Inter-species Transcriptomic Analysis Reveals a Constitutive Adaptation Against Oxidative Stress for the Highly Virulent Leptospira Species.

Transcriptomic analyses across large scales of evolutionary distance have great potential to shed light on regulatory evolution but are complicated by difficulties in establishing orthology and limited availability of accessible software. We introduce here a method and a graphical user interface wrapper, called Annotator-RNAtor, for performing interspecies transcriptomic analysis and studying intragenus evolution. The pipeline uses third-party software to infer homologous genes in various species and highlight differences in the expression of the core-genes. To illustrate the methodology and demonstrate its usefulness, we focus on the emergence of the highly virulent Leptospira subclade known as P1+, which includes the causative agents of leptospirosis. Here, we expand on the genomic study through the comparison of transcriptomes between species from P1+ and their related P1- counterparts (low-virulent pathogens). In doing so, we shed light on differentially expressed pathways and focused on describing a specific example of adaptation based on a differential expression of PerRA-controlled genes. We showed that P1+ species exhibit higher expression of the katE gene, a well-known virulence determinant in pathogenic Leptospira species correlated with greater tolerance to peroxide. Switching PerRA alleles between P1+ and P1- species demonstrated that the lower repression of katE and greater tolerance to peroxide in P1+ species was solely controlled by PerRA and partly caused by a PerRA amino-acid permutation. Overall, these results demonstrate the strategic fit of the methodology and its ability to decipher adaptive transcriptomic changes, not observable by comparative genome analysis, that may have been implicated in the emergence of these pathogens.

Neuropsychological functioning and its correlates at 1 year follow-up of severe COVID-19.

BACKGROUND: Short-term cognitive impairment is associated with SARS-CoV-2 infection but the long-term impact is yet to be examined in detail. We aim to study the evolution of these symptoms in severe COVID-19 patients admitted to the intensive care unit (ICU) between April and December 2020 1 year after hospital discharge and to analyze its clinical correlates. METHOD: A total of 58 patients agreed to participate in the 6 months follow-up and 30 at 1 year after hospital discharge. Demographic, clinical and laboratory data were collected and a comprehensive neuropsychological battery including validated tests for the main cognitive domains was administered. To test the magnitude of neurocognitive sequelae, two standard deviations below normative group were considered. To compare the neuropsychological performance at 6 and 12 months follow-up we used repeated measures tests. Finally, regression analyses were performed to test the main effects of medical and psychological factors on multiple cognition. RESULTS: Almost half of the sample continued to have impaired performance on neuropsychological tests at 12 months follow-up. In comparison with the results obtained at 6 months, significant improvements were found in immediate recall (d = 0.49), delayed recall (d = 0.45), and inhibitory control (d = 0.53). Medical variables predicted cognitive performance at 6 months but not at 12 months follow-up, while anxiety and depression predicted cognitive deficits in the long-term. CONCLUSIONS: A generalised improvement was observed in severe COVID-19 patients at follow-up. This improvement was particularly notable in verbal memory and executive functioning. However, a considerable proportion of the sample continued to present deficits at 1 year follow-up.

Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico.

The coronavirus disease 2019 (COVID-19) pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to enabling implementation of effective strategies for disease control and prevention. In this work, we present the full genome sequence for 17 SARS-CoV-2 isolates corresponding to the earliest sampled cases in Mexico. Global and local phylogenomics, coupled with mutational analysis, consistently revealed that these viral sequences are distributed within 2 known lineages, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage A/G, containing mostly sequences from North America, and lineage B/S, containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized 14 independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represented local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described for the country. Within this local transmission cluster, we also identified an H49Y amino acid change in the Spike protein. This mutation represents a homoplasy occurring independently through time and space and may function as a molecular marker to follow any further spread of these viral variants throughout the country. Our results provide a general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts.IMPORTANCE Understanding the introduction, spread, and establishment of SARS-CoV-2 within distinct human populations as well as the evolution of the pandemics is crucial to implement effective control strategies. In this work, we report that the initial virus strains introduced in Mexico came from Europe and the United States and that the virus was circulating locally in the country as early as mid-March. We also found evidence for early local transmission of strains with a H49Y mutation in the Spike protein, which could be further used as a molecular marker to follow viral spread within the country and the region.

Cognitive remediation to improve the vocational outcomes of people with severe mental illness.

