Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito

Background: The prediction of protein subcellular localization is a key step of the big effort towards protein functional annotation. Many computational methods exist to identify high-level protein subcellular compartments such as nucleus, cytoplasm or organelles. However, many organelles, like mitochondria, have their own internal compartmentalization. Knowing the precise location of a protein inside mitochondria is crucial for its accurate functional characterization. We recently developed DeepMito, a new method based on a 1-Dimensional Convolutional Neural Network (1D-CNN) architecture outperforming other similar approaches available in literature. Results: Here, we explore the adoption of DeepMito for the large-scale annotation of four sub-mitochondrial localizations on mitochondrial proteomes of five different species, including human, mouse, fly, yeast and Arabidopsis thaliana. A significant fraction of the proteins from these organisms lacked experimental information about sub-mitochondrial localization. We adopted DeepMito to fill the gap, providing complete characterization of protein localization at sub-mitochondrial level for each protein of the five proteomes. Moreover, we identified novel mitochondrial proteins fishing on the set of proteins lacking any subcellular localization annotation using available state-of-the-art subcellular localization predictors. We finally performed additional functional characterization of proteins predicted by DeepMito as localized into the four different sub-mitochondrial compartments using both available experimental and predicted GO terms. All data generated in this study were collected into a database called DeepMitoDB (available at http://busca.biocomp.unibo.it/deepmitodb), providing complete functional characterization of 4307 mitochondrial proteins from the five species. Conclusions: DeepMitoDB offers a comprehensive view of mitochondrial proteins, including experimental and predicted fine-grain sub-cellular localization and annotated and predicted functional annotations. The database complements other similar resources providing characterization of new proteins. Furthermore, it is also unique in including localization information at the sub-mitochondrial level. For this reason, we believe that DeepMitoDB can be a valuable resource for mitochondrial research

TRIS II: search for CMB spectral distortions at 0.60, 0.82 and 2.5 GHz

With the TRIS experiment we have performed absolute measurements of the sky brightness in a sky circle at $\delta = +42^{\circ}$ at the frequencies $\nu =$ 0.60, 0.82 and 2.5 GHz. In this paper we discuss the techniques used to separate the different contributions to the sky emission and give an evaluation of the absolute temperature of the Cosmic Microwave Background. For the black-body temperature of the CMB we get: $T_{cmb}^{th}=(2.837 \pm 0.129 \pm 0.066)K$ at $\nu=0.60$ GHz; $T_{cmb}^{th}=(2.803 \pm 0.051 ^{+0.430} _{-0.300})K$ at $\nu=0.82$ GHz; $T_{cmb}^{th}=(2.516 \pm 0.139 \pm 0.284)K$ at $\nu=2.5$ GHz. The first error bar is statistic (1$\sigma$) while the second one is systematic. These results represent a significant improvement with respect to the previous measurements. We have also set new limits to the free-free distortions, $-6.3 \times 10^{-6} < Y_{ff} < 12.6 \times 10^{-6}$, and slightly improved the Bose-Einstein upper limit, $|\mu| < 6 \times 10^{-5}$, both at 95% confidence level.Comment: accepted for publication in The Astrophysical Journa

TRIS I: Absolute Measurements of the Sky Brightness Temperature at 0.6, 0.82 and 2.5 GHz

At frequencies close to 1 GHz the sky diffuse radiation is a superposition of radiation of Galactic origin, the 3 K Relic or Cosmic Microwave Background Radiation, and the signal produced by unresolved extragalactic sources. Because of their different origin and space distribution the relative importance of the three components varies with frequency and depends on the direction of observation. With the aim of disentangling the components we built TRIS, a system of three radiometers, and studied the temperature of the sky at $\nu =0.6$, $\nu = 0.82$ and $\nu = 2.5$ GHz using geometrically scaled antennas with identical beams (HPBW = $18^{\circ} \times 23^{\circ}$). Observations included drift scans along a circle at constant declination $\delta=+42^{\circ}$ which provided the dependence of the sky signal on the Right Ascension, and absolute measurement of the sky temperature at selected points along the same scan circle. TRIS was installed at Campo Imperatore (lat. = $42^{\circ}~26'$ N, long.= $13^{\circ}~33'$, elevation = 2000 m a.s.l.) in Central Italy, close to the Gran Sasso Laboratory.Comment: Accepted for publication in The Astrophysical Journa

Predicting future cancer burden in the United States by artificial neural networks

