A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

Reply to comment by C. Morhange, C. Flaux, P.A. Pirazzoli, M.B. Carre on \u201cHolocene Sea level Change in Malta\u201d

The pits of Birzebbugia are located near the present-day mean sea level, and some are partially submerged. They were dated using pottery discovered in an archaeological site close to the coast, dated to the Bronze Age (Zammit, 1928; Abela, 1999). As they have been interpreted as sites for the retting of flax, during their utilization they should have remained dry and the sea could not submerge them. This is the reason why these structures are not directly related to the sea level, as suggested by Biolchi et al. (2011), so they represent an upper limit.peer-reviewe

Batoid abundances, spatial distribution, and life history traits in the strait of sicily (Central mediterranean sea): Bridging a knowledge gap through three decades of survey

Batoid species play a key role in marine ecosystems but unfortunately they have globally declined over the last decades. Given the paucity of information, abundance data and the main life history traits for batoids, obtained through about three decades of bottom trawl surveys, are presented and discussed. The surveys were carried out in two areas of the Central Mediterranean (South of Sicily and Malta Island), in a timeframe ranging from 1990 to 2018. Excluding some batoids, the abundance trends were stable or increasing. Only R. clavata, R. miraletus, and D. oxyrinchus showed occurrence and abundance indexes notable enough to carry out more detailed analysis. In particular, spatial distribution analysis of these species highlighted the presence of two main hotspots in Sicilian waters whereas they seem more widespread in Malta. The lengths at first maturity (L50) were 695 and 860, 635 and 574, and 364 and 349 mm total length (TL), respectively, for females and males of D. oxyrinchus, R. clavata, and R. miraletus. The asymptotic lengths (L∞) and the curvature coefficients (K) were 1365 and 1240 (K = 0.11 and 0.26), 1260 and 1100 (K = 0.16 and 0.26), and 840 and 800 mm TL (K = 0.36 and 0.41), respectively, for females and males of D. oxyrinchus, R. clavata, and R. miraletus. The lack of detailed quantitative historical information on batoids of Sicily and Malta does not allow to analytically judge the current status of the stocks, although the higher abundance of some species within Malta raises some concern for the Sicilian counterpart. In conclusion, suitable actions to protect batoids in the investigated area are recommended

Certains aspects des mécanismes de la compréhension et de l'expression, menés par l'étudiant dans un cadre contraignant, soit la traduction, soit le compte-rendu

Décrire certains aspects des mécanismes de la compréhension et de l'expression, menés par l'étudiant du Professorat et du Traductorat de Français de l'UNLP, dans un cadre contraignant, soit la traduction, soit le compte-rendu (C.-R.). Nous ne prendrons que quatre cas de fréquence occurrente qui semblent traduire les difficultés sur lesquelles se sont portés les Protocoles Verbaux, réalisés en Laboratoire de Langue, sous la direction de Mme. Jeanne Dancette.Departamento de Lenguas y Literaturas Moderna

Archaeology via underwater robots : mapping and localization within Maltese cistern systems

This paper documents the application of several underwater robot mapping and localization techniques used during an archaeological expedition. The goal of this project was to explore and map ancient cisterns located on the islands of Malta and Gozo. The cisterns of interest acted as water storage systems for fortresses, private homes, and churches. They often consisted of several connected chambers, still containing water. A sonar-equipped Remotely Operated Vehicle (ROV) was deployed into these cisterns to obtain both video footage and sonar range measurements. Four different mapping and localization techniques were employed including 1) Sonar image mosaics using stationary sonar scans, and 2) Simultaneous Localization and Mapping (SLAM) while the vehicle was in motion, 3) SLAM using stationary sonar scans, and 4) Localization using previously created maps. Two dimensional maps of 6 different cisterns were successfully constructed. It is estimated that the cisterns were built as far back as 300 B.C.peer-reviewe

Drag forces on inclusions in classical fields with dissipative dynamics

We study the drag force on uniformly moving inclusions which interact linearly with dynamical free field theories commonly used to study soft condensed matter systems. Drag forces are shown to be nonlinear functions of the inclusion velocity and depend strongly on the field dynamics. The general results obtained can be used to explain drag forces in Ising systems and also predict the existence of drag forces on proteins in membranes due to couplings to various physical parameters of the membrane such as composition, phase and height fluctuations.Comment: 14 pages, 7 figure

Quantitative analysis of prenylated RhoA interaction with its chaperone, RhoGDI

Small GTPases of the Rho family regulate cytoskeleton remodeling, cell polarity, and transcription, as well as the cell cycle, in eukaryotic cells. Membrane delivery and recycling of the Rho GTPases is mediated by Rho GDP dissociation inhibitor (RhoGDI), which forms a stable complex with prenylated Rho GTPases. We analyzed the interaction of RhoGDI with the active and inactive forms of prenylated and unprenylated RhoA. We demonstrate that RhoGDI binds the prenylated form of RhoA center dot GDP with unexpectedly high affinity (K-d = 5 pM). The very long half-life of the complex is reduced 25-fold on RhoA activation, with a concomitant reduction in affinity (K-d = 3 nM). The 2.8-angstrom structure of the RhoA center dot guanosine 5'-[beta,gamma-imido] triphosphate (GMPPNP)center dot RhoGDI complex demonstrated that complex formation forces the activated RhoA into a GDP-bound conformation in the absence of nucleotide hydrolysis. We demonstrate that membrane extraction of Rho GTPase by RhoGDI is a thermodynamically favored passive process that operates through a series of progressively tighter intermediates, much like the one that is mediated by RabGDI

