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Background Cardiac dysfunction, mainly assessed by biomarker alterations, has been described in COVID-19 infection. However, there are still areas of uncertainty regarding its effective role in disease evolution. Aim of this study was to evaluate early echocardiographic parameters in COVID pneumonia and their association with severity disease and prognosis. Methods An echocardiographic examination was performed within 72 h from admission in 64 consecutive patients hospitalized for COVID-19 pneumonia in our medium-intensity care unit, from March 30th to May 15th 2020. Six patients were excluded for inadequate acoustic window. Results Fifty-eight consecutive patients were finally enrolled, with a median age of 58 years. Twenty-two (38%) were classifiable as severe COVID-19 disease. Eight out of 58 patients experienced adverse evolution (six died, two were admitted to ICU and received mechanical ventilation), all of them in the severe pneumonia group. Severe pneumonia patients showed higher troponin, IL-6 and d-Dimer values. No significant new onset alterations of left and right ventricular systolic function parameters were observed. Patients with severe pneumonia showed higher mean estimated systolic pulmonary artery pressure (sPAP) (30.7 ± 5.2 mmHg vs 26.2 ± 4.3 mmHg, p = 0.006), even if in the normality range values. No differences in echocardiographic parameters were retrieved in patients with adverse events with respect to those with favorable clinical course. Conclusion A mild sPAP increase in severe pneumonia patients with respect to those with milder disease was the only significant finding at early echocardiographic examination, without other signs of new onset major cardiac dysfunction. Future studies are needed to deepen the knowledge regarding minor cardiac functional perturbation in the evolution of a complex systemic disorder, in which the respiratory involvement appears as the main character, at least in non-ICU patients.

As the availability of portable echocardiographic equipment is becoming more and more widespread, physicians can add a powerful tool to their bedside examination skills, thus helping them to more effectively face the growing complexity of patients admitted to internal medicine departments or the emergency room. Focused cardiac ultrasound (FoCUS) can be defined as a goal-directed, simplified, qualitative examination performed at the bedside using portable echocardiographic devices. FoCUS is not meant to be a substitute for a standard 2D color Doppler echocardiographic examination. Nevertheless, it can provide rapid and reliable information when limited to basic questions, even when performed by non-cardiologists with brief training. Furthermore, a focused cardiac ultrasound examination maximizes its diagnostic role when integrated with an ultrasonographic assessment of the lung, abdomen and deep veins, in a multisystem approach that is particularly dear to internists. In this article, we will focus on the specific targets of a focused cardiac ultrasound examination, as well as the most common pitfalls that can be encountered in ultrasonographic practice. We will also address the application of FoCUS in the management of two typical scenarios in clinical practice, such as dyspnea and non-post-traumatic hypotension. Mit der zunehmenden breiten Verfugbarkeit tragbarer echokardiografischer Gerate konnen Arzte eine leistungsstarke Methode hinzufugen, um ihre Fahigkeiten in der bettseitigen Untersuchung zu erweitern. So konnen sie der wachsenden Komplexitat der Patienten, die in den Abteilungen fur Innere Medizin oder in der Notaufnahme aufgenommen werden, wirksamer begegnen. Fokussierter kardialer Ultraschall (FoCUS) kann als zielgerichtete, vereinfachte, qualitative Untersuchung definiert werden, die am Krankenbett mittels tragbarer Echokardiografie-Gerate durchgefuhrt wird. FoCUS ist kein Ersatz fur eine standardmasige echokardiografische 2D-Farbdoppler-Untersuchung. Dennoch kann er bei Beschrankung auf grundlegende Fragestellungen schnelle und zuverlassige Informationen liefern, selbst wenn kurz ausgebildete Nicht-Kardiologen ihn durchfuhren. Daruber hinaus wird der diagnostische Wert des fokussierten kardialen Ultraschalls maximiert, wenn dieser in eine sonografische Beurteilung von Lunge, Abdomen und tiefen Venen integriert wird, und zwar in einem Multisystemansatz, der Internisten besonders am Herzen liegt. In diesem Artikel konzentrieren wir uns auf die spezifischen Ziele einer fokussierten kardialen Ultraschalluntersuchung sowie auf die haufigsten Fallstricke, die in der Ultraschallpraxis auftreten konnen. Wir werden uns auch mit der Anwendung von FoCUS bei der Behandlung von 2 typischen Szenarien in der klinischen Praxis befassen – Dyspnoe und nichtposttraumatische Hypotonie.