The present study investigates the effects of cognitive remediation (CR) training with Individual Placement and Support (IPS) in people suffering from severe mental illness in European population (Spanish). Sixty-five participants (83% with schizophrenia or bipolar disorder) were recruited from community mental health teams. Fifty-seven met the criteria and agreed to participate in the study. The conditions of cognitive rehabilitation were assigned randomly with support employment CR + IPS (n = 28) and IPS alone (n = 29). Two groups were followed at 8 and 12 months after the baseline. Participants in the CR + IPS group improved more than the IPS only group during the follow-up period in measures of cognitive functioning (significantly higher in executive functions, verbal learning and memory) and obtained higher employment percentages during the follow-up period, including people who got a job after 8 months (52.2% versus 29.2%, p = .023) and after 1 year (60.9% versus 37.5%, p = .025), as well as, in the weekly hours worked (37.2 versus 26.7 h, p = .023). Retention in the CR + IPS program was high (82.14%). The calculated global cognitive score showed that the evolution over time differed significantly between groups (p < .001).

How migratory populations become resident.

Migratory behaviour is rapidly changing in response to recent environmental changes, yet it is difficult to predict how migration will evolve in the future. To understand what determines the rate of adaptive evolutionary change in migratory behaviour, we simulated the evolution of residency using an individual-based threshold model, which allows for variation in selection, number of genes, environmental effects and assortative mating. Our model indicates that the recent reduction in migratory activity found in a population of Eurasian blackcaps (Sylvia atricapilla) is only compatible with this trait being under strong directional selection, in which residents have the highest fitness and fitness declines exponentially with migration distance. All other factors had minor effects on the adaptive response. Under this form of selection, a completely migratory population will become partially migratory in 6 and completely resident in 98 generations, demonstrating the persistence of partial migration, even under strong directional selection. Resident populations will preserve large amounts of cryptic genetic variation, particularly if migration is controlled by a large number of genes with small effects. This model can be used to realistically simulate the evolution of any threshold trait, including semi-continuous traits like migration, for predicting evolutionary response to natural selection in the wild.

Treatment of Depression in Primary Care with Computerized Psychological Therapies: Systematic Reviews.

Depression is one of the most important causes of disability due to illness in our environment. The primary care health system receives a high percentage of this consultation about psychological distress. Often this end in a pharmacological overtreatment in patients with mild depression, due to a lack of access to alternative tools for management. To analyze the evidence that exists by now about the effectiveness of computerized psychological therapies, in people with depression in primary care setting. The search process was mainly done through MEDLINE and Cochrane using keywords such as: "depression", "treatment", "primary care", "online", "internet", "computerized", "Cognitive Behavioral Therapy" and delimiting the search by years and types of studies. The Oxman quality scale was used to analyze quality of Systematic Reviews (SR). 11 previous SR were analyzed. Almost all research is experimental and has not been implemented in the public health network except in the United Kingdom, where there is a tradition in the use of the Beating the Blues program. It requires research in our country and development of programs in Spanish, or adaptation of those of other countries, to test the effectiveness in our health system and to study, in turn, the cost-efficiency. But it is proven to be effective in reducing depressive symptoms and must be study as a possible tool to be introduced in the management of depression in non-specialized care.

Effects of spring temperatures on the strength of selection on timing of reproduction in a long-distance migratory bird.

Climate change has differentially affected the timing of seasonal events for interacting trophic levels, and this has often led to increased selection on seasonal timing. Yet, the environmental variables driving this selection have rarely been identified, limiting our ability to predict future ecological impacts of climate change. Using a dataset spanning 31 years from a natural population of pied flycatchers (Ficedula hypoleuca), we show that directional selection on timing of reproduction intensified in the first two decades (1980-2000) but weakened during the last decade (2001-2010). Against expectation, this pattern could not be explained by the temporal variation in the phenological mismatch with food abundance. We therefore explored an alternative hypothesis that selection on timing was affected by conditions individuals experience when arriving in spring at the breeding grounds: arriving early in cold conditions may reduce survival. First, we show that in female recruits, spring arrival date in the first breeding year correlates positively with hatch date; hence, early-hatched individuals experience colder conditions at arrival than late-hatched individuals. Second, we show that when temperatures at arrival in the recruitment year were high, early-hatched young had a higher recruitment probability than when temperatures were low. We interpret this as a potential cost of arriving early in colder years, and climate warming may have reduced this cost. We thus show that higher temperatures in the arrival year of recruits were associated with stronger selection for early reproduction in the years these birds were born. As arrival temperatures in the beginning of the study increased, but recently declined again, directional selection on timing of reproduction showed a nonlinear change. We demonstrate that environmental conditions with a lag of up to two years can alter selection on phenological traits in natural populations, something that has important implications for our understanding of how climate can alter patterns of selection in natural populations.

