Miracle-dz/UniFAR-FTUs huggingface dataset:
Ethanol Stimulates Locomotion via a Gαs-Signaling Pathway in IL2 Neurons in Caenorhabditis elegans

Alcohol abuse is among the top causes of preventable death, generating considerable financial, health, and societal burdens. Paradoxically, alcohol. Alcohol is a potent pharmacological agent when consumed acutely at sufficient quantities and repeated overuse can lead to addiction and deleterious effects on health. Alcohol is thought to modulate neuronal function through low-affinity interactions with proteins, in particular with membrane channels and receptors. Paradoxically, alcohol acts as both a stimulant and a sedative. The exact molecular mechanisms for the acute effects of ethanol on neurons, as either a stimulant or a sedative, however remain unclear. We investigated the role that the heat shock transcription factor HSF-1 played in determining a stimulatory phenotype of Caenorhabditis elegans in response to physiologically relevant concentrations of ethanol (17 mM; 0.1% v/v). Using genetic techniques, we demonstrate that either RNA interference of hsf-1 or use of an hsf-1(sy441) mutant lacked the enhancement of locomotion in response to acute ethanol exposure evident in wild-type animals. We identify that the requirement for HSF-1 in this phenotype was IL2 neuron-specific and required the downstream expression of the α-crystallin ortholog HSP-16.48. Using a combination of pharmacology, optogenetics, and phenotypic analyses we determine that ethanol activates a Gαs-cAMP-protein kinase A signaling pathway in IL2 neurons to stimulate nematode locomotion. We further implicate the phosphorylation of a specific serine residue (Ser322) on the synaptic protein UNC-18 as an end point for the Gαs-dependent signaling pathway. These findings establish and characterize a distinct neurosensory cell signaling pathway that determines the stimulatory action of ethanol and identifies HSP-16.48 and HSF-1 as novel regulators of this pathway.
The importance of thermal history: costs and benefits of heat exposure in a tropical, rocky shore oyster

ABSTRACT Although thermal performance is widely recognised to be pivotal in determining species’ distributions, assessment of this performance is often based on laboratory-acclimated individuals, neglecting their proximate thermal history. The thermal history of a species sums the evolutionary history and, importantly, the thermal events recently experienced by individuals, including short-term acclimation to environmental variations. Thermal history is perhaps of greatest importance for species inhabiting thermally challenging environments and therefore assumed to be living close to their thermal limits, such as in the tropics. To test the importance of thermal history, the responses of the tropical oyster Isognomon nucleus to short-term differences in thermal environments were investigated. Critical and lethal temperatures and oxygen consumption were improved in oysters that previously experienced elevated air temperatures, and were associated with an enhanced heat shock response, indicating that recent thermal history affects physiological performance as well as inducing short-term acclimation to acute conditions. These responses were, however, associated with trade-offs in feeding activity, with oysters that experienced elevated temperatures showing reduced energy gain. Recent thermal history, therefore, seems to rapidly invoke physiological mechanisms that enhance survival of short-term thermal challenge but also longer term climatic changes and consequently needs to be incorporated into assessments of species’ thermal performances. Summary: Thermal responses and organismal vulnerability to climate largely depend on the proximate thermal history of individuals as exposure to acute heat events can enhance survival and thermal performance.
Exposing the Underlying Schema of LOD Sources

The Linked Data Principles defined by Tim-Berners Lee promise that a large portion of Web Data will be usable as one big interlinked RDF database. Today, with more than one thousand of Linked Open Data (LOD) sources available on the Web, we are assisting to an emerging trend in publication and consumption of LOD datasets. However, the pervasive use of external resources together with a deficiency in the definition of the internal structure of a dataset causes many LOD sources are extremely complex to understand. In this paper, we describe a formal method to unveil the implicit structure of a LOD dataset by building a (Clustered) Schema Summary. The Schema Summary contains all the main classes and properties used within the datasets, whether they are taken from external vocabularies or not, and is conceivable as an RDFS ontology. The Clustered Schema Summary, suitable for large LOD datasets, provides a more high level view of the classes and the properties used by gathering together classes that are object of multiple instantiations.
Multi-band GPS signal tracking in a high dynamic maneuvering situation

