Miracle-dz/UniFAR-FTUs huggingface dataset:
Multilocus Sequence Analysis and rpoB Sequencing of Mycobacterium abscessus (Sensu Lato) Strains (cid:1)

Mycobacterium abscessus , Mycobacterium bolletii , and Mycobacterium massiliense ( Mycobacterium abscessus sensu lato) are closely related species that currently are identiﬁed by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufﬁcient to discriminate between these species, and some authors have questioned their current taxonomic classiﬁcation. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The ﬁnal MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH , cya , glpK , gnd , murC , pgm , pta , and purH . The strains studied included the three type strains ( M. abscessus CIP 104536 T , M. massiliense CIP 108297 T , and M. bolletii CIP 108541 T ) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree conﬁrmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the clustering of strains. We found 10/120 (8.3%) isolates for which the concatenated MLSA gene sequence and rpoB sequence were discordant (e.g., M. massiliense MLSA sequence and M. abscessus rpoB sequence), suggesting the intergroup lateral transfers of rpoB . In conclusion, our study strongly supports the recent proposal that M. abscessus , M. massiliense , and M. bolletii should constitute a single species. Our ﬁndings also indicate that there has been a horizontal transfer of rpoB sequences between these subgroups, precluding the use of rpoB sequencing alone for the accurate identiﬁcation of the two proposed M. abscessus subspecies.
Development and Calibration of a New Dripper-Based Rainfall Simulator for Large-Scale Sediment Wash-O ﬀ Studies

: Rainfall simulators are useful tools for controlling the main variables that govern natural rainfall. In this study, a new drop-forming rainfall simulator, which consists of pressure-compensating dripper grids above a horizontal mesh that breaks and distributes raindrops, was developed to be applied in wash-o ﬀ experiments in a large-scale physical model of 36 m 2 . The mesh typology and size, and its distance to drippers, were established through a calibration where rain uniformity and distributions of raindrop sizes and velocities were compared with local natural rainfall. Finally, the rain properties of the ﬁnal solution were measured for the three rain intensities that the rainfall simulator is able to generate (30, 50 and 80 mm / h), obtaining almost uniform rainfalls with uniformity coe ﬃ cients of 81%, 89% and 91%, respectively. This, together with the very suitable raindrop size distribution obtained, and the raindrop velocities of around 87.5% of the terminal velocity for the mean raindrop diameter, makes the proposed solution optimal for wash-o ﬀ studies, where rain properties are key in the detachment of particles. In addition, the ﬂexibility seen in controlling rain characteristics increases the value of the proposed design in that it is adaptable to a wide range of studies.
Ultrasound-Guided Follicular Aspiration in Mares 1

The study was designed to develop a technique for collecting equine oocytes using ultrasoni- cally guided follicular aspiration. Recovery rate and morphology of cumulus-oocyte-complexes (COC) should be related to follicular diameter in cyclic and acyclic mares. On the basis of results of follicular aspiration in vitro, the follicles from ovaries of 27 warmblood horses were punctured by ultrasound control via the transcervical method. A 6.5-mHz sector scanner and a specially designed carrier with a bitubular needle were used for aspiration. Inner and outer diameters of the needle were 0.9 mm and 1.1 mm. A constant vacuum pressure of 0.3 bar was applied during in vivo aspiration. After aspiration, the follicles were flushed up to four times. The COC obtained were classified into four groups: compact COC (A), expanded COC (B), COC with few layers of cumulus cells (C), and denuded COC (D). The total number of aspirated follicles was 332. A mean of 12.3 follicles were aspirated per animal. The mean number of recovered COC per mare was 3.4. Aspiration of follicles with a diameter of up to 20 mm delivered 96% of all COC recovered. The recovery rate differed significantly between Day 5 and Day 12 of the estrous cycle. Oocytes with few layers of cumulus cells were found in almost equal proportions in follicles < 10 mm in diameter and 10-20 mm in diameter. Only one third of COC from follicles smaller than 20 mm had a compact cumulus.
A Generalized Approach to Predict the Availability of IPTV Services in Vehicular Networks Using an Analytical Model

— Currently, an increasing number of vehicles are getting equipped with components which offer the possibility of an Internet access with low expenditure. Therefore, entertainment services in VANETs are becoming more and more important. An interesting class of entertainment services comprises IP television (IPTV) services and, therefore, studies regarding the quality of experience (QoE) for IPTV in VANETs are becoming increasingly relevant. Such QoE analyses also constitute the main goal of this paper where we focus on QoE in terms of availability of IPTV services. Up to now, studies of IPTV service availability in VANETs have primarily been executed based on simulation models. In this paper, we make use of analytical models to predict availability of IPTV for VANET scenarios. For this purpose, we have elaborated an analytical model of rather low complexity which, nevertheless, is rather realistic as we will show by means of comprehensive validation studies. In addition, we propose a general proceeding which makes use of our analytical model and can be applied as a straight-forward approach to predict the availability of IPTV services in a flexible and efficient manner. Case studies demonstrate how our analytical model can be applied by a provider of IPTV services, offered via VANETs, in order to satisfy QoE requirements regarding the service availability as given by the IPTV users.
rapid communication Expression of metabotropic glutamate receptors in nodose ganglia and the nucleus of the solitary tract