Synthesis of Polysubstituted Tetrahydropyrans by Stereoselective Hydroalkoxylation of Silyl Alkenols: En Route to Tetrahydropyranyl Marine Analogues.

Tetrahydropyrans are abundantly found in marine natural products. The interesting biological properties of these compounds and their analogues make necessary the development of convenient procedures for their synthesis. In this paper, an atom economy access to tetrahydropyrans by intramolecular acid-mediated cyclization of silylated alkenols is described. p-TsOH has shown to be an efficient reagent to yield highly substituted tetrahydropyrans. Moreover, excellent diastereoselectivities are obtained both for unsubstituted and alkylsubstituted vinylsilyl alcohols. The methodology herein developed may potentially be applied to the synthesis of marine drugs derivatives.

Real-time prediction of pre-cooked Japanese sausage color with different storage days using hyperspectral imaging.

BACKGROUND: Redness can greatly influence the freshness of sausages. A precise, rapid and noncontact analytical method or tool is needed to quantify the color. Hyperspectral imaging (HSI) is an emerging technique that integrates spectroscopy and imaging to obtain the spectral and spatial information simultaneously. In the present study, the redness of cooked sausages stored up to 57 days was predicted using HSI in tandem with multivariate data analysis. The mean spectra of the sausages were extracted from the hyperspectral images. Partial least squares regression (PLSR) and forward stepwise multiple regression (FSMR) models were used to develop the relavent spectral profiles with the redness of the cooked sausages. RESULTS: Ten important wavelengths were selected based on the regression coefficient values from the PLSR model. The PLSR model established using the full wavelengths presented a good performance, with Rc of 0.934 and a root mean square error of calibration of 0.642 (redness ranged between 14.99 and 21.48). The prediction maps for demonstrating evolution of redness in sausages were developed for the first time using R statistics (R Foundation for Statistical Computing) and Matlab (MathWorks Inc., Natick, MA, USA). CONCLUSION: HSI combined with PLSR and FSMR can be used to quantify and visualize evolution of sausage redness under different storage days. © 2017 Society of Chemical Industry.

Implications of the Red Beet Ripening on the Colour and Betalain Composition Relationships.

The evolution during ripening of Beta vulgaris (var. Pablo) on colour and betalain composition, not previously conducted in conjunction in red beets, has been examined. According to the results, it could be asserted that the ripening stage significantly (p < 0.05) influenced on all the studied parameters. On the basis of the betalain content, the optimum ripening stage corresponded to a medium weigh-to-calibre ratio, in the light of the significantly (p < 0.05) higher content of betalains, especially betanin and vulgaxanthin I. Moreover, colour attributes also differed during ripening, having the medium-ripened beetroots a significantly (p < 0.05) more reddish hue (hab) and lower lightness (L*), probably due to the higher content of betaxanthins in this stage. The colour differences among red beets in the stage II and the rest of stages were visually appreciable (ΔE*ab > 3) and mainly qualitative. A new range of opportunities for diversification of colorant market, from a nutritional and colorimetric point of view, could be possible by employing red beets with different stages of ripening.

Analysis of Multifloral Bee Pollen Pellets by Advanced Digital Imaging Applied to Functional Food Ingredients.

Bee pollen is a hive product, resulting from floral pollen agglutination by worker bees and it is characterized by its excellent bioactive and nutritional composition. Currently, research is focused on bee pollen applications on food industry, because this product has been considered an excellent source of compounds for human nutrition. It is also important in some industries, where color and particle size are important characteristics for production. Due to the granular nature of bee pollen, conventional colorimetry does not allow describing color correctly; thus, digital image analysis is a better alternative. This technique could also allow classifying bee pollen according to its appearance beyond the color. Consequently, the aim of this work was to develop a novel methodology for image data processing to classify bee pollen as ingredient in food industry. Seven color groups in samples were established regarding harvest month and particle size. It was possible to calculate the percentage of each color group in all samples. This methodology also allowed selecting each fraction for different applications in food industry using colorimetry, granulometry and the relationship between both of them.

Measurement of ripening of raspberries (Rubus idaeus L) by near infrared and colorimetric imaging techniques.

This work includes the evaluation of 168 samples of raspberries 'Glen Lyon', representing whole maturation period, by colorimetric and near infrared imaging techniques, as well as the quantification of total phenols, total anthocyanins and antioxidant activity by chemical methods. Samples showed significant differences depending on the maturation stage using CIELAB colour parameters and total anthocyanins content. The application of partial least squares regression allowed predicting the chemical features from image analysis data, with coefficients of determination (R2) up to 0.75. The best prediction for total anthocyanins including colorimetric data was observed. The proposed methodology can be used as a reference method for assessing important quality attributes of raspberries. Moreover, it is useful, rapid and accurate automatic inspection method.

