallize phosphate as hydroxyapatite or struvite using only air stripping to reach the supersaturation pH. The classic composition of supernatant (alkalinity 3550 mgCaCO3/l, PO4 139 mg/l, Mg 24 mg/l) does not require any addition of chemicals for phosphate removal. Seventeen runs are performed in a bench scale FBR obtaining very high conversion and removal efficiency and phosphate loss in the effluent ≤3.5%. The use of Ca or Mg enriched supernatant has no meaningful influence on efficiency, but it determines the prevalent salt formed between MAP or HAP. Efficiency can be related to pH and sand contact time in a double saturational model. The half efficiency constants: 0.075 h for t and 7.75 pH, have an important role in the process knowledge and optimization of plant design. Exhaust sand analysis indicates the same composition at the top, bottom and mean of the sand bed (39% mol MAP and 61% mol HAP). This result together with the high half efficiency constant for contact time indicate that the phosphate growth on the bed is not competitive. Finally, the phosphate release from the plant is studied. Results show a weak release rate, equivalent to 2.8-10% d−1 phosphate as MAP, obtained at an operative pH range of 8.1-8.4.
Strategy-based feedback in a programming tutor (2014)

More and more people take up learning how to program: in schools and universities, in large open online courses or by learning it by themselves. A large number of tools have been developed over the years to support learners with the difficult task of building programs. Many of these tools focus on the resulting program and not on the process: they fail to help the student to take the necessary steps towards the final program.
Ignition of Propane&amp;ndash;Air Mixtures by a Repetitively Pulsed Nanosecond Discharge (2006)

Results of an experimental study of the efficiency of the ignition of propane-air mixtures by a high voltage repetitively pulsed nanosecond gas discharge (10 kV, 10 ns, 30 kHz) are presented for the pressure range 0.35-2.0 bar. The measured minimal energy for ignition is found to decrease with the pressure. A significant reduction of the ignition delay and a decrease of the overall combustion duration were obtained by using a train of high-voltage pulses. Spectroscopic measurements in a 1-bar air just after a 10-pulse train (300 mus) of about 10 mJ in total energy show the presence of N, N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> , O, and O <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> atomic species and a gas temperature increase up to 3000 K
Statistical interconnect metrics for physical-design optimization (2006)

In this paper, statistical models for the efficient analysis of interconnect delay and crosstalk noise in the presence of back-end process variations are developed. The proposed models enable closed-form computation of means and variances of interconnect-delay, crosstalk-noise peak, and coupling-induced-delay change for given magnitudes of variation in relevant process parameters, such as linewidth, metal thickness, metal spacing, and interlayer dielectric (ILD) thickness. The proposed approach is based on the observation that if the variations in different physical dimensions are assumed to be independent normal random variables, then the interconnect behavior also tends to have a Gaussian distribution. In the proposed statistical models, delay and noise are expressed directly as functions of changes in physical parameters. This formulation allows us to preserve all correlations and can be very useful in evaluating delay and noise sensitivities due to changes in various physical dimensions. For interconnect-delay computation, the authors express the resistance and capacitance of a line as a linear function of random variables and then use these to compute circuit moments. They show that ignoring higher order terms in the resulting variational moments does not result in a loss of accuracy. Finally, these variability-aware moments are used in known closed-form delay and slew metrics to compute interconnect-delay probability density functions (pdfs). Similarly for coupling noise and dynamic-delay analysis, the authors rely on the linearity (Gaussian) assumption, allowing us to truncate nonlinear terms and express noise and dynamic-delay pdfs as linear functions of variations in relevant geometric dimensions. They compare their approach to SPICE-based Monte Carlo simulations and report the error in mean and standard deviation of interconnect delay to be 1% and 4% on average, respectively
Linking Image and Text with 2-Way Nets (2017)

Linking two data sources is a basic building block in numerous computer vision problems. Canonical Correlation Analysis (CCA) achieves this by utilizing a linear optimizer in order to maximize the correlation between the two views. Recent work makes use of non-linear models, including deep learning techniques, that optimize the CCA loss in some feature space. In this paper, we introduce a novel, bi-directional neural network architecture for the task of matching vectors from two data sources. Our approach employs two tied neural network channels that project the two views into a common, maximally correlated space using the Euclidean loss. We show a direct link between the correlation-based loss and Euclidean loss, enabling the use of Euclidean loss for correlation maximization. To overcome common Euclidean regression optimization problems, we modify well-known techniques to our problem, including batch normalization and dropout. We show state of the art results on a number of computer vision matching tasks including MNIST image matching and sentence-image matching on the Flickr8k, Flickr30k and COCO datasets.