Large Pseudo-Counts and L2L_2-Norm Penalties Are Necessary for the Mean-Field Inference of Ising and Potts Models

Mean field (MF) approximation offers a simple, fast way to infer direct interactions between elements in a network of correlated variables, a common, computationally challenging problem with practical applications in fields ranging from physics and biology to the social sciences. However, MF methods achieve their best performance with strong regularization, well beyond Bayesian expectations, an empirical fact that is poorly understood. In this work, we study the influence of pseudo-count and $L_2$-norm regularization schemes on the quality of inferred Ising or Potts interaction networks from correlation data within the MF approximation. We argue, based on the analysis of small systems, that the optimal value of the regularization strength remains finite even if the sampling noise tends to zero, in order to correct for systematic biases introduced by the MF approximation. Our claim is corroborated by extensive numerical studies of diverse model systems and by the analytical study of the $m$-component spin model, for large but finite $m$. Additionally we find that pseudo-count regularization is robust against sampling noise, and often outperforms $L_2$-norm regularization, particularly when the underlying network of interactions is strongly heterogeneous. Much better performances are generally obtained for the Ising model than for the Potts model, for which only couplings incoming onto medium-frequency symbols are reliably inferred.Comment: 25 pages, 17 figure

Relationship between systolic time intervals and arterial blood pressure.

It has been suggested that systolic time intervals (STI) can be used to monitor the cardiac effects of antihypertensive treatments and also to evaluate hypertensive patients. STI changes observed in hypertensives have been ascribed to myocardial disease, although they could be due to the existence of a relationship between STI and blood pressure. A group of 37 subjects (18 normotensives and 19 hypertensives) with no signs of heart failure and left ventricular dysfunction were studied to examine the relationship of STI to blood pressure. Pacing with an external battery pulse generator was performed at the rate of 95 beats/min in order to eliminate differences in heart rate. STI were measured from good quality high speed (100 mm/s) recordings and the average value of 10 consecutive cardiac cycles was used for statistical analysis. Normal subjects showed significantly lower values of pre-ejection period (PEP), electromechanical systole (QS2), and pre-ejection period/left ventricular ejection time ratio (PEP/LVET). Moreover, a significant inverse relationship between diastolic pressure and LVET and significant direct relationships between diastolic pressure and PEP, systolic pressure and PEP, diastolic pressure and PEP/LVET, and between systolic pressure and PEP/LVET were demonstrated. We suggest to consider the relation of STI to blood pressure to provide regression equations to best appreciate and use STI

Meiofauna and nematode diversity in some Mediterranean subtidal areas of the Adriatic and Ionian Sea

Sediments of three different subtidal areas (15-705 m depth) of the Italian coasts (Manfredonia, Brindisi and Gallipoli) were investigated to study meiofauna and nematode composition. The nematodes were identified to the genus level and their abundances compared using multivariate analysis. Our data showed an evident depth gradient in meiofauna abundance: the shallowest sites had more diverse and abundant meiobenthic communities than the deeper ones. Nematodes were the dominant taxon (83-100%) at all sites, followed by Copepoda (0.5-8%). Sabatieria, Astomonema, Dorylaimopsis, Terschellingia and Daptonema were among the dominant nematode genera in the three areas. Nematode genus H’ diversities were not significantly dissimilar, though at community level some differences were detected among the study areas. The greatest differences were observed in the comparison of the communities from Manfredonia and Gallipoli. Furthermore, there was a difference between shallow (Astomonema, Dorylaimopsis, Sabatieria and Terschellingia)

Seed morphobiometry of wild and cultivated taxa of Phaseolus L. (Fabaceae)

A morphobiometric analysis of seeds of Phaseolus L. from 50 populations belonging to 31 wild and cultivated taxa was carried out. Based on the outcome of the study an identifi cation key was developed comprising 25 morphotypes of which 23 related to individual taxa The different patterns of seminal tegument allowed 31 taxa to cluster into three groups: (1) Phaseolus angustissimus Gray group (wrinkled seed coat) with two morphotypes, (2) Phaseolus lunatus L. group (smooth tegument with striae) with ten morphotypes and (3) Phaseolus vulgaris L. group (smooth tegument without striae) with 13 morphotypes. All the taxa exhibited uniformity in size and variability in tegument colour of seeds irrespective of the source of population and the type of habitat. Characterization of taxa into defi nite morphotypes and the groups could be useful for biosystematic investigations and the markerbased genetic selection approaches in this important leguminous crop

Phospho-HDAC6 Gathers Into Protein Aggregates in Parkinson’s Disease and Atypical Parkinsonisms

HDAC6 is a unique histone deacetylase that targets cytoplasmic non-histone proteins and has a specific ubiquitin-binding activity. Both of these activities are required for HDAC6-mediated formation of aggresomes, which contain misfolded proteins that will ultimately be degraded via autophagy. HDAC6 deacetylase activity is increased following phosphorylation on serine 22 (phospho-HDAC6). In human, HDAC6 localizes in neuronal Lewy bodies in Parkinson\u2019s disease (PD) and in oligodendrocytic Papp\u2013Lantos bodies in multiple system atrophy (MSA). However, the expression of phospho-HDAC6 in post-mortem human brains is currently unexplored. Here, we evaluate and compare the distribution of HDAC6 and its phosphorylated form in human brains obtained from patients affected by three forms of parkinsonism: two synucleinopathies (PD and MSA) and a tauopathy (progressive supranuclear palsy, PSP). We find that both HDAC6 and its phosphorylated form localize with pathological protein aggregates, including \u3b1-synuclein-positive Lewy bodies in PD and Papp\u2013Lantos bodies in MSA, and phospho-tau-positive neurofibrillary tangles in PSP. We further find a direct interaction of HDAC6 with \u3b1-synuclein with proximity ligation assay (PLA) in neuronal cell of PD patients. Taken together, our findings suggest that both HDAC6 and phospho-HDAC6 regulate the homeostasis of intra-neuronal proteins in parkinsonism

Italian consensus on the recommendations about the use of methotrexate for the treatment of rheumatic diseases with a focus on rheumatoid arthritis: results from the "3E initiative"

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