Correspondence Between Cognitive and Audiological Evaluations Among the Elderly: A Preliminary Report of an Audiological Screening Model of Subjects at Risk of Cognitive Decline With Slight to Moderate Hearing Loss

Epidemiological studies show increasing prevalence rates of cognitive decline and hearing loss with age, particularly after the age of 65 years. These conditions are reported to be associated, although conclusive evidence of causality and implications is lacking. Nevertheless, audiological and cognitive assessment among elderly people is a key target for comprehensive and multidisciplinary evaluation of the subject's frailty status. To evaluate the use of tools for identifying older adults at risk of hearing loss and cognitive decline and to compare skills and abilities in terms of hearing and cognitive performances between older adults and young subjects, we performed a prospective cross-sectional study using supraliminal auditory tests. The relationship between cognitive assessment results and audiometric results was investigated, and reference ranges for different ages or stages of disease were determined. Patients older than 65 years with different degrees of hearing function were enrolled. Each subject underwent an extensive audiological assessment, including tonal and speech audiometry, Italian Matrix Sentence Test, and speech audiometry with logatomes in quiet. Cognitive function was screened and then verified by experienced clinicians using the Montreal Cognitive Assessment Score, the Geriatric Depression Scale, and further investigations in some. One hundred twenty-three subjects were finally enrolled during 2016-2019: 103 were >65 years of age and 20 were younger participants (as controls). Cognitive functions showed a correlation with the audiological results in post-lingual hearing-impaired patients, in particular in those affected by slight to moderate hearing loss and aged more than 70 years. Audiological testing can thus be useful in clinical assessment and identification of patients at risk of cognitive impairment. The study was limited by its sample size (CI 95%; CL 10%), strict dependence on language, and hearing threshold. Further investigations should be conducted to confirm the reported results and to verify similar screening models

Munc18-1 is a molecular chaperone for α-synuclein, controlling its self-replicating aggregation

Munc 18-1 is a key component of the exocytic machinery that controls neurotransmitter release. Munc 18-1 heterozygous mutations cause developmental defects and epileptic phenotypes, including infantile epileptic encephalopathy (EIEE), suggestive of a gain of pathological function. Here, we used single-molecule analysis, gene-edited cells, and neurons to demonstrate that Munc 18-1 EIEE-causing mutants form large polymers that coaggregate wild-type Munc 18-1 in vitro and in cells. Surprisingly, Munc 18-1 EIEE mutants also form Lewy body like structures that contain a-synuclein (alpha-Syn). We reveal that Munc 18-1 binds alpha-Syn, and its EIEE mutants coaggregate alpha-Syn. Likewise, removal of endogenous Munc 18-1 increases the aggregative propensity of alpha-Syn(wT) and that of the Parkinson's disease-causing a-Syn(A30P) mutant, an effect rescued by Munc18-1(WT) expression, indicative of chaperone activity. Coexpression of the alpha-Syn(A30P) mutant with Munc 18-1 reduced the number of alpha-Syn(A30P) aggregates. Munc 18-1 mutations and haploinsufficiency may therefore trigger a pathogenic gain of function through both the corruption of native Munc 18-1 and a perturbed chaperone activity for a-Syn leading to aggregation-induced neurodegeneration

Circulating linoleic acid at the time of myocardial infarction and risk of primary ventricular fibrillation

Primary ventricular fibrillation (PVF) is a major driver of cardiac arrest in the acute phase of ST-segment elevation myocardial infarction (STEMI). Enrichment of cardiomyocyte plasma membranes with dietary polyunsaturated fatty acids (PUFA) reduces vulnerability to PVF experimentally, but clinical data are scarce. PUFA status in serum phospholipids is a valid surrogate biomarker of PUFA status in cardiomyocytes within a wide range of dietary PUFA. In this nested case-control study (n = 58 cases of STEMI-driven PVF, n = 116 control non-PVF STEMI patients matched for age, sex, smoking status, dyslipidemia, diabetes mellitus and hypertension) we determined fatty acids in serum phospholipids by gas-chromatography, and assessed differences between cases and controls, applying the Benjamini-Hochberg procedure on nominal P-values to control the false discovery rate (FDR). Significant differences between cases and controls were restricted to linoleic acid (LA), with PVF patients showing a lower level (nominal P = 0.002; FDR-corrected P = 0.027). In a conditional logistic regression model, each one standard deviation increase in the proportion of LA was related to a 42% lower prevalence of PVF (odds ratio = 0.58; 95% confidence interval, 0.37, 0.90; P = 0.02). The association lasted after the inclusion of confounders. Thus, regular consumption of LA-rich foods (nuts, oils from seeds) may protect against ischemia-driven malignant arrhythmias