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Sarcopenia is defined as a syndrome characterized by progressive and generalized loss of skeletal muscle mass and strength and it is diagnosed by measurements of muscle mass, muscle strength, and physical performance. Sarcopenia affects quality of life and is associated with several adverse health effects. Muscle decline is aggravated by a sedentary lifestyle and can be prevented through proper nutrition, together with adequate physical activity. Fish contains biologically active compounds, such as omega-3 polyunsaturated fatty acids, proteins, vitamin D, magnesium, and carnitine, which are able to intervene positively on muscle metabolism. This narrative literature review was performed to evaluate evidence regarding the actual benefit of fish consumption in the prevention of sarcopenia and the positive action on the muscle mass of the biological compounds present in fish. The results demonstrated that fish consumption has a protective and anti-inflammatory function on skeletal muscle and that its biologically active compounds help to maintain good muscle performance, preventing sarcopenia. Considering the nutritional and health benefits, elderly with sarcopenia should consume at least three servings per week of fish in order to have a minimum intake of 4-4.59 g daily of omega 3, and reaching the 50% RDA in Vitamin E and D. High biological value of proteins in 150 g of fish and its high available magnesium (20% of RDA in 150 g of fish) are an added value that could suggest fish as a "functional food" in order to prevent and treat sarcopenia., Competing Interests: The authors declare no conflicts of interest.

Background: Peri-implant marginal bone loss is influenced by the interaction between tissues and the implant–abutment complex. The implant–abutment connection geometry is considered to be one of the factors that most affects peri-implant bone remodelling. Purpose: The primary purpose was to compare the clinical and radiographical differences between implants sharing the same macrogeometry but with two different connections. The secondary aims were to measure implant success and survival rate, primary and secondary stability, and the correlation between changes in marginal bone level and clinical variables. Additionally, a neural network was developed and tested to anticipate the impact of the insertion torque curve on marginal bone loss. Materials and methods: Patients requiring at least two implants in the posterior region were randomly divided into two groups. The implants presented the same micro- and macrotopography with different internal connections, conical standard (CS) and internal hex (IH). Upon implant surgery (T0), insertion torque, implant stability (implant stability quotient values were recorded by resonance frequency analysis), soft tissue height and the amount of keratinised gingiva were assessed. Stability was remeasured at the time of prosthetic connection (stage-two surgery) using a one-abutment one-time protocol and a fully digital workflow. At 6 months and 1 year after implant loading, periodontal parameters were assessed and periapical radiographs were taken. To study the differences between the two groups and the different variables, paired t test and generalised estimating equations models were adopted. Cluster analysis was used to assess the correlation between torque insertion/clinical profiles and changes in marginal bone level. Results: A total of 33 patients (17 men, 16 women, mean age 67.4 ± 14.5 years) were included in the study. No dropouts were reported. Fifty-three implants (26 CS and 27 IH) were inserted in the maxilla, and 15 (8 CS and 7 IH) in the mandible. No implants failed. Marginal bone loss at 6 months after prosthetic loading was 0.33 ± 0.34 mm for CS and 0.43 ± 0.37 mm for IH (P = 0.125), and after 1 year was 0.48 ± 0.18 mm for CS and 0.57 ± 0.24 mm for IH. A statistically significant difference between the implant stabilty quotient values for the test and control groups was demonstrated at T0 (P = 0.03) and at stage-two surgery (P = 0.000122). The generalised estimating equations model showed that soft tissue height (P = 0.012), keratinised gingiva (P = 0.05) and insertion torque (P = 0.042) had a significant effect on marginal bone loss, while the other variables did not play a statistically significant role. The neural network showed good sensitivity, accuracy, precision and specificity. Conclusions: The present research showed that different implant–abutment connections with the same implant macrogeometry have a significant effect on marginal bone loss. Better outcomes were observed in the CS group compared to the IH group. Marginal bone loss was found to be influenced by different individual and clinical factors., Competing Interests: The authors declare no conflicts of interest related to this study.

Despite advances in medicine and numerous agents that counteract pain, millions of patients continue to suffer. Attention has been given to identify novel botanical interventions that produce analgesia by interacting with nociceptive-transducing channels. The aim of this review is to provide an overview of the actual knowledge of Acmella oleracea (L.) and its activities, particularly those that are anti-inflammatory, anti-oxidant, and painkiller. These activities are attributed to numerous bioactive compounds, such as phytosterols, phenolic compounds and N-alkylamides (spilanthol, responsible for many activities, primarily anesthetic). This review includes 99 eligible studies to consider the anti-inflammatory, anti-oxidant, and painkiller of Acmella. Studies reported in this review confirmed anti-inflammatory and anti-oxidant activities of Acmella, postulating that transcription factors of the nuclear factor-κB family (NF-κB) trigger the transcription iNOS and COX-2 and several other pro-inflammatory mediators, such as IL-6, IL-1β, and TNF-α. The antinociceptive effects has been demonstrated and have been related to different processes, including inhibition of prostaglandin synthesis, activation of opioidergic, serotoninergic and GABAergic systems, and anesthetic activity through blockage of voltage-gated Na Channels. acmella oleracea represents a promise for pain management, particularly in chronic degenerative diseases, where pain is a significant critical issue., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Plasma fatty acids (FAs) and oxidant status contribute to the etiology of sarcopenia in the elderly concurring to age-related muscle loss and elderly frailty through several mechanisms including changes in FA composition within the sarcolemma, promotion of chronic low-grade inflammation, and insulin resistance. The aim of this study was to determine the FA profile and pro-antioxidant status in sarcopenic frail elderly patients enrolled in a nutritional and physical activity program and to evaluate their correlation with clinical markers. Moreover, the possible changes, produced after a short-term clinical protocol, were evaluated. Plasma and erythrocyte FA composition and pro-antioxidant status were analyzed in sarcopenic elderly subjects recruited for the randomized clinical study and treated with a placebo or dietary supplement, a personalized diet, and standardized physical activity. Subjects were tested before and after 30 days of treatment. Pearson correlations between biochemical parameters and patients' characteristics at recruitment indicate interesting features of sarcopenic status such as negative correlation among the plasma FA profile, age, and physical characteristics. Physical activity and dietetic program alone for 30 days induced a decrease of saturated FA concentration with a significant increase of dihomo-gamma-linolenic acid. Supplementation plus physical activity induced a significant decrease of linoleic acid, omega-6 polyunsaturated FAs, and an increase of stearic and oleic acid concentration. Moreover, glutathione reductase activity, which is an indicator of antioxidant status, significantly increased in erythrocytes. Changes over time between groups indicate significant differences for saturated FAs, which suggest that the amino acid supplementation restores FA levels that are consumed during physical activity. A relationship between FA and clinical/metabolic status revealed unique correlations and a specific metabolic and lipidomic fingerprint in sarcopenic elderly. The results indicate the positive beneficial role of supplementation and physical activity on plasma FA status and the antioxidant system as a co-adjuvant approach in sarcopenic, frail, elderly patients.