In a GPS receiver, the goal of the signal tracking is to synchronize local generated code and carrier with the received signal. After a step of acquisition, the receiver tracks the shifting of the local code provoked by the movements of the receiver and satellites. In the future evolution of the GPS, the system will have several carrier frequencies, then it will be possible to have several tracking systems working simultaneously for a same satellite. We present in this article a detection method for the tracking of the future multi-band GPS signal. This method is applied to the localization of a vehicle which makes high dynamic maneuver. We define a MAP detection criterion to fuse the shifts discriminator detection achieved on multi carrier frequencies. This criterion is defined in the case when shifts are not necessary simultaneous and when there is a lack of information on one frequency provoked by the unlocking of the code tracking on one of the carrier. Indeed, there is a difference between the instants of shifts on the different carrier frequencies. This difference is due to the effect of ionospheric propagation. The experimentations achieved on synthetic GPS signals show the advantages of the method compared to the classical algorithm.
Incidence and clinical significance of bacterial and fungal contamination of the preservation solution in liver transplantation

M. Audet, T. Piardi, F. Panaro, E. Ghislotti, F. Gheza, M. Cag, T.M. Jarzembowski, H. Flicoteaux, P. Wolf, J. Cinqualbre. Incidence and clinical significance of bacterial and fungal contamination of the preservation solution in liver transplantation. Transpl Infect Dis 2011: 13: 84–88. All rights reserved
Technology for Assignment of Predicted Behavior of Subgrade Soils in the Design of Road Pavements

The paper discloses a technology for assignment of calculated values of moisture, strength, and deformability characteristics of clay subgrade soils. Main features of the geographical complex that determine the variability of characteristics of the water-and-thermal regime of subgrade soils are presented. Recommendations on assignment of calculated values of characteristics of the most common clay subgrade soils in the studied area are given.
An Empirical Investigation into Code Smell Elimination Sequences for Energy Efficient Software

Recent research has shown that maintainability improving activities, such as removing code smells using recommended refactoring activities, may degrade the energy consumption behavior of software systems. However, current research is still immature and requires considerable effort for transferring findings to practice. This work empirically investigates the impact of eliminating a set of three notorious code smells, individually as well as in all six possible sequences, on energy consumption behavior of software systems. It also analyzes whether any relationship exists between software architecture sustainability (in terms of energy efficiency) and maintainability within the context of individual and sequential code smell elimination. The study outcomes show that the selected code smell removal permutations yield variant levels of energy consumption values for the resulted refactored software versions. Also, a particular permutation is learned to yield most energy-efficient refactored software versions, when compared to all other code smell removal permutations.
Secretory Defect and Cytotoxicity

Background: D1080N mutation in interphotoreceptor retinoid-binding protein (IRBP) causes retinitis pigmentosa with unknown mechanisms. Results: The mutation abolished IRBP secretion and induced endoplasmic reticulum stress by forming insoluble IRBP-containing complexes via disulfide bonds. Conclusion: Loss of normal function and gain of cytotoxic function are the likely mechanisms for retinal degeneration. Significance: Chaperones that prevent misfolding of D1080N IRBP are therapeutic candidates. Interphotoreceptor retinoid-binding protein (IRBP) secreted by photoreceptors plays a pivotal role in photoreceptor survival and function. Recently, a D1080N mutation in IRBP was found in patients with retinitis pigmentosa, a frequent cause of retinal degeneration. The molecular and cellular bases for pathogenicity of the mutation are unknown. Here, we show that the mutation abolishes secretion of IRBP and results in formation of insoluble high molecular weight complexes via disulfide bonds. Co-expression of protein disulfide isomerase A2 that regulates disulfide bond formation or introduction of double Cys-to-Ala substitutions at positions 304 and 1175 in D1080N IRBP promoted secretion of the mutated IRBP. D1080N IRBP was not transported to the Golgi apparatus, but accumulated in the endoplasmic reticulum (ER), bound with the ER-resident chaperone proteins such as BiP, protein disulfide isomerase, and heat shock proteins. Splicing of X-box-binding protein-1 mRNA, expression of activating transcription factor 4 (ATF4), and cleavage of ATF6 were significantly increased in cells expressing D1080N IRBP. Moreover, D1080N IRBP induced up-regulation and nuclear translocation of the C/EBP homologous protein, a proapoptotic transcription factor associated with the unfolded protein response. These results indicate that loss of normal function (nonsecretion) and gain of cytotoxic function (ER stress) are involved in the disease mechanisms of D1080N IRBP. Chemical chaperones and low temperature, which help proper folding of many mutated proteins, significantly rescued secretion of D1080N IRBP, suggesting that misfolding is the molecular basis for pathogenicity of D1080N substitution and that chemical chaperones are therapeutic candidates for the mutation-caused blinding disease.
ANMLzoo: a benchmark suite for exploring bottlenecks in automata processing engines and architectures