Aims: To capture the complex relationships between risk factors and cancer incidences in the US and predict future cancer burden. Materials &amp; methods: Two artificial neural network (ANN) algorithms were adopted: a multilayer feed-forward network (MLFFNN) and a nonlinear autoregressive network with eXogenous inputs (NARX). Data on the incidence of the four most common tumors (breast, colorectal, lung and prostate) from 1992 to 2016 (available from National Cancer Institute online datasets) were used for training and validation, and data until 2050 were predicted. Results: The rapid decreasing trend of prostate cancer incidence started in 2010 will continue until 2018–2019; it will then slow down and reach a plateau after 2050, with several differences among ethnicities. The incidence of breast cancer will reach a plateau in 2030, whereas colorectal cancer incidence will reach a minimum value of 35 per 100,000 in 2030. As for lung cancer, the incidence will decrease from 50 per 100,000 (2017) to 31 per 100,000 in 2030 and 26 per 100,000 in 2050. Conclusion: This up-to-date prediction of cancer burden in the US could be a crucial resource for planning and evaluation of cancer-control programs

EBT2 Dosimetry of X-rays produced by the electron beam from PFMA-3, a Plasma Focus for medical applications

The electron beam emitted from the back of Plasma Focus devices is being studied as a radiation source for IORT (IntraOperative Radiation Therapy) applications. A Plasma Focus device is being developed to this aim, to be utilized as an X-ray source. The electron beam is driven to impinge on 50 {\mu}m brass foil, where conversion X-rays are generated. Measurements with gafchromic film are performed to analyse the attenuation of the X-rays beam and to predict the dose given to the culture cell in radiobiological experiments to follow.Comment: 10 pages, 14 figure

Ensuring healthcare workers’ safety in the management of Ebola virus disease : a novel competency assessment checklist for proper PPE use

Introduction: In response to EVD outbreak in Africa, Malta like many other countries in Europe, stepped up efforts to prepare and train in correct procedures for safe identification and management of potential EVD patients in the main acute tertiary hospital.peer-reviewe

Preliminary Estimation of Black Carbon Deposition from Nepal Climate Observatory-Pyramid Data and Its Possible Impact on Snow Albedo Changes Over Himalayan Glaciers During the Pre-Monsoon Season

The possible minimal range of reduction in snow surface albedo due to dry deposition of black carbon (BC) in the pre-monsoon period (March-May) was estimated as a lower bound together with the estimation of its accuracy, based on atmospheric observations at the Nepal Climate Observatory-Pyramid (NCO-P) sited at 5079 m a.s.l. in the Himalayan region. We estimated a total BC deposition rate of 2.89 g m-2 day-1 providing a total deposition of 266 micrograms/ square m for March-May at the site, based on a calculation with a minimal deposition velocity of 1.0 10(exp -4) m/s with atmospheric data of equivalent BC concentration. Main BC size at NCO-P site was determined as 103.1-669.8 nm by correlation analysis between equivalent BC concentration and particulate size distribution in the atmosphere. We also estimated BC deposition from the size distribution data and found that 8.7% of the estimated dry deposition corresponds to the estimated BC deposition from equivalent BC concentration data. If all the BC is deposited uniformly on the top 2-cm pure snow, the corresponding BC concentration is 26.0-68.2 microgram/kg assuming snow density variations of 195-512 kg/ cubic m of Yala Glacier close to NCO-P site. Such a concentration of BC in snow could result in 2.0-5.2% albedo reductions. From a simple numerical calculations and if assuming these albedo reductions continue throughout the year, this would lead to a runoff increases of 70-204 mm of water drainage equivalent of 11.6-33.9% of the annual discharge of a typical Tibetan glacier. Our estimates of BC concentration in snow surface for pre-monsoon season can be considered comparable to those at similar altitude in the Himalayan region, where glaciers and perpetual snow region starts in the vicinity of NCO-P. Our estimates from only BC are likely to represent a lower bound for snow albedo reductions, since a fixed slower deposition velocity was used and atmospheric wind and turbulence effects, snow aging, dust deposition, and snow albedo feedbacks were not considered. This study represents the first investigation about BC deposition on snow from atmospheric aerosol data in Himalayas and related albedo effect is especially the first track at the southern slope of Himalayas