Purpose: The purpose of this review was to identify the best solution for rapid and noninvasive diagnosis and long-term monitoring of patients affected by inflammatory gastrointestinal diseases, colon and gastric cancer, obesity in correlation to diet, and breast milk to evaluate exposure to VOCs in women and infants., Methods: This review included 20 previously published eligible studies. VOC analysis has allowed us to highlight differences in lifestyles, intestinal microbiota, and metabolism. New innovative methods have been described that allow the detection and quantification of a broad spectrum of metabolites present in exhaled breath even at very low levels, some of which have been shown to be indicators of pathological conditions., Results: Five studies were analyzed that involved VOC analysis in relation to type of diet. All of them showed that the type of diet can have an impact on metabolites excreted and therefore can be a useful tool in the nutritional studies related to metabolism and health and disease status. Two studies concerned VOC analysis in inflammatory bowel diseases, and the results showed that VOCs can distinguish active disease from remission; VOC profile is clearly different in patients. In particular, C 15 H 30 1-pentadecene, 3-methyl-1-butanal, octane, acetic acid, alpha-pinene, and m-cymene are elevated in active ulcerative colitis. Four studies examined VOCs in gastric and colorectal tumors showing a change in metabolic biomarkers of cancer patients compared to the control group. Finally, the study of VOCs in breast milk has improved the understanding of the potential health risks of exposure of children to chemical pollutants., Conclusions: VOC analysis allowed to highlight differences in behavior, lifestyle, and metabolism of individuals. Analytical methods are continuously developed to allow for better detection and quantification of metabolites, thus enabling the detection of a broader spectrum of pathophysiology and disease biomarkers., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2019 Mariangela Rondanelli et al.)

Osteoarthritis (OA) is the most common form of arthritis in the world and is characterized by pain, various disabilities and loss of quality of life. Chondroitin sulfate (CS) is recommended as first-line therapy. CS of non-animal origin is of great interest for safety and sustainability reasons. This study aims to investigate the anti-inflammatory effects, anti-pain and ability-enhancement of a short-term supplementation with non-animal CS in overweight subjects with OA. In a randomized, double-blind, placebo-controlled pilot study, 60 overweight adults with symptomatic OA were allocated to consume 600 mg of non-animal CS ( n = 30) or a placebo ( n = 30) daily for 12 consecutive weeks. The assessment of knee-pain, quality of life, related inflammation markers and body composition was performed at 0, 4 and 12 weeks. The Tegner Lysholm Knee Scoring (TLKS) scale of the experimental group showed a statistically significant increase (+10.64 points; confidence interval (95% confidence interval (CI) 5.57; 15.70; p < 0.01), while the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) score decreased (-12.24 points; CI 95% -16.01; -8.38; p < 0.01). The results also showed a decrease in the C-reactive protein (CRP) level (-0.14 mg/dL, CI 95% -0.26; -0.04; p < 0.01) and erythrocyte sedimentation rate (ESR) level (-5.01 mm/h, CI 95% -9.18; -0.84, p < 0.01) as well as the visual analogue scale (VAS) score in both knees. In conclusion, this pilot study demonstrates the effectiveness of non-animal CS supplementation in overweight subjects with knee OA in improving knee function, pain and inflammation markers.

Background: Fragile X-associated tremor/ataxia syndrome is a late-onset neurodegenerative disorder that affects about 40% of carriers of CGG-repeat expansions in the premutation range within the fragile X gene ( FMR1 ). Main clinical features include intention tremor, cerebellar ataxia, and parkinsonism. Recently, great emphasis on the deposition of soluble aggregates produced by a RAN translation process, as main pathogenic mechanism, has been given. These aggregates contain a small protein with a polyglycine stretch on the aminoterminal end named FMRpolyG and, so far, have been isolated and characterized in drosophila and mouse models, in post mortem brain of fragile X-associated tremor/ataxia syndrome patients, in fibroblasts of fragile primary ovarian insufficiency patients, but never in fibroblasts from a fragile X-associated tremor/ataxia living patients. In adult carriers the syndrome is frequently misdiagnosed due to the lack of specific markers., Methods: We standardized immunocytochemistry, immunoprecipitation and western blot procedures to study and biochemically characterize the FMRpolyG protein in fibroblasts from human skin biopsy., Results: We demonstrate for the first time, in fibroblasts from a patient affected by Fragile X-associated tremor/ataxia syndrome, the presence ex vivo of inclusions consisting of FMRpolyG- Hsp70 soluble aggregates., Conclusion: These observations can pave the way to develop a cellular model for studying ex vivo and in vitro the mechanisms involved in the production of FMRpolyG aggregates, their toxicity, and the role of the FMRpolyG-Hsp70 interaction in the pathogenesis of fragile X-associated tremor/ataxia syndrome.

Due to the limited field of view of the microscopes, acquisitions of macroscopic specimens require many parallel image stacks to cover the whole volume of interest. Overlapping regions are introduced among stacks in order to make it possible automatic alignment by means of a 3D stitching tool. Since state-of-the-art microscopes coupled with chemical clearing procedures can generate 3D images whose size exceeds the Terabyte, parallelization is required to keep stitching time within acceptable limits. In the present paper we discuss how multi-level parallelization reduces the execution times of TeraStitcher, a tool designed to deal with very large images. Two algorithms performing dataset partition for efficient parallelization in a transparent way are presented together with experimental results proving the effectiveness of the approach that achieves a speedup close to 300×, when both coarse- and fine-grained parallelism are exploited. Multi-level parallelization of TeraStitcher led to a significant reduction of processing times with no changes in the user interface, and with no additional effort required for the maintenance of code.

The field of dental implantology has made progress in recent years, allowing safer and predictable oral rehabilitations. Surely the rehabilitation times have also been reduced, thanks to the advent of the new implant surfaces, which favour the osseointegration phases and allow the clinician to rehabilitate their patients earlier. To carry out this study, a search was conducted in the Pubmed, Embase and Elsevier databases; the articles initially obtained according to the keywords used numbered 283, and then subsequently reduced to 10 once the inclusion and exclusion criteria were applied. The review that has been carried out on this type of surface allows us to fully understand the features and above all to evaluate all the advantages or not related. The study materials also are supported by a manufacturing company, which provided all the indications regarding surface treatment and confocal microscopy scans. In conclusion, we can say that, thanks to these new surfaces, it has been possible to shorten the time necessary to obtain osseointegration and, therefore, secondary stability on the part of implants. The surfaces, therefore, guarantee an improved cellular adhesion and thanks to the excellent wettability all the biological processes that derive from it, such as increases in the exposed implant surface, resulting in an increase in bone-implant contact (BIC).

