gebhart/patrepeval huggingface dataset:
Protein-DNA binding specificity predictions with structural models (2005)

Protein-DNA interactions play a central role in transcriptional regulation and other biological processes. Investigating the mechanism of binding affinity and specificity in protein-DNA complexes is thus an important goal. Here we develop a simple physical energy function, which uses electrostatics, solvation, hydrogen bonds and atom-packing terms to model direct readout and sequence-specific DNA conformational energy to model indirect readout of DNA sequence by the bound protein. The predictive capability of the model is tested against another model based only on the knowledge of the consensus sequence and the number of contacts between amino acids and DNA bases. Both models are used to carry out predictions of protein-DNA binding affinities which are then compared with experimental measurements. The nearly additive nature of protein-DNA interaction energies in our model allows us to construct position-specific weight matrices by computing base pair probabilities independently for each position in the binding site. Our approach is less data intensive than knowledge-based models of protein-DNA interactions, and is not limited to any specific family of transcription factors. However, native structures of protein-DNA complexes or their close homologs are required as input to the model. Use of homology modeling can significantly increase the extent of our approach, making it a useful tool for studying regulatory pathways in many organisms and cell types.
A Comparative In Vitro Surveillance Study of Gemifloxacin Activities against 2,632 Recent Streptococcus pneumoniae Isolates from across Europe, North America, and South America (2000)

From 1997 to 1999, 94 study centers in 15 European, 3 North American, and 2 South American countries contributed 2,632 isolates of Streptococcus pneumoniae to an international antimicrobial susceptibility testing study. Only 62.0% of isolates were susceptible to penicillin, while 22.3% were penicillin intermediate and 15.6% were penicillin resistant. Resistance to trimethoprim-sulfamethoxazole (24.4%), azithromycin (26.0%), and clarithromycin (27.1%) was also highly prevalent. For the penicillin-resistant isolates (n = 411), the MICs at which 90% of isolates are inhibited (MIC(90)s) for gemifloxacin, levofloxacin, ofloxacin, clarithromycin, and azithromycin were 0.03, 1, 2, >16, and >64 microgram/ml, respectively. Similarly, for isolates resistant to both azithromycin and clarithromycin (n = 649), gemifloxacin, levofloxacin, ofloxacin, and penicillin MIC(90)s were 0.03, 1, 2, and 4 microgram/ml, respectively. Overall rates of resistance to trovafloxacin (0.3%), levofloxacin (0.3%), grepafloxacin (0.6%), and ofloxacin (0.7%) were low. For ofloxacin-intermediate and -resistant isolates (n = 142), gemifloxacin had the lowest MIC(90) (0.12 microgram/ml) compared to the MIC(90)s of trovafloxacin (0.5 microgram/ml), grepafloxacin (1 microgram/ml), and levofloxacin (2 microgram/ml). For all S. pneumoniae isolates tested, gemifloxacin MICs were </=0.5 microgram/ml, suggesting that gemifloxacin has the potential to be used as a treatment for pneumococcal infections, including those arising from isolates resistant to beta-lactams and macrolides.
Spontaneous activity in developing turtle retinal ganglion cells: Statistical analysis (2000)

We report on the temporal properties of the spontaneous bursts of activity in the developing turtle retina. Quantitative statistical criteria were used to detect, cluster, and analyze the temporal properties of the bursts. The interburst interval, duration, firing rate, and number of spikes per burst varied widely among cells and from burst to burst in a single cell. Part of this variability was due to the positive correlation between a burst's duration and the interburst interval preceding that burst. This correlation indicated the influence of a refractory period on the bursts' properties. Further evidence of such a refractoriness came from the bursts' auto-covariance function, which gives the tendency of a spike to occur a given amount of time after another spike. This function showed a positive phase (between approximately 10 ms and 10 s) followed by a negative one (between 10 s and more than 100 s), suggestive of burst refractoriness. The bursts seemed to be propagating from cell to cell, because there was a long (symmetrically distributed) delay between the activation of two neighbor cells (median absolute delay = 2.3 s). However, the activity often failed to propagate from one cell to the other (median safety factor = 0.59). The number of spikes per burst in neighbor cells was statistically positively correlated, indicating that the activity in the two cells was driven by the same excitatory process. At least two factors contribute to the excitability during bursts, because the positive phase of the cross-covariance function (similar to auto-covariance but for two cells) had a temporally asymmetric fast component (1-3 ms) followed by a temporally symmetric slow component (1 ms to 10 s).
High accuracy retrieval with multiple nested ranker (2006)