From Silylated Trishomoallylic Alcohols to Dioxaspiroundecanes or Oxocanes: Catalyst and Substitution Influence.

A versatile method for the synthesis of dioxaspiroundecanes through a tandem Sakurai-Prins cyclization of allylsilyl alcohols in the presence of TMSOTf is described. The process is general and highly stereoselective with total control in the creation of three new stereogenic centers in a single step. Moreover, a very interesting chemoselectivity has been observed depending on the nature of the catalyst used or the substitution of the trishomoallylic alcohol, since the same reaction under BF3·OEt2 catalysis or using alcohols with allylic substituents provides exclusively the corresponding oxocanes, by a direct silyl-Prins cyclization.

Screening of anthocyanins in single red grapes using a non-destructive method based on the near infrared hyperspectral technology and chemometrics.

BACKGROUND: Anthocyanins are the main compounds responsible for the colour of red wines and therefore it may be important to evaluate the content of the aforesaid secondary metabolites during grape ripening due to the crucial importance to determine wine colour. Nowadays, there is a growing demand of rapid and non-destructive analytical tools for analysing grapes, such as the emerging hyperspectral analysis. RESULTS: The hyperspectral images of intact grapes (Vitis vinifera L. cv. Tempranillo, Graciano, Garnacha and Mazuelo red grape from vineyards located in the D.O.Ca. Rioja at two different developmental stages) were recorded using a near infrared hyperspectral imaging device (900-1700 nm). Reference values of anthocyanins were obtained by HPLC-DAD. Calibrations were performed by modified partial least squares regression and present a good potential (coefficient of determination of 0.72 and standard error of cross-validation values of 0.78 and 0.70 mg per grape for total and non-acylated anthocyanins respectively). CONCLUSION: The procedure reported here presents a good potential for a fast and reasonably inexpensive screening of these compounds in intact single berries. Moreover, the heterogeneity of anthocyanins within the same ripeness stage could be evaluated using this non-detructive tool.

Competitive silyl-Prins cyclization versus tandem Sakurai-Prins cyclization: an interesting substitution effect.

Two different mechanism pathways are observed for the reaction of allylsilyl alcohols 1 and aldehydes in the presence of trimethylsilyl trifluoromethanesulfonate (TMSOTf). In the case of allylsilyl alcohols without allylic substituents, the reaction gives dioxaspirodecanes, which are the products of a tandem Sakurai-Prins cyclization. In contrast, allylsilyl alcohols with an allylic substituent (R(2)≠H) selectively provide oxepanes, thus corresponding to a direct silyl-Prins cyclization. Both types of product are obtained with excellent stereoselectivity. Theoretical studies have been performed to obtain some rationalization for the observed stereoselectivity.

Evaluating Moisture Content in Immersion Vacuum-Cooled Sausages with Citrus Peel Extracts Using Hyperspectral Imaging.

The moisture content of immersion vacuum-cooled sausages with modified casings containing citrus fruit extracts under different storage conditions was studied using hyperspectral imaging (HSI) associated with chemometrics. Different pre-processing combinations were applied to improve the robustness of the model. The partial least squares regression model, employing the full reflectance spectrum with pre-treatment of the standard normal variate, showed calibration coefficients of determination (Rc2) of 0.6160 and a root mean square error of calibration (RMSEC) of 2.8130%. For the first time, prediction maps developed via HSI visualized the distribution of moisture content in the immersion vacuum-cooled sausages with unique modified casings in response to fluctuating storage conditions. The prediction maps showed exact parts with high water content, which will help us to monitor and prevent mold growth. The combination of HSI with multivariate analysis not only quantifies changes in moisture content but also visually represents them in response to various casing treatments under different storage conditions, illustrating the significant potential for real-time inspection and early mold detection in sausages within the processed meat industry.

Assessment of adenosine triphosphate content in sausages stuffed in different modified casing treatments added with orange extracts, utilising hyperspectral imaging combined with multivariate analysis.

