Optical mapping compendium of structural variants across global cattle breeds.

Structural variants (SV) have been linked to important bovine disease phenotypes, but due to the difficulty of their accurate detection with standard sequencing approaches, their role in shaping important traits across cattle breeds is largely unexplored. Optical mapping is an alternative approach for mapping SVs that has been shown to have higher sensitivity than DNA sequencing approaches. The aim of this project was to use optical mapping to develop a high-quality database of structural variation across cattle breeds from different geographical regions, to enable further study of SVs in cattle. To do this we generated 100X Bionano optical mapping data for 18 cattle of nine different ancestries, three continents and both cattle sub-species. In total we identified 13,457 SVs, of which 1,200 putatively overlap coding regions. This resource provides a high-quality set of optical mapping-based SV calls that can be used across studies, from validating DNA sequencing-based SV calls to prioritising candidate functional variants in genetic association studies and expanding our understanding of the role of SVs in cattle evolution.

Analysis of eyewitness testimony using electroencephalogram signals.

Face recognition and related psychological phenomenon have been the subject of neurocognitive studies during last decades. More recently the problem of face identification is also addressed to test the possibility of finding markers on the electroencephalogram signals. To this end, this work presents an experimental study where Brain Computer Interface strategies were implemented to find features on the signals that could discriminate between culprit and innocent. The feature extraction block comprises time domain and frequency domain characteristics of single-trial signals. The classification block is based on a support vector machine and its performance for the best ranked features. The data analysis comprises the signals of a cohort of 28 participants.

Mining EEG scalp maps of independent components related to HCT tasks.

This work presents an unsupervised mining strategy, applied to an independent component analysis (ICA) of segments of data collected while participants are answering to the items of the Halstead Category Test (HCT). This new methodology was developed to achieve signal components at trial level and therefore to study signal dynamics which are not available within participants' ensemble average signals. The study will be focused on the signal component that can be elicited by the binary visual feedback which is part of the HCT protocol. The experimental study is conducted using a cohort of 58 participants.

Event-related potentials modulated by the perception of sexual dimorphism: The influence of attractiveness and sex of faces.

Sexual dimorphism has been proposed as one of the facial traits to have evolved through sexual selection and to affect attractiveness perception. Even with numerous studies documenting its effect on attractiveness and mate choice, the neurophysiological correlates of the perception of sexual dimorphism are not yet fully understood. In the present study, event-related potentials (ERPs) were recorded during visualisation of faces that had been previously transformed in shape to appear more masculine or more feminine. The participants' task consisted of judging the attractiveness of half of the total number of faces, and performing a sex discrimination task on the other half. Both early and late potentials were modulated by the sex of faces, whereas the effect of the sexually dimorphic transform was mainly visible in the P2 (positive deflection around 200 ms after stimulus onset), EPN (early posterior negativity) and LPP (late positive potential) components. There was an effect of sexual dimorphism on P2 and EPN amplitudes when female participants visualised male faces, which may indicate that masculinity is particularly attended to when viewing opposite sex members. Also, ERP results seem to support the idea of sex differences in social categorisation decisions regarding faces, although differences were not evident on behavioural results. In general, these findings contribute to a better understanding of how humans perceive sexually dimorphic characteristics in other individuals' faces and how they affect attractiveness judgements.

ERP correlates of error processing during performance on the Halstead Category Test.

The Halstead Category Test (HCT) is a neuropsychological test that measures a person's ability to formulate and apply abstract principles. Performance must be adjusted based on feedback after each trial and errors are common until the underlying rules are discovered. Event-related potential (ERP) studies associated with the HCT are lacking. This paper demonstrates the use of a methodology inspired on Singular Spectrum Analysis (SSA) applied to EEG signals, to remove high amplitude ocular and movement artifacts during performance on the test. This filtering technique introduces no phase or latency distortions, with minimum loss of relevant EEG information. Importantly, the test was applied in its original clinical format, without introducing adaptations to ERP recordings. After signal treatment, the feedback-related negativity (FRN) wave, which is related to error-processing, was identified. This component peaked around 250ms, after feedback, in fronto-central electrodes. As expected, errors elicited more negative amplitudes than correct responses. Results are discussed in terms of the increased clinical potential that coupling ERP information with behavioral performance data can bring to the specificity of the HCT in diagnosing different types of impairment in frontal brain function.

In silico infrared and Raman spectroscopy under pressure: the case of CaSnO3 perovskite.