We compare bioimpedance analysis (BIA) with dual-energy X-ray absorptiometry (DXA) in the assessment of free fat mass (FFM), fat mass (FM) and percentage of body fat under different conditions in relation to age categories, hydration parameters, body mass index (BMI) and sarcopenia. A cross-sectional analysis of body composition was estimated by BIA and DXA in 379 hospitalized elderly patients. In addition, estimates of FFM, FM and percentage of body fat were investigated across different conditions. Paired t-tests, Bland-Altman plot and intraclass correlation coefficient analysis were used to compare methods. Data showed an underestimation of means (BIA versus DXA) of FFM (women: 0,97 kg, p<0,01; men: 1,99 kg; p<0,01), and an overestimation of both the FM (women: +1,11 kg; p<0,01; men: +1,67 kg; p<0,01) and percentage of body fat (women: +2,07 %, p<0,01; men: +2,82 %, p<0,01). BIA underestimated FFM and overestimated FM and percentage of body fat in patients from the age group of 75 to 85 years, in patients with a total body water content <60%, in underweight and normal weight patients and in patients with sarcopenia (p<0,01). The intraclass coefficient results were indicative of poor reproducibility between BIA and DXA for FFM (women: +0,197; men: +0,250) and FM (women: +0,141; men +0,144). BIA is a good alternative for estimation of FFM and FM only in overweight or obese patients or in patients with good hydration status. BIA, on the other hand, is not an accurate method for assessing FFM in sarcopenic patients.

The primary goal of precision medicine is to minimize side effects and optimize efficacy of treatments. Recent advances in medical imaging technology allow the use of more advanced image analysis methods beyond simple measurements of tumor size or radiotracer uptake metrics. The extraction of quantitative features from medical images to characterize tumor pathology or heterogeneity is an interesting process to investigate, in order to provide information that may be useful to guide the therapies and predict survival. This paper discusses the rationale supporting the concept of radiomics and the feasibility of its application to Non-Small Cell Lung Cancer in the field of radiation oncology research. We studied 91 stage III patients treated with concurrent chemoradiation and adaptive approach in case of tumor reduction during treatment. We considered 12 statistics features and 230 textural features extracted from the CT images. In our study, we used an ensemble learning method to classify patients' data into either the adaptive or non-adaptive group during chemoradiation on the basis of the starting CT simulation. Our data supports the hypothesis that a specific signature can be identified (AUC 0.82). In our experience, a radiomic signature mixing semantic and image-based features has shown promising results for personalized adaptive radiotherapy in non-small cell lung cancer., Competing Interests: The authors have declared that no competing interests exist.

The increment of recording atypical oral manifestation in young patients often related to systematic disease is today a challenge for the therapists. Sometime, the presence of tooth enamel lesions correlated with soft tissue lesions is just a symptom or a trigger sign for a deeper and undetermined disease. Recently, high impact has been developed toward the influence of the diet as a controlled and modifiable factor in patients affected by celiac pathologies. The celiac disease (CD) is a chronic immune-mediated disorder triggered by the ingestion of gluten that appears in genetically predisposed patients. Gluten is a proline-rich and glutamine-rich protein present in wheat (gliadin), barley (hordein), and rye (secalin). The gluten-free diet (GFD) seems to better influence the oral health status of the CD patients. For this reason, the main objective of this revision was to analyze the international data highlighting the relationship between celiac patients and the oral health impact profile. A comprehensive review of the current literature was conducted according to the PRISMA guidelines by accessing the NCBI PubMed database. Authors conducted the search of articles in the English language published from 2008 to 2018. The first analysis with filters recorded 67 manuscripts accordingly with the selected keywords. Finally, a number of 16 appropriate published papers were comprehended in the review. The studies were different in terms of the structure, findings, outcomes, and diet quality evaluation, and for this reason, it was not possible to accomplish a meta-analysis of the recorded data. This manuscript offers some observational evidence to justify the advantages of gluten-free diets related to a better oral health status in the patients involved.

Purpose: This study was aimed to investigate, over 5 years, bone response to "one-abutment onetime" (OA-OT) protocol in the restoration of implants inserted in the anterior maxilla. Additionally, influence of soft tissue biotype in the bone remodeling was investigated., Materials and Methods: From January 2011 to January 2012, all consecutive patients presented with a hopeless tooth in the maxillary area between canines were enrolled. Post-extraction ridge preservation was performed. After 6 months, implant was midcrestaly inserted and intraoperative impression was taken. Two months thereafter an immediate definitive abutment with a provisional crown was inserted. At final crown connection, patients underwent a standardized periapical radiograph (T0). At 12 (T1), 24 (T2), 36 (T3), 48 (T4), and 60 (T5) months, radiographic follow-up and clinical control were carried out. Independent sample t-test was conducted to compare bone loss at different times. To detect the potential role of biotype, groups (thick TK vs thin TH) were compared by analysis of variance with general linear model., Results: Twenty-five patients were enrolled, but only 22 patients concluded the study. The radiographic analysis showed a stable longitudinal condition of bone levels after the first-year significant increasing (0.17 ± 0.25mm, 0.33 ± 0.25mm, 0.28 ± 0.27mm, 0.25 ± 0.26mm, 0.31 ± 0.35mm, and 0.31 ± 0.29mm, respectively at T1, T2, T3, T4, and T5). No statistical significant differences in bone loss among the two groups TH vs TK over the time (P = 0.952) were demonstrated., Conclusion: Results showed that the OA-OT approach allow to obtain stable bone levels., (© 2018 Wiley Periodicals, Inc.)

The aim of this consensus conference was to provide clinical guidelines, based on the available evidence and on the author's daily practice and experience, for general dentistry and dental practitioners to allow them to delivery long-term successful restorations. Three groups of expert clinicians and dental technicians were invited to evaluate all of the scientific literature from 1967 up to March 2017 to identify relevant studies on assigned topics and to prepare in advance narrative/systematic review, written according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, to fulfill the consensus statement criteria. The three topics assigned to the three groups were abutment/framework materials and customization (metal vs. metal-free restorations), abutment/framework protocols and designs, and abutment/framework retentions (cemented- vs. screw-retained implant-supported prostheses). All the expert clinicians presented their results, and the lectures were followed by discussions. No significant differences in clinical parameters (marginal bone loss, bleeding on probing, and pocket probing depth) between screw- or cemented-retained were found for single and multiple implant-supported restorations. There is moderate evidence that nonoriginal abutments provide worse mechanical behavior than originals and high evidence that different implant neck designs do not offer any clinical or radiographic advantage. All the participants agreed that it is desirable to connect and remove abutments as few times as possible. There is medium evidence that an adequate platform switching tends to enhance tissue volume and stability in the medium- and long-term follow-up. No statistically significant differences exist between metal and zirconia as a framework material. The authors discussed and all agreed that retrievability and patient's expectation (function and esthetics) should guide the choice of the most adequate technique, component, and material., Competing Interests: There are no conflicts of interest.

