Miracle-dz/UniFAR-FTUs huggingface dataset:
A Survey of Overlooked Viral Infections in Biological Experiment Systems

It is commonly accepted that there are many unknown viruses on the planet. For the known viruses, do we know their prevalence, even in our experimental systems? Here we report a virus survey using recently published small (s)RNA sequencing datasets. The sRNA reads were assembled and contigs were screened for virus homologues against the NCBI nucleotide (nt) database using the BLASTn program. To our surprise, approximately 30% (28 out of 94) of publications had highly scored viral sequences in their datasets. Among them, only two publications reported virus infections. Though viral vectors were used in some of the publications, virus sequences without any identifiable source appeared in more than 20 publications. By determining the distributions of viral reads and the antiviral RNA interference (RNAi) pathways using the sRNA profiles, we showed evidence that many of the viruses identified were indeed infecting and generated host RNAi responses. As virus infections affect many aspects of host molecular biology and metabolism, the presence and impact of viruses needs to be actively investigated in experimental systems.
The S-Domain Receptor Kinase Arabidopsis Receptor Kinase2 and the U Box/Armadillo Repeat-Containing E3 Ubiquitin Ligase9 Module Mediates Lateral Root Development under Phosphate Starvation in Arabidopsis1[C][W][OPEN]

Autophagy plays an important role during lateral root development under phosphate starvation. When plants encounter nutrient-limiting conditions in the soil, the root architecture is redesigned to generate numerous lateral roots (LRs) that increase the surface area of roots, promoting efficient uptake of these deficient nutrients. Of the many essential nutrients, reduced availability of inorganic phosphate has a major impact on plant growth because of the requirement of inorganic phosphate for synthesis of organic molecules, such as nucleic acids, ATP, and phospholipids, that function in various crucial metabolic activities. In our screens to identify a potential role for the S-domain receptor kinase1-6 and its interacting downstream signaling partner, the Arabidopsis (Arabidopsis thaliana) plant U box/armadillo repeat-containing E3 ligase9 (AtPUB9), we identified a role for this module in regulating LR development under phosphate-starved conditions. Our results show that Arabidopsis double mutant plants lacking AtPUB9 and Arabidopsis Receptor Kinase2 (AtARK2; ark2-1/pub9-1) display severely reduced LRs when grown under phosphate-starved conditions. Under these starvation conditions, these plants accumulated very low to no auxin in their primary root and LR tips as observed through expression of the auxin reporter DR5::uidA transgene. Exogenous auxin was sufficient to rescue the LR developmental defects in the ark2-1/pub9-1 lines, indicating a requirement of auxin accumulation for this process. Our subcellular localization studies with tobacco (Nicotiana tabacum) suspension-cultured cells indicate that interaction between ARK2 and AtPUB9 results in accumulation of AtPUB9 in the autophagosomes. Inhibition of autophagy in wild-type plants resulted in reduction of LR development and auxin accumulation under phosphate-starved conditions, suggesting a role for autophagy in regulating LR development. Thus, our study has uncovered a previously unknown signaling module (ARK2-PUB9) that is required for auxin-mediated LR development under phosphate-starved conditions.
Monitoring coral reefs from space

Coral reefs are one of the world’s most biologically diverse and productive ecosystems. However, these valuable resources are highly threatened by human activities. Satellite remotely sensed observations enhance our understanding of coral reefs and some of the threats facing them by providing global spatial and time-series data on reef habitats and the environmental conditions influencing them in near-real time. This review highlights many of the ways in which satellites are currently used to monitor coral reefs and their threats, and provides a look toward future needs and capabilities.
A Framework for Recognizing Multi-Agent Action from Visual Evidence

A probabilistic framework for representing and visually recognizing complex multi-agent action is presented. Motivated by work in model-based object recognition and designed for the recognition of action from visual evidence, the representation has three components: (1) temporal structure descriptions representing the temporal relationships between agent goals, (2) belief networks for probabilistic ally representing and recognizing individual agent goals from visual evidence, and (3) belief networks automatically generated from the temporal structure descriptions that support the recognition of the complex action. We describe our current work on recognizing American football plays from noisy trajectory data.
Effect of anthracycline antibiotics on oxygen radical formation in rat heart.