High precision at the top ranks has become a new focus of research in information retrieval. This paper presents the multiple nested ranker approach that improves the accuracy at the top ranks by iteratively re-ranking the top scoring documents. At each iteration, this approach uses the RankNet learning algorithm to re-rank a subset of the results. This splits the problem into smaller and easier tasks and generates a new distribution of the results to be learned by the algorithm. We evaluate this approach using different settings on a data set labeled with several degrees of relevance. We use the normalized discounted cumulative gain (NDCG) to measure the performance because it depends not only on the position but also on the relevance score of the document in the ranked list. Our experiments show that making the learning algorithm concentrate on the top scoring results improves precision at the top ten documents in terms of the NDCG score.
Crystal structure of 3-(pyrazin-2-ylamino)-2-benzofuran-1(3H)-one, C12H9N3O2 (2014)

C 12 H 9 N 3 O 2 ,monoclinic, P2 1 /c (no. 14
DeepVoxels: Learning Persistent 3D Feature Embeddings (2019)

In this work, we address the lack of 3D understanding of generative neural networks by introducing a persistent 3D feature embedding for view synthesis. To this end, we propose DeepVoxels, a learned representation that encodes the view-dependent appearance of a 3D scene without having to explicitly model its geometry. At its core, our approach is based on a Cartesian 3D grid of persistent embedded features that learn to make use of the underlying 3D scene structure. Our approach combines insights from 3D geometric computer vision with recent advances in learning image-to-image mappings based on adversarial loss functions. DeepVoxels is supervised, without requiring a 3D reconstruction of the scene, using a 2D re-rendering loss and enforces perspective and multi-view geometry in a principled manner. We apply our persistent 3D scene representation to the problem of novel view synthesis demonstrating high-quality results for a variety of challenging scenes.
Uncertainty Analysis of Wideband Oxygen Sensor Based Strategy for Steady-State Biodiesel Blend Estimation (2008)

Real-time estimation and accommodation is critical for clean and efficient utilization of biodiesel blends in “fuel flexible” diesel engines. This paper utilizes a generalizable, physically-based, and experimentally-verified blend estimation strategy which uses exhaust oxygen sensor measurements coupled with engine control module (ECM) estimates of fuel and air flow to estimate the biodiesel blend fraction. The paper assesses the impact of uncertain variables on the estimation strategy. The strategy is essentially unaffected by biodiesel feedstock variations and, when applied to a Cummins 6.7-liter engine, is not susceptible to significant blend estimation discrepancies in response to expected fuel flow and oxygen sensor errors. However, observed errors in air flow estimates are expected to lead to large blend estimate errors. Use of direct air flow measurement or the use of a dynamic estimator (e.g., Kalman filter) synthesized from the model, the subject matter of future work, is expected to significantly reduce these errors.
Protein-Free Efavirenz Concentrations in Cerebrospinal Fluid and Blood Plasma Are Equivalent: Applying the Law of Mass Action To Predict Protein-Free Drug Concentration (2013)