Background: Parkinson's disease (PD) is the second most common neurodegenerative disorder, and the most common neurodegenerative form of parkinsonism. Recently, a pathogenic mutation (p.N855S) in DNAJC13 was linked to autosomal dominant Lewy body PD in a Dutch-German-Russian Mennonite multi-incident kindred, and was found in five additional patients. In this study, we performed a comprehensive screening of the DNAJC13 gene in familial PD and sporadic PD to assess the frequency of known and novel rare nonsynonymous variants., Methods: We screened 563 sporadic and 168 familial PD patients and a control series (n = 1000) for the coding region of DNAJC13., Results: Our sequencing analysis identified two carriers of the c.2708G > A (p.R903K) variant in exon 24 of DNAJC13. One of these carriers is a familial PD., Conclusion: The p. R903K variant was not found in 1000 healthy controls and it is localized in a functional domain of the DNAJC13 protein. Further studies are necessary to evaluate the role of DNAJC13 variants in PD., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Objective: Neurodegenerative diseases are often characterized by the presence of intracellular or extracellular protein aggregates in the central nervous system. Mutations of TARDBP gene have been shown to cause Amyotrophic Lateral Sclerosis and have been reported to present with clinical heterogeneity including parkinsonism. TDP-43 pathology has been observed across a spectrum of neurodegenerative disorders, including Alzheimer's and Parkinson's disease., Methods: In this study we screened 100 sporadic and 165 familial PD patients and control series (450) for the TARDBP gene. All cases and controls included in this study were born and living in Calabria., Results: The p.N267S heterozygous mutation was detected in one sporadic PD patient. The p.N267S mutation was not found in a control population of 450 healthy individuals and in our 165 familial PD., Conclusions: Sequencing of the TARDBP gene in our patient cohort identified one sporadic PD carrying the p.N267S mutation. This is the first analysis of TARDBP mutation in sporadic PD patient from South Italy., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Phospholipase A2-associated neurodegeneration (PLAN), a syndrome of Neurodegeneration with Brain Iron Accumulation (NBIA), is an autosomal recessive disorder caused by mutations in PLA2G6 gene. This gene encodes a calcium-independent group VI phospholipase A2 (iPLA-VI) critical in cell membrane homeostasis. PLAN syndrome encompasses a group of phenotypes with a different age of onset: classic infantile neuroaxonal dystrophy (INAD), atypical neuroaxonal dystrophy of childhood-onset (atypical NAD) and adult-onset PLA2G6-related dystonia-parkinsonism (PARK14). INAD is a severe progressive psychomotor disorder characterized by the presence of axonal spheroids throughout the central and peripheral nervous system. Here we report clinical, genetic and histopathological findings of an INAD consanguineous-family from Senegal. Sanger sequencing analysis revealed a new homozygous PLA2G6-mutation in the proband (c.1483C>T) and the co-segregation of the mutation in this family. Electron microscopy on skin biopsy showed degenerated axons confirming the phenotype. This study contributes to enrich the landscape of PLA2G6-associated INAD mutations and enforce the genotype-phenotype correlation., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Glycosylation, oxidation and other post-translational modifications of membrane and transmembrane proteins can alter lipid density, packing and interactions, and are considered an important factor that affects fluidity variation in membranes. Red blood cells (RBC) membrane physical state, showing pronounced alterations in Type 1 diabetes mellitus (T1DM), could be the ideal candidate for monitoring the disease progression and the effects of therapies. On these grounds, the measurement of RBC membrane fluidity alterations can furnish a more sensitive index in T1DM diagnosis and disease progression than Glycosylated hemoglobin (HbA1c), which reflects only the information related to glycosylation processes. Here, through a functional two-photon microscopy approach we retrieved fluidity maps at submicrometric scale in RBC of T1DM patients with and without complications, detecting an altered membrane equilibrium. We found that a phase separation between fluid and rigid domains occurs, triggered by systemic effects on membranes fluidity of glycation and oxidation. The phase separation patterns are different among healthy, T1DM and T1DM with complications patients. Blood cholesterol and LDL content are positively correlated with the extent of the phase separation patterns. To quantify this extent a machine learning approach is employed to develop a Decision-Support-System (DSS) able to recognize different fluidity patterns in RBC. Preliminary analysis shows significant differences(p<0.001) among healthy, T1DM and T1DM with complications patients. The development of an assay based on Phase separation of the plasma membrane of the Red Blood cells is a potential tool for diagnosis and progression monitoring of type 1 diabetes mellitus, and could allow customization and the selection of medical treatments in T1DM in clinical settings, and enable the early detection of complications.

The sensorimotor cortical system undergoes structural and functional changes across its lifespan. Some of these changes are physiological and parallel the normal aging process, while others might represent pathophysiological mechanisms underlying neurodegenerative disorders. In the last years, the study of possible age-related modifications in brain sensorimotor functional characteristics has been the focus of several research projects. Here we have used the transcranial magnetic stimulation (TMS)-electroencephalography (EEG) navigated co-registration to investigate the influence of physiological aging on the excitability and connectivity of the human sensorimotor cortical system. To this end, we compared the TMS-evoked EEG potentials (TEPs) collected after stimulating the dominant primary motor cortex (M1) in healthy young subjects (mean age 24.5years) with those collected in healthy older adults (mean age 67.6years). We have shown that, after stimulation of the left motor cortex, TEPs are significantly affected by physiological aging. This phenomenon has a clear spatio-temporal specificity and we speculate that normal aging per se leads to some changes in the excitability of specific cortical neural assemblies whereas other alterations could reflect compensatory mechanisms to such changes., (Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.)

It was recently demonstrated that the characteristics of EEG rhythms preceding a transcranial magnetic stimulation (TMS) of the motor cortex (M1) influence the motor-evoked potential (MEP) amplitude with a peculiar pattern, thus reflecting the M1 functional state. As physiological aging is related to a decrease in motor performance and changes in excitability and connectivity strength within cerebral sensorimotor circuits, we aimed to explore whether aging affects EEG-MEP interactions. Using MRI-navigated TMS and multichannel EEG, we compared the EEG-MEP interactions observed in healthy aged subjects with those observed in young volunteers. We divided the MEPs amplitude into two different subgroups consisting of "high" and "low" MEPs, based on the 50th percentile of their amplitude distribution. Then we analysed the characteristics of the pre-stimulus EEG from M1 and correlated areas separately for the "high" and "low" MEPs, comparing the two conditions. In both young and old subjects, significantly larger MEPs were evoked when the stimulated M1 was coupled in the beta-2 band with the homolateral prefrontal cortex. Conversely, only in young participants was the MEP size modulated when the M1 and homolateral parieto-occipital cortices were coupled in the delta band. The elderly didn't show this kind of pattern. Importantly, this coupling was significantly higher in elderly brains than in young brains, both for high and low MEPs. Our results suggest an age-related significant influence of time-varying coupling of spatially patterned EEG rhythms on motor cortex excitability in response to TMS., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Parkinson's disease (PD) is the most common form of degenerative Parkinsonism with a prevalence of 1% of those older than 65 years. PD is characterized by the combination of slowness of movement (bradykinesia), muscular rigidity, resting tremor, and postural instability. Recently, using a genome-wide linkage analysis and exome sequencing, a group identified a candidate gene (CHCHD2) in a large Japanese family with autosomal dominant Parkinson's disease. The aim of this study was to evaluate the presence of CHCHD2 mutations in a cohort of 165 familial patients with clinically diagnosed PD and 200 control subjects from South Italy. No mutations in CHCHD2 were found in our 165 PD patients. This result suggests that CHCHD2 mutations might not be the common cause of PD in South Italy., (Copyright © 2016 Elsevier Inc. All rights reserved.)