The CaSnO3 perovskite is investigated under geochemical pressure, up to 25 GPa, by means of periodic ab initio calculations performed at B3LYP level with local Gaussian-type orbital basis sets. Structural, elastic, and spectroscopic (phonon wave-numbers, infrared and Raman intensities) properties are fully characterized and discussed. The evolution of the Raman spectrum of CaSnO3 under pressure is reported to remarkably agree with a recent experimental determination [J. Kung, Y. J. Lin, and C. M. Lin, J. Chem. Phys. 135, 224507 (2011)] as regards both wave-number shifts and intensity changes. All phonon modes are symmetry-labeled and bands assigned. The single-crystal total spectrum is symmetry-decomposed into the six directional spectra related to the components of the polarizability tensor. The infrared spectrum at increasing pressure is reported for the first time and its main features discussed. All calculations are performed using the Crystal14 program, taking advantage of the new implementation of analytical infrared and Raman intensities for crystalline materials.

EEG study on affective valence elicited by novel and familiar pictures using ERD/ERS and SVM-RFE.

EEG signals have been widely explored in emotional processing analyses, both in time and frequency domains. However, in such studies, habituation phenomenon is barely considered in the discrimination of different emotional responses. In this work, spectral features of the event-related potentials (ERPs) are studied by means of event-related desynchronization/synchronization computation. In order to determine the most relevant ERP features for distinguishing how positive and negative affective valences are processed within the brain, support vector machine-recursive feature elimination is employed. The proposed approach was applied for investigating in which way the familiarity of stimuli affects the affective valence processing as well as which frequency bands and scalp regions are more involved in this process. In a group composed of young adult women, results prove that parietooccipital region and theta band are especially involved in the processing of novelty in emotional stimuli. Furthermore, the proposed method has shown to perform successfully using a moderated number of trials.

Individual EEG differences in affective valence processing in women with low and high neuroticism.

OBJECTIVE: In this study, individual differences in brain electrophysiology during positive and negative affective valence processing in women with different neuroticism scores are quantified. METHODS: Twenty-six women scoring high and low on neuroticism participated on this experiment. A support vector machine (SVM)-based classifier was applied on the EEG single trials elicited by high arousal pictures with negative and positive valence scores. Based on the accuracy values obtained from subject identification tasks, the most distinguishing EEG channels among participants were detected, pointing which scalp regions show more distinct patterns. RESULTS: Significant differences were obtained, in the EEG heterogeneity between positive and negative valence stimuli, yielding higher accuracy in subject identification using negative pictures. Regarding the topographical analysis, significantly higher accuracy values were reached in occipital areas and in the right hemisphere (p < 0.001). CONCLUSIONS: Mainly, individual differences in EEG can be located in parietooccipital regions. These differences are likely to be due to the different reactivity and coping strategies to unpleasant stimuli in individuals with high neuroticism. In addition, the right hemisphere shows a greater individual specificity. SIGNIFICANCE: An SVM-based classifier asserts the individual specificity and its topographical differences in electrophysiological activity for women with high neuroticism compared to low neuroticism.

Efeito do gel da babosa (Aloe barbadensis Mill. ) associado ao ultrassom em processo inflamatório agudo / Effect of aloe (Aloe barbadensis Mill. ) gel combined with ultrasound in the acute inflammatory process

O presente trabalho teve por objetivo analisar a ação antiinflamatória do gel da Babosa a 2 por cento (Aloe barbadensis Mill.) associado ao Ultrassom pulsátil no modelo de edema de pata. Foram utilizados 25 ratos Wistar, (200-250 g), divididos em 5 grupos de 5 animais cada. Grupo1 (controle): ratos tratados com solução salina a 0,9 por cento; Grupo 2: ratos tratados topicamente com gel de A. barbadensis Mill. a 2 por cento; Grupo 3: animais tratados com Ultrassom; Grupo 4: ratos tratados com gel de A. barbadensis Mill. a 2 por cento associado ao Ultrassom; Grupo 5 (controle positivo): ratos tratados com Indometacina na dose de 5 mg Kg-1. Os animais dos grupos 1 e 5 receberam os respectivos tratamentos por via intra-peritoneal 30 minutos antes da injeção intra-plantar de carragenina e os grupos 2, 3 e 4 foram tratados por aplicação tópica de gel de A. barbadensis Mill. a 2 por cento, Ultrassom pulsátil e gel de A. barbadensis Mill. associado ao Ultrassom respectivamente 15 minutos após a indução do edema. Os animais do grupo 04 demonstraram redução significativa do edema quando comparados ao grupo controle, ao mesmo tempo, que se mostrou comparável à indometacina. Observou-se que o gel de aloe associado à fonoforose é capaz reduzir a formação do edema de pata em ratos.