Expression of metabotropic glutamate receptors in nodose ganglia and the nucleus of the solitary tract. Am 281: H457–H462, 2001. —The purpose of this study was to identify the complement of metabotropic glutamate receptors (mGluRs) expressed in nodose ganglia and the nucleus tractus solitarius (NTS). mRNA from these tissues was isolated and ampliﬁed with standard RT-PCR with primers speciﬁc for each mGluR subtype. The results of this analysis showed that the NTS expresses all eight mGluR subtypes, whereas nodose ganglia express only group III mGluRs: mGluR4, mGluR6, mGluR7, and mGluR8. Application of the group III-speciﬁc mGluR agonist L -( 1 )-2-amino-4-phosphonobu-tyric acid (100 m M) reversibly inhibited voltage-gated calcium currents isolated from DiI-labeled aortic baroreceptor neurons and unlabeled nodose neurons. The results of this study suggest that group III mGluRs are the primary mGluR subtype expressed in visceral afferent neurons and that these receptors may be involved in afferent central transmission.
pp39mO Is Associated with p34cdc2 Kinase in c-mos'e-Transformed NIH 3T3 Cells

We investigated the possible interactions between pp39mOS and p34CdC2 kinase in NIH 3T3 cells transformed by c.mosXe. pp39" is coprecipitated with p34"""2 when using either anti-PSTAIR antibody or pl3Y""-Sepharose beads. Likewise, p34Cdc2 is coprecipitated with pp39"m4 when using anti-mos antibody. However, pp39""" was not present in histone Hi kinase-active p34CdC2 complexes precipitated with anti-p34fd2 C-terminal peptide antibody even during metaphase of the cell cycle. The molar ratio of p34 to pp39mOS in the p13`' complex is -2:1. Consistent with the tight association between pp39O and tubulin, tubulin was also present in equivalent amounts with pp39"mo and p34 in the pl3sucl complex. This pp39m-0p34cd2-tubulin complex may be important in transformation by the mos oncogene. The
Phone Inventories and Recognition for Every Language

Identifying phone inventories is a crucial component in language documentation and the preservation of endangered languages. However, even the largest collection of phone inventory only covers about 2000 languages, which is only 1/4 of the total number of languages in the world. A majority of the remaining languages are endangered. In this work, we attempt to solve this problem by estimating the phone inventory for any language listed in Glottolog, which contains phylogenetic information regarding 8000 languages. In particular, we propose one probabilistic model and one non-probabilistic model, both using phylogenetic trees (“language family trees”) to measure the distance between languages. We show that our best model outperforms baseline models by 6.5 F1. Furthermore, we demonstrate that, with the proposed inventories, the phone recognition model can be customized for every language in the set, which improved the PER (phone error rate) in phone recognition by 25%.
Identiﬁcation of a pheA Gene Associated with Streptococcus mitis by Using Suppression Subtractive Hybridization

We performed suppression subtractive hybridization to identify genomic differences between Streptococcus mitis and Streptococcus pneumoniae . Based on the pheA gene, a primer set speciﬁc to S. mitis detection was found in 18 out of 103 S. mitis -speciﬁc clones. Our ﬁndings would be useful for discrimination of S. mitis from other closely related cocci in the oral environment. S. software. The nucleotide sequence homologies of the genomic sub-tracted fragments of S. mitis KCTC 3556 T were evaluated using BLASTx searches against the GenBank databases. Oligonucleotide primers were designed to amplify the nucleotide sequences speciﬁc to S. mitis KCTC 3556 T using Primer3 software (30). PCRs were performed in 20- (cid:1) l reaction volumes containing 100 ng genomic DNA, 1 mM each primer, 2 (cid:1) l 10 (cid:4) reaction buffer (iNtRON), 1 (cid:1) l of 10 mM deoxynucleoside triphosphates (dNTPs;
Polysemy in Spoken Conversations and Written Texts

