Miracle-dz/UniFAR-FTUs huggingface dataset:
Turbulence and Mixing in the Intracluster Medium

The intracluster medium (ICM) is stably stratified in the hydrodynamic sense with the entropy s increasing outwards. However, thermal conduction along magnetic field lines fundamentally changes the stability of the ICM, leading to the “heat‐flux buoyancy instability” when dT/dr>0 and the “magnetothermal instability” when dT/dr 0 and parallel to r when dT/dr<0), without generating sustained convection. We show that after an anisotropically conducting plasma reaches this nonlinearly stable magnetic configuration, it experiences a buoyant restoring force that resists further distortions of the magnetic field. This restoring force is analogous to the buoyant restoring force experienced by a stably stratified adiabatic plasma. We argue that in order for a driving mechanism (e.g, galaxy mot.
Collision avoidance by a modified least-mean-square-error classification scheme for indoor autonomous land vehicle navigation

In this article, a new collision-avoidance scheme is proposed for autonomous land vehicle (ALV) navigation in indoor corridors. The goal is to conduct indoor collisionfree navigation of a three-wheel ALV among static obstacles with no a priori position information as well as moving obstacles with unknown trajectories. Based on the predicted positions of obstacles, a local collision-free path is computed by the use of a modified version of the least-mean-square-error (LMSE) classifier in pattern recognition. Wall and obstacle boundaries are sampled as a set of 2D coordinates, which are then viewed as feature points. Different weights are assigned to different feature points according to the distances of the feature points to the ALV location to reflect the locality of path planning. The trajectory of each obstacle is predicted by a real-time LMSE estimation method. And the maneuvering board technique used for nautical navigation is employed to determine the speed of the ALV for each navigation cycle. Smooth collision-free paths found in the simulation results are presented to show the feasibility of the proposed approach.
RX J0042.3+4115: a stellar mass black hole binary identified in M 31

Four XMM-Newton X-ray observations of the central region of the Andromeda Galaxy (M 31) have revealed an X-ray source that varies in luminosity over1 3 10 38 erg s 1 between observations and also displays significant variabil- ity over time-scales of a few hundred seconds. The power density spectra of lightcurves obtained in the 0.3-10 keV energy band from the three EPIC instruments on board XMM-Newton are typical of disc-accreting X-ray binaries at low accretion rates, observed in neutron star binaries only at much lower luminosities (10 36 erg s 1 ). However X-ray binaries with mas- sive black hole primaries have exhibited such power spectra for luminosities>10 38 erg s 1 . We discuss alternative possibilities where RX J0042.3+4115 may be a background AGN or foreground object in the field of view, but conclude that it is located within M 31 and hence use the observed power spectra and X-ray luminosities to identify the primary as a black hole candidate.
Long-Term Citalopram Treatment Alters the Stress Responses of the Cortical Dopamine and Noradrenaline Systems: the Role of Cortical 5-HT1A Receptors