This investigation examined the effect of the anthracycline antitumor agents on reactive oxygen metabolism in rat heart. Oxygen radical production by doxorubicin, daunorubicin, and various anthracycline analogues was determined in heart homogenate, sarcoplasmic reticulum, mitochondria, and cytosol, the major sites of cardiac damage by the anthracycline drugs. Superoxide production in heart sarcosomes was significantly increased by anthracycline treatment; for doxorubicin, the reaction appeared to follow saturation kinetics with an apparent Km of 112.62 microM, required NADPH as cofactor, was accompanied by the accumulation of hydrogen peroxide, and probably resulted from the transfer of electrons to molecular oxygen by the doxorubicin semiquinone after reduction of the drug by sarcosomal NADPH:cytochrome P-450 reductase (NADPH:ferricytochrome oxidoreductase, EC 1.6.2.4). Superoxide formation was also significantly enhanced by the anthracycline antibiotics in the mitochondrial fraction. Doxorubicin stimulated mitochondrial superoxide formation in a dose-dependent manner that also appeared to follow saturation kinetics (apparent Km of 454.55 microM); however, drug-related superoxide production by mitochondria required NADH rather than NADPH and was significantly increased in the presence of rotenone, which suggested that the proximal portion of the mitochondrial NADH dehydrogenase complex [NADH:(acceptor) oxidoreductase, EC 1.6. 99.3] was responsible for the reduction of doxorubicin at this site. In heart cytosol, anthracycline-induced superoxide formation and oxygen consumption required NADH and were significantly reduced by allopurinol, a potent inhibitor of xanthine oxidase (xanthine:oxygen oxidoreductase, EC 1.2.3.2). Reactive oxygen production was detected in all of our studies despite the presence of both superoxide dismutase (superoxide:superoxide oxidoreductase, EC 1.15.1.1) and glutathione peroxidase (glutathione:hydrogen peroxide oxidoreductase, EC 1.11.1.9) in each cardiac fraction. These results suggest that free radical formation by the anthracycline antitumor agents, which occurs in the same myocardial compartments that are subject to drug-induced tissue injury, may damage the heart by exceeding the oxygen radical detoxifying capacity of cardiac mitochondria and sarcoplasmic reticulum.
Effects of Canary hotspot volcanism on structure of oceanic crust off Morocco

Analysis of over 6400 km of multichannel seismics (MCS) and 50 sonobuoy reflection and refraction experiments reduced both in the domain of X-T and tau-p shows that a region within the Jurassic Quiet Zone off Morocco underwent dramatic changes as a result of the passage of the lithosphere over the Canary hotspot commencing approximately 60 Ma. A seismic unit (UCF), interpreted as volcanic in origin, is observed within the sediments in a region characterized by a broad bathymetric swell. It shows diffractions from its upper surface and an internally chaotic seismic facies and pinches out between sedimentary units of continuous, subparallel facies. A velocity inversion is noted between the UCF (4.7km/s) and the underlying sediment (3.1 km/s). The UCF is time transgressive; it lies near the Cretaceous/s Tertiary boundary in the northern portion of the study area and is younger to the south. Kinematic studies of the movement of the Canary hotspot relative to Africa show that the hotspot first appeared off NW Africa about 60 Ma and was located beneath oceanic crust in the region where the UCF is observed. Depth-to-basement measurements in areas not effected by the hotspot show a consistent linear trend of increased depth with age. In areas effected by the hotspot the thermal rejuvenation is evident as basement depths shoal with increased proximity to the present hotspot. The reheating of the crust resets the thermal age of the lithosphere with many of the properties of crust of a younger age. Subsidence curves of the reheated crust off Morocco show good correlation to subsidence curves of other reheated crust on a global basis. A zone characterized by high crustal velocities, (7.1–7.4 km/s) and greater crustal thicknesses (by ∼1–2 km) is observed in an area that corresponds to the bathymetric swell, the region of the UCF, and the reelevated basement. The high velocities and increased crustal thickness are interpreted to be the result of underplating and assimilation of existing oceanic crust caused by the Canary thermal anomaly. The presence of high crustal velocities coupled with a thickened crustal section has been noted on various passive margins of the world. They have generally been attributed to the thermal processes associated with continental rifting. Off Morocco, we believe that similar, thermally induced phenomena have occurred but that here; the heat anomaly was the midplate volcanism associated with the Canary hotspot.
Nitric oxide: pathophysiological mechanisms.

