Miracle-dz/UniFAR-FTUs huggingface dataset:
Heterogeneity in extracellular nucleotide hydrolysis among clinical isolates of Trichomonas vaginalis

Trichomonas vaginalis is a parasitic protozoan that causes trichomonosis, a sexually-transmitted disease, with serious sequelae to women and men. As the host–parasite relationship is complex, it is important to investigate biochemical aspects of the parasite that contribute to our understanding of trichomonal biology and pathogenesis. Nucleoside triphosphate diphosphohydrolase 1 (NTPDase 1), which hydrolyses extracellular ATP and ADP, and ecto-5′-nucleotidase, which hyrolyses AMP, have been characterized in laboratory isolates of T. vaginalis. Here we show that the extracellular ATP[ratio ]ADP hydrolysis ratio varies among fresh clinical isolates, which presented higher ATPase and ADPase activities than long-term-grown isolates. Growth of parasites in iron-replete and iron-depleted medium resulted in different, albeit minor, patterns in extracellular ATP and ADP hydrolysis among isolates. Importantly, some isolates had low or absent ecto-5′-nucleotidase activity, regardless of environmental conditions tested. For isolates with ecto-5′-nucleotidase activity, high- and low-iron trichomonads had increased and decreased levels of activity, respectively, compared to organisms grown in normal TYM-serum medium. This suggests a regulation in expression of either the enzyme amounts and/or activity under the control of iron. Finally, we found no correlation between the presence or absence of dsRNA virus infection among trichomonad isolates and NTPDase and ecto-5′-nucleotidase activities.
SeqPAM: A Sequence Clustering Algorithm for Web Personalization

With the growth in the number of Web users and necessity for making information available on the Web, the problem of Web personalization has become very critical and popular. Developers are trying to customize a Web site to the needs of specific users with the help of knowledge acquired from user navigational behavior. Since user page visits are intrinsically sequential in nature, efficient clustering algorithms for sequential data are needed. In this chapter, we introduce a similarity preserving function called sequence and set similarity measure S3M that captures both the order of occurrence of page visits as well as the content of pages. We conducted pilot experiments comparing the results of PAM, a standard clustering algorithm, with two similarity measures: Cosine and S3M. The goodness of the clusters resulting from both the measures was computed using a cluster validation technique based on average levensthein distance. Results on pilot dataset established the effectiveness of S3M for sequential data. Based on these results, we proposed a new clustering algorithm, SeqPAM for clustering sequential data. We tested the new algorithm on two datasets namely, cti and msnbc datasets. We provided recommendations for Web personalization based on the clusters obtained from SeqPAM for msnbc dataset.
Retrieval of cloud geometrical properties using optical remote sensing data

It is of great interest to investigate the properties on the cloud optical, microphysical, and geometrical parameters, in particular, of low-level marine clouds which play crucial influence on the global climate system. Top height, base height, and geometrical thickness of cloud layer are considered here as cloud geometrical parameters. These parameters are very important to retrieve, because top and base heights are the factors which govern the strength of greenhouse effect through the thermal radiation from/to cloud layer, whereas the geometrical thickness is the key parameter for the estimation of gaseous absorption in cloud layer where multiple scattering process dominates. In this study, an algorithm was developed to retrieve simultaneously cloud optical thickness, effective particle radius, top height, and geometrical thickness of cloud layer from the spectral information of visible, near infrared, thermal infrared, and oxygen A band channels. This algorithm was applied to FIRE (First ISCCP Regional Experiment, 1987) airborne data which included the above four channels and targeted at the low-level marine clouds off the coast of California in summer. The retrieved results seems to be comparable to the in situ microphysical observation although further validation studies are required for the cloud geometrical parameters in particular.
Importance of Circulation Changes to Atlantic Heat Storage Rates on Seasonal and Interannual Time Scales

