Finite mixture clustering of human tissues with different levels of IGF-1 splice variants mRNA transcripts

BACKGROUND: This study addresses a recurrent biological problem, that is to define a formal clustering structure for a set of tissues on the basis of the relative abundance of multiple alternatively spliced isoforms mRNAs generated by the same gene. To this aim, we have used a model-based clustering approach, based on a finite mixture of multivariate Gaussian densities. However, given we had more technical replicates from the same tissue for each quantitative measurement, we also employed a finite mixture of linear mixed models, with tissue-specific random effects. RESULTS: A panel of human tissues was analysed through quantitative real-time PCR methods, to quantify the relative amount of mRNA encoding different IGF-1 alternative splicing variants. After an appropriate, preliminary, equalization of the quantitative data, we provided an estimate of the distribution of the observed concentrations for the different IGF-1 mRNA splice variants in the cohort of tissues by employing suitable kernel density estimators. We observed that the analysed IGF-1 mRNA splice variants were characterized by multimodal distributions, which could be interpreted as describing the presence of several sub-population, i.e. potential tissue clusters. In this context, a formal clustering approach based on a finite mixture model (FMM) with Gaussian components is proposed. Due to the presence of potential dependence between the technical replicates (originated by repeated quantitative measurements of the same mRNA splice isoform in the same tissue) we have also employed the finite mixture of linear mixed models (FMLMM), which allowed to take into account this kind of within-tissue dependence. CONCLUSIONS: The FMM and the FMLMM provided a convenient yet formal setting for a model-based clustering of the human tissues in sub-populations, characterized by homogeneous values of concentrations of the mRNAs for one or multiple IGF-1 alternative splicing isoforms. The proposed approaches can be applied to any cohort of tissues expressing several alternatively spliced mRNAs generated by the same gene, and can overcome the limitations of clustering methods based on simple comparisons between splice isoform expression levels

Characterization of two new alleles at the goat CSN1S2 locus.

Two novel alleles at the goat CSN1S2 locus have been identified: CSN1S2(F) and CSN1S2(D). Sequence analyses revealed that the CSN1S2(F) allele is characterized by a G --> A transition at the 13th nucleotide in exon 3 changing the seventh amino acid of the mature protein from Val to Ile. The CSN1S2(D) allele, apparently associated with a decreased synthesis of alpha s2-casein, is characterized by a 106-bp deletion, involving the last 11 bp of the exon 11 and the first 95 bp of the following intron. Methods (PCR-RFLP and PCR) for identification of carriers of these alleles have been developed

Study of the 27 Al(d, α) 25 Mg and 27 Al(d, p) 28 al nuclear reactions at 2 MeV deuteron energy

Differential excitation functions and angular distributions from 30° to 150° have been measured for the27Al(d, α)26Mg and27Al(d, p)28Al reactions leading to the ground state and to the first excited states of the residual nuclei25Mg and28Al, in the deuteron energy range (1.4≪2.3) MeV. The overall energy resolution was 10 keV for the differential excitation functions and 2 0 keV for the angular distributions. Fluctuations occurring in the differential excitation functions as well as in the integrated cross-sections have been analysed on the basis of the statistical theory. In particular, with the use of correlation functions, values of Γ=(40±10)keV and θ0≃30° have been deduced for the « coherence » energy and the « coherence » angle, respectively. The theoretical values of Γ and the average values of the integrated cross-sections have been evaluated using a consistent set of parameters. The analysis showed that the predictions of the statistical model agree with the experimental results for the27Al(d, α)25Mg reactions. Both statistical and nonstatistioal effects have been found to contribute to the27Al(d, p)28Al reaction for the proton transitions leading to the low-lying levels of the residual nucleus

Biogeographical boundaries, functional group structure and diversity of rocky shore communities along the Argentinean coast