TRIS III: the diffuse galactic radio emission at δ=+42∘\delta=+42^{\circ}

We present values of temperature and spectral index of the galactic diffuse radiation measured at 600 and 820 MHz along a 24 hours right ascension circle at declination $\delta = +42^{\circ}$. They have been obtained from a subset of absolute measurements of the sky temperature made with TRIS, an experiment devoted to the measurement of the Cosmic Microwave Background temperature at decimetric-wavelengths with an angular resolution of about $20^{\circ}$. Our analysis confirms the preexisting picture of the galactic diffuse emission at decimetric wavelength and improves the accuracy of the measurable quantities. In particular, the signal coming from the halo has a spectral index in the range $2.9-3.1$ above 600 MHz, depending on the sky position. In the disk, at TRIS angular resolution, the free-free emission accounts for the 11% of the overall signal at 600 MHz and 21% at 1420 MHz. The polarized component of the galactic emission, evaluated from the survey by Brouw and Spoelstra, affects the observations at TRIS angular resolution by less than 3% at 820 MHz and less than 2% at 600 MHz. Within the uncertainties, our determination of the galactic spectral index is practically unaffected by the correction for polarization. Since the overall error budget of the sky temperatures measured by TRIS at 600 MHz, that is 66 mK(systematic)$+$18 mK (statistical), is definitely smaller than those reported in previous measurements at the same frequency, our data have been used to discuss the zero levels of the sky maps at 150, 408, 820 and 1420 MHz in literature. Concerning the 408 MHz survey, limiting our attention to the patch of sky corresponding to the region observed by TRIS, we suggest a correction of the base-level of $(+3.9\pm 0.6)$K.Comment: Accepted for publication in the Astrophysical Journa

Influence of root maturity or periodontal involvement on dentinal collagen changes following NaOCL irrigation: an ex-vivo study

Abstract Aims: To refine FTIR protocol for detection of NaOCl-induced dentinal collagen changes using an ex- vivo irrigation model, and to apply it to determine the collagen change within 0.5mm of canal or root surfaces, with or without mature roots or periodontal involvement. Methodology: Extracted human roots were irrigated with control saline (n=3) or 5% NaOCl (n=3) and sectioned into transverse discs for FTIR analyses, 0.5mm from both the canal lumen and root surface, before and after surface-treatment with 17% EDTA. Amide I/phosphate and amide II/phosphate absorbance ratios were compared using the Wilcoxon sign rank test. Mature roots without periodontal involvement were irrigated with: saline (n=7), 5% NaOCl (n=7), or 5% NaOCl+17% EDTA (n=7); those with periodontal involvement (n=7) or immature roots (n=7) were irrigated with 5% NaOCl. Dentine discs were then prepared for FTIR analyses. The effects of irrigant/root-maturity/periodontal involvement were analysed using linear mixed models. Results: FTIR analyses of the irrigated samples revealed significant (P < 0.05) reduction in collagen bands near the canal lumen after NaOCl irrigation using surface-EDTA treated samples. Irrigation with test solutions resulted in significant (P < 0.0001) dentinal collagen changes in the mature roots, whilst those in the immature roots were significantly (P < 0.05) greater compared with the mature roots with or without periodontal involvement; but there were no difference between the latter groups. Conclusion: EDTA surface-treatment of polished dentine surfaces enhanced FTIR detection of NaOCl-induced collagen changes. Both root maturity and irrigation protocol influenced the ability of NaOCl to alter dentinal collagen up to 0.5mm from the canal lumen

Febrile Neutropenia Duration Is Associated with the Severity of Gut Microbiota Dysbiosis in Pediatric Allogeneic Hematopoietic Stem Cell Transplantation Recipients

Febrile neutropenia (FN) is a common complication in pediatric patients receiving al-logeneic hematopoietic stem cell transplantation (HSCT). Frequently, a precise cause cannot be identified, and many factors can contribute to its genesis. Gut microbiota (GM) has been recently linked to many transplant-related complications, and may also play a role in the pathogenesis of FN. Here, we conducted a longitudinal study in pediatric patients receiving HSCT from three centers in Europe profiling their GM during the transplant course, particularly at FN onset. We found that a more stable GM configuration over time is associated with a shorter duration of fever. Moreover, patients with longer lasting fever exhibited higher pre-HSCT levels of Collinsella, Megasphaera, Prevotella and Roseburia and increased proportions of Eggerthella and Akkermansia at the engraftment. These results suggest a possible association of the GM with the genesis and course of FN. Data seem consistent with previous reports on the relationship of a so-called “healthy” GM and the reduction of transplant complications. To our knowledge, this is the first report in the pediatric HSCT setting. Future studies are warranted to define the underling biological mechanisms and possible clinical implications