AbstractOcean heat budgets and transports are diagnosed to elucidate the importance of general circulation changes to Atlantic Ocean heat storage rates. The focus is on low- and midlatitude regions and on seasonal and interannual time scales. An estimate of the ocean state over 1993–2004, produced by a coarse-resolution general circulation model fit to observations via the method of Lagrange multipliers, is used. Meridional heat transports are first decomposed into contributions from time-mean and time-variable velocity and temperature and second from zonally symmetric baroclinic (overturning, including Ekman) and zonally asymmetric (gyre and other spatially correlated) circulations. Heat storage rates are then ascribed to ocean–atmosphere heat exchanges, diffusive mixing, and advective processes related to the various components of the meridional heat transport. Results show that seasonal heat storage changes generally represent a local response to surface heat inputs, but seasonal advective changes are .
Siboglinid-bacteria endosymbiosis

Siboglinid worms are a group of gutless marine annelids which are nutritionally dependent upon endosymbiotic bacteria.1-2 Four major groups of siboglinids are known including vestimentiferans, Osedax spp. , frenulates, and moniliferans.3-5 Very little is known about the diversity of bacterial endosymbionts associated with frenulate or monoliferan siboglinids. This lack of knowledge is surprising considering the global distribution of siboglinids; this system is likely among the most common symbioses in the deep sea. At least three distinct clades of endosymbiotic γ-proteobacteria associate with siboglinid annelids.6 Frenulates harbor a clade of γ–proteobacteria that are divergent from both the thiotrophic bacteria of vestimentiferans and monoliferans as well as the heterotrophic bacteria of Osedax spp.6-7 We also discuss priorities for future siboglinid research and the need to move beyond descriptive studies. A promising new method, laser-capture microdissection (LCM), allows for the precise excision of tissue regions of interest.8 This method, when used in concert with molecular and genomic techniques, such as Expressed Sequence Tag surveys using pyrosequencing technology, will likely enable investigations into physiological processes and mechanisms in these symbioses. Furthermore, adopting a comparative approach using different siboglinid groups, such as worms harboring thiotrophic versus methanotrophic endosymbionts, may yield considerable insight into the ecology and evolution of the Siboglinidae.
Biometrics and Identity Management: First European Workshop, BIOID 2008, Roskilde, Denmark, May 7-9, 2008. Revised Selected Papers

Bargaining with reading habit is no need. Reading is not kind of something sold that you can take or not. It is a thing that will change your life to life better. It is the thing that will give you many things around the world and this universe, in the real world and here after. As what will be given by this biometrics and identity management first european workshop bioid 2008 roskilde denmark may 7 9 2008 revised selected papers author ben schouten feb 2009, how can you bargain with the thing that has many benefits for you?
The seismic attenuation structure of the East Pacific Rise

Abstract : Studies of seismic propagation through oceanic crust have contributed enormously to our understanding of the generation and evolution of oceanic crust. However, such work has largely been confined to the seismic velocity structure. This thesis presents results from a study of seismic attenuation using a data set collected for three-dimensional tomographic imaging of a fast- spreading ridge. The experiment location at 9 deg 30 min N on the East Pacific Rise is the site of a strong mid-crustal seismic reflector which has been inferred to be the roof of a small axial magma chamber at about 1.6 km depth.
High Sugar-Induced Insulin Resistance in Drosophila Relies on the Lipocalin Neural Lazarillo

In multicellular organisms, insulin/IGF signaling (IIS) plays a central role in matching energy needs with uptake and storage, participating in functions as diverse as metabolic homeostasis, growth, reproduction and ageing. In mammals, this pleiotropy of action relies in part on a dichotomy of action of insulin, IGF-I and their respective membrane-bound receptors. In organisms with simpler IIS, this functional separation is questionable. In Drosophila IIS consists of several insulin-like peptides called Dilps, activating a unique membrane receptor and its downstream signaling cascade. During larval development, IIS is involved in metabolic homeostasis and growth. We have used feeding conditions (high sugar diet, HSD) that induce an important change in metabolic homeostasis to monitor possible effects on growth. Unexpectedly we observed that HSD-fed animals exhibited severe growth inhibition as a consequence of peripheral Dilp resistance. Dilp-resistant animals present several metabolic disorders similar to those observed in type II diabetes (T2D) patients. By exploring the molecular mechanisms involved in Drosophila Dilp resistance, we found a major role for the lipocalin Neural Lazarillo (NLaz), a target of JNK signaling. NLaz expression is strongly increased upon HSD and animals heterozygous for an NLaz null mutation are fully protected from HSD-induced Dilp resistance. NLaz is a secreted protein homologous to the Retinol-Binding Protein 4 involved in the onset of T2D in human and mice. These results indicate that insulin resistance shares common molecular mechanisms in flies and human and that Drosophila could emerge as a powerful genetic system to study some aspects of this complex syndrome.
User-centric local mobile cloud-assisted D2D communications in heterogeneous cloud-rans