Nitric oxide is a double-edged sword. Produced by mammalian cells at an appropriate magnitude and tempo, it serves as a key signaling molecule in physiological processes as diverse as host-defense, neuronal communication, and vascular regulation (for reviews, see 13 1 , 1 32, 172). On the other hand, excessive and unregulated NO synthesis has been implicated as causal or contributing to pathophysiological conditions induding many lethal and de­ bilitating diseases of humans: vascular shock, stroke, diabetes, neurodegenera­ tion, arthritis, and chronic inflammation. Contrary to conventional biosignaling molecules that act by binding to specific receptor molecules, NO manifests its biological actions via a wide range of chemical reactions. NO is a small, relatively stable, free-radical gas that readily diffuses into cells and cell mem­ branes where it reacts with molecular targets. The precise reactions, which are realized in any biological setting, depend on the concentration of NO achieved and often on subtle variations in the composition of the intraand extracellular milieu. This review summarizes the present knowledge of cellular events that lead to NO overproduction in mammalian systems and discusses reactions of NO that may contribute to cell damage or death. Our primary aim is to interpret rather than exhaustively summarize the large body of accumulated NO litera-
Structural analysis of the Sulfolobus solfataricus MCM protein N-terminal domain†

The Mini-Chromosome Maintenance (MCM) proteins are candidates of replicative DNA helicase in eukarya and archaea. Here we report a 2.8 Å crystal structure of the N-terminal domain (residues 1–268) of the Sulfolobus solfataricus MCM (Sso MCM) protein. The structure reveals single-hexameric ring-like architecture, at variance from the protein of Methanothermobacter thermoautotrophicus (Mth). Moreover, the central channel in Sso MCM seems significantly narrower than the Mth counterpart, which appears to more favorably accommodate single-stranded DNA than double-stranded DNA, as supported by DNA-binding assays. Structural analysis also highlights the essential role played by the zinc-binding domain in the interaction with nucleic acids and allows us to speculate that the Sso MCM N-ter domain may function as a molecular clamp to grasp the single-stranded DNA passing through the central channel. On this basis possible DNA unwinding mechanisms are discussed.
Firewatch: Use Of Satellite Imagery By Remote Communities In Northern Australia For Fire Risk Communications

This paper presents the contextual background and early findings from a new research project funded by the Australian Research Council titled Using community engagement and enhanced visual information to promote FireWatch satellite communications as a support for collaborative decision-making. FireWatch (provided by Landgate in Western Australia) is an internet-based public information service based on near real time satellite data showing timely information relevant to bushfire safety within Australia. However, it has been developed in a highly technical environment and is currently used chiefly by experts. This project aims to redesign FireWatch for ordinary users and to engage a remote community in Northern Australia in this process, leading to improved decision making surrounding bushfire risk.
Impact of atmospheric forcing data on simulations of the Laptev Sea polynya dynamics using the sea‐ice ocean model FESOM

