A Hitchhiker's Guide to Functional Magnetic Resonance Imaging

Functional Magnetic Resonance Imaging (fMRI) studies have become increasingly popular both with clinicians and researchers as they are capable of providing unique insights into brain functions. However, multiple technical considerations (ranging from specifics of paradigm design to imaging artifacts, complex protocol definition, and multitude of processing and methods of analysis, as well as intrinsic methodological limitations) must be considered and addressed in order to optimize fMRI analysis and to arrive at the most accurate and grounded interpretation of the data. In practice, the researcher/clinician must choose, from many available options, the most suitable software tool for each stage of the fMRI analysis pipeline. Herein we provide a straightforward guide designed to address, for each of the major stages, the techniques, and tools involved in the process. We have developed this guide both to help those new to the technique to overcome the most critical difficulties in its use, as well as to serve as a resource for the neuroimaging community.

The functional connectome of cognitive reserve

Cognitive Reserve (CR) designates the brain's capacity to actively cope with insults through a more efficient use of its resources/networks. It was proposed in order to explain the discrepancies between the observed cognitive ability and the expected capacity for an individual. Typical proxies of CR include education and Intelligence Quotient but none totally account for the variability of CR and no study has shown if the brain's greater efficiency associated with CR can be measured. We used a validated model to estimate CR from the residual variance in memory and general executive functioning, accounting for both brain anatomical (i.e., gray matter and white matter signal abnormalities volume) and demographic variables (i.e., years of formal education and sex). Functional connectivity (FC) networks and topological properties were explored for associations with CR. Demographic characteristics, mainly accounted by years of formal education, were associated with higher FC, clustering, local efficiency and strength in parietal and occipital regions and greater network transitivity. Higher CR was associated with a greater FC, local efficiency and clustering of occipital regions, strength and centrality of the inferior temporal gyrus and higher global efficiency. Altogether, these findings suggest that education may facilitate the brain's ability to form segregated functional groups, reinforcing the view that higher education level triggers more specialized use of neural processing. Additionally, this study demonstrated for the first time that CR is associated with more efficient processing of information in the human brain and reinforces the existence of a fine balance between segregation and integration. Hum Brain Mapp 37:3310–3322, 2016.. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

The association between stress and mood across the adult lifespan on default mode network

Aging of brain structure and function is a complex process characterized by high inter- and intra-individual variability. Such variability may arise from the interaction of multiple factors, including exposure to stressful experience and mood variation, across the lifespan. Using a multimodal neuroimaging and neurocognitive approach, we investigated the association of stress, mood and their interaction, in the structure and function of the default mode network (DMN), both during rest and task-induced deactivation, throughout the adult lifespan. Data confirmed a decreased functional connectivity (FC) and task-induced deactivation of the DMN during the aging process and in subjects with lower mood; on the contrary, an increased FC was observed in subjects with higher perceived stress. Surprisingly, the association of aging with DMN was altered by stress and mood in specific regions. An increased difficulty to deactivate the DMN was noted in older participants with lower mood, contrasting with an increased deactivation in individuals presenting high stress, independently of their mood levels, with aging. Interestingly, this constant interaction across aging was globally most significant in the combination of high stress levels with a more depressed mood state, both during resting state and task-induced deactivations. The present results contribute to characterize the spectrum of FC and deactivation patterns of the DMN, highlighting the crucial association of stress and mood levels, during the adult aging process. These combinatorial approaches may help to understand the heterogeneity of the aging process in brain structure and function and several states that may lead to neuropsychiatric disorders.

