Reti neurali e modelli fisico-predittivi: Dati clinici e analisi di trattamenti in tomotherapy

Il lavoro è parte integrante di un progetto di ricerca del Ministero della Salute ed è stato sviluppato presso la Fisica Sanitaria ed il reparto di Radioterapia Oncologica dell’Azienda Ospedaliero Universitaria di Modena. L’obiettivo è la realizzazione di modelli predittivi e di reti neurali per tecniche di warping in ambito clinico. Modifiche volumetrico-spaziali di organi a rischio e target tumorali, durante trattamenti tomoterapici, possono alterare la distribuzione di dose rispetto ai constraints delineati in fase di pianificazione. Metodologie radioterapiche per la valutazione di organ motion e algoritmi di registrazione ibrida permettono di generare automaticamente ROI deformate e quantificare la divergenza dal piano di trattamento iniziale. Lo studio si focalizzata sulle tecniche di Adaptive Radiation Therapy (ART) mediante la meta-analisi di 51 pazienti sottoposti a trattamento mediante Tomotherapy. Studiando il comportamento statistico del campione, sono state generate analisi predittive per quantificare in tempo reale divergenze anatomico dosimetriche dei pazienti rispetto al piano originale e prevedere la loro ripianificazione terapeutica. I modelli sono stati implementati in MATLAB, mediante Cluster Analysis e Support Vector Machines; l’analisi del dataset ha evidenziato il valore aggiunto apportabile dagli algoritmi di deformazione e dalle tecniche di ART. La specificità e sensibilità della metodica è stata validata mediante l’utilizzo di analisi ROC. Gli sviluppi del presente lavoro hanno aperto una prospettiva di ricerca e utilizzo in trattamenti multicentrici e per la valutazione di efficacia ed efficienza delle nuove tecnologie in ambito RT.

The role of bifidobacteria in newborn health and the intestinal microbial balance

Gut microbial acquisition during the early stage of life is an extremely important event since it affects the health status of the host. In this contest the healthy properties of the genus Bifidobacterium have a central function in newborns. The aim of this thesis was to explore the dynamics of the gut microbial colonization in newborns and to suggest possible strategies to maintain or restore a correct balance of gut bacterial population in infants. The first step of this work was to review the most recent studies on the use of probiotics and prebiotics in infants. Secondly, in order to prevent or treat intestinal disorders that may affect newborns, the capability of selected Bifidobacterium strains to reduce the amount of Enterobacteriaceae and against the infant pathogen Streptococcus agalactiae was evaluated in vitro. Furthermore, the ability of several commercial fibers to stimulate selectively the growth of bifidobacterial strains was checked. Finally, the gut microbial composition in the early stage of life in response to the intrapartum antibiotic prophylaxis (IAP) against group B Streptococcus was studied using q-PCR, DGGE and next generation sequencing. The results globally showed that Bifidobacterium breve B632 strain is the best candidate for the use in a synbiotic product coupled to a mixture of two selected prebiotic fibers (galactooligosaccharides and fructooligosaccharides) for gastrointestinal disorders in infants. Moreover, the early gut microbial composition was affected by IAP treatment with infants showing lower counts of Bifidobacterium spp. and Bacteroides spp. coupled to a decrement of biodiversity of bacteria, compared to control infants. These studies have shown that IAP could affect the early intestinal balance in infants and they have paved the way to the definition of new strategies alternative to antibiotic treatment to control GBS infection in pregnant women.

Stress abiotici e trattamenti ultra-diluiti: effetti fisiologici e molecolari sulla crescita in vitro di frumento