Mobile cloud computing has been widely used to offload the execution of computation-intensive applications to a cloud for mobile devices. One concern of computation offloading is the energy consumption of transmission due to the long air interface distance between the user and the cloud. Therefore, we introduce device-to-device communications into computation offloading, and then propose a framework of user-centric local mobile cloud-assisted D2D communications in heterogeneous cloud RANs (H-CRANs). In this framework, resource-poor devices can utilize other users' vacant computing resources. Following that, we consider an energy- aware subtask allocation strategy with limited fronthaul data transfer in H-CRAN. Finally, simulation results illustrate that the proposed strategy consumes less transmission energy than conventional computation offloading strategies with fronthaul usage fairness guaranteed.
ECOLOGICAL DISTRIBUTION OF RECENT DEEP-WATER FORAMINIFERA AROUND NEW ZEALAND

Census counts (>63 μm) of 461 species in 361 samples are used as the basis for recognizing and mapping associations of deep-sea benthic foraminifera (50–5000-m depth) around New Zealand, southwest Pacific (28–60°S, 155°E–170°W). Fourteen faunal associations are identified by cluster analysis with five of these subdivided into 20 subassociations. The deepest associations, dominated by Nuttallides spp. , Globocassidulina subglobosa , and diverse agglutinated species, occur at middle–lower abyssal depths (>3600 m) right around New Zealand, where they have been impacted by differing levels of taphonomic modifications. Two large associations are widespread throughout the region: one ( Alabaminella weddellensis-Epistominella exigua ) at lower bathyal–middle abyssal depths (~1500–4000 m) and the other ( Cassidulina carinata - A. weddellensis - Abditodentrix pseudothalmanni ) mostly at mid-bathyal–upper abyssal depths (~500–3000 m). Two deep-water associations occur on current-swept submarine highs: one ( Trifarina angulosa-Ehrenbergina glabra ) at lower bathyal–upper abyssal depths (1000–2400 m) along the southeastern margin of the Camp-bell and Bounty plateaux and the other ( Bolivina robusta-Globocassidulina canalisuturata ) at mid–upper bathyal depths in coarse sediment east and southeast of New Zealand. Two large associations occur at mid-shelf–uppermost-bathyal depths (50–400 m): one ( Cassidulina carinata - Bulimina marginata - Gavelinopsis praegeri ) around the coast beneath warm Subtropical Water and the other ( C. carinata - T. angulosa - G. praegeri ) further south beneath the cooler Subtropical Front and Subantarctic Water. A major reason for this study was to understand the environmental drivers of foraminiferal faunal distribution in this region to assist in paleoenvironmental interpretations of fossil faunas which have a significant regional character. Canonical correspondence analysis indicates that the distribution of bathyal and abyssal associations is more strongly influenced by depth-related variables, while shallower associations are influenced by latitude-related differences in surface-water characteristics. Environmental variables that influence faunal patterns at abyssal and bathyal depths appear to be, in decreasing order: food supply (organic-carbon flux, chlorophyll- a proxies), bottom-oxygen concentration, and carbonate corrosiveness (Fragmentation Index, planktic % proxies). Latitude-related variables driving mid-shelf–uppermost bathyal faunal patterns are water temperature, followed by primary productivity (phosphate and chlorophyll- a proxies). Environmental variables related to bottom-current strength appear to drive the faunal composition of three associations at shelf and bathyal depths. Cluster analysis enables the recognition of 22 anomalously deep faunas that are inferred to have a significant displaced content. There are no significant diversity trends correlated with depth, but species diversity decreases with increasing latitude at all depths.
Broad-Spectrum Anti-biofilm Peptide That Targets a Cellular Stress Response