Efavirenz (EFV) is one of the most commonly prescribed antiretroviral drugs (ARVs) for the treatment of HIV. Highly protein-bound drugs, like EFV, have limited central nervous system (CNS) penetration when measured using total drug concentration gradients between blood plasma (BP) and cerebrospinal fluid (CSF). However, the more relevant pharmacologically active protein-free drug concentrations are rarely assessed directly in clinical studies. Using paired BP and CSF samples obtained from 13 subjects on an EFV-containing regimen, both the protein-free and total concentrations of EFV were determined. Despite a median (interquartile range [IQR]) total EFV BP/CSF concentration ratio of 134 (116 to 198), the protein-free EFV BP/CSF concentration ratio was 1.20 (0.97 to 2.12). EFV median (IQR) protein binding was 99.78% (99.74 to 99.80%) in BP and 76.19% (74.47 to 77.15%) in CSF. In addition, using the law of mass action and an in vitro-derived EFV-human serum albumin dissociation constant, we have demonstrated that the predicted median (IQR) protein-free concentration in BP, 4.59 ng/ml (4.02 to 9.44 ng/ml), compared well to that observed in BP, 4.77 ng/ml (3.68 to 6.75 ng/ml). Similar results were also observed in CSF and seminal plasma. This method provides a useful predictive tool for estimating protein binding in varied anatomic compartments. Our results of equivalent protein-free EFV concentrations in BP and CSF do not support prior concerns of the CNS as a pharmacological sanctuary from EFV. As CSF penetration of ARVs may increase our understanding of HIV-associated neurological dysfunction and antiretroviral effect, assessment of protein-free CSF concentrations of other highly protein-bound ARVs is warranted.
<title>Thermal plastic metal coatings on optical fiber sensors</title> (1991)

Optical fiber sensors coated with linear work hardening elastic-plastic materials are analytically explored to determine the effects which the coating properties have on the sensor performance. The optical fiber system is subjected to both an axial load and an arbitrary thermal gradient. An important consequence of the non-linear analysis is the discovery that this coated fiber system can be exploited to serve as an alternative to the conventional fiber breakage sensor for sensing impact damage. The non-linear analysis reveals a mechanism for designing coatings which provide a 'memory' to the fiber-optic sensor by undergoing permanent deformations in response to large thermal or mechanical strain excursions. Such sensors can be utilized to maintain a permanent record of the load/damage history of a loaded structure.
Stereochemical course of the reduction of cinnamaldehyde and cinnamyl alcohol to 3-phenylpropanol by fermenting Baker's yeast (1975)

Reduction of cinnamyl alcohol by fermenting baker's yeast proceeds with formal trans addition of hydrogen across the double bond, a pro-R hydrogen atom being introduced at position 2; (1S)-3-phenyl[1-2H1]pro- panol is obtained from [formyl-2H]cinnamaldehyde and from [1-2H2]cinnamyl alcohol under the same conditions.
Enzymatic Preparation of 14C-Labeled Phytoene, Squalene, and Geranylgeranyl Pyrophosphate from [2-14C]Mevalonic Acid (1980)

Methods are described for an enzymatic preparation of 14 C-labeled terpenoids. With a cell-free system of a white mutant of Phycomyces blakesleeanus (Mucoraceae) [ 14 C]squalene and [ 14 C- cis]phytoene can be synthesized from [2- 14 C]mevalonate. The application of norflurazon, a phenyl- pyridazinone herbicide, helps to increase the yield of squalene. Furthermore, the liquid endosperm of Echinocystis lobata (Cucurbitaceae) was used for the formation of either [ 14 C(-)]kaurene from [ 14 C]mevalonic acid or [ 14 C-/ra/w]geranylgeranyl pyrophosphate in the presence of Amo 1618. The hydrocarbons formed were purified by alumina-column chromatography and preparative thin-layer chromatography (TLC). Geranylgeranyl pyrophosphate was separated by DE-column chromatography followed by TLC.
ChemInform Abstract: (μ‐Oxo)bis(trichloroferrate(III)) Dianion Revisited. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Multiple transforms for video coding (2015)