Gli stress abiotici determinando modificazioni a livello fisiologico, biochimico e molecolare delle piante, costituiscono una delle principali limitazioni per la produzione agricola mondiale. Nel 2007 la FAO ha stimato come solamente il 3,5% della superficie mondiale non sia sottoposta a stress abiotici. Il modello agro-industriale degli ultimi cinquant'anni, oltre ad avere contribuito allo sviluppo economico dell'Europa, è stato anche causa di inquinamento di acqua, aria e suolo, mediante uno sfruttamento indiscriminato delle risorse naturali. L'arsenico in particolare, naturalmente presente nell'ambiente e rilasciato dalle attività antropiche, desta particolare preoccupazione a causa dell'ampia distribuzione come contaminante ambientale e per gli effetti di fitotossicità provocati. In tale contesto, la diffusione di sistemi agricoli a basso impatto rappresenta una importante risorsa per rispondere all'emergenza del cambiamento climatico che negli anni a venire sottoporrà una superficie agricola sempre maggiore a stress di natura abiotica. Nello studio condotto è stato utilizzato uno stabile modello di crescita in vitro per valutare l'efficacia di preparati ultra diluiti (PUD), che non contenendo molecole chimiche di sintesi ben si adattano a sistemi agricoli sostenibili, su semi di frumento preventivamente sottoposti a stress sub-letale da arsenico. Sono state quindi condotte valutazioni sia a livello morfometrico (germinazione, lunghezza di germogli e radici) che molecolare (espressione genica valutata mediante analisi microarray, con validazione tramite Real-Time PCR) arricchendo la letteratura esistente di interessanti risultati. In particolare è stato osservato come lo stress da arsenico, determini una minore vigoria di coleptile e radici e a livello molecolare induca l'attivazione di pathways metabolici per proteggere e difendere le cellule vegetali dai danni derivanti dallo stress; mentre il PUD in esame (As 45x), nel sistema stressato ha indotto un recupero nella vigoria di germoglio e radici e livelli di espressione genica simili a quelli riscontrati nel controllo suggerendo un effetto "riequilibrante" del metabolismo vegetale.

Chitinase expression in parotid glands of non-obese diabetic mice

OBJECTIVE: This investigation was a basal study that used a mouse model of xerostomia to identify protein biomarkers of xerostomia in saliva. We identified genes expressed differently in parotid glands from non-obese diabetic mice with diabetes and those from control mice; subsequently, we investigated expression of the proteins encoded by these genes in parotid glands and saliva. MATERIALS AND METHODS: DNA microarray and real-time PCR analyses were performed to detect differences between NOD/ShiJcl and C57BL/6JJcl (control) female mice in gene expression from parotid glands or parotid acinar cells. Subsequently, protein expression was assessed using immunoblotting and immunohistochemistry. Similarly, enzyme activity in saliva was assessed using zymography. RESULTS: Based on gene expression analyses, Chia expression was higher in diabetic mice than non-diabetic mice and control mice; similarly, expression of chitinase, the protein encoded by Chia, was higher in diabetic mice. Saliva from NOD/ShiJcl mice had more chitinase than saliva from control mice. CONCLUSIONS: Chitinase was highly expressed in parotid acinar cells from diabetic mice compared with non-diabetic and control mice. Increased chitinase expression and enzyme activity may characterize the autoimmune diabetes in mice; however, further investigation is required to assess its use as a biomarker of xerostomia in humans.

Impact of antibiotic use on carbapenem resistance in Pseudomonas aeruginosa: is there a role for antibiotic diversity?

In this study, we aimed to evaluate the relationship between the rates of resistance of Pseudomonas aeruginosa to carbapenems and the levels and diversity of antibiotic consumption. Data were retrospectively collected from 20 acute care hospitals across 3 regions of Switzerland between 2006 and 2010. The main outcome of the present study was the rate of resistance to carbapenems among P. aeruginosa. Putative predictors included the total antibiotic consumption and carbapenem consumption in defined daily doses per 100 bed days, the proportion of very broad-spectrum antibiotics used, and the Peterson index. The present study confirmed a correlation between carbapenem use and carbapenem resistance rates at the hospital and regional levels. The impact of diversifying the range of antibiotics used against P. aeruginosa resistance was suggested by (i) a positive correlation in multivariate analysis between the above-mentioned resistance and the proportion of consumed antibiotics having a very broad spectrum of activity (coefficient = 1.77; 95% confidence interval, 0.58 to 2.96; P < 0.01) and (ii) a negative correlation between the resistance and diversity of antibiotic use as measured by the Peterson homogeneity index (coefficient = -0.52; P < 0.05). We conclude that promoting heterogeneity plus parsimony in the use of antibiotics appears to be a valuable strategy for minimizing the spread of carbapenem resistance in P. aeruginosa in hospitals.