Persistent and non-persistent strains of Listeria monocytogenes: A focus on growth kinetics under different temperature, salt, and pH conditions and their sensitivity to sanitizers

This study aimed to investigate the effect of different conditions, including temperature (37 °C, 22 °C, and 4 °C), NaCl concentrations (2.5%, 4%, and 8%), and acidity (pH = 5), on the growth response of persistent and non-persistent isolates of Listeria monocytogenes. The resistance to two common sanitizers (benzalkonium chloride and hydrogen peroxide) was also investigated. A selected group of 41 persistent and non-persistent L. monocytogenes isolates recovered from three cheese processing plants during a previous longitudinal study was assembled. Average lag time was similar for persistent and non-persistent isolates grown at 37 °C, 22 °C and 4 °C but significantly shorter (p < 0.05) for persistent isolates grown at 2.5%, 4% and 8% NaCl, and at pH 5. Average growth rates were significantly higher (p < 0.05) for persistent than for non-persistent isolates when grown at 22 °C, 2.5%, 4% and 8% NaCl, and at pH 5. These results suggest that persistent strains may be better adapted to grow under stressful conditions frequently encountered in food processing environments than non-persistent strains. No relation between persistence and resistance to the tested sanitizers was found.

Brain structure across the lifespan: the influence of stress and mood

Normal brain aging is an inevitable and heterogeneous process characterized by a selective pattern of structural changes. Such heterogeneity arises as a consequence of cumulative effects over the lifespan, including stress and mood effects, which drive different micro- and macro-structural alterations in the brain. Investigating these differences in healthy age-related changes is a major challenge for the comprehension of the cognitive status. Herein we addressed the impact of normal aging, stress, mood, and their interplay in the brain gray and white matter (WM) structure. We showed the critical impact of age in the WM volume and how stress and mood influence brain volumetry across the lifespan. Moreover, we found a more profound effect of the interaction of aging/stress/mood on structures located in the left hemisphere. These findings help to clarify some divergent results associated with the aging decline and to enlighten the association between abnormal volumetric alterations and several states that may lead to psychiatric disorders.

The learning curve for narrow-band imaging in the diagnosis of precancerous gastric lesions by using Web-based video

BACKGROUND

A simplified narrow-band imaging (NBI) endoscopy classification of gastric precancerous and cancerous lesions was derived and validated in a multicenter study. This classification comes with the need for dissemination through adequate training.

OBJECTIVE

To address the learning curve of this classification by endoscopists with differing expertise and to assess the feasibility of a YouTube-based learning program to disseminate it.

DESIGN

Prospective study.

SETTING

Five centers.

PARTICIPANTS

Six gastroenterologists (3 trainees, 3 fully trained endoscopists [FTs]).

INTERVENTIONS

Twenty tests provided through a Web-based program containing 10 randomly ordered NBI videos of gastric mucosa were taken. Feedback was sent 7 days after every test submission.

MAIN OUTCOME MEASUREMENTS

Measures of accuracy of the NBI classification throughout the time.

RESULTS

From the first to the last 50 videos, a learning curve was observed with a 10% increase in global accuracy, for both trainees (from 64% to 74%) and FTs (from 56% to 65%). After 200 videos, sensitivity and specificity of 80% and higher for intestinal metaplasia were observed in half the participants, and a specificity for dysplasia greater than 95%, along with a relevant likelihood ratio for a positive result of 7 to 28 and likelihood ratio for a negative result of 0.21 to 0.82, were achieved by all of the participants. No constant learning curve was observed for the identification of Helicobacter pylori gastritis and sensitivity to dysplasia. The trainees had better results in all of the parameters, except specificity for dysplasia, compared with the FTs. Globally, participants agreed that the program's structure was adequate, except on the feedback, which should have consisted of a more detailed explanation of each answer.

LIMITATIONS

No formal sample size estimate.

CONCLUSION

A Web-based learning program could be used to teach and disseminate classifications in the endoscopy field. In this study, an NBI classification for gastric mucosal features seems to be easily learned for the identification of gastric preneoplastic lesions.