State of the art video codecs use transforms to ensure a compact signal representation. The transform stage is where compression takes place, however, little variety is observed in the type of transforms used for standardised video coding schemes: often, a single transform is considered, usually a Discrete Cosine Transform (DCT). Recently, other transforms have started being considered in addition to the DCT. For instance, in the latest video coding standard, High Efficiency Video Coding (HEVC), the 4x4 sized blocks can make use of the Discrete Sine Transform (DST) and, in addition, it also possible not to transform them. This fact reveals an increasing interest to consider a plurality of transforms to achieve higher compression rates. This thesis focuses on extending HEVC through the use of multiple transforms. After a general introduction to video compression and transform coding, two transform designs are studied in detail: the Karhunen Loeve Transform (KLT) and a Rate-Distortion Optimised Transform are considered. These two methods are compared against each other by replacing the transforms in HEVC. This experiment validates the appropriateness of the design. A coding scheme that incorporates and boosts the use of multiple transforms is introduced: several transforms are made available to the encoder, which chooses the one that provides the best rate-distortion trade-off. Consequently, a design method for building systems using multiple transforms is also described. With this coding scheme, significant amounts of bit-rate savings are achieved over HEVC, especially when using many complex transforms. However, these improvements come at the expense of increased complexity in terms of coding, decoding and storage requirements. As a result, simplifications are considered while limiting the impact on bit-rate savings. A first approach is introduced, in which incomplete transforms are used. This kind of transforms use one single base vector and are conceived to work as companions of the HEVC transforms. This technique is evaluated and provides significant complexity reductions over the previous system, although the bit-rate savings are modest. A systematic method, which specifically determines the best trade-offs between the number of transforms and bit-rate savings, is designed. This method uses two different types of transforms based separable orthogonal transforms and Discrete Trigonometric Transforms (DTTs) in particular. Several designs are presented, allowing for different complexity and bitrate savings trade-offs. These systems reveal the interest of using multiple transforms for video coding.
Morphological Transformations of Top Electrodes on YMnO<sub>3</sub> Caused by Filamentary Resistive Switching in the Oxide Matrix (2015)

Unipolar resistive switching in YMnO 3 with large-scale bottom and small-scale top electrodes is analyzed in detail by tracking the morphological transformations of the top electrodes induced by applied writing voltages. Micro-scale digital images are taken after each subsequent quasi-static current-voltage sweep. Current mapping after electrical investigations indicates a shift in the conductivity at the localized areas of the morphologically transformed top electrodes. Those changes are assigned to the heat induced structural and compositional changes within YMnO 3 which lead to the formation and rupture of conductive filaments observed as unipolar resistive switching. Presented results underline the importance of Joule heating in the fostering of resistive switching and its adverse impact on the device endurance.
Role of microRNAs in allergic asthma (2015)

There may be a potential role for using circulating miRNAs as biomarkers of disease status or response to therapy. The use of miRNAs as asthma therapy remains to be determined.
Comprehensive Multimodality Imaging Review of Complications of Penile Prostheses (2018)

Complications of a PP can be categorized into three groups: first, malpositioning, which includes buckling, floppy glans, erosion, migration, and crossover; second, mechanical failure, which includes fracture, aneurysm, and leakage; and, third, infection. Radiography, sonography, CT, and MRI are useful in the detection of these complications and complement each other, with MRI being the most useful imaging modality among them.
New ANN-Based Algorithms for Detecting HIFs in Multigrounded MV Networks (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Application of two new ANN-based algorithms for arcing high impedance fault (HIF) detection in multigrounded medium-voltage (MV) distribution networks is presented in this paper. The paper provides an evaluation of two new structures of artificial neural networks (ANNs) that may be used for reliable HIF detection in multigrounded as well as isolated, compensated, and grounded via small resistance distribution grids. The results obtained by use of both neural nets are presented. The performance was tested using data obtained from staged HIFs in real MV network as well as from Electromagnetic Transients Program–Alternative Transients Program simulations. A small number of necessary neurons in developed ANNs, short measuring sliding data window, and easy interpretation of obtained output signals are the main advantages of the proposed approach. Satisfactory results of ANN performance were observed for all examined HIF cases in which the ground fault current was greater than 16 A. The selected ANNs of best performance show high reliability and immunity to transients resulting from switching operations in protected feeders and from capacitor bank switching. </para>
Model-Based Image Processing Algorithms for CT Image Reconstruction, Artifact Reduction and Segmentation (2015)