High-performance automata-processing engines are traditionally evaluated using a limited set of regular expression-rulesets. While regular expression rulesets are valid real-world examples of use cases for automata processing, they represent a small proportion of all use cases for automata-based computing. With the recent availability of architectures and software frameworks for automata processing, many new applications have been found to benefit from automata processing. These show a wide variety of characteristics that differ from prior, popular regular-expression benchmarks, and these should be considered when designing new systems for automata processing. This paper presents ANMLZoo, a benchmark repository for automata-based applications as well as automata engines for both von-Neumann and reconfigurable dataflow architectures. To demonstrate the usefulness of ANMLZoo, we first characterize diversity in the benchmark suite. We then present insights from five experiments showing how ANMLZoo can be used to expose bottlenecks in both automata-processing software engines and hardware architectures.
Different inhibitory effects on the proliferation and apoptosis of human and laboratory Borna disease virus-infected human neuroblastoma SH-SY5Y cells in vitro

Borna disease virus (BDV) is a neurotropic and non-cytolytic virus, which causes behavioral disorders in a wide range of warm-blooded species. It is well established that BDV induces neurodegeneration by impairing neurogenesis and interfering with neuronal functioning in the limbic system. In the present study, the potential role of BDV infection in SH-SY5Y cells was identified, and comparisons of two original BDV strains (the human Hu-H1 and the laboratory Strain V) were performed to further elucidate the phenotypes of BDV pathogenesis with strain differences. Cell Counting Kit-8 and flow cytometric analyses revealed that the two BDV strain-infected groups exhibited marked anti-proliferation and cell cycle arrest compared with the control group, and the Hu-H1 strain caused more evident effects. However, the Hu-H1 strain did not exert effects on the apoptosis of SH-SH5Y cells, while Strain V led to a marked increase in apoptosis upon initial infection. Western blot analysis confirmed the upregulation of apoptosis regulator BAX protein and the downregulation of apoptosis regulator Bcl-2 protein caused by the two BDV strains. The results of the present study provided evidence that infection with BDV suppressed SH-SY5Y cellular functioning and exhibited divergent antiproliferative and apoptotic roles in cells between the two strains. The present study provided an insight for future investigation of strain differences and underlying pathomechanisms.
Description of the biogeochemical features of the subtropical southeastern Atlantic and the Southern Ocean south of South Africa during the austral summer of the International Polar Year

