gebhart/patrepeval huggingface dataset:
Biotransformation of the Neonicotinoid Insecticide Thiacloprid by the Bacterium Variovorax boronicumulans Strain J1 and Mediation of the Major Metabolic Pathway by Nitrile Hydratase (2011)

A neonicotinoid insecticide thiacloprid-degrading bacterium strain J1 was isolated from soil and identified as Variovorax boronicumulans by 16S rRNA gene sequence analysis. Liquid chromatography-mass spectrometry and nuclear magnetic resonance analysis indicated the major pathway of thiacloprid (THI) metabolism by V. boronicumulans J1 involved hydrolysis of the N-cyanoimino group to form an N-carbamoylinino group containing metabolite, THI amide. Resting cells of V. boronicumulans J1 degraded 62.5% of the thiacloprid at a concentration of 200 mg/L in 60 h, and 98% of the reduced thiacloprid was converted to the final metabolite thiacloprid amide. A 2.6 kb gene cluster from V. boronicumulans J1 that includes the full length of the nitrile hydratase gene was cloned and investigated by degenerate primer polymerase chain reaction (PCR) and inverse PCR. The nitrile hydratase gene has a length of 1304 bp and codes a cobalt-type nitrile hydratase with an α-subunit of 213 amino acids and a β-subunit of 221 amino acids. The nitrile hydratase gene was recombined into plasmid pET28a and overexpressed in Escherichia coli BL21 (DE3). The resting cells of recombinant E. coli BL21 (DE3)-pET28a-NHase with overexpression of nitrile hydratase transformed thiacloprid to its amide metabolite, whereas resting cells of the control E. coli BL21 (DE3)-pET28a did not. Therefore, the major hydration pathway of thiacloprid is mediated by nitrile hydratase.
A Computational Study of the Interfacial Structure and Capacitance of Graphene in [BMIM][PF6] Ionic Liquid (2012)

A combination of graphene-like electrodes and ionic liquid (IL) electrolytes has emerged as a viable and attractive choice for electrochemical double layer (EDL) capacitors. Based on combined classical molecular dynamics and density functional theory calculations, we present the interfacial capacitance between planar graphene and [BMIM][PF6] IL, with particular attention to the relative contributions of the electric double layer capacitance at the graphene/IL interface and the quantum capacitance of graphene. The microstructure of [BMIM][PF6] near the graphene electrode with varying charge densities are investigated to provide a molecular description of EDLs, including BMIM/PF6 packing and orientation, cation-anion segregation, and electrode charge screening. Although the IL interfacial structures exhibit an alternative cation/anion layering extending a few nanometers, the calculated potential profiles provide evidence of one-ion thick compact EDL formation. The capacitance-potential curve of the EDL is convex- or bell-shaped, whereas the quantum capacitance of graphene is found to have concave- or U-shaped characteristics with a minimum of nearly zero. Consequently, we find that the total interfacial capacitance exhibits a U-shaped trend, consistent with existing experimental observations at a typical carbon/IL interface. Our work highlights the importance of the quantum capacitance in the overall performance of graphene-based EDL capacitors.
Probabilistic Kernels for the Classification of Auto-Regressive Visual Processes (2005)

We present a framework for the classification of visual processes that are best modeled with spatio-temporal autoregressive models. The new framework combines the modeling power of a family of models known as dynamic textures and the generalization guarantees, for classification, of the support vector machine classifier. This combination is achieved by the derivation of a new probabilistic kernel based on the Kullback-Leibier divergence (KL) between Gauss-Markov processes. In particular, we derive the KL-kernel for dynamic textures in both 1) the image space, which describes both the motion and appearance components of the spatio-temporal process, and 2) the hidden state space, which describes the temporal component alone. Together, the two kernels cover a large variety of video classification problems, including the cases where classes can differ in both appearance and motion and the cases where appearance is similar for all classes and only motion is discriminant. Experimental evaluation on two databases shows that the new classifier achieves superior performance over existing solutions.
Resveratrol: More than a phytochemical (2015)