Introduction: An investigation was conducted using a hyperspectral imaging (HSI) system to non-invasively estimate adenosine triphosphate (ATP) content in vacuum packaged sausages in different modified casing treatments added with orange extracts after a year of storage at 4°C. Methods: Various pre-processing combinations were applied to the spectra to enhance the performance of partial least squares regression (PLSR). Results and discussion: PLSR models, utilising the full absorbance spectrum with pre-treatment of standard normal variate combined with 1st derivative,exhibited prediction coefficients of determination (Rp2) reaching up to 0.6629. A distribution map developed through MATLAB was employed to display the location and concentration of ATP content in these unique sausages for the first time. The integration of HSI and multivariate analysis not only quantifies but also visually represents the changes in ATP content response to the different casing treatments, demonstrating the significant potential for real-time inspection in the processed meat industry.

Characterization and bioaccessibility assessment of bioactive compounds from camu-camu (Myrciaria dubia) powders and their food applications.

Camu-camu (Myrciaria dubia) is a tropical fruit known for its content of bioactive compounds. This study aimed to evaluate physicochemically, morphologically, andsensorialpowders from camu-camu obtained by spray-drying at two inlet temperatures (150 °C and 180 °C) with three encapsulating agents (maltodextrin, whey protein and a 50:50 mixture of both) and by freeze-drying of whole fruit. The use of maltodextrin protected bet anthocyanins (cyanidin-3-glucoside (C3G) and delphinidin-3-glucoside (D3G)), but whey protein showed a better protective effect on ascorbic and malic acids. These facts were confirmed during the storage stability test, finding that relative humidity is a critical variable in preserving the bioactive compounds of camu-camu powders. The powders with the highest content of bioactive compounds were added to a yogurt and a white grape juice, and then sensory evaluated. The bioaccessibility studies in gastric and intestinal phases showed better recovery percentages of bioactive compounds in camu-camu powders (up to 60.8 %) and beverages (up to 90 %) for C3G, D3G, ascorbic acid, and malic acid than in the fruit juice. Dehydration of camu-camu (M. dubia) is a strategy to increase the bioactive compounds stability, modulate the fruit sensory properties, and improve their bioavailability after incorporation in food matrices.

Comparison of hyperspectral imaging and spectrometers for prediction of cheeses composition.

Artisanal cheeses are part of the heritage and identity of different countries or regions. In this work, we investigated the spectral variability of a wide range of traditional Brazilian cheeses and compared the performance of different spectrometers to discriminate cheese types and predict compositional parameters. Spectra in the visible (vis) and near infrared (NIR) region were collected, using imaging (vis/NIR-HSI and NIR-HSI) and conventional (NIRS) spectrometers, and it was determined the chemical composition of seven types of cheeses produced in Brazil. Principal component analysis (PCA) showed that spectral variability in the vis/NIR spectrum is related to differences in color (yellowness index) and fat content, while in NIR there is a greater influence of productive steps and fat content. Partial least squares discriminant analysis (PLSDA) models based on spectral information showed greater accuracy than the model based on chemical composition to discriminate types of traditional Brazilian cheeses. Partial least squares (PLS) regression models based on vis/NIR-HSI, NIRS, NIR-HSI data and HSI spectroscopic data fusion (vis/NIR + NIR) demonstrated excellent performance to predict moisture content (RPD > 2.5), good ability to predict fat content (2.0 < RPD < 2.5) and can be used to discriminate between high and low protein values (∼1.5 < RPD < 2.0). The results obtained for imaging and conventional equipment are comparable and sufficiently accurate, so that both can be adapted to predict the chemical composition of the Brazilian traditional cheeses used in this study according to the needs of the industry.

Current selection for lower migratory activity will drive the evolution of residency in a migratory bird population.

Global warming is impacting biodiversity by altering the distribution, abundance, and phenology of a wide range of animal and plant species. One of the best documented responses to recent climate change is alterations in the migratory behavior of birds, but the mechanisms underlying these phenotypic adjustments are largely unknown. This knowledge is still crucial to predict whether populations of migratory birds will adapt to a rapid increase in temperature. We monitored migratory behavior in a population of blackcaps (Sylvia atricapilla) to test for evolutionary responses to recent climate change. Using a common garden experiment in time and captive breeding we demonstrated a genetic reduction in migratory activity and evolutionary change in phenotypic plasticity of migration onset. An artificial selection experiment further revealed that residency will rapidly evolve in completely migratory bird populations if selection for shorter migration distance persists. Our findings suggest that current alterations of the environment are favoring birds wintering closer to the breeding grounds and that populations of migratory birds have strongly responded to these changes in selection. The reduction of migratory activity is probably an important evolutionary process in the adaptation of migratory birds to climate change, because it reduces migration costs and facilitates the rapid adjustment to the shifts in the timing of food availability during reproduction.