Miracle-dz/UniFAR-FTUs huggingface dataset:
Aerosol analysis and forecast in the European Centre for Medium‐Range Weather Forecasts Integrated Forecast System: 2. Data assimilation

[1] This study presents the new aerosol assimilation system, developed at the European Centre for Medium-Range Weather Forecasts, for the Global and regional Earth-system Monitoring using Satellite and in-situ data (GEMS) project. The aerosol modeling and analysis system is fully integrated in the operational four-dimensional assimilation apparatus. Its purpose is to produce aerosol forecasts and reanalyses of aerosol fields using optical depth data from satellite sensors. This paper is the second of a series which describes the GEMS aerosol effort. It focuses on the theoretical architecture and practical implementation of the aerosol assimilation system. It also provides a discussion of the background errors and observations errors for the aerosol fields, and presents a subset of results from the 2-year reanalysis which has been run for 2003 and 2004 using data from the Moderate Resolution Imaging Spectroradiometer on the Aqua and Terra satellites. Independent data sets are used to show that despite some compromises that have been made for feasibility reasons in regards to the choice of control variable and error characteristics, the analysis is very skillful in drawing to the observations and in improving the forecasts of aerosol optical depth.
Regional cerebral glucose metabolism of patients with malignant diseases in different clinical phases.

BACKGROUND Psychological and psychiatric aspects of cancer patients have not been studied well in terms of functional neuroimaging. The aim of this pilot study was to investigate the relationship between regional cerebral metabolism and different clinical phases. MATERIAL AND METHODS Relative cerebral glucose metabolism of 77 Japanese patients with various types of malignant diseases was studied by positron emission tomography with 18F-fluorodeoxyglucose. They were subgrouped into the 1) pre-treatment, 2) post-treatment, 3) recurrence and 4) terminal patient groups. These subgroups were compared to the control group of 17 in-patients with benign diseases, using voxel-based Statistic Parametrical Mapping software (SPM). RESULTS Relative reduction in the regional cerebral metabolism was detected in the prefrontal and basolateral (inferolateral) prefrontal cortex, orbitofrontal cortex, anterior and posterior cingulate gyrus, insula, basal ganglia, hippocampus and thalamus in the pre-treatment group. The anterior and posterior cingulate gyri were hypometabolic only in the pre-treatment group. Hypometabolic areas were detected only in the basolateral prefrontal cortex, orbitofrontal cortex, ventral part of cingulate gyrus and insula in the post-treatment group. In the terminal group, the hypometabolic pattern seemed very close to that in the pre-treatment group. The results seemed to suggest that hypometabolic findings before treatments could reverse after treatments but became prominent again in terminal stages. These results do not contradict with previous epidemiological findings that high incidence of adjustment disorders was seen in earlier stages and more brain organic syndromes were seen in terminal stages. CONCLUSION It could be speculated that decreased metabolism in early stages reflects state-dependent changes and that decreased metabolism in the terminal stages reflects organic brain damages. brain of cancer patients show a fluctuation in the regional metabolism. This finding might give a suggestion that functional imaging could be used as a supplementary method for psychological evaluation of patients with severe diseases.
The effect of tyrosine‐specific protein phosphorylation on the assembly of adherens‐type junctions.

Adherens‐type junctions (AJs) are major subcellular targets for tyrosine specific protein phosphorylation [Volberg et al. (1991) Cell Regul. , 2, 105–120]. Here we report on the apparent effect of such phosphorylation events on the assembly and integrity of AJs. We show that incubation of MDCK cells with potent inhibitors of tyrosine‐specific phosphatases (PTP), namely H2O2 and vanadate, leads to a dramatic increase in AJ‐associated phosphotyrosine which was apparent already within 2–5 min of treatment and progressed upon further incubation. Examination of H2O2 vanadate treated cells at later time points indicated that intercellular AJs rapidly deteriorated, concomitantly with a marked increase in the number and size of vinculin and actin containing focal contacts. In parallel, major changes were observed in cell structure and topology, as revealed by electron microscopy. These were manifested by rapid rounding‐up of the cells followed by reorganization of the cell monolayer. Other intercellular junctions, including desmosomes and tight junctions, visualized by staining with desmoplakin and ZO‐I antibodies, were not significantly affected. To verify that modulation of AJs was indeed related to tyrosine phosphorylation, we have carried out reciprocal experiments in which Rovs Sarcoma virus (RSV) transformed chick lens cells, expressing high levels of pp60src kinase, were treated with inhibitors of tyrosine kinases, (tyrphostins). We show that following such treatment, intercellular AJs which were deteriorated in the transformed cells, were reformed. Based on these observations, we propose that specific tyrosine phosphorylation of AJ components is involved in the downregulation of these cellular contacts.
Impulse Origin and Propagation in a Bipolar Sensory Neuron