Foci of contamination of Listeria monocytogenes in different cheese processing plants

Listeria monocytogenes is a ubiquitous bacterium widely distributed in the environment that can cause a severe disease in humans when contaminated foods are ingested. Cheese has been implicated in sporadic cases and in outbreaks of listeriosis worldwide. Environmental contamination, in several occasions by persistent strains, has been considered an important source of finished product contamination. The objectives of this research were to (i) evaluate the presence of L. monocytogenes within the factory environments and cheeses of three processing plants, artisanal producer of raw ewe's milk cheeses (APC), small-scale industrial cheese producer (SSI) and industrial cheese producer (ICP) each producing a distinct style of cheese, all with history of contamination by L. monocytogenes (ii) and identify possible sources of contamination using different typing methods (arsenic and cadmium susceptibility, geno-serotyping, PFGE). The presence of markers specific for 3 epidemic clones (ECI-ECIII) of L. monocytogenes was also investigated. Samples were collected from raw milk (n = 179), whey (n = 3), cheese brining solution (n = 7), cheese brine sludge (n = 505), finished product (n = 3016), and environment (n = 2560) during, at least, a four-year period. Listeria monocytogenes was detected in environmental, raw milk and cheese samples, respectively, at 15.4%, 1.1% and 13.6% in APC; at 8.9%, 2.9% and 3.4% in SSI; and at 0%, 21.1% and 0.2% in ICP. Typing of isolates revealed that raw ewe's milk and the dairy plant environment are important sources of contamination, and that some strains persisted for at least four years in the environment. Although cheeses produced in the three plants investigated were never associated with any case or outbreak of listeriosis, some L. monocytogenes belonging to specific PFGE types that caused disease (including putative epidemic clone strains isolated from final products) were found in this study.

TLR7 and TLR9 in SLE: when sensing self goes wrong

Autoreactive B and T cells are present in healthy, autoimmunity-free individuals, but they are kept in check by various regulatory mechanisms. In systemic lupus erythematosus (SLE) patients, however, autoreactive cells are expanded, activated, and produce large quantities of autoantibodies, directed especially against nuclear antigens. These antibodies form immune complexes with self-nucleic acids present in SLE serum. Since self-DNA and self-RNA in the form of protein complexes can act as TLR9 and TLR7 ligands, respectively, TLR stimulation is suggested as an additional signal contributing to activation and/or modulation of the aberrant adaptive immune response. Data from mouse models suggest a pathogenic role for TLR7 and a protective role for TLR9 in the pathogenesis of SLE. Future investigations are needed to elucidate the underlying modulatory mechanisms and the role of TLR7 and TLR9 in the complex pathogenesis of human SLE.

Behaviour of Listeria monocytogenes isolates through gastro-intestinal tract passage simulation, before and after two sub-lethal stresses

The effects of previous exposure to sub-lethal acidic and osmotic stresses on the survival of Listeria monocytogenes during exposure to gastro-intestinal (GI) tract simulation, was investigated. Six L. monocytogenes strains isolated from cheeses were selected and exposed to high salt concentrations or acidic conditions and their viability compared in quick and slow digestions. The results demonstrated that (i) all isolates were more sensitive to the exposure to acidic than to osmotic sub-lethal conditions (ii) significant differences (p < 0.05) between the two types of digestion were observed; in slow digestion, the log reduction was higher for all the tested isolates (iii) all isolates were inhibited in the presence of bile salts for both types of digestion (iv) differences between quick and slow digestion were not observed (p > 0.05) after exposure to either osmotic or acidic stress (v) a higher cellular inactivation (p < 0.001) was observed during the passage through the GI tract simulation after exposure to osmotic than to acidic stresses and (vi) neither osmotic nor acidic sub-lethal stresses conferred resistance to simulated GI tract conditions.