The polynyas of the Laptev Sea are regions of particular interest due to the strong formation of Arctic sea-ice. In order to simulate the polynya dynamics and to quantify ice production, we apply the Finite Element Sea-Ice Ocean Model FESOM. In previous simulations FESOM has been forced with daily atmospheric NCEP (National Centers for Environmental Prediction) 1. For the periods 1 April to 9 May 2008 and 1 January to 8 February 2009 we examine the impact of different forcing data: daily and 6-hourly NCEP reanalyses 1 (1.875° × 1.875°), 6-hourly NCEP reanalyses 2 (1.875° × 1.875°), 6-hourly analyses from the GME (Global Model of the German Weather Service) (0.5° × 0.5°) and high-resolution hourly COSMO (Consortium for Small-Scale Modeling) data (5 km × 5 km). In all FESOM simulations, except for those with 6-hourly and daily NCEP 1 data, the openings and closings of polynyas are simulated in principle agreement with satellite products. Over the fast-ice area the wind fields of all atmospheric data are similar and close to in situ measurements. Over the polynya areas, however, there are strong differences between the forcing data with respect to air temperature and turbulent heat flux. These differences have a strong impact on sea-ice production rates. Depending on the forcing fields polynya ice production ranges from 1.4 km3 to 7.8 km3 during 1 April to 9 May 2011 and from 25.7 km3 to 66.2 km3 during 1 January to 8 February 2009. Therefore, atmospheric forcing data with high spatial and temporal resolution which account for the presence of the polynyas are needed to reduce the uncertainty in quantifying ice production in polynyas.
Keeping global change honest

In my reading and travels I frequently come across statements regarding the importance of biological cycles in the ocean to the uptake of CO2 produced by fossil fuel burning and forest cutting. While these are often prefaced with an admission that physical processes are more important, the listener or reader comes away with a feeling that somehow biology has a very important role to play. This supposed importance is being used as a defense for the funding of a wide range of biologically oriented ocean programs. I challenge this defense.
Performance of generalized multicarrier DS-CDMA using various chip waveforms

We extend our investigation of generalized multicarrier direct-sequence code-division multiple access by considering two additional types of chip waveforms, namely, the time-domain half-sine and raised-cosine chip waveforms, in addition to the rectangular chip waveform. A range of closed-form equations are provided for quantifying the effect of both the multipath interference and the multiuser interference, when using partially overlapping subcarriers. These closed-form formulas allow us to evaluate the bit-error rate performance of arbitrary code-division multiple access schemes using overlapping subbands with the aid of the standard Gaussian approximation.
Overview of IgG4 – Related Disease

Rationale (hypothesis): IgG4-related disease (IgG4-RD) is a pathological entity recently recognized by the medical world that can affect any organ or system. However, there is insufficient data about this disease in medical literature. Aim (objective): A more extensive clarification of the IgG4 molecule, the diversified aspects of IgG4-related disease, and the response of this disease to treatment, will provide a crucial understanding of the immune system and other diseases now known to be associated with IgG4. Methods and results: The MEDLINE online medical database was used, and, after a comprehensive review of medical articles regarding IgG4-RD, published after 2003, using the search words “IgG4- related disease” and “IgG4 molecule”, we have described the clinical, pathological and therapeutic features of IgG4-RD, as well as the presence of the IgG4 molecule in the evolution, diagnosis and management of this syndrome. We characterized the potential disease mechanisms and discussed early observations related to treatment. Discussion: Given the response to immunosuppressive therapy, it is hypothesized that IgG4-related disease is most likely an autoimmune disease. Therefore, IgG4-related disease is a fibro-inflammatory condition that can affect any organ and can lead to the formation of pseudotumoral lesions requiring differential diagnosis with various malignancies. Positive diagnostic criteria are histopathological and require at least two features out of the following three: dense limphoplasmocitary infiltrate, storiform fibrosis, obliterative phlebitis.
Norges Teknisk-naturvitenskapelige Universitet on Discontinuous Galerkin Methods and Commutator-free Exponential Integrators for Advection Problems on Discontinuous Galerkin Methods and Commutator-free Exponential Integrators for Advection Problems