In recent years, alternative and complementary medicine including the plant-based drugs with antioxidant and neuroptotective effects has attracted a growing interest. Resveratrol, a polyphenolic compound which is found in various plant species, has emerged as a promising nutraceutical with therapeutic potentials in neuropsychiatric, cardiometabolic and cancer diseases, also aging. The abundance of research providing promising findings about the multi-spectrum therapeutic applications of resveratrol and its encouraging potential to treat or prevent chronic and age-related disorders has raised a considerable number of clinical trials. Recently, resveratrol is implicated the biology of nerve growth factor (NGF), a critical player in the maintenance of neuronal growth and function. Furthermore, resveratrol affects the endocannabinoid signalling (eCBs) which exerts modulatory effects in the survival signalling pathways, neural plasticity, and a variety of neuroinflammatory and neurodegenerative processes. The therapeutic effects of this ubiquitous signalling system in Alzheimer`s disease, epilepsy, multiple sclerosis, mood and movement disorders, spinal cord injury, and stroke have been well-documented. In the present review, the implication of NGF and eCBs in the mechanism of action of resveratrol, that may be of therapeutic significance in neurological and non-neurological disorders, is highlighted. Biomed Rev 2015; 26: 13-21.
Development and Application of Lunar ''Concrete'' for Habitats (2006)

This paper reports the results of an ongoing research effort aimed at developing "waterless" concretes based on JSC-1 lunar regolith simulant. "Waterless" concrete, composed of lunar regolith used as an aggregate, and either a provisioned binder or a binder extracted from lunar regolith, such as sulfur, which is used as a cementitious material. The paper also presents several concepts utilizing this concrete for lunar habitat integrated construction. Integrated construction technology trade study data are presented, along with conceptual designs of these concrete application methods. Results of initial technology prototype development efforts are reported.
A Fast Algorithm for Sparse Reconstruction Based on Shrinkage, Subspace Optimization, and Continuation (2010)

We propose a fast algorithm for solving the $\ell_1$-regularized minimization problem $\min_{x\in\mathbb{R}^n}\mu\|x\|_1+\|Ax-b\|^2_2$ for recovering sparse solutions to an undetermined system of linear equations $Ax=b$. The algorithm is divided into two stages that are performed repeatedly. In the first stage a first-order iterative “shrinkage” method yields an estimate of the subset of components of x likely to be nonzero in an optimal solution. Restricting the decision variables x to this subset and fixing their signs at their current values reduces the $\ell_1$-norm $\|x\|_1$ to a linear function of x. The resulting subspace problem, which involves the minimization of a smaller and smooth quadratic function, is solved in the second phase. Our code FPC_AS embeds this basic two-stage algorithm in a continuation (homotopy) approach by assigning a decreasing sequence of values to $\mu$. This code exhibits state-of-the-art performance in terms of both its speed and its ability to recover sparse signals.
Modifications of Etioplasts in Cotyledons during Prolonged Dark Growth of Sugar Beet Seedlings (Identification of Etiolation-Related Plastidial Aminopeptidase Activities) (1994)

We studied the effects of prolonged dark growth on proplastids and etioplasts in cotyledons of sugar beet (Beta vulgaris L.) seedlings. Differentiation of proplastids into etioplasts occurred between d 4 and d 6 after imbibition, with the typical characteristics of increased synthesis of plastidial proteins, protein and carotenoid accumulation, size increase, development of plastid membranes and of the prolamellar body, and increase of the greening capacity. However, this situation of efficient greening capacity was short-lived. The greening capacity started to decline from d 6 after imbibition. This decline was due in part to reserve depletion and glucose limitation and also to irreversible damage to plastids. Indeed, electron microscopy observations in situ showed some signs of plastidial damage, such as accumulation of plastoglobuli and membrane alterations. The biochemical characterization of purified plastids also showed a decrease of proteins per plastid. Aminopeptidase activities, and to a lesser extent, neutral endopeptidase activities, were found to increase in plastids during this degenerative process. We identified two plastidial aminopeptidases showing a sharp increase of activity at the onset of the degenerative process. One of them, an alanyl aminopeptidase, was shown to be inactivated by exposure to light or addition of exogenous glucose, thus confirming the relationship with prolonged dark growth and indicating a relationship with glucose limitation.
Irregularity-Aware Graph Fourier Transforms (2018)