Distribution and characterization of Listeria monocytogenes clinical isolates in Portugal, 1994-2007

In recent years, the number of cases of listeriosis has increased worldwide. Ninety-five isolates of Listeria monocytogenes recovered from Portuguese human cases of listeriosis have been characterized by biotyping (cadmium and arsenic sensitivity), polymerase chain reaction (PCR) grouping, and by pulsed-field gel electrophoresis (PFGE) applying the enzymes AscI and ApaI. Isolates were classified into one of three PCR groups; IVb (71.6%), IIb (17.9%), and IIa (10.5%). Four biotypes were differentiated: sensitive to arsenic/cadmium (48.4%), arsenic-sensitive and cadmium-resistant (25.3%), resistant to arsenic and sensitive to cadmium (18.9%), and resistant to both heavy metals (7.4%). Combined analyses of AscI and ApaI patterns yielded a total of 58 PFGE types with five sets (G, Jb, KKa, Me, and U) of Portuguese strains, each of which were indistinguishable by PFGE typing. In the present study, it was demonstrated that there are recurrent pulsotypes and that some were the same pulsotypes linked to outbreaks in France. In addition, there are some pulsotypes spread throughout the country, while others only appear in a restricted region. This study allowed the assembly of a first large pulsotype database of Portuguese clinical strains.

Effective Cryopreservation of Neural Stem or Progenitor Cells without Serum or Proteins by Vitrification

Development of effective cryopreservation protocols will be essential to realizing the potential for clinical application of neural stem and progenitor cells. Current cryopreservation protocols have been largely employed in research, which does not require as stringent consideration of viability and sterility. Therefore, these protocols involve the use of serum and protein additives, which can potentially introduce contaminants, and slow cooling with DMSO/glycerol-based cryopreservation solutions, which impairs cell survival. We investigated whether serum- and protein-free vitrification is effective for functional cryopreservation of neurosphere cultures of neural stem or progenitor cells. To protect the samples from introduction of other contaminants during handling and cryostorage, an original “straw-in-straw” method (250 μl sterile straw placed in 500 μl straw) for direct immersion into liquid nitrogen and storing the samples was also introduced. The protocol employed brief step-wise exposure to vitrification solution composed of ethylene glycol (EG) and sucrose (40% v/v EG, 0.6 M sucrose) and removal of vitrification solution at room temperature. Evaluation of the effects of vitrification revealed that there were no differences between control and vitrified neural stem or progenitor cells in expression of the neural stem or progenitor cell markers, proliferation, or multipotent differentiation. This sterile method for the xeno-free cryopreservation of murine neurospheres without animal or human proteins may have the potential to serve as a starting point for the development of cryopreservation protocols for human neural stem and progenitor cells for clinical use.

Effective cryopreservation of neural stem or progenitor cells without serum or proteins by vitrification

Development of effective cryopreservation protocols will be essential to realizing the potential for clinical application of neural stem and progenitor cells. Current cryopreservation protocols have been largely employed in research, which does not require as stringent consideration of viability and sterility. Therefore, these protocols involve the use of serum and protein additives, which can potentially introduce contaminants, and slow cooling with DMSO/glycerol-based cryopreservation solutions, which impairs cell survival. We investigated whether serum- and protein-free vitrification is effective for functional cryopreservation of neurosphere cultures of neural stem or progenitor cells. To protect the samples from introduction of other contaminants during handling and cryostorage, an original "straw-in-straw" method (250 microl sterile straw placed in 500 microl straw) for direct immersion into liquid nitrogen and storing the samples was also introduced. The protocol employed brief step-wise exposure to vitrification solution composed of ethylene glycol (EG) and sucrose (40% v/v EG, 0.6 M sucrose) and removal of vitrification solution at room temperature. Evaluation of the effects of vitrification revealed that there were no differences between control and vitrified neural stem or progenitor cells in expression of the neural stem or progenitor cell markers, proliferation, or multipotent differentiation. This sterile method for the xeno-free cryopreservation of murine neurospheres without animal or human proteins may have the potential to serve as a starting point for the development of cryopreservation protocols for human neural stem and progenitor cells for clinical use.