preprint numerics no. 6/2011 norwegian university of science and technology trondheim, norway Discontinuous Galerkin (DG) finite-element methods are well-known to be suitable for solving convection-dominated convection diffusion problems. High order Runge-Kutta methods such as the RKDG and SSP methods have been developed and tested to work quite well for convection-dominated problems(see e. An issue of concern remains the strong CFL restrictions on the discretization parameters. Restelli et al. (2006) proposed combining the DG methods with the semi-Lagrangian methods in what they called semi-Lagragian discontinuous Galerkin (SLDG) methods. Proposed implementations of the SLDG methods however suffer from limited spatial accuracy as opposed to the RKDG methods. We hereby propose a method in the framework of Lie-group exponential integrators (see Cellodoni et al. [6, 5]), that uses a modified version of the SLDG method as a building block for computing compositions of convection flows and maintain the good properties of the DG formulations.
The Ultrastructure of the Heart in Systole and Diastole: >Changes In Sarcomere Length

The relations between ultrastructure and function have been examined in the canine left ventricle under known hemodynamic conditions. Left ventricles of normal dogs were fixed acutely by rapid perfusions of the coronary arteries in either diastole or systole, and also following acute ventricular distension, or potentiation of contraction. Sarcomere lengths at the midwall of the left ventricle averaged 2.07 μ at end diastole and 1.81 μ at end systole, changes that are adequate to explain the degree of normal ventricular emptying. Following marked ventricular emptying induced by postextrasystolic potentiation, sarcomeres shortened to an average of 1.60 μ; with acute ventricular distension resulting from over-transfusion, average sarcomere length in diastole increased to 2.25 μ. In each instance, sarcomere lengths correlated with the changes in sarcomere length predicted from changes in the dimensions of a thick-walled sphere. The importance of dispersion of sarcomere length within a given layer of the ventricular wall was noted and its potential significance discussed.
Data hiding on 3-D triangle meshes

In this paper, we present a new scheme for digital steganography of three-dimensional (3-D) triangle meshes. This scheme is robust against translation, rotation, and scaling operations. It is based on a substitutive procedure in the spatial domain. The key idea is to consider a triangle as a two-state geometrical object. We discuss its performance in terms of capacity, complexity, visibility, and security. We validate the use of a principal component analysis (PCA) to make our scheme signal-dependent in the line of second generation watermarking scheme. We also define a simple specific metric for distortion evaluation that has been validated by many tests. We conclude by giving some other solutions, including open steganographic schemes that could be derived from the basic ideas presented here.
Interaction between facilitation and presynaptic inhibition at the crayfish neuromuscular junction

SUMMARY Action potential-mediated calcium (Ca) entry into excitor nerve terminal boutons during presynaptic inhibition and the effects of co-activation of the inhibitor on the kinetics of muscle contraction were studied at crayfish claw opener muscle. Inhibition reduced postsynaptic excitatory junction potentials (EJPs) below the threshold to initiate contraction. Upon cessation of inhibition, EJP amplitudes immediately increased several-fold due to the build-up of presynaptic facilitation during inhibition. Consequently, muscle contraction was initiated more rapidly after a period of inhibitor-excitor coactivation. Presynaptic inhibition reduced Ca entry into presynaptic excitor terminal boutons (range 0-50%, mean ± s.e.m.=20±1%, N=122 terminals; 12 preparations) and reduced the EJP amplitude (range 30-70%, mean± s.e.m.=51±2%, N=27 cells). The decline in the EJP was proportional to the reduction of Ca influx raised to the power of 2.8. Since presynaptic inhibition reduces the number of Ca channels opened by an action potential, our data suggest cooperativity between Ca channel microdomains to initiate vesicle fusion at this synapse. The amount of inhibition of Ca influx into an excitor bouton was not correlated with either the distance to the closest inhibitor bouton or the main excitor branch, although slightly more inhibition was seen for excitor boutons on tertiary versus secondary branches. Unlike inhibitor axon stimulation, bath application of GABA caused inhibition of Ca influx that steadily increased from proximal to distal terminal boutons on a branch. We propose a model where presynaptic inhibition causes localized shunting of an actively propagated action potential in the vicinity of release sites, which can recover its amplitude outside the shunted region.