Background: Cortical dopamine and noradrenaline are involved in the stress response. Citalopram, a selective serotonin reuptake inhibitor, has direct and indirect effects on the serotonergic system. Furthermore, long-term treatment with citalopram affects the dopamine and noradrenaline systems, which could contribute to the therapeutic action of antidepressants. Methods: The effects of long-term treatment with citalopram on the responses of the dopamine and noradrenaline systems in the rat prefrontal cortex to acute handling stress were evaluated using in vivo microdialysis. Results: Acute handling stress increased dopamine and noradrenaline levels in the prefrontal cortex. The dopamine and noradrenaline responses were suppressed by local infusion of a 5-HT1A receptor agonist, 7-(Dipropylamino)-5,6,7,8-tetrahydronaphthalen-1-ol;hydrobromide, into the prefrontal cortex. The dopamine response was abolished by long-term treatment with citalopram, and the abolished dopamine response was reversed by local infusion of a 5-HT1A receptor antagonist, (Z)-but-2-enedioic acid;N-[2-[4-(2-methoxyphenyl)piperazin-1-yl]ethyl]-N-pyridin-2-ylcyclohexanecarboxamide into the prefrontal cortex. On the other hand, long-term treatment with citalopram reduced the basal noradrenaline levels (approximately 40% of the controls), but not the basal dopamine levels. The noradrenaline response was maintained despite the low basal noradrenaline levels. Signaling from the 5-HT1A receptors and α2-adrenoceptors was not involved in the decrease in the basal noradrenaline levels but partially affected the noradrenaline response. Conclusions: Chronic citalopram treatment differentially suppresses the dopamine and noradrenaline systems in the prefrontal cortex, and the dopamine stress response was preferentially controlled by upregulating 5-HT1A receptor signaling. Our findings provide insight into how antidepressants modulate the dopamine and noradrenaline systems to overcome acute stress.
Fucci2a: A bicistronic cell cycle reporter that allows Cre mediated tissue specific expression in mice

Markers of cell cycle stage allow estimation of cell cycle dynamics in cell culture and during embryonic development. The Fucci system incorporates genetically encoded probes that highlight G1 and S/G2/M phases of the cell cycle allowing live imaging. However the available mouse models that incorporate Fucci are beset by problems with transgene inactivation, varying expression level, lack of conditional potential and/or the need to maintain separate transgenes—there is no transgenic mouse model that solves all these problems. To address these shortfalls we re-engineered the Fucci system to create 2 bicistronic Fucci variants incorporating both probes fused using the Thosea asigna virus 2A (T2A) self cleaving peptide. We characterize these variants in stable 3T3 cell lines. One of the variants (termed Fucci2a) faithfully recapitulated the nuclear localization and cell cycle stage specific florescence of the original Fucci system. We go on to develop a conditional mouse allele (R26Fucci2aR) carefully designed for high, inducible, ubiquitous expression allowing investigation of cell cycle status in single cell lineages within the developing embryo. We demonstrate the utility of R26Fucci2aR for live imaging by using high resolution confocal microscopy of ex vivo lung, kidney and neural crest development. Using our 3T3 system we describe and validate a method to estimate cell cycle times from relatively short time-lapse sequences that we then apply to our neural crest data. The Fucci2a system and the R26Fucci2aR mouse model are compelling new tools for the investigation of cell cycle dynamics in cell culture and during mouse embryonic development.
Single strand transposition at the host replication fork

Members of the IS200/IS605 insertion sequence family differ fundamentally from classical IS essentially by their specific single-strand (ss) transposition mechanism, orchestrated by the Y1 transposase, TnpA, a small HuH enzyme which recognizes and processes ss DNA substrates. Transposition occurs by the ‘peel and paste’ pathway composed of two steps: precise excision of the top strand as a circular ss DNA intermediate; and subsequent integration into a specific ssDNA target. Transposition of family members was experimentally shown or suggested by in silico high-throughput analysis to be intimately coupled to the lagging strand template of the replication fork. In this study, we investigated factors involved in replication fork targeting and analysed DNA-binding properties of the transposase which can assist localization of ss DNA substrates on the replication fork. We showed that TnpA interacts with the β sliding clamp, DnaN and recognizes DNA which mimics replication fork structures. We also showed that dsDNA can facilitate TnpA targeting ssDNA substrates. We analysed the effect of Ssb and RecA proteins on TnpA activity in vitro and showed that while RecA does not show a notable effect, Ssb inhibits integration. Finally we discuss the way(s) in which integration may be directed into ssDNA at the replication fork.
A monsoon depression over north-western Australia . Part III : Motion