Our discourses are full of potential lexical ambiguities, due in part to the pervasive use of words having multiple senses. Sometimes, one word may even be used in more than one sense throughout a text. But, to what extent is this true for different kinds of texts? Does the use of polysemous words change when a discourse involves two people, or when speakers have time to plan what to say? We investigate these questions by comparing the polysemy level of texts of different nature, with a focus on spontaneous spoken dialogs; unlike previous work which examines solely scripted, written, monolog-like data. We compare multiple metrics that presuppose different conceptualizations of text polysemy, i.e., they consider the observed or the potential number of senses of words, or their sense distribution in a discourse. We show that the polysemy level of texts varies greatly depending on the kind of text considered, with dialog and spoken discourses having generally a higher polysemy level than written monologs. Additionally, our results emphasize the need for relaxing the popular “one sense per discourse” hypothesis.
Comparison between anaerobic threshold determined by ventilatory variables and blood lactate response in cyclists

Many investigations have shown that the coincidence between the ventilatory thresholds and those thresholds using the lactate response does not happen all of the time, suggesting that there is no relationship between the cause-effect between these phenomena. Thus, the present study had as main purpose to compare and correlate the Oxygen consumption (VO 2 ), the power (W), and the heart rate (HR) values attained using protocols to determine the Ventilatory Threshold (VT) and the Individual Anaerobic Threshold (IAT). The sampling was constituted by eight State and National level cyclists (age: 27.88 ± 8.77 years; body mass: 65.19 ± 4.40 kg; height: 169.31 ± 5,77 cm). The IAT was determined starting from a three minutes 50 W warm up with progressive increases of 50 W.3min-1 up to achieving the voluntary exhaustion, when the blood was collected in the last 20 seconds of each phase, and during the recovering period. In order to determine the VT, it was used the same protocol used to determine the IAT, but without performing the blood collection. The VT was identified through the changes in the pulmonary ventilation, as well as of the ventilatory equivalent of the O 2 and CO 2 . The t-Student test showed no significant statistical difference in any of the attained variables. The associations found were high and significant. The VO 2 (ml.kg1.min.-1), P (W), and HR (bpm) corresponding to the VT and IAT, as well as the associations between variables were respectively: 48.00 ± 3.82 vs. 48.08 ± 3.71 (r = 0.90); 256.25 ± 32.04 vs. 246.88 ± 33.91 (r = 0.84); 173.75 ± 9.18 vs. 171.25 ± 12.02 (r = 0.97). According to the results attained, it can be concluded that the IAT and the VT produce similar VO 2 , W, and HR values, favoring the adoption of the VT because it is a non-invasive method to determine the anaerobic threshold in cyclists.
Improvements to the Implicit Hitting Set Approach to Pseudo-Boolean Optimization

The development of practical approaches to efficiently reasoning over pseudo-Boolean constraints has recently increasing attention as a natural generalization of Boolean satisfiability (SAT) solving. Analogously, solvers for pseudo-Boolean optimization draw inspiration from techniques developed for maximum satisfiability (MaxSAT) solving. Recently, the first practical solver lifting the implicit hitting set (IHS) approach – one of the most efficient approaches in modern MaxSAT solving – to the realm of PBO was developed, employing a PB solver as a core extractor together with an integer programming solver as a hitting set solver. In this work, we make practical improvements to the IHS approach to PBO. We propose the integration of solution-improving search to the PBO-IHS approach, resulting in a hybrid approach to PBO which makes use of both types of search towards an optimal solution. Furthermore, we explore the potential of different variants of core extraction within PBO-IHS – including recent advances in PB core extraction, allowing for extracting more general PB constraints compared to the at-least-one constraints typically relied on in IHS – in speeding up PBO-IHS search. We show that the empirical efficiency of PBO-IHS – recently shown to outperform other specialized PBO solvers – is further improved by the integration of these techniques. Computing Competence Infrastructure (FCCI) for supporting this project with computational and data storage resources.
Stomatin-deﬁcient cryohydrocytosis results from mutations in SLC2A1 : a novel form of GLUT1 deﬁciency syndrome

The hereditary stomatocytoses are a se-ries of dominantly inherited hemolytic anemias in which the permeability of the erythrocyte membrane to monovalent cations is pathologically increased. The causative mutations for some forms of hereditary stomatocytosis have been found in the transporter protein genes, RHAG and SLC4A1 . Glucose transporter 1 (glut1) deﬁciency syndromes (glut1DSs) result from mutations in SLC2A1 , encoding glut1. Glut1 is the main glucose transporter in the mammalian blood-brain barrier, and glut1DSs are manifested by an array of neurologic symptoms. We have previously reported 2 cases of stomatin-deﬁcient cryohydrocytosis (sdCHC), a rare form of stomatocytosis associated with a cold-induced cation leak, hemo-lyticanemia,andhepatosplenomegalybut also with cataracts, seizures, mental retardation, and movement disorder. We now show that sdCHC is associated with mutations in SLC2A1 that cause both loss of glucose transport and a cation leak, as shown by expression studies in Xenopus oocytes. On the basis of a 3-dimensional model of glut1, we propose potential mechanisms underlying the phenotypes of the 2 mutations found. We investigated the loss of stomatin during erythropoiesis and ﬁnd this occurs during reticulocyte maturation and involves endocyto-sis. The molecular basis of the glut1DS, paroxysmal exercise-induced dyskinesia, and sdCHC phenotypes are compared and discussed. ( Blood . 2011;118(19): 5267-5277)
The role of elasticity in slab bending Geochemistry, Geophysics, Geosystems PUBLICATIONS