The reconstruction of neuron morphology allows to investigate how the brain works, which is one of the foremost challenges in neuroscience. This process aims at extracting the neuronal structures from microscopic imaging data. The great advances in microscopic technologies have made a huge amount of data available at the micro-, or even lower, resolution where manual inspection is time consuming, prone to error and utterly impractical. This has motivated the development of methods to automatically trace the neuronal structures, a task also known as neuron tracing. This paper surveys the latest neuron tracing methods available in the scientific literature as well as a selection of significant older papers to better place these proposals into context. They are categorized into global processing, local processing and meta-algorithm approaches. Furthermore, we point out the algorithmic components used to design each method and we report information on the datasets and the performance metrics used.

The co-registration of transcranial magnetic stimulation and electroencephalography (TMS-EEG) is emerging as a successful technique for causally exploring cortical mechanisms and connections. However, various artefacts could affect TMS-EEG signals. Correct artefacted channels reconstruction is crucial to obtain accurate topographical representation and consequently accurate inverse problem solution, in order to map in a proper way the global brain responses after the stimulation of one particular brain region of interest. In this paper, we discuss the problem of artefacted channels interpolation in TMS-EEG signals. Aim of the study was to investigate two different interpolation methods evaluating their performance in two datasets: one constituted by 19 EEG channels montage (low-density spatial resolution) and the other one by 60 EEG channels montage (high-density spatial resolution). In addition, these evaluations took place in two different contexts of application: after the averaging of TMS Evoked Potentials (TEPs) in a time interval to obtain a global information in the considered range, and at fixed latencies 100 ms and 300 ms after the TMS stimulus. The results showed that the global reconstruction error was lower at fixed latencies for the high-density electrodes spatial resolution montage.

Several studies have shown that, in spite of the fact that motor symptoms manifest late in the course of Alzheimer's disease (AD), neuropathological progression in the motor cortex parallels that in other brain areas generally considered more specific targets of the neurodegenerative process. It has been suggested that motor cortex excitability is enhanced in AD from the early stages, and that this is related to disease's severity and progression. To investigate the neurophysiological hallmarks of motor cortex functionality in early AD we combined transcranial magnetic stimulation (TMS) with electroencephalography (EEG). We demonstrated that in mild AD the sensorimotor system is hyperexcitable, despite the lack of clinically evident motor manifestations. This phenomenon causes a stronger response to stimulation in a specific time window, possibly due to locally acting reinforcing circuits, while network activity and connectivity is reduced. These changes could be interpreted as a compensatory mechanism allowing for the preservation of sensorimotor programming and execution over a long period of time, regardless of the disease's progression. Hum Brain Mapp 37:2083-2096, 2016. © 2016 Wiley Periodicals, Inc., (© 2016 Wiley Periodicals, Inc.)

The objective of our study was to investigate the association of two single nucleotide polymorphisms (SNPs) with genetic risk of dementia. In 212 patients with Parkinson's disease (PD), we investigated two polymorphisms within the G-protein coupled receptor kinase 5 (GRK5) gene (rs2420616, rs4752293) to determine a possible risk factor for dementia. We identified two alleles most significantly present in PD patients with dementia: G and T alleles. We also identified risk haplotypes: GC, and AT. We demonstrated that the SNPs and the related haplotypes could play a central role in predisposing PD patients to cognitive impairment., (Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.)

In vivo two-photon imaging combined with targeted fluorescent indicators is currently extensively used for attaining critical insights into brain functionality and structural plasticity. Additional information might be gained from back-scattered photons from the near-infrared (NIR) laser without introducing any exogenous labelling. Here, we describe a complimentary and versatile approach that, by collecting the reflected NIR light, provides structural details on axons and blood vessels in the brain, both in fixed samples and in live animals under a cranial window. Indeed, by combining NIR reflectance and two-photon imaging of a slice of hippocampus from a Thy1-GFPm mouse, we show the presence of randomly oriented axons intermingled with sparsely fluorescent neuronal processes. The back-scattered photons guide the contextualization of the fluorescence structure within brain atlas thanks to the recognition of characteristic hippocampal structures. Interestingly, NIR reflectance microscopy allowed the label-free detection of axonal elongations over the superficial layers of mouse cortex under a cranial window in vivo. Finally, blood flow can be measured in live preparations, thus validating label free NIR reflectance as a tool for monitoring hemodynamic fluctuations. The prospective versatility of this label-free technique complimentary to two-photon fluorescence microscopy is demonstrated in a mouse model of photothrombotic stroke in which the axonal degeneration and blood flow remodeling can be investigated.

Comprehensive mapping and quantification of neuronal projections in the central nervous system requires high-throughput imaging of large volumes with microscopic resolution. To this end, we have developed a confocal light-sheet microscope that has been optimized for three-dimensional (3-D) imaging of structurally intact clarified whole-mount mouse brains. We describe the optical and electromechanical arrangement of the microscope and give details on the organization of the microscope management software. The software orchestrates all components of the microscope, coordinates critical timing and synchronization, and has been written in a versatile and modular structure using the LabVIEW language. It can easily be adapted and integrated to other microscope systems and has been made freely available to the light-sheet community. The tremendous amount of data routinely generated by light-sheet microscopy further requires novel strategies for data handling and storage. To complete the full imaging pipeline of our high-throughput microscope, we further elaborate on big data management from streaming of raw images up to stitching of 3-D datasets. The mesoscale neuroanatomy imaged at micron-scale resolution in those datasets allows characterization and quantification of neuronal projections in unsectioned mouse brains.