This paper is Part III in a series examining aspects of a monsoon depression that formed within the monsoon trough near the coast of northwestern Australia in February 1994. The depression was a prominent feature in that area for about a week. Aspects of the structure and evolution of the depression are described in Part I by Hell and Smith (1998). In Part II, Dengler and Smith (1998) describe idealised model calculations pertaining to the event using a three-layer baroclinic model. In this paper we examine aspects of the depression’s motion. Aust. Met. Mag. 49 (2000) 1-21
Feature Selection in Document Classification

Text classification, as part of text mining domain, is the problem of classifying text documents into a set of predefined classes. After extracting the features, documents are represented as a vector containing a huge number of features. When working on large collections of documents both time and memory restrictions are prohibitive and, therefore, we have to apply feature selection methods to reduce the dimensionality of the vector. In this paper, we evaluate three feature selection methods: one based on the 1R classifier, Information Gain and Gain Ratio. The best results were obtained with the Information Gain method and for a relatively small dimension of the feature vector. The best accuracy of 93.58% was obtained using only 27.14% of features.
Response of the Microaerophilic Bifidobacterium Species, B. boum and B. thermophilum, to Oxygen

ABSTRACT We investigated the effects of O2 on Bifidobacterium species using liquid shaking cultures under various O2 concentrations. Although most of the Bifidobacterium species we selected showed O2 sensitivity, two species, B. boum and B. thermophilum, demonstrated microaerophilic profiles. The growth of B. bifidum and B. longum was inhibited under high-O2 conditions accompanied by the accumulation of H2O2 in the medium, and growth was restored by adding catalase to the medium. B. boum and B. thermophilum grew well even under 20% O2 conditions without H2O2 accumulation, and growth was stimulated compared to anoxic growth. H2O-forming NADH oxidase activities were detected dominantly in cell extracts of B. boum and B. thermophilum under acidic reaction conditions (pH 5.0 to 6.0).
Quantifying the sustainability impact of data center availability

Data center availability is critical considering the explosive growth in Internet services and people's dependence on them. Furthermore, in recent years, sustainability has become important. However, data center designers have little information on the sustainability impact of data center availability architectures. In this paper, we present an approach to estimate the sustainability impact of such architectures. Availability is computed using Stochastic Petri Net (SPN) models while an exergy-based lifecycle assessment (LCA) approach is used for quantifying sustainability impact. The approach is demonstrated on real life data center power infrastructure architectures. Five different architectures are considered and initial results show that quantification of sustainability impact provides important information to a data center designer in evaluating availability architecture choices.
Containment maneuvering of marine surface vessels

The containment maneuvering problem involves two tasks. The first, called the geometric formation task, is to force the vessel outputs to converge to convex hull spanned by multiple parameterized paths. The second task, called the dynamic task, is to satisfy a desired dynamic behavior along the paths. A modular design approach is presented to develop the adaptive containment maneuvering controllers. Specifically, a predictor module using echo state network is proposed for estimating the model uncertainty and ocean disturbances, which is able to identify the vessel dynamics as fast as possible. Then, a controller module is designed based on a modified dynamic surface control technique. The stability of the closed-loop network system is established via cascade theory. The proposed design results in decoupled estimate and control, and can achieve fast adaptation without incurring high-frequency signals.
Automatically deriving information-theoretic bounds for adaptive side-channel attacks

We present a model of adaptive attacks which we combine with information-theoretic metrics to quantify the information revealed to an adaptive adversary. This enables us to express an adversary's remaining uncertainty about a secret as a function of the number of interactions with the system under attack. We present algorithms and approximation methods for computing this function. The main application area for our approach is the analysis of side-channels in cryptographic algorithms and we give examples of how it can be used to characterize the vulnerability of hardware implementations to timing and power attacks. We also show the generality of our approach by using it to quantify the information leaked by a security protocol.
Epitope-directed processing of specific antigen by B lymphocytes