Bacteria form multicellular communities known as biofilms that cause two thirds of all infections and demonstrate a 10 to 1000 fold increase in adaptive resistance to conventional antibiotics. Currently, there are no approved drugs that specifically target bacterial biofilms. Here we identified a potent anti-biofilm peptide 1018 that worked by blocking (p)ppGpp, an important signal in biofilm development. At concentrations that did not affect planktonic growth, peptide treatment completely prevented biofilm formation and led to the eradication of mature biofilms in representative strains of both Gram-negative and Gram-positive bacterial pathogens including Pseudomonas aeruginosa, Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, methicillin resistant Staphylococcus aureus, Salmonella Typhimurium and Burkholderia cenocepacia. Low levels of the peptide led to biofilm dispersal, while higher doses triggered biofilm cell death. We hypothesized that the peptide acted to inhibit a common stress response in target species, and that the stringent response, mediating (p)ppGpp synthesis through the enzymes RelA and SpoT, was targeted. Consistent with this, increasing (p)ppGpp synthesis by addition of serine hydroxamate or over-expression of relA led to reduced susceptibility to the peptide. Furthermore, relA and spoT mutations blocking production of (p)ppGpp replicated the effects of the peptide, leading to a reduction of biofilm formation in the four tested target species. Also, eliminating (p)ppGpp expression after two days of biofilm growth by removal of arabinose from a strain expressing relA behind an arabinose-inducible promoter, reciprocated the effect of peptide added at the same time, leading to loss of biofilm. NMR and chromatography studies showed that the peptide acted on cells to cause degradation of (p)ppGpp within 30 minutes, and in vitro directly interacted with ppGpp. We thus propose that 1018 targets (p)ppGpp and marks it for degradation in cells. Targeting (p)ppGpp represents a new approach against biofilm-related drug resistance.
Scheduling and deployment of large-scale applications on Cloud platforms. (Ordonnancement et déploiement d'applications de gestion de données à grande échelle sur des plates-formes de type Clouds)

Infrastructure as a service (IaaS) Cloud platforms are increasingly used in the IT industry. IaaS platforms are providers of virtual resources from a catalogue of predefined types. Improvements in virtualization technology make it possible to create and destroy virtual machines on the fly, with a low overhead. As a result, the great benefit of IaaS platforms is the ability to scale a virtual platform on the fly, while only paying for the used resources. From a research point of view, IaaS platforms raise new questions in terms of making efficient virtual platform scaling decisions and then efficiently scheduling applications on dynamic platforms. The current thesis is a step forward towards exploring and answering these questions. The first contribution of the current work is focused on resource management. We have worked on the topic of automatically scaling cloud client applications to meet changing platform usage. There have been various studies showing self-similarities in web platform traffic which implies the existence of usage patterns that may or may not be periodical. We have developed an automatic platform scaling strategy that predicted platform usage by identifying non-periodic usage patterns and extrapolating future platform usage based on them. Next we have focused on extending an existing grid platform with on-demand resources from an IaaS platform. We have developed an extension to the DIET (Distributed Interactive Engineering Toolkit) middleware, that uses a virtual market based approach to perform resource allocation. Each user is given a sum of virtual currency that he will use for running his tasks. This mechanism help in ensuring fair platform sharing between users. The third and final contribution targets application management for IaaS platforms. We have studied and developed an allocation strategy for budget-constrained workflow applications that target IaaS Cloud platforms. The workflow abstraction is very common amongst scientific applications. It is easy to find examples in any field from bioinformatics to geology. In this work we have considered a general model of workflow applications that comprise parallel tasks and permit non-deterministic transitions. We have elaborated two budget-constrained allocation strategies for this type of workflow. The problem is a bi-criteria optimization problem as we are optimizing both budget and workflow makespan. This work has been practically validated by implementing it on top of the Nimbus open source cloud platform and the DIET MADAG workflow engine. This is being tested with a cosmological simulation workflow application called RAMSES. This is a parallel MPI application that, as part of this work, has been ported for execution on dynamic virtual platforms. Both theoretical simulations and practical experiments have shown encouraging results and improvements.
Reorienting companies' hiring behaviour: an innovative `back-to-work' method in France