This work aimed to evaluate the anti-inflammatory action of 2 percent aloe (Aloe barbadensis Mill.) gel combined with pulsed ultrasound in the paw edema model. Twenty-five Wistar rats (200-250 g) were divided into 5 groups of 5 animals each. Group1 (control): rats treated with 0.9 percent saline; Group 2: rats topically treated with 2 percent aloe gel; Group 3: rats treated with ultrasound; Group 4: rats treated with 2 percent aloe gel combined with ultrasound; Group 5 (positive control): rats treated with indomethacin at 5 mg Kg-1. Animals of groups 1 and 5 were intraperitoneally treated 30 min before intraplantar carrageenan injection and groups 2, 3 and 4 were treated by topical application of 2 percent aloe gel, pulsed ultrasound and aloe gel combined with ultrasound, respectively, 15 min after edema induction. Animals of group 4 had a significant reduction in edema relative to controls and showed to be comparable to indomethacin. Aloe gel combined with phonophoresis is capable of reducing paw edema formation in rats.

Clustering evoked potential signals using subspace methods.

This work proposes a clustering technique to analyze evoked potential signals. The proposed method uses an orthogonal subspace model to enhance the single-trial signals of a session and simultaneously a subspace measure to group the trials into clusters. The ensemble averages of the signals of the different clusters are compared with ensemble averages of visually selected trials which are free of any artifact. Preliminary results consider recordings from an occipital channel where evoked response P100 wave is most pronounced.

Deficits in facial, body movement and vocal emotional processing in autism spectrum disorders.

BACKGROUND: Previous behavioural and neuroimaging studies of emotion processing in autistic spectrum disorder (ASD) have focused on the use of facial stimuli. To date, however, no studies have examined emotion processing in autism across a broad range of social signals. METHOD: This study addressed this issue by investigating emotion processing in a group of 23 adults with ASD and 23 age- and gender-matched controls. Recognition of basic emotions ('happiness', 'sadness', 'anger', disgust' and 'fear') was assessed from facial, body movement and vocal stimuli. The ability to make social judgements (such as approachability) from facial stimuli was also investigated. RESULTS: Significant deficits in emotion recognition were found in the ASD group relative to the control group across all stimulus domains (faces, body movements and voices). These deficits were seen across a range of emotions. The ASD group were also impaired in making social judgements compared to the control group and this correlated with impairments in basic emotion recognition. CONCLUSIONS: This study demonstrates that there are significant and broad-ranging deficits in emotion processing in ASD present across a range of stimulus domains and in the auditory and visual modality; they cannot therefore be accounted for simply in terms of impairments in face processing or in the visual modality alone. These results identify a core deficit affecting the processing of a wide range of emotional information in ASD, which contributes to the impairments in social function seen in people with this condition.

A common neural system mediating two different forms of social judgement.

BACKGROUND: A wide range of neuropsychiatric conditions, including schizophrenia and autistic spectrum disorder (ASD), are associated with impairments in social function. Previous studies have shown that individuals with schizophrenia and ASD have deficits in making a wide range of social judgements from faces, including decisions related to threat (such as judgements of approachability) and decisions not related to physical threat (such as judgements of intelligence). We have investigated healthy control participants to see whether there is a common neural system activated during such social decisions, on the basis that deficits in this system may contribute to the impairments seen in these disorders. METHOD: We investigated the neural basis of social decision making during judgements of approachability and intelligence from faces in 24 healthy participants using functional magnetic resonance imaging (fMRI). We used conjunction analysis to identify common brain regions activated during both tasks. RESULTS: Activation of the amygdala, medial prefrontal cortex, inferior prefrontal cortex and cerebellum was seen during performance of both social tasks, compared to simple gender judgements from the same stimuli. Task-specific activations were present in the dorsolateral prefrontal cortex in the intelligence task and in the inferior and middle temporal cortex in the approachability task. CONCLUSIONS: The present study identified a common network of brain regions activated during the performance of two different forms of social judgement from faces. Dysfunction of this network is likely to contribute to the broad-ranging deficits in social function seen in psychiatric disorders such as schizophrenia and ASD.