Vitrification Successfully Preserves Hepatocyte Spheroids

This is the first report on low-temperature preservation of self-assembled cell aggregates by vitrification, which is both a time- and cost-effective technology. We developed an effective protocol for vitrification (ice-free cryopreservation) of hepatocyte spheroids that employs rapid stepwise exposure to cryoprotectants (10.5 min) at room temperature and direct immersion into liquid nitrogen (-196°C). For this, three vitrification solutions (VS) were formulated and their effects on vitrified-warmed spheroids were examined. Cryopreservation using ethylene glycol (EG)-sucrose VS showed excellent preservation capability whereby highly preserved cell viability and integrity of vitrified spheroids were observed, through confocal and scanning electron microscopy imaging, when compared to untreated control. The metabolic functions of EG-sucrose VS-cryopreserved spheroids, as assessed by urea production and albumin secretion, were not significantly different from those of control within the same day of observation. In both the vitrification and control groups, albumin secretion was consistently high, ranging from 47.57 ± 14.39 to 70.38 ± 11.29 μg/106 cells and from 56.84 ± 14.48 to 71.79 ± 16.65 μg/106 cells, respectively, and urea production gradually increased through the culture period. The efficacy of vitrification procedure in preserving the functional ability of hepatocyte spheroids was not improved by introduction of a second penetrating cryoprotectant, 1,2-propanediol (PD). Spheroids cryopreserved with EG-PD-sucrose VS showed maintained cell viability; however, in continuous culture, levels of both metabolic functions were lower than those cryopreserved with EG-sucrose VS. EG-PD VS, in which nonpenetrating cryoprotectant (sucrose) was excluded, provided poor protection to spheroids during cryopreservation. This study demonstrated that sucrose plays an important role in the effective vitrification of self-assembled cell aggregates. In a broad view, the excellent results obtained suggest that the developed vitrification strategy, which is an alternative to freezing, may be effectively used as a platform technology in the field of cell transplantation.

Development of a standard set of microsatellite reference alleles for identification of grape cultivars

In order to investigate the comparability of microsatellite profiles obtained in different laboratories, ten partners in seven countries analyzed 46 grape cultivars at six loci (VVMD5, VVMD7, VVMD27, VVS2, VrZAG62, and VrZAG79). No effort was made to standardize equipment or protocols. Although some partners obtained very similar results, in other cases different absolute allele sizes and, sometimes, different relative allele sizes were obtained. A strategy for data comparison by means of reference to the alleles detected in well-known cultivars was proposed. For each marker, each allele was designated by a code based on the name of the reference cultivar carrying that allele. Thirty-three cultivars, representing from 13 to 23 alleles per marker, were chosen as references. After the raw data obtained by the different partners were coded, more than 97% of the data were in agreement. Minor discrepancies were attributed to errors, suboptimal amplification and visualization, and misscoring of heterozygous versus homozygous allele pairs. We have shown that coded microsatellite data produced in different laboratories with different protocols and conditions can be compared, and that it is suitable for the identification and SSR allele characterization of cultivars. It is proposed that the six markers employed here, already widely used, be adopted as a minimal standard marker set for future grapevine cultivar analyses, and that additional cultivars be characterized by means of the coded reference alleles presented here. The complete database is available at http://www.genres.de/eccdb/vitis/ Cuttings of the 33 reference cultivars are available on request from the Institut National de la Recherche Agronomique Vassal collection (didier.vares@ensam.inra.fr).

[@HOME is a new Eu-Project in Tele Home care]

@Home is a robust platform for real-time remote monitoring of patients at their home by doctors at the hospital. Health monitoring sensors, which have the capability to measure quick and easy vital parameters such as blood pressure, pulse rate, temperature, oxygen saturation (SpO2), as well as ECG 12 leads are used. Additionally, an advantage of the platform is that all the sensors are wearable and the patient is able to walk around indoors or outdoors. Moreover, the sensors are able to convey the recorded data over Bluetooth, a short-range wireless communication, to any Bluetooth enabled device such as Desktop computer or a Pocket PC.

