A pre seismic radio anomaly revealed in the area where the Abruzzo earthquake ( M =6.3) occurred on 6 April 2009

Abstract. On 6 April 2009 a strong (Mw=6.3) earthquake occurred in the Abruzzo region (central Italy). Since 1996, the intensity of CLT (f=189 kHz, Sicily, Italy), MCO (f=216 kHz, France) and CZE (f=270 kHz, Czech Republic) broadcast signals has been collected with a ten minutes sampling rate by a receiver operating in a place located about 13 km far from the epicenter. During March 2009, the old receiver was substituted with a new one able to measure, with one minute sampling rate, the intensity of five VLF signals and five LF signals radiated by transmitters located in different zones of Europe. The MCO and CZE transmitters mentioned above are included among them. From 31 March to 1 April the intensity of the MCO radio signal dropped and this drop was observed only in this signal. The possibility that the drop was connected to problems in the transmitter or in the receiver was investigated and excluded. So, the drop indicates a defocusing of the radiated signal. Since no particular meteorological situation along the path transmitter-receiver happened, the defocusing must be related to other causes, and a possibility is presented that it is a precursor of the Abruzzo earthquake

Finite-size scaling analysis of the distributions of pseudo-critical temperatures in spin glasses

Using the results of large scale numerical simulations we study the probability distribution of the pseudo critical temperature for the three-dimensional Edwards-Anderson Ising spin glass and for the fully connected Sherrington-Kirkpatrick model. We find that the behavior of our data is nicely described by straightforward finite-size scaling relations.Comment: 23 pages, 9 figures. Version accepted for publication in J. Stat. Mec

Retrospective analysis for detecting seismic precursors in groundwater argon content

We examined the groundwater Argon content data sampled from 1988 to 2001 at two wells in Kamchatka (Russia) and anomalous increases appeared clearly during June-July&nbsp;1996. On 21&nbsp;June, a shallow (1km) earthquake with <i>M</i>=7.1 occurred at a distance less than 250km from the wells and so the previous increases could be related to this earthquake and, in particular, could be considered premonitory anomalies. In order to support this raw interpretation, we analysed the data collected in details. At first we smoothed out the high frequency fluctuations arising from the errors in a single measurement. Next we considered the known external effects on the water of a well that are the slow tectonic re-adjustment processes, the meteorology and the gravity tides and we separated these effects applying band-pass filters to the Argon content raw trends. Then we identified the largest fluctuations in these trends applying the 3 σ criterion and we found three anomalies in a case and two anomalies in other case. Comparing the time occurrence of the anomalies at the two wells we found out that a coincidence exists only in the case of the premonitory anomalies we are studying. The simultaneous appearance of well definite anomalies in the residual trends of the same parameter at two different sites supports their meaning and the possibility that they are related to some large scale effect, as the occurrence of a strong earthquake. But, other earthquakes similar to the June&nbsp;1996 event took place during the Argon content measurements time and no anomaly appeared in this content. In the past, some of the authors of this paper studied the Helium content data collected in three natural springs of the Caucasus during seven years. A very similar result, that is the simultaneous appearance of clear premonitory anomalies only on the occasion of a strong (<i>M</i>=7.0) but shallow (2–4km) earthquake, was obtained. The correspondence with the case of the Caucasus validates the interpretation of the Kamchatkian anomalies as precursors

A pre seismic radio anomaly revealed in the area where the Abruzzo earthquake (<i>M</i>=6.3) occurred on 6 April 2009

On 6 April 2009 a strong (Mw=6.3) earthquake occurred in the Abruzzo region (central Italy). Since 1996, the intensity of CLT (f=189 kHz, Sicily, Italy), MCO (f=216 kHz, France) and CZE (f=270 kHz, Czech Republic) broadcast signals has been collected with a ten minutes sampling rate by a receiver operating in a place located about 13 km far from the epicenter. During March 2009, the old receiver was substituted with a new one able to measure, with one minute sampling rate, the intensity of five VLF signals and five LF signals radiated by transmitters located in different zones of Europe. The MCO and CZE transmitters mentioned above are included among them. From 31 March to 1 April the intensity of the MCO radio signal dropped and this drop was observed only in this signal. The possibility that the drop was connected to problems in the transmitter or in the receiver was investigated and excluded. So, the drop indicates a defocusing of the radiated signal. Since no particular meteorological situation along the path transmitter-receiver happened, the defocusing must be related to other causes, and a possibility is presented that it is a precursor of the Abruzzo earthquake

Expanding the phenotype associated to KMT2A variants: overlapping clinical signs between Wiedemann&#8211;Steiner and Rubinstein&#8211;Taybi syndromes

Lysine-specific methyltransferase 2A (KMT2A) is responsible for methylation of histone H3 (K4H3me) and contributes to chromatin remodeling, acting as \u201cwriter\u201d of the epigenetic machinery. Mutations in KMT2A were first reported in Wiedemann\u2013Steiner syndrome (WDSTS). More recently, KMT2A variants have been described in probands with a specific clinical diagnosis comprised in the so-called chromatinopathies. Such conditions, including WDSTS, are a group of overlapping disorders caused by mutations in genes coding for the epigenetic machinery. Among them, Rubinstein\u2013Taybi syndrome (RSTS) is mainly caused by heterozygous pathogenic variants in CREBBP or EP300. In this work, we used next generation sequencing (either by custom-made panel or by whole exome) to identify alternative causative genes in individuals with a RSTS-like phenotype negative to CREBBP and EP300 mutational screening. In six patients we identified different novel unreported variants in KMT2A gene. The identified variants are de novo in at least four out of six tested individuals and all of them display some typical RSTS phenotypic features but also WDSTS specific signs. This study reinforces the concept that germline variants affecting the epigenetic machinery lead to a shared molecular effect (alteration of the chromatin state) determining superimposable clinical conditions

Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies

[Image: see text] Proteogenomics has the potential to advance genome annotation through high quality peptide identifications derived from mass spectrometry experiments, which demonstrate a given gene or isoform is expressed and translated at the protein level. This can advance our understanding of genome function, discovering novel genes and gene structure that have not yet been identified or validated. Because of the high-throughput shotgun nature of most proteomics experiments, it is essential to carefully control for false positives and prevent any potential misannotation. A number of statistical procedures to deal with this are in wide use in proteomics, calculating false discovery rate (FDR) and posterior error probability (PEP) values for groups and individual peptide spectrum matches (PSMs). These methods control for multiple testing and exploit decoy databases to estimate statistical significance. Here, we show that database choice has a major effect on these confidence estimates leading to significant differences in the number of PSMs reported. We note that standard target:decoy approaches using six-frame translations of nucleotide sequences, such as assembled transcriptome data, apparently underestimate the confidence assigned to the PSMs. The source of this error stems from the inflated and unusual nature of the six-frame database, where for every target sequence there exists five “incorrect” targets that are unlikely to code for protein. The attendant FDR and PEP estimates lead to fewer accepted PSMs at fixed thresholds, and we show that this effect is a product of the database and statistical modeling and not the search engine. A variety of approaches to limit database size and remove noncoding target sequences are examined and discussed in terms of the altered statistical estimates generated and PSMs reported. These results are of importance to groups carrying out proteogenomics, aiming to maximize the validation and discovery of gene structure in sequenced genomes, while still controlling for false positives

Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. The annotation process is now performed almost exclusively in an automated fashion to balance the large number of sequences generated. One possible way of reducing errors inherent to automated computational annotations is to apply data from omics measurements (i.e. transcriptional and proteomic) to the un-annotated genome with a proteogenomic-based approach. Here, the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species. Transcriptomic and proteomic data derived from highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis Pestoides F, and Y. pseudotuberculosis PB1/+) was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 incorrect (i.e., observed frameshifts, extended start sites, and translated pseudogenes) protein-coding sequences within the three current genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent pathogen, thus the discovery of many translated pseudogenes, including the insertion-ablated argD, underscores a need for functional analyses to investigate hypotheses related to divergence. Refinements included the discovery of a seemingly essential ribosomal protein, several virulence-associated factors, a transcriptional regulator, and many hypothetical proteins that were missed during annotation

Hospital-acquired influenza infections detected by a surveillance system over six seasons, from 2010/2011 to 2015/2016

In addition to outbreaks of nosocomial influenza, sporadic nosocomial influenza infections also occur but are generally not reported in the literature. This study aimed to determine the epidemiologic characteristics of cases of nosocomial influenza compared with the remaining severe cases of severe influenza in acute hospitals in Catalonia (Spain) which were identified by surveillance. An observational case-case epidemiological study was carried out in patients aged ≥18 years from Catalan 12 hospitals between 2010 and 2016. For each laboratory-confirmed influenza case (nosocomial or not) we collected demographic, virological and clinical characteristics. We defined patients with nosocomial influenza as those admitted to a hospital for a reason other than acute respiratory infection in whom ILI symptoms developed ≥48 h after admission and influenza virus infection was confirmed using RT-PCR. Mixed-effects regression was used to estimate the crude and adjusted OR. One thousand seven hundred twenty-two hospitalized patients with severe laboratory-confirmed influenza virus infection were included: 96 (5.6%) were classified as nosocomial influenza and more frequently had > 14 days of hospital stay (42.7% vs. 27.7%, P <.001) and higher mortality (18.8% vs. 12.6%, P <.02). The variables associated with nosocomial influenza cases in acute-care hospital settings were chronic renal disease (aOR 2.44 95% CI 1.44-4.15) and immunodeficiency (aOR 1.79 95% CI 1.04-3.06). Nosocomial infections are a recurring problem associated with high rates of chronic diseases and death. These findings underline the need for adherence to infection control guidelines

Unpredictability of metabolism—the key role of metabolomics science in combination with next-generation genome sequencing

Next-generation sequencing provides technologies which sequence whole prokaryotic and eukaryotic genomes in days, perform genome-wide association studies, chromatin immunoprecipitation followed by sequencing and RNA sequencing for transcriptome studies. An exponentially growing volume of sequence data can be anticipated, yet functional interpretation does not keep pace with the amount of data produced. In principle, these data contain all the secrets of living systems, the genotype–phenotype relationship. Firstly, it is possible to derive the structure and connectivity of the metabolic network from the genotype of an organism in the form of the stoichiometric matrix N. This is, however, static information. Strategies for genome-scale measurement, modelling and predicting of dynamic metabolic networks need to be applied. Consequently, metabolomics science—the quantitative measurement of metabolism in conjunction with metabolic modelling—is a key discipline for the functional interpretation of whole genomes and especially for testing the numerical predictions of metabolism based on genome-scale metabolic network models. In this context, a systematic equation is derived based on metabolomics covariance data and the genome-scale stoichiometric matrix which describes the genotype–phenotype relationship