Previous studies showed that plate rheology exerts a dominant control on the shape and velocity of subducting plates. Here, we perform a systematic investigation of the role of elasticity in slab bending, using fully dynamic 2-D models where an elastic, viscoelastic, or viscoelastoplastic plate subducts freely into a purely viscous mantle. We derive a scaling relationship between the bending radius of viscoelastic slabs and the Deborah number, De , which is the ratio of Maxwell time over deformation time. We show that De controls the ratio of elastically stored energy over viscously dissipated energy and ﬁnd that at De > 10 2 2 , substantially less energy is required to bend a viscoelastic slab to the same shape as a purely viscous slab with the same intrinsic viscosity. Elastically stored energy at higher De favors retreating modes of subduction via unbending, while trench advance only occurs for some cases with De < 10 2 2 . We estimate the apparent Deborah numbers of natural subduction zones and ﬁnd values ranging from 10 2 3 to > 1, where most zones have low De < 10 2 2 , but a few young plates have De > 0.1. Slabs with De < 10 2 2 either have very low viscosities or they may be yielding, in which case our De estimates may be underestimated by up to an order of magnitude, potentially pointing towards a signiﬁcant role of elasticity in (cid:2) 60% of the subduction zones. In support of such a role of elasticity in subduction, we ﬁnd that increasing De correlates with increasing proportion of larger seismic events in both instrumental and historic catalogues. mantle of density q M and viscosity g M , achieving a subduction velocity U p , deﬂection w and slab dip h . Slab deformation is modeled in 2-D, but the analytically cal- culated mantle drag that is applied along the slab’s sides and tip is for 3-D ﬂow around a ﬁnite-width plate. The plate is supported in the top few kilometers by a Winkler foundation of thickness h w . The top surface and the trailing edge are free.
777 The transcription cycle of RNA polymerase II in living

UK NA polymerase II transcribes most eukaryotic genes. Its catalytic subunit was tagged with green ﬂuorescent protein and expressed in Chinese hamster cells bearing a mutation in the same subunit; it complemented the defect and so was functional. Photobleaching revealed two kinetic fractions of polymerase in living nuclei: (cid:2) 75% moved rapidly, but (cid:2) 25% was transiently immobile (association t 1/2 (cid:2) 20 min) and transcriptionally active, as incubation with 5,6-dichloro-1- (cid:2) - D -ribofuranosylbenzimidazole eliminated it. No immobile but inactive fraction was detected, providing little support for the existence of a stable holoenzyme, or the slow stepwise assembly of a preinitiation complex R promoters or the nuclear substructure. Actinomycin D decreased the rapidly moving fraction, suggesting that engaged polymerases stall at intercalated molecules while others initiate. When wild-type cells containing only the endogenous enzyme were incubated with [ 3 H]uridine, nascent transcripts became saturated with tritium with similar kinetics (t 1/2 (cid:2) 14 min). These data are consistent with a polymerase being mobile for one half to ﬁve sixths of a transcription cycle, and rapid assembly into the preinitiation complex. Then, most expressed transcription units would spend signiﬁcant times unassociated with engaged
A genome-wide study of reproductive barriers between allopatric populations of a homosporous richardii

Biological factors involved in reproductive barriers between two divergent of Ceratopteris richardii were investigated. We used a combination of spore germination rates, QTL analysis of spore germination rates, and transmission ratio distortion (TRD) of 729 RFLP, AFLP, and isozyme markers distributed across the genome based on hybrid populations of 488 doubled haploid lines (DHLs) and 168 F 2 s. Substantial reproductive barriers were found between the parental races, predominantly in the form of spore inviability (23.7% F 1 spore viability). Intrinsic genetic factors such as Bateson-Dobzhansky-Muller (BDM) incompatibilities, involving both nuclear-nuclear and nuclear-cytoplasmic factors, and chromosomal rearrangements appear to contribute to intrinsic postzygotic isolation. The genome-wide distribution patterns of TRD loci support the hypothesis that reproductive barriers are a byproduct of divergence in allopatry and that the strong reproductive barriers are attributable to a small number of genetic elements scattered throughout the genome.