Long-term culture of multibacillary leprosy macrophages isolated from skin lesions: a new model to study Mycobacterium leprae-human cell interaction.

BACKGROUND: Leprosy is characterized by a disease spectrum having two polar clinical forms dependent on the presence or not of cell-mediated immunity. In the tuberculoid forms, granuloma-activated macrophages kill Mycobacterium leprae in conjunction with a Th1 response while, in multibacillary (MB) lesions, M. leprae nonactivated macrophages infiltrate the nerves and internal organs together with a Th2 response. The functional properties and activation pathways of macrophages isolated from patients with MB leprosy remain only partially understood. OBJECTIVES: To establish an ex vivo methodology capable of evaluating the activation pathways, grade and fate of cultured macrophages isolated from MB lesions. METHODS: Skin biopsies from patients with borderline tuberculoid, bordeline lepromatous and lepromatous leprosy (LL) were characterized by immunohistochemistry and transcriptional analysis. To isolate inflammatory cells, a portion of the samples was submitted to enzymatic digestion. These same cells, maintained in culture for a minimum 7-day period, were characterized morphologically and via flow cytometry at different culture time points. Cytokine [interferon (IFN)-gamma, tumour necrosis factor (TNF)-alpha and interleukin (IL)-10] mRNA levels were quantified by real-time polymerase chain reaction and protein secretion in the culture supernatants was measured by enzyme-linked immunosorbent assay and the nitric oxide levels by Griess reagent. RESULTS: RNA expression in tuberculoid and MB lesions showed the profile expected of characteristic Th1 and Th2 responses, respectively. The inflammatory cells in all biopsies were successfully isolated. Although the number of cells varied between biopsies, it was highest in LL biopsies. The frequency of isolated CD14+ and CD3+ cells measured by flow cytometry correlated with the percentages of macrophages and lymphocytes in the lesions. Throughout the culture period, CD68+ macrophages showed morphological changes. A progressive increase in cell number and reduction of infected cells were perceptible in the cultures. In contrast to the biopsies, TNF-alpha, IFN-gamma and IL-10 expression in the tuberculoid and MB leprosy cells in 24-h culture and the cytokine levels in the supernatants did not differ significantly. During the culture period, cytokine expression in the MB cells progressively declined, whereas, from days 1 to 7, nitrite levels progressively increased. After day 40, the remaining macrophages were able to ingest fluorescein isothiocyanate-labelled M. leprae. These data need to be confirmed. CONCLUSIONS: This study confirmed the feasibility of obtaining ex vivo macrophages from leprosy lesions and keeping them in long-term culture. This procedure may open new pathways to studying the interaction between M. leprae and human macrophages, which might, in turn, lead to the development of therapeutic tools capable of overcoming the specific anergy found in patients with MB leprosy.

New and simple plate test for screening relative transfructosylation activity of fungi

Several microorganisms are reported to have transfructosylation activity due to fructosyltransferase and/or fructofuranosidase activities. However, the search for other fungi with higher transfructosylation activity remains a challenge. So, a presumptive and indirect colorimetric plate assay for the evaluation of transfructosylation activity in fungi was developed which involved the simultaneous determination in the same plate of glucose and fructose released from sucrose. The method entailed the (a) glucose oxidase-peroxidase coupled reaction using phenol and 4-aminoantipyrine for determination of glucose; and (b) fructose dehydrogenase oxidation in the presence of a tetrazolium salt for determination of fructose. The presence of enzymes with transfructosylation activity was identified by the formation of pink (presence of glucose) and blue (presence of fructose) halos around the fungal colony. In conclusion, the results showed that the method is suitable for screening a large number of fungi due to its simplicity, reproducibility and rapidity and also gives a relative quantitative idea of the transfructosylation activity of different fungi species(AU)

Analysis of the consequences of premature termination codons within factor VIII coding sequences.