Long-term patterns of subjective wellbeing in schizophrenia: cluster, predictors of cluster affiliation, and their relation to recovery criteria in 2842 patients followed over 3 years

To study the longitudinal patterns of subjective wellbeing in schizophrenia using cluster analysis and their relation to recovery criteria, further to examine predictors for cluster affiliation, and to evaluate the sensitivity and specificity of baseline subjective wellbeing cut-offs for cluster affiliation.

Molecular epidemiology of vancomycin-resistant Enterococcus faecium: a prospective, multicenter study in South American hospitals.

Enterococcus faecium has emerged as an important nosocomial pathogen worldwide, and this trend has been associated with the dissemination of a genetic lineage designated clonal cluster 17 (CC17). Enterococcal isolates were collected prospectively (2006 to 2008) from 32 hospitals in Colombia, Ecuador, Perú, and Venezuela and subjected to antimicrobial susceptibility testing. Genotyping was performed with all vancomycin-resistant E. faecium (VREfm) isolates by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. All VREfm isolates were evaluated for the presence of 16 putative virulence genes (14 fms genes, the esp gene of E. faecium [espEfm], and the hyl gene of E. faecium [hylEfm]) and plasmids carrying the fms20-fms21 (pilA), hylEfm, and vanA genes. Of 723 enterococcal isolates recovered, E. faecalis was the most common (78%). Vancomycin resistance was detected in 6% of the isolates (74% of which were E. faecium). Eleven distinct PFGE types were found among the VREfm isolates, with most belonging to sequence types 412 and 18. The ebpAEfm-ebpBEfm-ebpCEfm (pilB) and fms11-fms19-fms16 clusters were detected in all VREfm isolates from the region, whereas espEfm and hylEfm were detected in 69% and 23% of the isolates, respectively. The fms20-fms21 (pilA) cluster, which encodes a putative pilus-like protein, was found on plasmids from almost all VREfm isolates and was sometimes found to coexist with hylEfm and the vanA gene cluster. The population genetics of VREfm in South America appear to resemble those of such strains in the United States in the early years of the CC17 epidemic. The overwhelming presence of plasmids encoding putative virulence factors and vanA genes suggests that E. faecium from the CC17 genogroup may disseminate in the region in the coming years.

Acquisition of a natural resistance gene renders a clinical strain of methicillin-resistant Staphylococcus aureus resistant to the synthetic antibiotic linezolid.

Linezolid, which targets the ribosome, is a new synthetic antibiotic that is used for treatment of infections caused by Gram-positive pathogens. Clinical resistance to linezolid, so far, has been developing only slowly and has involved exclusively target site mutations. We have discovered that linezolid resistance in a methicillin-resistant Staphylococcus aureus hospital strain from Colombia is determined by the presence of the cfr gene whose product, Cfr methyltransferase, modifies adenosine at position 2503 in 23S rRNA in the large ribosomal subunit. The molecular model of the linezolid-ribosome complex reveals localization of A2503 within the drug binding site. The natural function of cfr likely involves protection against natural antibiotics whose site of action overlaps that of linezolid. In the chromosome of the clinical strain, cfr is linked to ermB, a gene responsible for dimethylation of A2058 in 23S rRNA. Coexpression of these two genes confers resistance to all the clinically relevant antibiotics that target the large ribosomal subunit. The association of the ermB/cfr operon with transposon and plasmid genetic elements indicates its possible mobile nature. This is the first example of clinical resistance to the synthetic drug linezolid which involves a natural resistance gene with the capability of disseminating among Gram-positive pathogenic strains.