We investigate the extent to which functional structure and spatial variability of intertidal communities coincide with major biogeographical boundaries, areas where extensive compositional changes in the biota are observed over a limited geographic extension. We then investigate whether spatial variation in the biomass of functional groups, over geographic (10′s km) and local (10′s m) scales, could be associated to species diversity within and among these groups. Functional community structure expressed as abundance (density, cover and biomass) and composition of major functional groups was quantified through field surveys at 20 rocky intertidal shores spanning six degrees of latitude along the southwest Atlantic coast of Argentina and extending across the boundaries between the Argentinean and Magellanic Provinces. Patterns of abundance of individual functional groups were not uniformly matched with biogeographical regions. Only ephemeral algae showed an abrupt geographical discontinuity coincident with changes in biogeographic boundaries, and this was limited to the mid intertidal zone. We identified 3–4 main ‘groups’ of sites in terms of the total and relative abundance of the major functional groups, but these did not coincide with biogeographical boundaries, nor did they follow latitudinal arrangement. Thus, processes that determine the functional structure of these intertidal communities are insensitive to biogeographical boundaries. Over both geographical and local spatial scales, and for most functional groups and tidal levels, increases in species richness within the functional group was significantly associated to increased total biomass and reduced spatial variability of the group. These results suggest that species belonging to the same functional group are sufficiently uncorrelated over space (i.e. metres and site-to-site ) to stabilize patterns of biomass variability and, in this manner, provide a buffer, or “insurance”, against spatial variability in environmental conditions

Relationship between External and Internal Workloads in Elite Soccer Players : Comparison between Rate of Perceived Exertion and Training Load

The use of machine learning (ML) in soccer allows for the management of a large amount of data deriving from the monitoring of sessions and matches. Although the rate of perceived exertion (RPE), training load (S-RPE), and global position system (GPS) are standard methodologies used in team sports to assess the internal and external workload; how the external workload affects RPE and S-RPE remains still unclear. This study explores the relationship between both RPE and SRPE and the training workload through ML. Data were recorded from 22 elite soccer players, in 160 training sessions and 35 matches during the 2015/2016 season, by using GPS tracking technology. A feature selection process was applied to understand which workload features influence RPE and SRPE the most. Our results show that the training workloads performed in the previous week have a strong effect on perceived exertion and training load. On the other hand, the analysis of our predictions shows higher accuracy for medium RPE and S-RPE values compared with the extremes. These results provide further evidence of the usefulness of ML as a support to athletic trainers and coaches in understanding the relationship between training load and individual-response in team sports

Star-forming dwarf galaxies in the Virgo cluster: the link between molecular gas, atomic gas, and dust

We present $^{12}$CO(1-0) and $^{12}$CO(2-1) observations of a sample of 20 star-forming dwarfs selected from the Herschel Virgo Cluster Survey, with oxygen abundances ranging from 12 + log(O/H) ~ 8.1 to 8.8. CO emission is observed in ten galaxies and marginally detected in another one. CO fluxes correlate with the FIR 250 $\mu$m emission, and the dwarfs follow the same linear relation that holds for more massive spiral galaxies extended to a wider dynamical range. We compare different methods to estimate H2 molecular masses, namely a metallicity-dependent CO-to-H2 conversion factor and one dependent on H-band luminosity. The molecular-to-stellar mass ratio remains nearly constant at stellar masses <~ 10$^9$ M$_{\odot}$, contrary to the atomic hydrogen fraction, M$_{HI}$/M$_*$, which increases inversely with M$_*$. The flattening of the M$_{H_2}$/M$_*$ ratio at low stellar masses does not seem to be related to the effects of the cluster environment because it occurs for both HI-deficient and HI-normal dwarfs. The molecular-to-atomic ratio is more tightly correlated with stellar surface density than metallicity, confirming that the interstellar gas pressure plays a key role in determining the balance between the two gaseous components of the interstellar medium. Virgo dwarfs follow the same linear trend between molecular gas mass and star formation rate as more massive spirals, but gas depletion timescales, $\tau_{dep}$, are not constant and range between 100 Myr and 6 Gyr. The interaction with the Virgo cluster environment is removing the atomic gas and dust components of the dwarfs, but the molecular gas appears to be less affected at the current stage of evolution within the cluster. However, the correlation between HI deficiency and the molecular gas depletion time suggests that the lack of gas replenishment from the outer regions of the disc is lowering the star formation activity.Comment: 19 pages, 11 figures, accepted for publication in Astronomy & Astrophysic