In this paper, we present a novel generalization of the graph Fourier transform (GFT). Our approach is based on separately considering the definitions of signal energy and signal variation, leading to several possible orthonormal GFTs. Our approach includes traditional definitions of the GFT as special cases, while also leading to new GFT designs that are better at taking into account the irregular nature of the graph. As an illustration, in the context of sensor networks we use the Voronoi cell area of vertices in our GFT definition, showing that it leads to a more sensible definition of graph signal energy even when sampling is highly irregular.
Radiative lifetime measurement of the a 3Σ+ metastable state of NO+ using a new type of electrostatic ion trap (1999)

A new type of ion trap is used to measure the radiative lifetime of the NO+(a 3Σ+) metastable state. The ion trap is designed to store ion beams with an energy of a few keV and is well suited for the study of metastable states. The measured value for the radiative lifetime is τr=760±30 ms, in good agreement with the last experimental values of Calamai and Yoshino [J. Chem. Phys. 101, 9480 (1994)], and with the theoretical value of Kuo et al. [J. Chem. Phys. 92, 4849 (1990)].
What’s So Different about Blockchain? — Blockchain is a Probabilistic State Machine (2016)

Blockchain is a distributed timestamp server technology introduced for realization of Bitcoin, a digital cash system. It has been attracting much attention especially in the areas of financial and legal applications. But such applications would fail if they are designed without knowledge of the fundamental differences in blockchain from existing technology. We show that blockchain is a probabilistic state machine in which participants can never commit on decisions, we also show that this probabilistic nature is necessarily deduced from the condition where the number of participants remains unknown. This work provides useful abstractions to think about blockchain, and raises discussion for promoting the better use of the technology.
The Escherichia coli pcnB gene promotes adenylylation of antisense RNAI of ColE1-type plasmids in vivo and degradation of RNAI decay intermediates. (1993)

Previous work has shown that RNase E-mediated cleavage of RNAI, an antisense repressor of the replication of ColE1-type plasmids, relieves repression in vivo by endonucleolytically converting RNAI to a rapidly decaying product. We report that mutations in the Escherichia coli pcnB gene result in a 10-fold prolongation of the half-life of RNAI decay intermediates and also of truncated RNAI primary transcripts lacking sites attacked by RNase E. Using Northern blotting, primer extension analysis, [32P]GTP capping of 5'-triphosphate termini, and PCR amplification methods, we show that pcnB-mediated acceleration of RNAI degradation is associated with posttranscriptional 3' addition of adenosine residues in vivo to native and processed forms of RNAI. Accumulation of antisense RNAI decay products in pcnB mutants potentially explains the reduced copy number of ColE1-type plasmids seen in the mutated bacteria.
STARTRAC analyses of scRNAseq data from tumor models reveal T cell dynamics and therapeutic targets (2021)

Single-cell RNA sequencing is a powerful tool to examine cellular heterogeneity, novel markers and target genes, and therapeutic mechanisms in human cancers and animal models. Here, we analyzed single-cell RNA sequencing data of T cells obtained from multiple mouse tumor models by PCA-based subclustering coupled with TCR tracking using the STARTRAC algorithm. This approach revealed various differentiated T cell subsets and activation states, and a correspondence of T cell subsets between human and mouse tumors. STARTRAC analyses demonstrated peripheral T cell subsets that were developmentally connected with tumor-infiltrating CD8+ cells, CD4+ Th1 cells, and T reg cells. In addition, large amounts of paired TCRα/β sequences enabled us to identify a specific enrichment of paired public TCR clones in tumor. Finally, we identified CCR8 as a tumor-associated T reg cell marker that could preferentially deplete tumor-associated T reg cells. We showed that CCR8-depleting antibody treatment provided therapeutic benefit in CT26 tumors and synergized with anti-PD-1 treatment in MC38 and B16F10 tumor models.
A theory of tie‐set graph and its application to information network management (2001)