Model-based image processing is a collection of techniques that provides a systematic framework for solving inverse problems in imaging systems. In this dissertation, three problems that arise in CT imaging systems are addressed using the model- based approach: image reconstruction for the single energy X-ray CT with both 2D parallel-beam and 3D multi-slice geometries, simultaneous image reconstruction and beam hardening correction for the single energy X-ray CT, and simultaneous metal artifact reduction and image segmentation for CT images. In the first topic, the methodology of model-based iterative reconstruction (MBIR) for solving CT image reconstruction problems is studied. Recent research indicates that the MRIR has potential to improve image quality and remove artifacts comparing to traditional filtered back-projection (FBP) methods. The MBIR algorithms for both 2D parallel-beam and 3D multi-slice helical CT geometries are developed using the formulation under the statistical framework and the reconstruction is solved using optimization techniques. The result on the real CT baggage dataset is presented, which illustrates the image quality improvement and noise and artifact reduction. The second topic studies the beam hardening correction problem in the single-energy X-ray CT. Beam hardening is the effect that material preferably attenuates more low-energy X-ray than high-energy, and with a broad X-ray source spectrum, assumption that distinct materials can be separated according to their densities, a more accurate forward model that accounts for the X-ray spectrum is developed and a MBIR algorithm that incorporates this new model is proposed. The overall algorithms works by alternating estimation of the image and the unknown model parameters, therefore no additional information is required. Results on both the simulated and real CT scan data show that the proposed method significantly reduces metal streak artifacts in the reconstruction. The third problem is the segmentation of CT images with metal artifacts and without the access to the CT data. Segmenting interesting objects from CT images has a wide range of applications in medical diagnosis and security inspection. How- ever, raw CT images often contain artifacts such as streak due to the dense metal objects, and these artifacts can make accurate segmentation difficult. A novel model- based approach that jointly estimates both the segmentation and the restored image is proposed and the unified cost function consists of three terms: 1) a data fidelity term that relates the raw and restored image and incorporates a streak mask; 2) a dictionary-based image prior which regularizes the restored image; 3) a term based on the continuous-relaxed Potts model which couples the restored image intensities and segmentation labels. Results on both simulated and real CT data are presented and support that the joint segmentation and MAR can produce superior results without the use of the raw CT data.
Heterogeneity of Mycobacterium tuberculosis strains in Makassar, Indonesia (2012)

Only a few genetically identical clustered isolates were identified within the 9-month study period, and most isolates were genetically diverse. Furthermore, 15 spoligopatterns identified in our study have not been reported previously. To our knowledge, this is the first comprehensive study describing genotypes of M. tuberculosis clinical isolates in Sulawesi.
Spoof Surface Plasmon Polaritons Power Divider with large Isolation (2018)

Periodic corrugated metal structure is designed to support and propagate spoof surface plasmon polaritons (SSPPs) wave in the microwave frequencies. In this paper, firstly a plasmonic waveguide consisting of oval-ring shaped cells is proposed with the performance of high transmission efficiency in a wide frequency range. The coplanar waveguides (CPWs) with 50 Ω impedance are adopted to feed the energies or extract signals at both ends of the plasmonic waveguide. Then a well-isolated power divider is constructed based on the SSPPs waveguides aiming to equally split the energy of the SSPPs wave into two equal parts. The stepped-impedances are co-designed with the three input/output ports of the power divider to achieve the impedance-matching between the SSPPs waveguides and the coplanar waveguides. Besides, a single resistor is placed in the middle of two symmetrical half oval-rings to realize the isolation between the two output ports over the spectrum of 4.5-7.5 GHz. Finally, both plasmonic waveguide and the power divider are fabricated and tested to verify the predicted characteristics.
Compensation of IQ imbalance in OFDM systems (2004)

Today a lot of attention is spent on developing inexpensive OFDM receivers. Especially, zero-IF receivers are very appealing, because they avoid costly IF filters. However, this implies IQ demodulation at RF, which therefore cannot be done digitally and thus introduces IQ mismatch. Unfortunately, OFDM is very sensitive to receiver IQ imbalance. Therefore, we developed a new compensation scheme to combat the IQ imbalance at baseband. In this paper, we describe the algorithm and represent the performance results. Our compensation scheme eliminates the IQ imbalance almost perfect. This leads to tremendous improvements, especially in multi-path channels (up to 10 dB performance gain), and enables low-cost zero-IF receivers.