Mechanisms of protein regulation in rat skeletal muscle during resistance exercise and training

The cellular mechanisms through which adult rat skeletal muscle protein is regulated during resistance exercise and training was investigated. A model of non-voluntary resistance exercise was described which involves the electrically-stimulated contraction of the lower leg muscles of anesthetized rats against a weighted pulley-bar. Muscle protein synthesis rates were measured by in vivo constant infusion of $\sp3$H-leucine following a single bout of resistance exercise. Specific messenger RNA levels were determined by dot-blot hybridization analysis using $\sp{32}$P-labelled DNA probes after a single bout and multiple bouts of phasic training. The effects of phasic training on increasing skeletal muscle mass was assessed. Between 12 and 36 hours following a single resistance exercise bout (24-192 contractions), total mixed and myofibril protein synthesis rates were significantly increase (32%-65%) after concentric (gastrocnemius m.) and eccentric (tibialis anterior m.) contractions. Eccentric contractions had greater effects on myofibril synthesis with more prolonged increases in synthesis rates. Lower numbers of eccentric than concentric contractions were required to increase synthesis. Cellular RNA was increased after exercise but the relative levels of skeletal $\alpha$-actin and cytochrome c mRNAs were unchanged. Since increases in synthesis rates exceeded increases in RNA, post-transcriptional mechanisms may be primarily responsible for increased protein synthesis after a resistance exercise bout. After 10-22 weeks of phasic eccentric resistance training, muscle enlargement (16%-30%) was produced in the tibialis anterior m. after all training paradigms examined. In contrast, gastrocnemius m. enlargement after phasic concentric training occurred after moderate (24/bout) but not after high (192/bout) repetition training. The absence of muscle growth in the gastrocnemius m. after high repetition training despite increased synthesis rates after the initial bout and RNA and possibly mRNA accumulation during training suggests a role for post-translational mechanisms (protein degradation) in the control of muscle growth in the gastrocnemius m. It is concluded that muscle protein during resistance exercise and training is regulated at several cellular levels. The particular response may be influenced by the exercise intensity and duration, the training frequency and the type of contractile work (eccentric vs. concentric) performed. ^

Fine-scale population structure analysis of seven local Swiss sheep breeds using genome-wide SNP data

As part of the global sheep Hapmap project, 24 individuals from each of seven indigenous Swiss sheep breeds (Bundner Oberländer sheep (BOS), Engadine Red sheep (ERS), Swiss Black-Brown Mountain sheep (SBS), Swiss Mirror sheep (SMS), Swiss White Alpine (SWA) sheep, Valais Blacknose sheep (VBS) and Valais Red sheep (VRS)), were genotyped using Illumina’s Ovine SNP50 BeadChip. In total, 167 animals were subjected to a detailed analysis for genetic diversity using 45 193 informative single nucleotide polymorphisms. The results of the phylogenetic analyses supported the known proximity between populations such as VBS and VRS or SMS and SWA. Average genomic relatedness within a breed was found to be 12 percent (BOS), 5 percent (ERS), 9 percent (SBS), 10 percent (SMS), 9 percent (SWA), 12 percent (VBS) and 20 percent (VRS). Furthermore, genomic relationships between breeds were found for single individuals from SWA and SMS, VRS and VBS as well as VRS and BOS. In addition, seven out of 40 indicated parent–offspring pairs could not be confirmed. These results were further supported by results from the genome-wide population cluster analysis. This study provides a better understanding of fine-scale population structures within and between Swiss sheep breeds. This relevant information will help to increase the conservation activities of the local Swiss sheep breeds.

Results of bulk sediment X-ray diffraction analysis and quantification of mineral phases based on the RockJock and on the QUAX quantitative analysis

We have performed quantitative X-ray diffraction (qXRD) analysis of 157 grab or core-top samples from the western Nordic Seas between (WNS) ~57°-75°N and 5° to 45° W. The RockJock Vs6 analysis includes non-clay (20) and clay (10) mineral species in the <2 mm size fraction that sum to 100 weight %. The data matrix was reduced to 9 and 6 variables respectively by excluding minerals with low weight% and by grouping into larger groups, such as the alkali and plagioclase feldspars. Because of its potential dual origins calcite was placed outside of the sum. We initially hypothesized that a combination of regional bedrock outcrops and transport associated with drift-ice, meltwater plumes, and bottom currents would result in 6 clusters defined by "similar" mineral compositions. The hypothesis was tested by use of a fuzzy k-mean clustering algorithm and key minerals were identified by step-wise Discriminant Function Analysis. Key minerals in defining the clusters include quartz, pyroxene, muscovite, and amphibole. With 5 clusters, 87.5% of the observations are correctly classified. The geographic distributions of the five k-mean clusters compares reasonably well with the original hypothesis. The close spatial relationship between bedrock geology and discrete cluster membership stresses the importance of this variable at both the WNS-scale and at a more local scale in NE Greenland.