Meridional and vertical distributions of several biogeochemical parameters were studied along a section in the southeastern Atlantic and the Southern Ocean south of South Africa during the austral summer 2008 of the International Polar Year to characterize the biogeochemical provinces and to assess the seasonal net diatom production. Based on analyses of macro-nutrients, ammonium (NH4), chlorophyll a, (Chl a), phaeopigments, biogenic silica (BSi), particulate inorganic carbon (PIC), and particulate organic carbon and nitrogen (POC and PON, respectively), four biogeochemical domains were distinguished along the section: the subtropical Atlantic, the confluence zone of the subtropical and subantarctic domains, the Polar Frontal Zone (PFZ) in the Antarctic Circumpolar Current (ACC), and the north-eastern branch of the Weddell Gyre. The subtropical region displayed extremely low nutrient concentrations featuring oligotrophic conditions, and sub-surface maxima of Chl a and phaeopigments never exceeded 0.5 µg L−1 and 0.25 µg L−1, respectively. The anticyclonic and cyclonic eddies crossed in the Cape Basin were characterized by a deepening and a rise, respectively, of the nutrients isoclines. The confluence zone of the subtropical domain and the northern side of the ACC within the subantarctic domain displayed remnant nitrate and phosphate levels, whereas silicate concentrations kept to extremely low levels. In this area, Chl a level of 0.4–0.5 µg L−1 distributed homogenously within the mixed layer, and POC and PON accumulated to values up to 10 µM and 1.5 µM, respectively, indicative of biomass accumulation along the confluence zone during the late productive period. In the ACC domain, the Polar Frontal Zone was marked by a post-bloom of diatoms that extended beyond the Polar Front (PF) during this late summer condition, as primarily evidenced by the massive depletion of silicic acid in the surface waters. The accumulation of NH4 to values up to 1.25 µM at 100 m depth centred on the PF and the accumulation of BSi up to 0.5 µM in the surface waters of the central part of the PFZ also featured a late stage of the seasonal diatom bloom. The silica daily net production rate based on the seasonal depletion of silicic acid was estimated to be 11.9 ± 6.5 mmol m−2 d−1 in the domain of the vast diatom post-bloom, agreeing well with the previously recorded values in this province. The Weddell Gyre occasionally displayed relative surface depletion of silicic acid, suggesting a late stage of a relatively minor diatom bloom possibly driven by iceberg drifting releases of iron. In this domain the estimated range of silica daily net production rate (e.g. 21.1 ± 8.8 mmol m−2 d−1) is consistent with previous studies, but was not significantly higher than that in the Polar Front region.
Physical and Genetic Interactions Between Uls1 and the Slx5–Slx8 SUMO-Targeted Ubiquitin Ligase

The Slx5–Slx8 complex is a ubiquitin ligase that preferentially ubiquitylates SUMOylated substrates, targeting them for proteolysis. Mutations in SLX5, SLX8, and other SUMO pathway genes were previously identified in our laboratory as genomic suppressors of a point mutation (mot1-301) in the transcriptional regulator MOT1. To further understand the links between the SUMO and ubiquitin pathways, a screen was performed for high-copy suppressors of mot1-301, yielding three genes (MOT3, MIT1, and ULS1). MOT3 and MIT1 have characteristics of prions, and ULS1 is believed to encode another SUMO-targeted ubiquitin ligase (STUbL) that functionally overlaps with Slx5-Slx8. Here we focus on ULS1, obtaining results suggesting that the relationship between ULS1 and SLX5 is more complex than expected. Uls1 interacted with Slx5 physically in to yeast two-hybrid and co-immunoprecipitation assays, a uls1 mutation that blocked the interaction between Uls1 and Slx5 interfered with ULS1 function, and genetic analyses indicated an antagonistic relationship between ULS1 and SLX5. Combined, our results challenge the assumption that Uls1 and Slx5 are simply partially overlapping STUbLs and begin to illuminate a regulatory relationship between these two proteins.
Functional Knockout of the Adenosine 5′-Phosphosulfate Reductase Gene in Physcomitrella patens Revives an Old Route of Sulfate Assimilation*

The reduction of adenosine 5′-phosphosulfate (APS) to sulfite catalyzed by adenosine 5′-phosphosulfate reductase is considered to be the key step of sulfate assimilation in higher plants. However, analogous to enteric bacteria, an alternative pathway of sulfate reduction via phosphoadenosine 5′-phosphosulfate (PAPS) was proposed. To date, the presence of the corresponding enzyme, PAPS reductase, could be neither confirmed nor excluded in plants. To find possible alternative routes of sulfate assimilation we disrupted the adenosine 5′-phosphosulfate reductase single copy gene inPhyscomitrella patens by homologous recombination. This resulted in complete loss of the correct transcript and enzymatic activity. Surprisingly, the knockout plants grew on sulfate as the sole sulfur source, and the concentration of thiols in the knockouts did not differ from the wild type plants. However, when exposed to a sublethal concentration of cadmium, the knockouts were more sensitive than wild type plants. When fed [35S]sulfate, the knockouts incorporated 35S in thiols; the flux through sulfate reduction was ∼50% lower than in the wild type plants. PAPS reductase activity could not be measured with thioredoxin as reductant, but a cDNA and a gene coding for this enzyme were detected inP. patens. The moss Physcomitrella patens is thus the first plant species wherein PAPS reductase was confirmed on the molecular level and also the first organism wherein both APS- and PAPS-dependent sulfate assimilation co-exist.
DTFS: exploiting the similarity of data versions to design a write-efficient file system in phase-change memory