Objective: To define surface, mechanical, microstructural and metallurgical features of conventional OneShape (OShape) and heat-treated OneCurve (OCurve) nickel-titanium instruments. Methods: Instruments were analysed by scanning electron microscopy (SEM) on new instruments and after simulated clinical use (SCU). Cyclic fatigue testing was performed and the number of cycles to fracture (NCF) and the length of the fractured instruments were measured (Mann-Whitney test). Fractured instruments during cyclic fatigue testing were then inspected by SEM fractographic analysis. Field emission gun scanning scanning electron microscopy (FEG-SEM), energy-dispersive X-ray spectroscopy (EDX) and micro-Raman spectroscopy were used to assess alloy surface chemistry. Focused ion beam (FIB) was performed to analyse the oxide layer on the surface of OCurve before and after SCU. X-Ray diffraction (XRD), metallographic evaluation and differential scanning calorimetry (DSC) were used to determine martensitic/austenitic phase transformation temperatures. Results: SEM observations on new instruments revealed a smooth regular surface with flattened milling grooves. No wear features were detected after SCU. OCurve exhibited a higher cyclic fatigue resistance (P

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds&rsquo, performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities&rsquo, composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

Background Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to facilitate data analysis. Results Here we describe QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. Instead of being designed on specific datasets, it works on a general XML schema specifying formats and criteria of each data source. Thanks to this flexibility, new criteria can be easily added for future expansion. Currently, up to 70 user-selectable criteria are available, including a wide range of gene and variant features. Moreover, rather than progressively discarding variants taking one criterion at a time, the prioritization is achieved by a global positive selection process that considers all transcript isoforms, thus producing reliable results. QueryOR is easy to use and its intuitive interface allows to handle different kinds of inheritance as well as features related to sharing variants in different patients. QueryOR is suitable for investigating single patients, families or cohorts. Conclusions QueryOR is a comprehensive and flexible web platform eligible for an easy user-driven variant prioritization. It is freely available for academic institutions at http://queryor.cribi.unipd.it/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1654-4) contains supplementary material, which is available to authorized users.

HIV-positive patients have a 60- to 200-fold increased incidence of Non-Hodgkin Lymphomas (NHL) because of their impaired cellular immunity. Some NHL are considered Acquired Immunodeficiency Syndrome (AIDS) defining conditions. Diffuse large B-cell Lymphoma (DLBC) and Burkitt Lymphoma (BL) are the most commonly observed, whereas Primary Effusion Lymphoma (PEL), Central Nervous System Lymphomas (PCNSL), Plasmablastic Lymphoma (PBL) and classic Hodgkin Lymphoma (HL) are far less frequent. Multicentric Castleman disease (MCD) is an aggressive lymphoproliferative disorder highly prevalent in HIV-positive patients and strongly associated with HHV-8 virus infection. In the pre-Combination Antiretroviral Therapy (CART) era, patients with HIV-associated lymphoma had poor outcomes with median survival of 5 to 6 months. By improving the immunological status, CART extended the therapeutic options for HIV positive patients with lymphomas, allowing them to tolerate standard chemotherapies regimen with similar outcomes to those of the general population. The combination of CART and chemotherapy/ immuno-chemotherapy treatment has resulted in a remarkable prolongation of survival among HIVinfected patients with lymphomas. In this short communication, we briefly review the problems linked with the treatment of lymphoproliferative diseases in HIV patients. Combination Antiretroviral Therapy (CART) not only reduces HIV replication and restores the immunological status improving immune function of the HIV-related lymphomas patients but allows patients to deal with standard doses of chemotherapies. The association of CART and chemotherapy allowed to obtain better results in terms of overall survival and complete responses. In the setting of HIVassociated lymphomas, many issues remain open and their treatment is complicated by the patient’s immunocompromised status and the need to treat HIV concurrently.