Operator and replicability bias in comparative taphonomic studies

The operator effect is a well-known methodological bias already quantified in some taphonomic studies. However, the replicability effect, i.e., the use of taphonomic attributes as a replicable scientific method, has not been taken into account to the present. Here, we quantified for the first time this replicability bias using different multivariate statistical techniques, testing if the operator effect is related to the replicability effect. We analyzed the results reported by 15 operators working on the same dataset. Each operator analyzed 30 biological remains (bivalve shells) from five different sites, considering the attributes fragmentation, edge rounding, corrasion, bioerosion and secondary color. The operator effect followed the same pattern reported in previous studies, characterized by a worse correspondence for those attributes having more than two levels of damage categories. However, the effect did not appear to have relation with the replicability effect, because nearly all operators found differences among sites. Despite the binary attribute bioerosion exhibited 83% of correspondence among operators it was the taphonomic attributes that showed the highest dispersion among operators (28%). Therefore, we conclude that binary attributes (despite showing a reduction of the operator effect) diminish replicability, resulting in different interpretations of concordant data. We found that a variance value of nearly 8% among operators, was enough to generate a different taphonomic interpretation, in a Q-mode cluster analysis. The results reported here showed that the statistical method employed influences the level of replicability and comparability of a study and that the availability of results may be a valid alternative to reduce bias.

Geochemical provenance analysis of fine-grained sediment of sediment core AND1-1

Bulk chemical fine-grained sediment compositions from southern Victoria Land glacimarine sediments provide significant constraints on the reconstruction of sediment provenance models in the McMurdo Sound during Late Cenozoic time. High-resolution (~ 1 ka) geochemical data were obtained with a non-destructive AVAATECH XRF Core Scanner (XRF-CS) on the 1285 m long ANDRILL McMurdo Ice Shelf Project (MIS) sediment core AND-1B. This data set is complemented by high-precision chemical analyses (XRF and ICP-OES) on discrete samples. Statistical analyses reveal three geochemical facies which are interpreted to represent the following sources for the sediments recovered in the AND-1B core: 1) local McMurdo Volcanic Group (MVG) rocks, 2) Transantarctic Mountain rocks west of Ross Island (W TAM), and 3) Transantarctic Mountain rocks from more southerly areas (S TAM). Data indicate in combination with other sediment facies analyses (McKay et al., 2009, doi:10.1130/B26540.1) and provenance scenarios (Talarico and Sandroni, 2009, doi:10.1016/j.gloplacha.2009.04.007) that diamictites at the drill site are largely dominated by local sources (MVG) and are interpreted to indicate cold polar conditions with dry-based ice. MVG is interpreted to indicate cold polar condition with dry-based ice. A mixture of MVG and W TAM is interpreted to represent polar conditions and the S TAM facies is interpreted to represent open-marine conditions. Down-core variations in geochemical facies in the AND-1B core are interpreted to represent five major paleoclimate phases over the past 14 Ma. Cold polar conditions with major MVG influence occur below 1045 mbsf and above 120 mbsf. A section of warmer climate conditions with extensive peaks of S TAM influence characterizes the rest of the core, which is interrupted by a section from 525 to 855 mbsf of alternating influences of MVG and W TAM.