Intracellular recording techniques were used to study electrical activity in bipolar sensory cells associated with crayfish tactile receptors. Several lines of evidence indicate that spikes evoked by natural stimulation of the receptor originate at a dendritic locus. Although overshooting spikes are recorded in the soma in response to both natural and antidromic stimulation receptor potentials are observed only rarely, and, when present, their amplitude is less than 5 mv. Impulses propagating centrifugally into the soma following antidromic stimulation always exhibit an inflection in the rising phase of the spike; however, orthodromic spikes are usually uninflected. Occasionally, orthodromic responses (in the soma) exhibit rather unusual wave forms. Such spikes evoked by natural stimuli are indistinguishable from those elicited electrically in the dendrite, but they do not resemble antidromic impulses. Because the axonal and dendritic boundaries of the soma have a low safety factor for spike transmission, at high frequencies invasion of the soma by dendritic spikes is impeded and often blocked. The soma region can thus act as a low-pass filter. The significance of this self-limiting mechanism for the behavior of the animal is not known; it is suggested, however, that this impediment is a potentially critical one, and may, in other situations, have encouraged the evolution of alternative arrangements.
Agents that activate protein kinase C reduce acetylcholine sensitivity in cultured myotubes

We have examined acetylcholine (ACh)-elicited potentials or currents in current- or voltage-clamped cultured myotubes exposed to 12-O- tetradecanoyl-phorbol-13-acetate (TPA), a potent tumor promoter that activates protein kinase C. Although this agent had little action on either membrane resting potential or electrical resistance, a reversible decrease in ACh sensitivity was induced on 3-4-d-old chick myotubes. Depression of transmitter action by TPA was extended to 7-8-d mouse myotubes only when they were treated with phosphatidylserine. Glyceryl dioleate had effects on myotubes similar to those of TPA but with a reduced efficacy. We conclude that the activation of protein kinase C might be involved with the capacity of ACh receptors to respond to transmitter stimulation.
Fleet Management for Vehicle Sharing Operations

Astochastic, mixed-integer program (MIP) involving joint chance constraints is developed that generates least-cost vehicle redistribution plans for shared-vehicle systems such that a proportion of all near-term demand scenarios are met. The model aims to correct short-term demand asymmetry in shared-vehicle systems, where flow from one station to another is seldom equal to the flow in the opposing direction. The model accounts for demand stochasticity and generates partial redistribution plans in circumstances when demand outstrips supply. This stochastic MIP has a nonconvex feasible region. A novel divide-and-conquer algorithm for generating p-efficient points, used to transform the problem into a set of disjunctive, convex MIPs and handle dual-bounded chance constraints, is proposed. Assuming independence of random demand across stations, a faster cone-generation method is also presented. In a real-world application for a system in Singapore, the potential of redistribution as a fleet management strategy and the value of accounting for inherent stochasticities are demonstrated.
A Linked Data Based Approach to Similarity Reasoning

SemSim is a semantic similarity reasoning method that has been conceived to be used as a service for the Semantic Web. SemSim is based on a Weighted Reference Ontology, which is used to semantically annotate a collection of digital resources (e.g., documents) to be searched. In this paper we present a new approach to SemSim implementation based on Linked Data, that significantly increments its usability in the Semantic Web.
Single Cell Isolation and Analysis

Individual cell heterogeneity within a population can be critical to its peculiar function and fate. Subpopulations studies with mixed mutants and wild types may not be as informative regarding which cell responds to which drugs or clinical treatments. Cell to cell differences in RNA transcripts and protein expression can be key to answering questions in cancer, neurobiology, stem cell biology, immunology, and developmental biology. Conventional cell-based assays mainly analyze the average responses from a population of cells, without regarding individual cell phenotypes. To better understand the variations from cell to cell, scientists need to use single cell analyses to provide more detailed information for therapeutic decision making in precision medicine. In this review, we focus on the recent developments in single cell isolation and analysis, which include technologies, analyses and main applications. Here, we summarize the historical background, limitations, applications, and potential of single cell isolation technologies.
Plasma Lipid Levels in the Elderly Are Not Associated with the Risk of Mild Cognitive Impairment

Background: There are conflicting data relating plasma lipids to the risk of Alzheimer‘s disease (AD). We explored the association of plasma lipids to mild cognitive impairment (MCI), a transitional stage between normal cognition and dementia, in a prospective community-based cohort study among randomly sampled Medicare recipients ≧65 years. Baseline data were collected from 1992 to 1994, follow-up data were collected at 18-month intervals. Methods: Multivariate proportional hazards regression was used to relate plasma lipid levels to incident total MCI, amnestic MCI and nonamnestic MCI in 854 persons without MCI or dementia at baseline. Results: There were 324 cases of incident MCI, 153 cases of amnestic MCI and 171 cases of nonamnestic MCI during 4,189 person-years of follow-up. Higher levels of total cholesterol and LDL were associated with a decreased risk of total MCI in models adjusting for age and sex. However, these associations were attenuated after adjusting for ethnicity, education, APOEΕ4 and vascular risk factors. There was no association between lipids and the risk of amnestic or nonamnestic MCI, and there was no effect of lipid-lowering treatment on MCI risk. Conclusions: Plasma lipid levels or lipid-lowering treatment in the elderly are not associated with the risk of MCI.
Yersinia pestis grows within phagolysosomes in mouse peritoneal macrophages