Von Willebrand factor (vWF) cleaving protease ADAMTS-13 has a key role for maintaining normal size of vWF. A deficiency or dysfunction of vWF cleaving protease is associated with ultra large vWF multimers and thrombotic microangiopathy. Patients with cancers have reduced levels of vWF cleaving protease. In this pilot study, we have evaluated whether or not deficiencies of ADAMTS-13 were present in myelodysplastic syndromes (MDS). Moreover, we assessed if a reduction in basal levels of ADAMTS-13 may play a role in the prognosis of MDS.We measured and compared the levels of vWF cleaving protease ADAMTS-13 in 100 patients with MDS and 35 healthy controls. Patients were divided into 2 groups according to the International Prognostic Scoring System: group I consisting of 44 patients with low-risk MDS and group II of 56 patients with high-risk MDS. Patients with high-risk and low-risk MDS presented significantly lower levels of ADAMTS-13 than controls (P .001 and P = .0177, respectively). High-risk patients had significantly lower levels of ADAMTS-13 when compared with the low-risk group (P .001).We found that reduced levels of ADAMTS-13 have a relationship with overall survival (P .001). Statistical analysis showed that ADAMTS-13 correlates with cytogenetics (P .001) and a tendency of slight correlation with platelet count and basal levels of ADAMTS-13 (R, 0.35; P value, 0.001). Moreover, we found that levels of ADAMTS-13 have correlation with response to treatment (P .001).ADAMTS-13 in MDS might represent a surrogate marker of prognosis, response to therapy, or disease progression. Further studies are needed.

Grapheme-colour synaesthesia (GCS) is defined by additional perceptual experiences, which are automatically and consistently triggered by specific inducing stimuli. The associative nature of GCS has motivated attempts to induce synaesthesia by means of associative learning. Two recent studies have shown that extensive associative training can generate not only behavioural (consistency and automaticity) and neurophysiological markers of GCS, but also synaesthesia-like phenomenology [1,2]. However, these studies provided only superficial descriptions regarding the training-related changes in subjective experience: they did not directly assess how closely induced synaesthetic experiences mirror those found in natural GCS. Here we report an extended qualitative analysis of the transcripts of the semi-structured interviews obtained following the completion of the associative training protocol used by [2]. In addition, we performed a comparable analysis of responses to an interview with a new population of natural occurring grapheme-colour synaesthetes (NOS), allowing us to directly compare the phenomenological dimensions of induced and naturally occurring synaesthetic experience. Our results provide an extensive addition to the description of the phenomenology of NOS experience, revealing a high degree of heterogeneity both within and across all experiential categories. Capitalising on this unique level of detail, we identified a number of shared experiential categories between NOS and induced synaesthesia-like (ISL) groups, including: stability of experience, location of colour experience, shape of co-occurring colour experience, relative strength of colour experience and automaticity of colour experience. Only the automaticity of colour experience differed significantly between the two groups: NOS experience was reported as being mostly automatic, whereas induced ISL were mostly described as being ‘wilful’. We observed three additional experiential categories relating to the automaticity of synaesthetic experience within the NOS group: contextually varied experience, semi-automatic experience and reflective association, which suggests that, as with other experiential categories, the automaticity of synaesthetic experience is also highly heterogeneous. Our results provide new evidence that that intensive training of letter-colour associations can alter conscious perceptual experiences in non-synaesthetes, and that such alterations produce synaesthesia-like phenomenology which substantially resembles similarities to natural grapheme-colour synaesthesia.

The myelodysplastic syndromes (MDSs) are clonal hematopoietic stem cell disorders. The International Prognostic Score System (IPSS) groups MDS in lower-risk (IPSS low and intermediate-1) and higher-risk disease (IPSS intermediate-2 and high). AML transformation is the main concern in higher-risk MDS, while anemia and transfusion dependency represent the major issues for low-risk MDS patients. Improving erythropoiesis, and eliminating fatigue and symptoms, is the main therapeutic goal for low-risk MDS patients. Around 50% of MDS patients present with anemia with an Hb level

BACKGROUND: arterial and venous complications are major causes of morbidity and mortality in myeloproliferative neoplasms (MPNs). MPNs patients, frequently receive heparin. Heparin-induced thrombocytopenia (HIT) is a rare but potentially life-threatening complication resulting in a severe acquired thrombophilic condition. PATIENTS AND METHODS: we carried out a retrospective analysis to evaluate occurrence of new thrombotic events during heparin therapy in essential thrombocythemia (ET) patients. We studied 108 ET patients on heparin for treatment of previous thrombotic events or in thromboprophilaxis. Fifty-eight of them carried JAK 2 V617F mutation while fifty patients were without V617F mutation. RESULTS: Ten patients, among those with JAK 2 V617F mutation after a median of 10 days from heparin treatment presented a platelet drop, new thrombotic events and in 10/10 cases heparin-related antibodies were found. In the other group, 2 patients (4%) presented a platelet drop, thrombotic manifestations and heparin related antibodies. CONCLUSIONS: Our data show that HIT is more frequent, during heparin treatment, in patients with ET carrying V617F mutation, as compared with patients without mutations (P=0.029). ET with V617F mutation seems to be associated with higher risk of thrombotic complications during heparin treatment. Monitoring platelet counts very closely during the course of heparin is essential especially in ET patients in which platelet drop may be hidden by constitutional thrombocytosis.

Myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic disorders characterized by ineffective hematopoiesis and peripheral cytopenia, and their possible transformation into acute myeloid leukemia (AML). They typically affect the elderly but, when making treatment decisions, considering chronological age may be insufficient because it poorly correlates with patient frailty: the challenge is to select the optimal treatment in these patients by balancing efficacy and toxicity. Areas covered: This review discusses the rationale for and methods of personalizing the treatment of elderly MDS patients. Expert commentary: Decisions concerning treatment strategies for elderly MDS patients should be made after assessing their frailty on the basis of a geriatric assessment and an estimate of age-adjusted life expectancy. We suggest that all elderly MDS patients should undergo a timed up and go test (TUGT) as a preliminary means of identifying frail patients, and that all non-frail patients should then undergo a comprehensive geriatric assessment (CGA) in order to distinguish fit and pre-frail patients. Fit patients should receive standard dose treatment; pre-frail patients should receive individualized therapy; and frail patients should receive symptom-related therapy. A repeated CGA may be useful to evaluate the hematological, cognitive and socio-relational effects of MDS treatment.

Summary Recent experimental data indicate a pathogenic role of complement activation in congestive heart failure (CHF). The aim of this study was to evaluate contact and complement systems activation in patients hospitalized for an acute episode of CHF. Forty-two of 80 consecutive patients admitted at our hospital with confirmed diagnosis of acute CHF were enrolled. They underwent blood sampling within 24 h from admission (T0) and at clinical stability (T1). Patients were stratified for ejection fraction (EF) based on echocardiographic test. We measured plasma levels of C3, C4, sC5b-9 and cleaved high molecular weight kininogen (contact activation marker). At T1, C3 levels increased significantly compared to T0 (97 ± 2 versus 104 ± 3% of total pooled plasma, P < 0·01). Classifying patients according to EF, only patients with preserved EF presented a significant increase of C3 from T0 to T1 (99 ± 3 versus 108 ± 4%, P = 0·03). When the sample was stratified according to clinical outcome, C3 (98 ± 3 versus 104 ± 4%, P = 0·03) and sC5b-9 levels (204 ± 10 versus 230 ± 11 ng/ml, P = 0·03) were increased in patients who had positive outcome after hospitalization. CHF patients with preserved EF and positive outcome after hospitalization showed higher levels of sC5b-9 in the T1 period compared with T0 (211 ± 14 versus 243 ± 14 ng/ml, P = 0·04). Our results suggest that the complement system reacts differently if CHF occurs with preserved or reduced EF. This finding is interesting if we consider the difference in epidemiology, pathogenesis and possible therapeutic approaches of these two clinical entities.

Nannochloropsis is rapidly emerging as a model organism for the study of biofuel production in microalgae. Here, we report a high-quality genomic assembly of Nannochloropsis gaditana , consisting of large contigs, up to 500 kbp long, and scaffolds that in most cases span the entire length of the chromosomes. We identified 10646 complete genes and characterized possible alternative transcripts. The annotation of the predicted genes and the analysis of cellular processes revealed traits relevant for the genetic improvement of this organism such as genes involved in DNA recombination, RNA silencing, and cell wall synthesis. We also analyzed the modification of the transcriptional profile in nitrogen deficiency—a condition known to stimulate lipid accumulation. While the content of lipids increased, we did not detect major changes in expression of the genes involved in their biosynthesis. At the same time, we observed a very significant down-regulation of mitochondrial gene expression, suggesting that part of the Acetyl-CoA and NAD(P)H, normally oxidized through the mitochondrial respiration, would be made available for fatty acids synthesis, increasing the flux through the lipid biosynthetic pathway. Finally, we released an information resource of the genomic data of N. gaditana , available online at www.nannochloropsis.org. SUMMARY The paper describes the genome sequence, gene annotation, and transcriptional profiling of the microalga Nannochloropsis gaditana B-31. The study identifies possible targets of genetic modification that could improve the yield of the strain for biodiesel production. The genome resource is available online at www.nannochloropsis.org with multiple tools for information retrieval.