Abstract This paper presents a new circuit theoretical concept based on the principal partition theorem for distributed network management focusing on loops of an information network. To realize a simple network management with the minimum number of local agents, namely the topological degrees of freedom of a graph, a reduced loop agent graph generated by contracting the minimal principal minor is proposed. To investigate the optimal distribution of the loop agents, a theory of tie‐set graph is proposed. Considering the total processing load of loop agents, a complexity of a tie‐set graph is introduced to obtain the simplest tie‐set graph with the minimum complexity. As for the simplest tie‐set graph search, an experimental result shows that the computational time depends heavily on the nullity of the original graph. Therefore, a tie‐set graph with the smallest nullity is essential for network management. Copyright © 2001 John Wiley &amp; Sons, Ltd.
Implementation of the Air Quality Monitoring Network at Agadir City in Morocco (2017)

Air pollution is a major global issue with widely known harmful effects on human health and the environment. This pollution is a very complex phenomenon given the diversity of pollutants that may be present in the atmosphere. The air quality in urban areas is of a great concern for residents living in cities and represents a current issue that requires an adequate management. So that air quality policy is driven by health concerns. In this paper, we present an overview on the experience of Agadir city to establish the air quality management policy, local authority on the whole have developed a good understanding of air quality in the area. Indeed for several years, efforts have been made to monitor the air quality in this city, this translated by air quality assessment since 2006 using mobile laboratory and fixed station. Our goals in this study were to review the operation of Local Air Quality Management (LAQM) making better use of available resources to improve its outcomes and make recommendations with a view to improving air quality issues. This work highlights the requirement to revise periodically the LAQM for generating priority for air quality issues within local authority and the need to implement the optimizing Air Quality Monitoring Network (AQMN).
UV Resonance Raman Detection of Artificial Sweetener in Soda Pop—Just for the Fun of it (1987)

Ultraviolet resonance Raman (UVRR) spectroscopy has recently demonstrated its potential as a powerful technique for the study of biomolecular structure and for probing chromophores in complex systems. UVRR investigations of proteins and peptides have demonstrated selective enhancement of the aromatic amino acid ring vibrations of small peptide chains and proteins. UVRR is particularly useful for studying aromatic ring systems in complicated fuel, coal liquid, and petroleum mixtures. An increase of up to six orders of magnitude in sensitivity can occur compared with that for normal Raman spectroscopy, because of the resonance phenomenon.
Universal Work Function of Metal Oxides Exposed to Air (2019)

Abstract Metal oxides are the cornerstone of thin‐film electronics, a multibillion dollar industry, because they possess a wide variety of optoelectronic properties, exhibit novel functionalities, and can typically be fabricated from cheap, nontoxic raw materials. However, for thin‐film electronics to achieve further market penetration, it is necessary to replace expensive vacuum‐based fabrication processes with low‐cost, large‐scale solution‐based methods. Here, the influence of exposure to air on the band energies of metal oxides is investigated, which is crucial for predicting the operation of thin‐film devices under realistic conditions. A universal reduction in the work function is observed across 18 oxides, and for a subset, n‐type doping of the surfaces is observed after they have been exposed to atmosphere for extended periods of time. These effects arise from charge transfer events with the ubiquitous water layer that forms on surfaces in air. A quantitative analysis of the changes is provided based on the electrochemical transfer doping model, and the amount of transferred charge and the equilibrium work function of oxides in air are calculated which are in agreement with the measurements.
Infectious Tenosynovitis in Young Turkeys (1982)

Two viruses serologically related to the tenosynovitis virus of chickens were isolated from two flocks of turkeys experiencing outbreaks of tenosynovitis. Both viruses produced a tenosynovitis when injected into the foot pad of young turkeys. Staphylococcus aureus was not isolated from either flock, nor was there any evidence of Mycoplasma synoviae antibody in either flock.
Traffic Monitoring System using Image Processing based on Rotation Vector Matching (2006)

In order to prevent traffic accidents on expressways, it is necessary to give drivers information regarding existing danger in advance. Many different sensors have been developed for detecting danger on expressways. In current traffic monitoring systems, visual sensors are often applied, and humans directly survey the expressways through monitors. However, the performance of current systems usually fails when undesirable images are generated under a poor environment such as brightness changes and low contrast. A vehicle detection method was developed based on Rotation Vector Matching, and it was confirmed that this system works effectively even when operating in a poor environment. For the covering abstract see ITRD E134653.
Activity, Folding and Z-DNA Formation of the 8-17 DNAzyme in the Presence of Monovalent Ions (2009)