Transmission electron microscopy was used to determine the intracellular localization of Yersinia pestis growing within cultured resident peritoneal macrophages of mice. Monolayers fixed immediately, or as long as 4.5 h, after infection contained yersiniae closely surrounded by a membrane. The vesicles containing the yersiniae were determined to be phagolysosomes by labeling secondary lysosomes of macrophages with electron-dense particles of thorium dioxide. The presence of the label within vesicles containing yersiniae indicates that this pathogen grows within the lysosomal compartment of its target host cell.
Efficient noise-tolerant learning from statistical queries

In this paper, we study the problem of learning in the presence of classification noise in the probabilistic learning model of Valiant and its variants. In order to identify the class of “robust” learning algorithms in the most general way, we formalize a new but related model of learning from statistical queries. Intuitively, in this model, a learning algorithm is forbidden to examine individual examples of the unknown target function, but is given access to an oracle providing estimates of probabilities over the sample space of random examples. One of our main results shows that any class of functions learnable from statistical queries is in fact learnable with classification noise in Valiant’s model, with a noise rate approaching the informationtheoretic barrier of 1/2. We then demonstrate the generality of the statistical query model, showing that practically every class learnable in Valiant’s model and its variants can also be learned in the new model (and thus can be learned in the presence of noise). A notable exception to this statement is the class of parity functions, which we prove is not learnable from statistical queries, and for which no noise-tolerant algorithm is known.
Characterizing podcast services: publishing, usage, and dissemination

In this paper, we aim at characterizing podcast services both from publishers' and users' perspectives, and at analyzing the implications of these characteristics on the design of efficient dissemination systems. Specifically, our goal is to characterize how podcasting content is generated and published, and how users subscribe and consume podcasts. We are also interested in understanding whether podcast episodes are efficiently disseminated to users just using a sporadic direct access to the Internet (which is the current way of downloading podcast episodes), or whether the use of peer-to-peer mobile device-to-device dissemination systems could help enhancing the performance of podcast services. Our study is based on traces of podcast episode releases, subscriptions, and play times from major podcast service providers. An extensive analysis of the traces allows us to develop a comprehensive model of current podcast services, and provide statistics about the type and content of the typical podcasts, the size and the release frequencies of their episodes, as well as their popularity. By studying podcast usage, we show that the service is delay-tolerant, as users may well play podcast episodes a long time after their actual release. An interesting consequence of this delay tolerance is that mobile device-to-device dissemination systems would not be very useful for the current typical podcasts, while they may become more attractive for future interactive podcast services.
Timing Semantics for Abstraction and Execution of Synthesized High-Level Robot Control

The use of formal methods for synthesis has recently enabled the automated construction of verifiable high-level robot control. Most approaches use a discrete abstraction of the underlying continuous domain, and make assumptions about the physical execution of actions given a discrete implementation; examples include when actions will complete relative to each other, and possible changes in the robot's environment while it is performing various actions. Relaxing these assumptions give rise to a number of challenges during the continuous implementation of automatically synthesized hybrid controllers. This paper presents several distinct timing semantics for controller synthesis, and compares them with respect to the assumptions they make on the execution of actions. It includes a discussion of when each set of assumptions is reasonable, and the computational tradeoffs inherent in relaxing them at synthesis time.
An efficient Multiscale Phase Spectrum Based Salient Object Detection Technique

Automatic image segmentation is emerging field in image processing research domain. Many researchers have developed various techniques for segmenting the interested region in an image. Saliency based image segmentation is one of the keen area of research. In a visual scene, the objects which are different from their surroundings get more visual importance and get high gaze attention of the viewer. There are several other applications also where saliency detection is used as core module such as object based surveillance, content adaptive data delivery for low data rate systems, automatic foveation system. In this paper, an efficient multiscale phase spectrum based salient object detection method is proposed. It is observed that, a fixed scale of the original image may not predict properly the salient objects. Saliency predicted in one resolution may not predict the same fixation region on another resolution. It is proposed to apply saliency detection algorithm to multiple scales of the original image. As it known that, positional information is contained in the phase spectrum whereas amplitude spectrum contains the presence of frequency components, hence it is proposed to detect saliency using phase spectrum of Fourier transform. The proposed method performs much better than other previous methods and predicts more precisely salient objects. In experimental set-up, results of four state-of-art techniques for salient object detection are analyzed compared against the proposed method. The performance of the proposed method is measured on the basis of objective and subjective analysis.
Table-based polynomials for fast hardware function evaluation