Proteolytic processing of specific antigen was studied using Epstein Barr virus transformed B-lymphoblastoid cells expressing membrane IgG against tetanus toxin. As previously reported (Watts, C., and H.W. Davidson. 1988. EMBO (Eur. Mol. Biol. Organ.) J. 7:1937-1945), receptor- mediated endocytosis of monovalent antigen bound at 0 degrees C began immediately upon shifting the cells to 37 degrees C. In contrast, degradation of antigen, assessed either by the release of acid-soluble radiolabel into the incubation medium, or by SDS-PAGE analysis of total cell-associated antigen, proceeded after a lag of 10-20 min. Degradation was abolished by exposure of the cells to metabolic inhibitors, or by incubation at 20 degrees C, and inhibited in a dose- dependent fashion by chloroquine and by the lysosomal protease inhibitors leupeptin, E-64, and pepstatin A. Analysis of the cell- associated radiolabel by SDS-PAGE and autoradiography after incubations at 37 degrees C revealed the time-dependent generation of distinct antigen fragments. Virtually quantitative immunoprecipitation of these fragments was obtained using a monoclonal anti-human IgG antibody, indicating that the antigen/mIg complex is the initial substrate for processing. We show that the pattern of fragmentation observed varies from one B cell line to another (a) depending on the epitope through which the antigen is bound and endocytosed and (b) depending on whether additional epitopes in the antigen are complexed with anti-tetanus Fabs. The implications of these results for the presentation of major histocompatibility complex restricted antigen fragments, and for intracellular trafficking of ligand/receptor complexes are discussed.
Three-Dimensional Blood Vessel Quantification via Centerline Deformation

It is clinically important to quantify the geometric parameters of an abnormal vessel, as this information can aid radiologists in choosing appropriate treatments or apparatuses. Centerline and cross-sectional diameters are commonly used to characterize the morphology of vessel in various clinical applications. Due to the existence of stenosis or aneurysm, the associated vessel centerline is unable to truly portray the original, healthy vessel shape and may result in inaccurate quantitative measurement. To remedy such a problem, a novel method using an active tube model is proposed. In the method, a smoothened centerline is determined as the axis of a deformable tube model that is registered onto the vessel lumen. Three types of regions, normal, stenotic, and aneurysmal regions, are defined to classify the vessel segment under-analyzed by use of the algorithm of a cross-sectional-based distance field. The registration process used on the tube model is governed by different region-adaptive energy functionals associated with the classified vessel regions. The proposed algorithm is validated on the 3-D computer-generated phantoms and 3-D rotational digital subtraction angiography (DSA) datasets. Experimental results show that the deformed centerline provides better vessel quantification results compared with the original centerline. It is also shown that the registered model is useful for measuring the volume of aneurysmal regions.
The Role of Rab Proteins in Neuronal Cells and in the Trafficking of Neurotrophin Receptors

Neurotrophins are a family of proteins that are important for neuronal development, neuronal survival and neuronal functions. Neurotrophins exert their role by binding to their receptors, the Trk family of receptor tyrosine kinases (TrkA, TrkB, and TrkC) and p75NTR, a member of the tumor necrosis factor (TNF) receptor superfamily. Binding of neurotrophins to receptors triggers a complex series of signal transduction events, which are able to induce neuronal differentiation but are also responsible for neuronal maintenance and neuronal functions. Rab proteins are small GTPases localized to the cytosolic surface of specific intracellular compartments and are involved in controlling vesicular transport. Rab proteins, acting as master regulators of the membrane trafficking network, play a central role in both trafficking and signaling pathways of neurotrophin receptors. Axonal transport represents the Achilles' heel of neurons, due to the long-range distance that molecules, organelles and, in particular, neurotrophin-receptor complexes have to cover. Indeed, alterations of axonal transport and, specifically, of axonal trafficking of neurotrophin receptors are responsible for several human neurodegenerative diseases, such as Huntington’s disease, Alzheimer’s disease, amyotrophic lateral sclerosis and some forms of Charcot-Marie-Tooth disease. In this review, we will discuss the link between Rab proteins and neurotrophin receptor trafficking and their influence on downstream signaling pathways.
Epothilones in breast cancer: review of clinical experience.