Background: Primary familial brain calcification (PFBC) is a rare neurodegenerative disease characterized by bilateral calcifications mostly located in the basal ganglia and in the thalami, cerebellum and subcortical white matter. Clinical manifestations of this disease include a large spectrum of movement disorders and neuropsychiatric disturbances. PFBC is genetically heterogeneous and typically transmitted in an autosomal dominant fashion. Three causative genes have been reported: SLC20A2, PDGFRB and PDGFB., Objective: We screened three PFBC Italian families for mutations in the SLC20A2, PDGFRB and PDGFB genes., Methods: Phenotypic data were obtained by neurologic examination, CT scan and magnetic resonance imaging. Mutation screening of SLC20A2, PDGFRB and PDGFB was performed by sequencing., Results: We identified a new heterozygous deletion c.21&#95;21delG (p.L7Ffs*10) in SLC20A2 gene in one of these families. No mutations were detected in the other two families., Conclusions: Our data confirm that mutations in SLC20A2 are a major cause of familial idiopathic basal ganglia calcification., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Knowledge of the sequences and structures of proteins produced by microbial pathogens is continuously increasing. Besides offering the possibility of unraveling the mechanisms of pathogenesis at the molecular level, structural information provides new tools for vaccine development, such as the opportunity to improve viral and bacterial vaccine candidates by rational design. Structure-based rational design of antigens can optimize the epitope repertoire in terms of accessibility, stability, and variability. In the present study, we used epitope mapping information on the well-characterized antigen of Neisseria meningitidis factor H binding protein (fHbp) to engineer its gonococcal homologue, Ghfp. Meningococcal fHbp is typically classified in three distinct antigenic variants. We introduced epitopes of fHbp variant 1 onto the surface of Ghfp, which is naturally able to protect against meningococcal strains expressing fHbp of variants 2 and 3. Heterologous epitopes were successfully transplanted, as engineered Ghfp induced functional antibodies against all three fHbp variants. These results confirm that structural vaccinology represents a successful strategy for modulating immune responses, and it is a powerful tool for investigating the extension and localization of immunodominant epitopes., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)

Characterizing the cytoarchitecture of mammalian central nervous system on a brain-wide scale is becoming a compelling need in neuroscience. For example, realistic modeling of brain activity requires the definition of quantitative features of large neuronal populations in the whole brain. Quantitative anatomical maps will also be crucial to classify the cytoarchtitectonic abnormalities associated with neuronal pathologies in a high reproducible and reliable manner. In this paper, we apply recent advances in optical microscopy and image analysis to characterize the spatial distribution of Purkinje cells (PCs) across the whole cerebellum. Light sheet microscopy was used to image with micron-scale resolution a fixed and cleared cerebellum of an L7-GFP transgenic mouse, in which all PCs are fluorescently labeled. A fast and scalable algorithm for fully automated cell identification was applied on the image to extract the position of all the fluorescent PCs. This vectorized representation of the cell population allows a thorough characterization of the complex three-dimensional distribution of the neurons, highlighting the presence of gaps inside the lamellar organization of PCs, whose density is believed to play a significant role in autism spectrum disorders. Furthermore, clustering analysis of the localized somata permits dividing the whole cerebellum in groups of PCs with high spatial correlation, suggesting new possibilities of anatomical partition. The quantitative approach presented here can be extended to study the distribution of different types of cell in many brain regions and across the whole encephalon, providing a robust base for building realistic computational models of the brain, and for unbiased morphological tissue screening in presence of pathologies and/or drug treatments.

Extensive mapping of neuronal connections in the central nervous system requires high-throughput µm-scale imaging of large volumes. In recent years, different approaches have been developed to overcome the limitations due to tissue light scattering. These methods are generally developed to improve the performance of a specific imaging modality, thus limiting comprehensive neuroanatomical exploration by multi-modal optical techniques. Here, we introduce a versatile brain clearing agent (2,2'-thiodiethanol; TDE) suitable for various applications and imaging techniques. TDE is cost-efficient, water-soluble and low-viscous and, more importantly, it preserves fluorescence, is compatible with immunostaining and does not cause deformations at sub-cellular level. We demonstrate the effectiveness of this method in different applications: in fixed samples by imaging a whole mouse hippocampus with serial two-photon tomography; in combination with CLARITY by reconstructing an entire mouse brain with light sheet microscopy and in translational research by imaging immunostained human dysplastic brain tissue.

This study tested the possible damage to the internal implant connection provoked by repeated disconnection and reconnection of prosthetic components. Using a light-structured scanner, connection deformation was inferred by threedimensional (3D) positional changes of a "reference" abutment before and after multiple dis- and reconnections. Measurements were taken after 1, 2, 5, 10, and 20 insertions of titanium abutments in 16 internal hexagon implants. Statistical analysis revealed that multiple dis- and reconnections could cause a deformation in the implant-abutment connection, proportional to the number of insertion procedures. However, below the threshold of 10 cycles, 3D deformation values were minimal.

Objective: To evaluate neurophysiological features of M1 excitability and plasticity in Subcortical Ischemic Vascular Dementia (SIVD), by means of a TMS mapping study., Methods: Seven SIVD and nine AD patients, along with nine control subjects were tested. The M1 excitability was studied by resting thresholds, area and volume of active cortical sites for forearm and hand's examined muscles. For M1 plasticity, coordinates of the hot-spot and the center of gravity (CoG) were evaluated. The correlation between the degree of hyperexcitability and the amount of M1 plastic rearrangement was also calculated., Results: Multivariate analysis of excitability measures demonstrated similarly enhanced cortical excitability in AD and SIVD patients with respect to controls. SIVD patients showed a medial and frontal shift of CoG from the hot-spot, not statistically different from that observed in AD. A significant direct correlation was seen between parameters related to cortical excitability and those related to cortical plasticity., Conclusions: The results suggest the existence of common compensatory mechanisms in different kind of dementing diseases supporting the idea that cortical hyperexcitability can promote cortical plasticity., Significance: This study characterizes neurophysiological features of motor cortex excitability and plasticity in SIVD, providing new insights on the correlation between cortical excitability and plasticity., (Copyright © 2014 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.)

Background: A lack of evidence is present in literature regarding the clinical relevance of micropollution and bacterial contamination present on customized titanium abutments following laboratory stages and steaming cleaning procedures. To preserve abutments from such pollutants, plasma of argon cleaning of customized abutments was advocated., Aim: The aim of this prospective, randomized, match-paired, triple-blinded, controlled, clinical trial is to longitudinally assess radiographical marginal bone-level changes around implants restored according to the platform switching and "one-abutment-one-time" concepts, using commercially available abutments, with and without plasma of argon cleaning treatment after customization., Materials and Methods: Thirty patients with thin gingival biotype, a history of periodontal disease, and in general good health received one implant in the anterior maxilla or premolar region. Patients were randomly assigned to control (abutment subjected only to usually adopted cleaning protocol by steam) and test group (abutment subjected to plasma of argon treatment). Periapical standardized digital radiographs were taken at the time of crown connection (T0), 6 (T1) and 24 months after the final restoration (T2). Average mesial-distal bone-level changes mean values with standard deviations (SD) were calculated. The Mann-Whitney U-test was selected to identify differences in bone-level changes between test and control groups., Results: An average interproximal bone loss of 0.16 mm (SD: 0.17) and 0.07 mm (SD: 0.34) was revealed in the control and test group at 6 months (T1), respectively, while after 24 months, groups showed a mean bone-level changes of 0.38 mm (SD: 0.44) and 0.11 mm (SD: 0.14), respectively. Statistically significant differences among control and test groups were found at both time points. Intergroup comparison relived absence of statistically significant difference., Conclusion: Plasma-cleaning treatment of implant titanium abutments, together with platform switching and one-abutment-one-time concepts, could be favorable in terms of hard-tissue-level changes, also in critical conditions such as in patients with a history of periodontal disease, presenting thin gingival biotype., (© 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Achieving a comprehensive knowledge of the human brain cytoarchitecture is a fundamental step to understand how the nervous system works, i.e., one of the greatest challenge of 21(st) century science. The recent development of biological tissue labeling and automated microscopic imaging systems has permitted to acquire images at the micro-resolution, which produce a huge quantity of data that cannot be manually analyzed. In case of mammals brain, automatic methods to extract objective information at the microscale have been applied until now to mice, macaque and cat 3D volume images. Here we report a method to automatically localize neurons in a sample of human brain removed during a surgical procedure for the treatments of drug resistant epilepsy in a child with hemimegalencephaly, whose neurons and neurites were fluorescence labelled and finally imaged using the two-photon fluorescence microscope. The method provides the map of both parvalbuminergic neurons and all other cells nuclei with a satisfactory f-score measured using more than two thousand human labelled soma.