Many general table-based methods for the evaluation in hardware of elementary functions have been published. The bipartite and multipartite methods implement a first-order approximation of the function using only table lookups and additions. Recently, a single multiplier second order method of similar inspiration has also been published. This paper extends such methods to approximations of arbitrary order, using adders, small multipliers, and very small ad hoc powering units. We obtain implementations that are both smaller and faster than previously published approaches. This paper also deals with the FPGA implementation of such methods. Previous work have consistently shown that increasing the approximation degree lead to not only smaller but also faster designs, as the reduction of the table size meant a reduction of its lookup time, which compensated for the addition and multiplication time. The experiments in this paper suggest that this still holds when going from order 2 to order 3, but no longer when using higher order approximations, where a tradeoff appears.
Physical Intrusion Games—Optimizing Surveillance by Simulation and Game Theory

The protection of cyber-physical networks is a topic of increasing importance. The evolution of IT (cyber) systems that control and supervise the underlying physical system has grown over decades, whereas security has not become a concern until quite recently. Advanced persistent threats (APTs) have proven to be a difficult but significant challenge for practitioners. This paper adopts a game-theoretic modeling of APTs and applies it to the (sub) problem of physical intrusion in an infrastructure. The gap between defining a good theoretical model and practically instantiating it is considered in particular. The model description serves to illustrate what is needed to put it into practice. The main contribution of this paper is the demonstration of how simulation, physical understanding of an infrastructure, and theoretical methods can be combined toward a practical solution to the physical intrusion avoidance problem. Numerical results are given to show how the physical intrusion game is being set up, and how the results obtained from its analysis can be interpreted and used for an optimized defense.
Degradation of Methanethiol by Methylotrophic Methanogenic Archaea in a Lab-Scale Upflow Anaerobic Sludge Blanket Reactor

ABSTRACT In a lab-scale upflow anaerobic sludge blanket reactor inoculated with granular sludge from a full-scale wastewater treatment plant treating paper mill wastewater, methanethiol (MT) was degraded at 30°C to H2S, CO2, and CH4. At a hydraulic retention time of 9 h, a maximum influent concentration of 6 mM MT was applied, corresponding to a volumetric loading rate of 16.5 mmol liter−1 day−1. The archaeal community within the reactor was characterized by anaerobic culturing and denaturing gradient gel electrophoresis analysis, cloning, and sequencing of 16S rRNA genes and quantitative PCR. Initially, MT-fermenting methanogenic archaea related to members of the genus Methanolobus were enriched in the reactor. Later, they were outcompeted by Methanomethylovorans hollandica, which was detected in aggregates but not inside the granules that originated from the inoculum, the microbial composition of which remained fairly unchanged. Possibly other species within the Methanosarcinacaea also contributed to the fermentation of MT, but they were not enriched by serial dilution in liquid media. The archaeal community within the granules, which was dominated by Methanobacterium beijingense, did not change substantially during the reactor operation. Some of the species related to Methanomethylovorans hollandica were enriched by serial dilutions, but their growth rates were very low. Interestingly, the enrichments could be sustained only in the presence of MT and did not utilize any of the other typical substrates for methylotrophic methanogens, such as methanol, methyl amine, or dimethylsulfide.
Correlated mutations in hydroxysteroid dehydrogenases family

Abstract Background Hydroxysteroid dehydrogenase enzymes belong to the short-chain dehydrogenase/reductase (SDR) superfamily and aldo-keto reductases (AKRs). SDR is involved in the metabolism of many compounds (hormones, lipids, etc.) and is present in almost all studied genomes. Two hundred members of hydroxysteroid dehydrogenases have been analysed in terms of natural mutational variability. The second superfamily comprises AKR superfamily group enzymes whose function is catalysing the oxidation and reduction of many substrates by binding NAD(P)H as a cofactor. This kind of study is the first approach for the hydroxysteroid dehydrogenase family. This information grants practical meaning to designing potential specific drugs to fight specific diseases caused by mutations. Methods In the research, amino acid sequences of representatives of the hydroxysteroid dehydrogenase family were extracted from the UniProt database. In total, the analysed 200 sequences with the highest degree of similarity were shown by BLAST searches. In the sequence analyses, we used the following software: ClustalX (multiple sequence alignment), Consensus Constructor (creating consensus sequence), and CORM (finding correlated mutations). Results The CORM program identified potential sites of correlated mutations in hydroxysteroid dehydrogenases. This program generated 18 tables of results that contain the amino acid positions of mutations. Seven of these are presented in this paper. Conclusions The primary structure of the hydroxysteroid dehydrogenase family shows high variation.