Resilience-Performance Tradeoff Analysis of a Deep Neural Network Accelerator

Nowadays, Deep Neural Networks (DNNs) are one of the most computationally-intensive algorithms because of the (i) huge amount of data to be transferred from/to the memory, and (ii) the huge amount of matrix multiplications to compute. These issues motivate the design of custom DNN hardware accelerators. These accelerators are widely used for low-latency safety-critical applications such as object detection in autonomous cars. Safety-critical applications have to be resilient with respect to hardware faults and Deep Learning (DL) accelerators are subjected to hardware faults that can cause functional failures, potentially leading to catastrophic consequences. Although DNNs possess a certain level of intrinsic resilience, it varies depending on the hardware on which they are run. The intent of the paper is to assess the resilience of a systolic-array-based DNN accelerator in the presence of hardware faults, in order to identify the architectural parameters that may mainly impact the DNN resilience

Climate Justice in the City: Mapping Heat-Related Risk for Climate Change Mitigation of the Urban and Peri-Urban Area of Padua (Italy)

The mitigation of urban heat islands (UHIs) is crucial for promoting the sustainable development of urban areas. Geographic information systems (GISs) together with satellite-derived data are powerful tools for investigating the spatiotemporal distribution of UHIs. Depending on the availability of data and the geographic scale of the analysis, different methodologies can be adopted. Here, we show a complete open source GIS-based methodology based on satellite-driven data for investigating and mapping the impact of the UHI on the heat-related elderly risk (HERI) in the Functional Urban Area of Padua. Thermal anomalies in the territory were mapped by modelling satellite data from Sentinel-3. After a socio-demographic analysis, the HERI was mapped according to five levels of risk. The highest vulnerability levels were localised within the urban area and in three municipalities near Padua, which represent about 20% of the entire territory investigated. In these municipalities, a percentage of elderly people over 20%, a thermal anomaly over 2.4 °C, and a HERI over 0.65 were found. Based on these outputs, it is possible to define nature-based solutions for reducing the UHI phenomenon and promote a sustainable development of cities. Stakeholders can use the results of these investigations to define climate and environmental policies

Vegetated ditches for the mitigation of pesticides runoff in the po valley

In intensive agricultural systems runoff is one of the major potential diffuse pollution path- ways for pesticides and poses a risk to surface water. Ditches are common in the Po Valley and can potentially provide runoff mitigation for the protection of watercourses. The effec- tiveness depends on ditch characteristics, so there is an urgent need for site-specific field trials. The use of a fugacity model (multimedia model) can allows recognition of the mitiga- tion main processes. A field experiment was conducted in order to evaluate the mitigation capacity of a typical vegetated ditch, and results were compared with predictions by a fugacity model. To evaluate herbicide mitigation after an extreme runoff, the ditch was flooded with water containing mesotrione, S-metolachlor and terbuthylazine. Two other sub- sequent floods with uncontaminated water were applied 27 and 82 days later to evaluate herbicides release. Results show that the ditch can immediately reduce runoff concentration of herbicides by at least 50% even in extreme flooding conditions. The half-distances were about 250 m. As a general rule, a runoff of 1 mm from 5 ha is mitigated by 99% in 100 m of vegetated ditch. Herbicides retention in the vegetated ditch was reversible, and the second flood mobilized 0.03-0.2% of the previous one, with a concentration below the drinking water limit of 0.1 \u3bcg L-1. No herbicide was detected in the third flood, because the residual amount in the ditch was too low. Fugacity model results show that specific physical-chemi- cal parameters may be used and a specific soil-sediment-plant compartment included for modelling herbicides behaviour in a vegetated ditch, and confirm that accumulation is low or negligible for herbicides with a half-life of 40 days or less. Shallow vegetated ditches can thus be included in a general agri-environment scheme for the mitigation of pesticides runoff together with wetlands and linear buffer strips. These structures are present in the land- scape, and their environmental role can be exploited by proper management