Distribution of deep-sea foraminifera in surface sediments east of New Zealand

Paleobathymetric assessments of fossil foraminiferal faunas play a significant role in the analysis of the paleogeographic, sedimentary, and tectonic histories of New Zealand's Neogene marine sedimentary basins. At depths >100 m, these assessments often have large uncertainties. This study, aimed at improving the precision of paleodepth assessments, documents the present-day distribution of deep-sea foraminifera (>63 µm) in 66 samples of seafloor sediment at 90-700 m water depth (outer shelf to mid-abyssal), east of New Zealand. One hundred and thirty-nine of the 465 recorded species of benthic foraminifera are new records for the New Zealand region. Characters of the foraminiferal faunas which appear to provide the most useful information for estimating paleobathymetry are, in decreasing order of reliability: relative abundance of common benthic species; benthic species associations; upper depth limits of key benthic species; and relative abundance of planktic foraminifera. R mode cluster analysis on the quantitative census data of the 58 most abundant species of benthic foraminifera produced six species associations within three higher level clusters: (1) calcareous species most abundant at mid-bathyal to outer shelf depths (<1000 m); (2) calcareous species most abundant at mid-bathyal and greater depths (>600 m); (3) agglutinated species mostly occurring at deep abyssal depths (>3000 m). A detrended correspondence analysis ordination plot exhibits a strong relationship between these species associations and bathymetry. This is manifest in the bathymetric ranges of the relative abundance peaks of many of the common benthic species (e.g., Abditodentrix pseudothalmanni 500-2800 m, Bolivina robusta 200-650 m, Bulimina marginata f. marginata 20-600 m, B. marginata f. aculeata 400-3000 m, Cassidulina norvangi 1000-4500 m, Epistominella exigua 1000-4700 m, and Trifarina angulosa 10-650 m), which should prove useful in paleobathymetric estimates. The upper depth limits of 28 benthic foraminiferal species (e.g., Fursenkoina complanata 200 m, Bulimina truncana 450 m, Melonis affinis 550 m, Eggerella bradyi 750 m, and Cassidulina norvangi 1000 m) have potential to improve the precision of paleobathymetric estimates based initially on the total faunal composition. The planktic percentage of foraminiferal tests increases from outer shelf to upper abyssal depths followed by a rapid decline within the foraminiferal lysocline (below c. 3600 m). A planktic percentage <50% is suggestive of shelf depths, and >50% is suggestive of bathyal or abyssal depths above the CCD. In the abyssal zone there is dramatic taphonomic loss of most agglutinated tests (except some textulariids) at burial depths of 0.1-0.2 m, which negates the potential usefulness of these taxa in paleobathymetric assessments.

Late Quaternary benthic foraminiferal record of the Bounty Trough, east of New Zealand

The Bounty Trough, east of New Zealand, lies along the southeastern edge of the present-day Subtropical Front (STF), and is a major conduit via the Bounty Channel, for terrigenous sediment supply from the uplifted Southern Alps to the abyssal Bounty Fan. Census data on 65 benthic foraminiferal faunas (>63 µm) from upper bathyal (ODP 1119), lower bathyal (DSDP 594) and abyssal (ODP 1122) sequences, test and refine existing models for the paleoceanographic and sedimentary history of the trough through the last 150 ka (marine isotope stages, MIS 6-1). Cluster analysis allows recognition of six species groups, whose distribution patterns coincide with bathymetry, the climate cycles and displaced turbidite beds. Detrended canonical correspondence analysis and comparisons with modern faunal patterns suggest that the groups are most strongly influenced by food supply (organic carbon flux), and to a lesser extent by bottom water oxygen and factors relating to sediment type. Major faunal changes at upper bathyal depths (1119) probably resulted from cycles of counter-intuitive seaward-landward migrations of the Southland Front (SF) (north-south sector of the STF). Benthic foraminiferal changes suggest that lower nutrient, cool Subantarctic Surface Water (SAW) was overhead in warm intervals, and higher nutrient-bearing, warm neritic Subtropical Surface Water (STW) was overhead in cold intervals. At lower bathyal depths (594), foraminiferal changes indicate increased glacial productivity and lowered bottom oxygen, attributed to increased upwelling and inflow of cold, nutrient-rich, Antarctic Intermediate Water (AAIW) and shallowing of the oxygen-minimum zone (upper Circum Polar Deep Water, CPDW). The observed cyclical benthic foraminiferal changes are not a result of associations migrating up and down the slope, as glacial faunas (dominated by Globocassidulina canalisuturata and Eilohedra levicula at upper and lower bathyal depths, respectively) are markedly different from those currently living in the Bounty Trough. On the abyssal Bounty Fan (1122), faunal changes correlate most strongly with grain size, and are attributed to varying amounts of mixing of displaced and in-situ faunas. Most of the displaced foraminifera in turbiditic sand beds are sourced from mid-outer shelf depths at the head of the Bounty Channel. Turbidity currents were more prevalent during, but not restricted to, glacial intervals.