RNA editing is a widespread post-transcriptional molecular phenomenon that can increase proteomic diversity, by modifying the sequence of completely or partially non-functional primary transcripts, through a variety of mechanistically and evolutionarily unrelated pathways. Editing by base substitution has been investigated in both animals and plants. However, conventional strategies based on directed Sanger sequencing are time-consuming and effectively preclude genome wide identification of RNA editing and assessment of partial and tissue-specific editing sites. In contrast, the high-throughput RNA-Seq approach allows the generation of a comprehensive landscape of RNA editing at the genome level. Short reads from Solexa/Illumina GA and ABI SOLiD platforms have been used to investigate the editing pattern in mitochondria of Vitis vinifera providing significant support for 401 C-to-U conversions in coding regions and an additional 44 modifications in non-coding RNAs. Moreover, 76% of all C-to-U conversions in coding genes represent partial RNA editing events and 28% of them were shown to be significantly tissue specific. Solexa/Illumina and SOLiD platforms showed different characteristics with respect to the specific issue of large-scale editing analysis, and the combined approach presented here reduces the false positive rate of discovery of editing events.

Kopf, Anna ... et. al.-- 5 pages, 1 figure.-- This manuscript is NOAA-GLERL contribution number 1763, Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits, This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589

Real-time monitoring of pipeline integrity is a key factor for the environmental sustainability of oil & gas industry. eni launched in 2009 an R&D project for developing a real-time technology based upon vibroacoustic sensing. In principle any interaction with a pipe filled with gas or liquid generates pressure waves that are guided within the fluid for long distances, carrying information on the source event. Among these events, leaks (due to corrosion, incidents, theft, etc.) are the ones where real-time monitoring has a paramount value. Starting from 2010, acquisition campaigns in controlled scenarios were carried out and a validation of the mathematical models of pressure wave's propagation in fluid filled pipes was performed. More recently, background noise removal algorithms have been developed to further increase the sensitivity of the system in terms of decreased leak size and false alarm rate. In late 2013 the technology fulfilled the technology innovation qualification system of eni. Since 2007, NAOC (eni's Nigerian affiliate) has registered a significant increase of oil spill events due to sabotage and oil theft activities. The situation that has arisen posed such risks for the safety of people and for the protection of the environment, that it has been decided to investigate new detection and monitoring systems. In fact, monitoring of the pipelines with other real-time systems which require the presence of sensors all along the pipes (for instance fiber optics technologies) are neither difficult nor economic to implement in the Nigerian existing pipelines. The innovative technology presented here overcomes this weakness, by allowing detecting and locating leaks taking place up to a distance of 35 km from the sensors.

Background The deep-sea bacterium Photobacterium profundum is an established model for studying high pressure adaptation. In this paper we analyse the parental strain DB110 and the toxR mutant TW30 by massively parallel cDNA sequencing (RNA-seq). ToxR is a transmembrane DNA-binding protein first discovered in Vibrio cholerae, where it regulates a considerable number of genes involved in environmental adaptation and virulence. In P. profundum the abundance and activity of this protein is influenced by hydrostatic pressure and its role is related to the regulation of genes in a pressure-dependent manner. Results To better characterize the ToxR regulon, we compared the expression profiles of wt and toxR strains in response to pressure changes. Our results revealed a complex expression pattern with a group of 22 genes having expression profiles similar to OmpH that is an outer membrane protein transcribed in response to high hydrostatic pressure. Moreover, RNA-seq allowed a deep characterization of the transcriptional landscape that led to the identification of 460 putative small RNA genes and the detection of 298 protein-coding genes previously unknown. We were also able to perform a genome-wide prediction of operon structure, transcription start and termination sites, revealing an unexpected high number of genes (992) with large 5′-UTRs, long enough to harbour cis-regulatory RNA structures, suggesting a correlation between intergenic region size and UTR length. Conclusion This work led to a better understanding of high-pressure response in P. profundum. Furthermore, the high-resolution RNA-seq analysis revealed several unexpected features about transcriptional landscape and general mechanisms of controlling bacterial gene expression.

Genome sequencing projects are either based on whole genome shotgun (WGS) or on a BAC-by-BAC strategy. Although WGS is in most cases the preferred choice, sometimes the BAC-by-BAC approach may be better because it requires a much simpler assembly process. Furthermore, when the study is limited to specific regions of the genome, the WGS would require an unjustified effort, making the BAC-by-BAC the only feasible strategy. In this paper we describe an informatics pipeline called PABS (Platform Assisted BAC-by-BAC Sequencing) that we developed to provide a tool to optimize the BAC-by-BAC sequencing strategy. PABS has two main functions: (i) PABS-Select, to choose suitable overlapping clones; and (ii) PABS-Validate, to verify whether a BAC under analysis is actually overlapping the neighboring BAC.