Background: Detection of RNA structure similarities is still one of the major computational problems in the discovery of RNA functions. A case in point is the study of the new appreciated long non-coding RNAs (lncRNAs), emerging as new players involved in many cellular processes and molecular interactions. Among several mechanisms of action, some lncRNAs show specific substructures that are likely to be instrumental for their functioning. For instance, it has been reported in literature that some lncRNAs have a guiding or scaffolding role by binding chromatin-modifying protein complexes. Thus, a functionally characterized lncRNA (reference) can be used to infer the function of others that are functionally unknown (target), based on shared structural motifs., Methods: In our previous work we presented a tool, MONSTER v1.0, able to identify structural motifs shared between two full-length RNAs. Our procedure is mainly composed of two ad-hoc developed algorithms: nbRSSP&#95;extractor for characterizing the folding of an RNA sequence by means of a sequence-structure descriptor (i.e., an array of non-overlapping substructures located on the RNA sequence and coded by dot-bracket notation); and SSD&#95;finder, to enable an effective search engine for groups of matches (i.e., chains) common to the reference and target RNA based on a dynamic programming approach with a new score function. Here, we present an updated version of the previous one (MONSTER v1.1) accounting for the peculiar feature of lncRNAs that are not expected to have a unique fold, but appear to fluctuate among a large number of equally-stable folds. In particular, we improved our SSD&#95;finder algorithm in order to take into account all the alternative equally-stable structures., Results: We present an application of MONSTER v1.1 on lincRNAs, which are a specific class of lncRNAs located in genomic regions which do not overlap protein-coding genes. In particular, we provide reliable predictions of the shared chains between HOTAIR, ANRIL and COLDAIR. The latter are lincRNAs which interact with the same protein complexes of the Polycomb group and hence they are expected to share structural motifs.

Motivation: Recently, confocal light sheet microscopy has enabled high-throughput acquisition of whole mouse brain 3D images at the micron scale resolution. This poses the unprecedented challenge of creating accurate digital maps of the whole set of cells in a brain., Results: We introduce a fast and scalable algorithm for fully automated cell identification. We obtained the whole digital map of Purkinje cells in mouse cerebellum consisting of a set of 3D cell center coordinates. The method is accurate and we estimated an F1 measure of 0.96 using 56 representative volumes, totaling 1.09 GVoxel and containing 4138 manually annotated soma centers., Availability and Implementation: Source code and its documentation are available at http://bcfind.dinfo.unifi.it/. The whole pipeline of methods is implemented in Python and makes use of Pylearn2 and modified parts of Scikit-learn. Brain images are available on request., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author 2014. Published by Oxford University Press.)

Three-dimensional (3D) bioimaging, visualization and data analysis are in strong need of powerful 3D exploration techniques. We develop virtual finger (VF) to generate 3D curves, points and regions-of-interest in the 3D space of a volumetric image with a single finger operation, such as a computer mouse stroke, or click or zoom from the 2D-projection plane of an image as visualized with a computer. VF provides efficient methods for acquisition, visualization and analysis of 3D images for roundworm, fruitfly, dragonfly, mouse, rat and human. Specifically, VF enables instant 3D optical zoom-in imaging, 3D free-form optical microsurgery, and 3D visualization and annotation of terabytes of whole-brain image volumes. VF also leads to orders of magnitude better efficiency of automated 3D reconstruction of neurons and similar biostructures over our previous systems. We use VF to generate from images of 1,107 Drosophila GAL4 lines a projectome of a Drosophila brain.

Introduction: In recent years, there has been an increased demand for computer-aided diagnosis (CAD) tools to support clinicians in the field of indirect immunofluorescence. To this aim, academic and industrial research is focusing on detecting antinuclear, anti-neutrophil, and anti-double-stranded (anti-dsDNA) antibodies. Within this framework, we present a CAD system for automatic analysis of dsDNA antibody images using a multi-step classification approach. The final classification of a well is based on the classification of all its images, and each image is classified on the basis of the labeling of its cells., Methods: We populated a database of 342 images--74 positive (21.6%) and 268 negative (78.4%)-- belonging to 63 consecutive sera: 15 positive (23.8%) and 48 negative (76.2%). We assessed system performance by using k-fold cross-validation. Furthermore, we successfully validated the recognition system on 83 consecutive sera, collected by using different equipment in a referral center, counting 279 images: 92 positive (33.0%) and 187 negative (67.0%)., Results: With respect to well classification, the system correctly classified 98.4% of wells (62 out of 63). Integrating information from multiple images of the same wells recovers the possible misclassifications that occurred at the previous steps (cell and image classification). This system, validated in a clinical routine fashion, provides recognition accuracy equal to 100%., Conclusion: The data obtained show that automation is a viable alternative for Crithidia luciliae immunofluorescence test analysis.