Inhibitor antibody formation is a complication of factor VIII (FVIII) replacement therapy due to a failure to synthesize sufficient FVIII protein to induce immune tolerance. The incidence of nonsense mutations in inhibitor patients is high, however, this association is variable according to the position of the mutation. We have studied the effect of nonsense mutations on accumulation of FVIII mRNA, protein translation and secretion. Appropriately processed mRNA was detected in cells transfected with wild-type R1966X and R2116X expression constructs and no evidence of nonsense-mediated decay was observed. All constructs directed the translation of detectable intracellular FVIII antigen, however, secreted FVIII was detected only in conditioned media of cells transfected with wild-type cDNA. We have also analyzed ectopic FVIII mRNA transcripts in the lymphocytes of six hemophilia A patients with nonsense mutations (Q139X, R583X, R1941X, R1966X and two unrelated patients with R2116X). FVIII mRNA was detectable in every case. In R1941X and R1966X only normally spliced transcripts were present. In Q139X, R583X and R2116X aberrantly spliced transcripts were observed with two distinct patterns in two individuals with the R2116X mutation. No correlation between mutation, transcript pattern and incidence of inhibitor development was apparent.

The effect of culture preservation techniques on patulin and citrinin production by Penicillium expansum Link.

AIMS: To study the influence of culture preservation methods and culture conditions on the production of the mycotoxins patulin and citrinin by Penicillium expansum. METHODS AND RESULTS: Ten strains of Penicillium expansum were preserved using subculture and maintenance at 4 degrees C, mineral oil, drying on silica gel and freeze-drying. Patulin and citrinin production was assessed on yeast extract sucrose agar (YES) and grape juice agar (GJ), using TLC before and after 0.5, 2-3, 6 and 12 months preservation. Citrinin was detected in all cultures for all preservation techniques on YES. The patulin profiles obtained differed with strain and culture media used. CONCLUSIONS: Citrinin production seems to be a stable character for the tested strains. There is a tendency for patulin detection with time apparently more consistent for silica gel storage and freeze-drying, especially when the strains are grown on GJ. SIGNIFICANCE AND IMPACT OF THE STUDY: Variability in the profiles of the mycotoxins tested seems to be more strain-specific than dependent on the preservation technique used.

Biodegradation of bioaccessible textile azo dyes by Phanerochaete chrysosporium.

Azo dyes are important chemical pollutants of industrial origin. Textile azo dyes with bioaccessible groups for lignin degrading fungi, such as 2-methoxyphenol (guaiacol) and 2,6-dimethoxyphenol (syringol), were synthesised using different aminobenzoic and aminosulphonic acids as diazo components. The inocula of the best biodegradation assays were obtained from a pre-growth medium (PAM), containing one of the synthesised dyes. The results of the dye biodegradation assays were evaluated every 7 days, by the decrease of the absorbance at the maximum wavelength of the dye, by the decrease of the sucrose concentration in the culture medium and by the increase of the biomass during the 28 days of assay. It was observed that the extent of dye biodegradation depended on the sucrose concentration, on the degraded dye structure and, on the dye present in the PAM medium.

Stable recombinant expression and characterization of the two haemophilic factor VIII variants C329S (CRM(-)) and G1948D (CRM(r)).

In haemophilia A, the functional defect at the molecular level of most factor VIII (FVIII) missense mutations remains unknown. Site-directed mutagenesis of B domain-deleted FVIII cDNA (FVIIISQ) was used to introduce two mutations associated with severe cross-reacting material (CRM)-negative (FVIII-C329S) or mild/moderate CRM-reduced (FVIII-G1948D) haemophilia A. Wild-type (FVIIISQ-WT) and variant FVIIISQ proteins were successfully expressed after stable transfection in Chinese hamster ovary (CHO) cells, and partially characterized at the intracellular, molecular and functional levels. Reverse transcription polymerase chain reaction analysis confirmed that both transcription and mRNA processing appeared normal in CHO cells transfected with both the wild-type and two variant constructs. In contrast to FVIIISQ-WT, immunofluorescence analysis of both CRM(-) and CRM(r) variants showed intracellular FVIII accumulation within the rough endoplasmic reticulum, suggesting secretion defects in transfected CHO cells. Immunoblot analysis of the FVIIISQ variant proteins that were secreted showed that they were expressed as mixed populations of uncleaved 170 kDa polypeptides, processed 90 kDa heavy chains and 80 kDa light chains, similar to FVIIISQ-WT. Phenotypic analysis of the B domain-deleted FVIIISQ variants expressed in CHO cells correlated well with the patients' reduced FVIII activity and, in addition, surface plasmon resonance studies demonstrated that both missense mutations were associated with increased rates of A2 domain dissociation following thrombin activation. We conclude that the mutations found are responsible for the haemophilia A phenotype, through intracellular retention and decreased stability of the active cofactor FVIIIa.