The effect of monovalent ions on both the reactivity and global folding of the 8-17 DNAzyme is investigated, and the results are compared with those of the hammerhead ribozyme, which has similar size and secondary structure. In contrast to the hammerhead ribozyme, the 8-17 DNAzyme activity is not detectable in the presence of 4 M K(+), Rb(+), or Cs(+) or in the presence of 80 mM, [Co(NH(3))(6)](3+). Only 4 M Li(+), NH(4)(+) and, to a lesser extent, Na(+) conferred detectable activity. The observed rate constants (k(obs) approximately 10(-3) min(-1) for Li(+) and NH(4)(+)) are approximately 1000-fold lower than that in the presence of 10 mM Mg(2+), and approximately 200,000-fold slower than that in the presence of 100 microM Pb(2+). Since the hammerhead ribozyme displays monovalent ion-dependent activity that is often within approximately 10-fold of divalent metal ion-dependent activity, these results suggest that the 8-17 DNAzyme, obtained by in vitro selections, has evolved to have a more stringent divalent metal ion requirement for high activity as compared to the naturally occurring ribozymes, making the 8-17 DNAzyme an excellent choice as a Pb(2+) sensor with high selectivity. In contrast to the activity data, folding was observed in the presence of all the monovalent ions investigated, although those monovalent ions that do not support DNAzyme activity have weaker binding affinity (K(d) approximately 0.35 M for Rb(+) and Cs(+)), while those that confer DNAzyme activity possess stronger affinity (K(d) approximately 0.22 M for Li(+), Na(+) and NH(4)(+)). In addition, a correlation between metal ion charge density, binding affinity and enzyme activity was found among mono- and divalent metal ions except Pb(2+); higher charge density resulted in stronger affinity and higher activity, suggesting that the observed folding and activity is at least partially due to electrostatic interactions between ions and the DNAzyme. Finally, circular dichroism (CD) study has revealed Z-DNA formation with the monovalent metal ions, Zn(2+) and Mg(2+); the K(d) values obtained using CD were in the same range as those obtained from folding studies using FRET. However, Z-DNA formation was not observed with Pb(2+). These results indicate that Pb(2+)-dependent function follows a different mechanism from the monovalent metal ions and other divalent metal ions; in the presence of latter metal ions, metal-ion dependent folding and structural changes, including formation of Z-DNA, play an important role in the catalytic function of the 8-17 DNAzyme.
Cell culture models for reactive gliosis: New perspectives (1998)

Reactive gliosis, which occurs in response to any damage or disturbance to the central nervous system, has been recognized for many years, but is still not completely understood. The hallmark is the increased expression of glial fibrillary acidic protein (GFAP), yet studies in GFAP knockout mice suggest that GFAP may not be required for an astrocyte to become hypertrophic. In this review, we describe a series of tissue culture models that have been established in order to address: 1) the biochemical phenotype of reactive astrocytes; 2) the factor and/or cell responsible for induction of gliosis; 3) the mechanisms by which one might block the induction. These models range from cultures of astrocytes, both neonatal and adult, to co-cultures of astrocytes with either neurons or microglia, to organ cultures. None is ideal: each addresses a different set of questions, but taken together, they are beginning to provide useful information which should allow a better understanding of the plasticity response of astrocytes to brain injury.
Geometric registration of remotely sensed data with SAMIR (2015)

The commercial market offers several software packages for the registration of remotely sensed data through standard one-to-one image matching. Although very rapid and simple, this strategy does not take into consideration all the interconnections among the images of a multi-temporal data set. This paper presents a new scientific software, called Satellite Automatic Multi-Image Registration (SAMIR), able to extend the traditional registration approach towards multi-image global processing. Tests carried out with high-resolution optical (IKONOS) and high-resolution radar (COSMO-SkyMed) data showed that SAMIR can improve the registration phase with a more rigorous and robust workflow without initial approximations, user’s interaction or limitation in spatial/spectral data size. The validation highlighted a sub-pixel accuracy in image co-registration for the considered imaging technologies, including optical and radar imagery.