Current `back-to-work' programmes, particularly in France, tend to be built on a concept of personal responsibility for (long-term) unemployment and follow an `adaptive' approach: improving the `employability' of the unemployed, which is seen as an individual capacity, independent of the work and evaluation context. Our contribution justifies an alternative approach to back-to-work initiatives, so that society's share of responsibilities for long-term unemployment and social exclusion is taken into account within a collective, emergent and context-related conception of employability. Our study is based on observation of an innovative back-to-work programme in France (IOD) which seeks to change employers' assessment and recruitment practices to help vulnerable candidates who are generally discriminated against when seeking work.This interventionist approach aims to alter the demand side of the labour market and bring about changes in companies' practices to encourage more stable jobs and reduce selectivity in hiring.
Improved Channel Estimation for TDS-OFDM Based on Flexible Frequency-Binary Padding

By adopting the pseudo-random noise (PN) sequences as the guard interval (GI) as well as the training sequence, time domain synchronous orthogonal frequency division multiplexing (TDS-OFDM) outperforms the conventional OFDM using the cyclic prefix (CP) in the spectral efficiency at the cost of the iterative padding subtraction (IPS) in channel estimation (CE). To avoid the high computational complexity of the IPS, an improved frequency domain CE scheme based on a newly designed frame structure is proposed. To further improve the CE accuracy, the time domain training sequences, which are frequency binary (FB) after the fast Fourier transform (FFT), are flexibly padded as the frame header instead of the PN sequences. Theoretical analyses and computer simulations show that the proposed scheme can improve the system performance under the time frequency doubly selective channels, even in the presence of large channel delays in the single frequency networks.
Armitage Lecture 2011: the design and analysis of life history studies

Life history studies collect information on events and other outcomes during people's lifetimes. For example, these may be related to childhood development, education, fertility, health, or employment. Such longitudinal studies have constraints on the selection of study members, the duration and frequency of follow‐up, and the accuracy and completeness of information obtained. These constraints, along with factors associated with the definition and measurement of certain outcomes, affect our ability to understand, model, and analyze life history processes. My objective here is to discuss and illustrate some issues associated with the design and analysis of life history studies. Copyright © 2013 John Wiley & Sons, Ltd.
Thermal structure of the martian thermosphere: LMD-IAA GCM and MTGCM intercomparisons

F. González-Galindo, Instituto de Astrofı́sica de Andalucı́a, Granada, CSIC, Spain (ggalindo@iaa.es), S. Bougher, Department of Atmospheric, Oceanic and Space Science, University of Michigan, USA, M.A. López-Valverde, Instituto de Astrofı́sica de Andalucı́a, Granada, CSIC, Spain, F. Forget, Laboratoire de Météorologie Dynamique, Institut Pierre Simon Laplace, Paris, France, J. Bell, Department of Atmospheric, Oceanic and Space Science, University of Michigan, USA.
The fate of fluids released from subducting slab in northern Cascadia

Abstract. Large amounts of water carried down in subduction zones are driven upward into the overlying forearc upper mantle and crust as increasing temperatures and pressure dehydrate the subducting crust. Through seismic tomography velocities we show (a) the overlying forearc mantle in northern Cascadia is hydrated to serpentinite, and (b) there is low Poisson's ratio at the base of the forearc lower crust that may represent silica deposited from the rising fluids. From the velocities observed in the forearc mantle, the volume of serpentinite estimated is ∼30 %. This mechanically weak hydrated forearc region has important consequences in limits to great earthquakes and to collision tectonics. An approximately 10 km thick lower crustal layer of low Poisson's ratio (σ = 0.22) in the forearc is estimated to represent a maximum addition of ∼14 % by volume of quartz (σ = 0.09). If this quartz is removed from rising silica-saturated fluids over long times, it represents a significant addition of silica to the continental crust and an important contributor to its average composition.