Aim: To assess and characterize pollution micro-particles and bacterial growth on customized titanium abutments after steaming, ultrasonic and plasma cleaning treatments., Materials and Methods: Thirty commercially available implant abutments, after customization, were randomly divided into 3 groups of 10 and cleansed by steam (considered as control group), ultrasonic cleaning (test group 1) and plasma of Argon (test group 2). For all specimens, SEM analysis and EDAX microanalysis were performed to count and characterize pollution micro-particles, both on the abutment surface and implant-abutment connection. For the control and test groups, mean values and standard deviations were calculated for number and density of micro-particles. Statistical differences were determined by one-way ANOVA with Scheffe multiple comparison test. The level of statistical significance was set at P ≤ 0.05. Additional microbiologic analysis was performed to detect bacterial contamination on the abutment surface., Results: In the control group, the number of micro-particles on average was 117.5, and 14.1, respectively, on the abutment surface and connection. In the test groups, no pollution was revealed on the abutment (average of 1.09 and 1.13 spots, respectively, in test group 1 and test group 2) and connection (1.28 and 1.41, respectively, in test group 1 and test group 2). The analysis of variance (ANOVA) showed a statistically significant difference for all the variables examined. For each variable, at least one of the groups differs from the others. Scheffe multiple comparison test showed that all comparisons for every variables between the control group and both groups are significant, while there were some comparisons between test group 1 and test group 2 that were not significant. EDAX microanalysis identified micro-particles as residual of lubricant mixed with traces of Titanium and other metals. Microbiologic analysis demonstrated the presence of bacterial growth on the abutment surface only in the control group (111.5 ± 11.43 CFU/ml/implant-abutment as mean value). In the test groups, absence of growing microorganisms was found., Conclusions: This study confirmed that both plasma and ultrasonic treatments can be beneficially adopted for abutment cleaning process after laboratory technical stages, to supposedly favor soft tissue healing and implant-prosthetic connection stability., (© 2012 John Wiley & Sons A/S.)

Open-Source 3D Visualization-Assisted Analysis (Vaa3D) is a software platform for the visualization and analysis of large-scale multidimensional images. In this protocol we describe how to use several popular features of Vaa3D, including (i) multidimensional image visualization, (ii) 3D image object generation and quantitative measurement, (iii) 3D image comparison, fusion and management, (iv) visualization of heterogeneous images and respective surface objects and (v) extension of Vaa3D functions using its plug-in interface. We also briefly demonstrate how to integrate these functions for complicated applications of microscopic image visualization and quantitative analysis using three exemplar pipelines, including an automated pipeline for image filtering, segmentation and surface generation; an automated pipeline for 3D image stitching; and an automated pipeline for neuron morphology reconstruction, quantification and comparison. Once a user is familiar with Vaa3D, visualization usually runs in real time and analysis takes less than a few minutes for a simple data set.

Autoimmune diseases are very serious and also invalidating illnesses. The benchmark procedure for their diagnosis is the indirect immunofluorescence (IIF) assay performed on the HEp-2 substrate. Medical doctors first determine the fluorescence intensity exhibited by HEp-2 wells and then report the staining pattern. Despite its pivotal role, IIF is affected by inter- and intra-laboratory variabilities demanding for the development of computer-aided-diagnosis tools supporting medical doctor decisions. With reference to staining pattern recognition, state-of-the-art approaches recognize five main patterns characterized by well-defined cell edges. These approaches are based on cell segmentation, a task that recent work suggests to be harder than the classification itself. In this paper, we extend the panel of detectable HEp-2 staining patterns, introducing the recognition of centromere and cytoplasmic patterns, which have a high specific match with certain autoimmune diseases, from other stainings. Since image segmentation algorithms fail on these samples, we developed a classification system integrating local descriptors and the bag of visual word approach, which represents image contents without the burden of segmentation. We tested our approach on a large dataset of HEp-2 images with high variability in both fluorescence intensity and staining patterns correctly recognizing the 97.12 % of samples. The system has also been validated in a daily routine fashion on 108 consecutive IIF analyses of hospital outpatients and inpatients, achieving an accuracy rate of 97.22 %.

This paper proposes a new method for removing noise and blurring from 3D microscopy images. The main contribution is the definition of a space-variant generating model of a 3-D signal, which is capable to stochastically describe a wide class of 3-D images. Unlike other approaches, the space-variant structure allows the model to consider the information on edge locations, if available. A suitable description of the image acquisition process, including blurring and noise, is then associated to the model. A state-space realization is finally derived, which is amenable to the application of standard Kalman filter as an image restoration algorithm. The so obtained method is able to remove, at each spatial step, both blur and noise, via a linear minimum variance recursive one-shot procedure, which does not require the simultaneous processing of the whole image. Numerical results on synthetic and real microscopy images confirm the merit of the approach.

Understanding the architecture of mammalian brain at single-cell resolution is one of the key issues of neuroscience. However, mapping neuronal soma and projections throughout the whole brain is still challenging for imaging and data management technologies. Indeed, macroscopic volumes need to be reconstructed with high resolution and contrast in a reasonable time, producing datasets in the TeraByte range. We recently demonstrated an optical method (confocal light sheet microscopy, CLSM) capable of obtaining micron-scale reconstruction of entire mouse brains labeled with enhanced green fluorescent protein (EGFP). Combining light sheet illumination and confocal detection, CLSM allows deep imaging inside macroscopic cleared specimens with high contrast and speed. Here we describe the complete experimental pipeline to obtain comprehensive and human-readable images of entire mouse brains labeled with fluorescent proteins. The clearing and the mounting procedures are described, together with the steps to perform an optical tomography on its whole volume by acquiring many parallel adjacent stacks. We showed the usage of open-source custom-made software tools enabling stitching of the multiple stacks and multi-resolution data navigation. Finally, we illustrated some example of brain maps: the cerebellum from an L7-GFP transgenic mouse, in which all Purkinje cells are selectively labeled, and the whole brain from a thy1-GFP-M mouse, characterized by a random sparse neuronal labeling.

Aim: This study was aimed to assess contaminants on the abutment surface close to the implant-abutment interface and the connection, after common technical protocols., Materials and Methods: A total of 40 abutments were divided into four groups: control group (abutment removed from the plastic envelop), test group1 (milled), test group2 (milled and polished), test group3 (milled, polished and steamed). Groups were subjected to scanning electron microscope (SEM) analysis. Pollution particles were counted and measured. Mean values and standard deviation (SD) were calculated. To evaluate any difference between groups Wilcoxon Signed Rank Test was conducted. In addition, contaminant chemical characterization was investigated by Energy-dispersive X-ray spectroscopy (EDX)., Results: Control group presented minimal amount of pollution (mean value of 2.1 spots [SD: 1.66] covering 0.004% of the surface). On the other hand, SEM analysis revealed on the abutment surface a mean value of 115.9 (SD: 32.27), 162 (SD: 21.17), and 32.5 (SD: 9.73) spots, respectively, in Test group 1, 2, and 3. Micro-particles covered the 0.025%, 0.057%, 0.0404% of the surface, respectively, in Test group 1, 2, and 3. On the connection, SEM analysis revealed a mean value of 61.9 (SD: 9.07), 39 (SD: 12.35), 42.1 (SD: 8.59) spots, respectively, in Test group 1, 2, and 3. Micro-particles covered the 0.0774%, 0.0869%, and 0.0392% of the surface, respectively, in Test group 1, 2, and 3. Spots were identified by EDX as micro-particles of lubricant and titanium smear layer. All differences were statistically significant., Conclusions: After technical procedures, presence of contaminants on the abutment surface in contact with the peri-implant tissues was confirmed. To prevent that such debris could interfere with biological stability of peri-implant tissues and, thus, enhance the implant-prosthesis integration, different cleaning protocols should be evaluated., (© 2012 John Wiley & Sons A/S.)