BACKGROUND Drugs that target microtubules, including paclitaxel (Taxol) and docetaxel (Taxotere), are among the most commonly prescribed anticancer therapies. However, the utility of taxane-based therapies is limited by difficulties with formulation, administration, and resistance induced by P-glycoprotein. The epothilones are a novel class of antimicrotubule agents that have demonstrated antitumor activity in the setting of resistance. DESIGN This review summarizes clinical studies of epothilones in patients with metastatic breast cancer. Data were identified by searches of PubMed and the Proceedings of the American Society of Clinical Oncology annual meetings from 2000 to 2006. RESULTS The epothilones have demonstrated promising antitumor activity and manageable toxicity in phase II studies of heavily pretreated patients with metastatic breast cancer, including patients with resistance to taxanes and other cytotoxic agents. Neuropathy associated with ixabepilone appears to be schedule dependent and comparable to that observed with paclitaxel. Ixabepilone appears to be active in combination with capecitabine. CONCLUSIONS Ongoing and planned trials promise to elucidate the benefits of ixabepilone in combination with other agents including capecitabine, bevacizumab, and trastuzumab in patients with metastatic breast cancer as well as those receiving neo-adjuvant therapy.
Hepatitis B Diagnosis Using Logical Inference and Self-Organizing Map

Despite all the standardization efforts made, medical diagnosis is still regarded as an art owing to the fact that that medical diagnosis requires an expertise in handling the uncertainty which is unavailable in today's computing machinery. Though artificial intelligence is not a new concept it has been widely recognized as a new technology in computer science. Numerous areas such as education, business, medical and manufacturing have made use of artificial intelligence. Problem statement: The proposed study investigated the potential of artificial intelligence techniques principally for medical applications. Neural network algorithms could possible provide an enhanced solution for medical problems. This study analyzed the application of artificial intelligence in conventional hepatitis B diagnosis. Approach: In this research, an intelligent system that worked on basis of logical inference utilized to make a decision on the type of hepatitis that is likely to appear for a patient, if it is hepatitis B or not. Then kohonen's self-organizing map network was applied to hepatitis data for predictions regarding the Hepatitis B which gives severity level on the patient. Results: SOM which is a class of unsupervised network was used as a classifier to predict the accuracy of Hepatitis B. Conclusion: We concluded that the proposed model gives faster and more accurate prediction of hepatitis B and it works as promising tool for predicting of routine hepatitis B from the clinical laboratory data.
K-coverage Formation for Target Tracking Using Nonholonomic Agents

Formation control is an important problem in multi-agent systems. In this paper, it is assumed that a target is moving with a disturbed dynamics, and then, a k-coverage formation control is designed for every nonholonomic agent to improve tracking qualities. A virtual agent approach is adopted in the formation control design. The stability of the tracking error system is analyzed. Finally, some numerical simulations are given to validate the proposed tracking algorithms. Keywords—formation control, k-coverage, nonholonomic dynamics, multi-agent systems, target tracking
Longitudinal Changes in Individual BrainAGE in Healthy Aging, Mild Cognitive Impairment, and Alzheimer’s Disease

We recently proposed a novel method that aggregates the multidimensional aging pattern across the brain to a single value. This method proved to provide stable and reliable estimates of brain aging - even across different scanners. While investigating longi- tudinal changes in BrainAGE in about 400 elderly subjects, we discovered that patients with Alzheimer's disease and subjects who had converted to AD within 3 years showed accelerated brain atrophy by +6 years at baseline. An additional increase in BrainAGE accumulated to a score of about +9 years during follow-up. Accelerated brain aging was related to prospective cognitive decline and disease severity. In conclusion, the BrainAGE framework indicates discrepancies in brain aging and could thus serve as an indicator for cognitive func- tioning in the future.