IgVH-genes analysis from psoriatic arthritis shows involvement of antigen-activated synovial B-lymphocytes

The pathogenesis of psoriatic arthritis (PA), which occurs in 5-7% of patients with psoriasis vulgaris, is enigmatic. There are no molecular data about synovial B-cells of chronic synovitis of PA. In order to understand the B-cell response in PA, we analysed IgVH genes and specified replacement to silent mutation (R/S) ratios of the complementarity determining regions (CDR) and framework regions (FR) as well as VH families. To prove the existence of a common pattern we additionally analysed the IgVH genes at the amino-acid level. From 5 PA patients we took cryo-tissue sections with somatically mutated IgVH genes (sum R/sum S in the CDRs: 2.5-6.8), 62 of which were analysed. In one patient two cases of clonally related IgVH genes were observed. Identical amino-acid replacements in IgVH1 and IgVH4 were found at the same mutational "cold spot". These data indicate that antigen-activated B-cells participate in the formation of chronic synovitis of PA. Since, neither histopathologically nor immunohistochemically, no germinal centres could be detected, the clonally related IgVH genes may be interpreted as residues of a germinal centre reaction that occurred before synovectomy. The existence of identical amino-acid replacement mutations in IgVH1 and IgVH4 genes suggests that a limited number of antigens are common to all PA patients analysed. The recombinant expression of the IgVH could help to define B-cell specificities underlying the pathogenesis of chronic synovitis and dermatitis of PA.

[Integration, exclusion and solidarity in the current social policy debate]

The current global trend involving transformation of work and the crisis in large government economic development and intervention projects in the market are raising new challenges for social policies to combat poverty. This study reconstitutes and analyzes the tensions, paradoxes, and main consequences of this process, focusing on problems concerned with combining solidarity strategies and public welfare systems.

[Experimental cirrhosis induced by carbon tetrachloride inhalation: adaptation of the technique and evaluation of lipid peroxidation]

BACKGROUND

Long-term administration of carbon tetrachloride is an accepted experimental model to produce hepatic fibrosis. Oxidative stress has been postulated as a major molecular mechanism involved in carbon tetrachloride hepatotoxicity, where the reactive oxygen species play an important role in the pathogenesis of liver fibrosis.

AIMS

This study was conducted to evaluate the effectiveness of an experimental model of hepatic cirrhosis induced by carbon tetrachloride inhalation as well as the importance of lipid peroxidation and the characteristics of the ascitic fluid in this model.

METHODS

At first the hepatic histologic findings were assessed using the hematoxilineosin technique in different moments of carbon tetrachloride inhalation (5th, 7th, 9th, 12th weeks). Later, at the end of 15 weeks of the study the rats were divided in three groups (control; control + phenobarbital; and carbon tetrachloride + phenobarbital) for lipid peroxidation, ascitic fluid and histologic characteristics evaluation. For the lipid peroxidation analysis, thiobarbituric acid and QL techniques were used. Cytologic and bacteriologic parameters were analysed in the ascitic fluid.

RESULTS

Cirrhosis was established in 100% of carbon tetrachloride rats between the 12th and 15th weeks with an elevation in the lipid peroxidation carbon tetrachloride rats' livers. Ascitic fluid infection was observed in one of seven rats who has developed ascites.

CONCLUSIONS

The carbon tetrachloride inhalation method developed in this study is effective in cirrhosis induction and ascites formation, and the carbon tetrachloride cirrhosis physiopathogenesis is probably related to the oxidative stress installation.

Vitis vinifera must varietal authentication using microsatellite DNA analysis (SSR)

A microsatellite DNA-based method for Vitis vinifera grape must authentication is presented. Five of the most important port wine producing grape cultivars (Tinta Roriz, Tinto Cão, Touriga Francesa, Touriga Nacional, and Tinta Barroca) were typed at four microsatellite loci described by Bowers et al. (Genome 1996, 39, 628-633) and Thomas and Scott (Theor. Appl. Genet. 1993, 86, 985-990). The corresponding 5 varietal musts and 26 must mixtures that result from the combination of the five varieties were also typed at the four loci. There were no differences between the corresponding leaf and varietal must profiles. All must combinations showed the expected band profiles corresponding to the sum of the varietal band profile components. Among the 26 must mixtures, 8 could be discriminated using the four loci.