Phase-change memory (PCM) has emerged as one of the most promising technologies to incorporate into the storage hierarchy of future computer systems. However, PCM has critical weaknesses in performing write operations. Specifically, the access latency and the energy consumption that occur during a write operation are about 6--10 times larger than those of a read operation in PCM. To cope with this situation, we analyze the write access characteristics of file systems, and observe that a large percentage of file write I/Os incurs small changes from the previous version. Based on this observation, we design a novel file system for PCM called DTFS (dual-tree file system) that incurs minimal writes to PCM. DTFS performs better than legacy file systems, but its reliability is as high as any file systems based on journaling or copy-on-write. Experiments with various workload conditions show that DTFS improves the file system performance and the energy consumption by 47% and 67% on average, respectively, compared to copy-on-write file systems such as ZFS and BtrFS.
Phylogenetic Evidence for the Existence of Multiple Strains of Rickettsia parkeri in the New World

ABSTRACT The bacterium Rickettsia parkeri has been reported to infect ticks of the “Amblyomma maculatum species complex” in the New World, where it causes spotted fever illness in humans. In South America, three additional rickettsial strains, namely, Atlantic rainforest, NOD, and Parvitarsum, have been isolated from the ticks Amblyomma ovale, Amblyomma nodosum, and Amblyomma parvitarsum, respectively. These three strains are phylogenetically closely related to R. parkeri, Rickettsia africae, and Rickettsia sibirica. Herein, we performed a robust phylogenetic analysis encompassing 5 genes (gltA, ompA, virB4, dnaA, and dnaK) and 3 intergenic spacers (mppE-pur, rrl-rrf-ITS, and rpmE-tRNAfMet) from 41 rickettsial isolates, including different isolates of R. parkeri, R. africae, R. sibirica, Rickettsia conorii, and strains Atlantic rainforest, NOD, and Parvitarsum. In our phylogenetic analyses, all New World isolates grouped in a major clade distinct from the Old World Rickettsia species (R. conorii, R. sibirica, and R. africae). This New World clade was subdivided into the following 4 clades: the R. parkeri sensu stricto clade, comprising the type strain Maculatum 20 and all other isolates of R. parkeri from North and South America, associated with ticks of the A. maculatum species complex; the strain NOD clade, comprising two South American isolates from A. nodosum ticks; the Parvitarsum clade, comprising two South American isolates from A. parvitarsum ticks; and the strain Atlantic rainforest clade, comprising six South American isolates from the A. ovale species complex (A. ovale or Amblyomma aureolatum). Under such evidences, we propose that strains Atlantic rainforest, NOD, and Parvitarsum are South American strains of R. parkeri. IMPORTANCE Since the description of Rickettsia parkeri infecting ticks of the “Amblyomma maculatum species complex” and humans in the New World, three novel phylogenetic close-related rickettsial isolates were reported in South America. Herein, we provide genetic evidence that these novel isolates, namely, strains Atlantic rainforest, NOD, and Parvitarsum, are South American strains of R. parkeri. Interestingly, each of these R. parkeri strains seems to be primarily associated with a tick species group, namely, R. parkeri sensu stricto with the “Amblyomma maculatum species group,” R. parkeri strain NOD with Amblyomma nodosum, R. parkeri strain Parvitarsum with Amblyomma parvitarsum, and R. parkeri strain Atlantic rainforest with the “Amblyomma ovale species group. ” Such rickettsial strain-tick species specificity suggests a coevolution of each tick-strain association. Finally, because R. parkeri sensu stricto and R. parkeri strain Atlantic rainforest are human pathogens, the potential of R. parkeri strains NOD and Parvitarsum to be human pathogens cannot be discarded.