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Abstract Many aquatic organisms utilize suction-based organs to adhere to diverse substrates in unpredictable environments. For multiple fish species, these adhesive discs include a softer disc margin consisting of surface structures called papillae, which stabilize and seal on variable substrates. The size, arrangement, and density of these papillae are quite diverse among different species, generating complex disc patterns produced by these structures. Considering papillae arrangements in three fish species, the Northern Clingfish (Gobiesox maeandricus), Tidepool Snailfish (Liparis florae), and Chilean Clingfish (Sicyases sanguineus), we fabricated physical disc models that tested relevant surface pattern parameters under shear loading conditions. Parameters of interest included the area of papillae-like structures, the spacing between adjacent structures (channel spacing), and the percent coverage of elements relative to the total disc area. To create our models, a soft silicone elastomer was added to a stiff circular suction cup, which was then “stamped” using a laser-etched and thermoformed mold base to create the desired surface patterning. Discs were tested using a robotic arm equipped with a force sensor, which sheared them across smooth and rough surfaces at a fixed speed and distance. The arm was also used to vary the initial compression to test performance under both suction-dominant and friction-dominant preloads. For our designs, patterns with smaller papillae-like structures and channel spacing often produced higher peak forces than those with larger features. However, the design that withstood the highest shear load featured an intermediate pad size and channel spacing, potentially highlighting a balance between overall surface area and fluid channeling. Additionally, discs with surface patterns often outperformed the control discs (no pattern) on both smooth and rough surfaces, but performance was highly dependent on preload, with patterned discs exhibiting benefits with the higher “friction-dominant” preloads.

For the past thirty years, hemoglobin-based oxygen carriers (HBOCs) have been under development as a red blood cell substitute. Side-effects such as vasoconstriction, oxidative injury, and cardiac toxicity have prevented clinical approval of HBOCs. Recently, high molecular weight (MW) polymerized human hemoglobin (PolyhHb) has shown positive results in rats. Studies have demonstrated that high MW PolyhHb increased O2 delivery, with minimal effects on blood pressure, without vasoconstriction, and devoid of toxicity. In this study, we used guinea pigs to evaluate the efficacy and safety of high MW PolyhHb, since like humans guinea pigs cannot produce endogenous ascorbic acid, which limits the capacity of both species to deal with oxidative stress. Hence, this study evaluated the efficacy and safety of resuscitation from severe hemorrhagic shock with high MW PolyhHb, fresh blood, and blood stored for 2 weeks. Animals were randomly assigned to each experimental group, and hemorrhage was induced by the withdrawal of 40% of the blood volume (BV, estimated as 7.5% of body weight) from the carotid artery catheter. Hypovolemic shock was maintained for 50 min. Resuscitation was implemented by infusing 25% of the animal's BV with the different treatments. Hemodynamics, blood gases, total hemoglobin, and lactate were not different before hemorrhage and during shock between groups. The hematocrit was lower for the PolyhHb group compared to the fresh and stored blood groups after resuscitation. Resuscitation with stored blood had lower blood pressure compared to fresh blood at 2 h. There was no difference in mean arterial pressure between groups at 24 h. Resuscitation with PolyhHb was not different from fresh blood for most parameters. Resuscitation with PolyhHb did not show any remarkable change in liver injury, inflammation, or cardiac damage. Resuscitation with stored blood showed changes in liver function and inflammation, but no kidney injury or systemic inflammation. Resuscitation with stored blood after 24 h displayed sympathetic hyper-activation and signs of cardiac injury. These results suggest that PolyhHb is an effective resuscitation alternative to blood. The decreased toxicities in terms of cardiac injury markers, vital organ function, and inflammation following PolyhHb resuscitation in guinea pigs indicate a favorable safety profile. These results are promising and support future studies with this new generation of PolyhHb as alternative to blood when blood is unavailable.

Abstract Measuring the carbon stable isotope ratio (13C/12C, expressed as δ13CCO2) in geogenic CO2 fluids is a crucial geochemical tool for studying Earth's degassing. Carbon stable isotope analysis is traditionally performed by bulk mass spectrometry. Although Raman spectroscopy distinguishes 12CO2 and 13CO2 isotopologue bands in spectra, using this technique to determine CO2 isotopic signature has been challenging. Here, we report on in-situ non-destructive analyses of the C stable isotopic composition of CO2, applying a novel high-resolution Raman configuration on 42 high-density CO2 fluid inclusions in mantle rocks from the Lake Tana region (Ethiopia) and El Hierro (Canary Islands). We collected two sets of three spectra with different acquisition times at high spectral resolution in each fluid inclusion. Among the 84 sets of spectra, 58 were characterised by integrated 13CO2/12CO2 band area ratios with reproducibility better than 4‰. Our results demonstrate the determination of δ13CCO2 by Raman spectroscopy in individual fluid inclusions with an error better than 2.5 ‰, which satisfactorily matches bulk mass spectrometry analyses in the same rock samples, supporting the accuracy of the measurements. We thus show that Raman Spectroscopy can provide a fundamental methodology for non-destructive, site-specific, and spatially resolved carbon isotope labelling at the microscale.

Abstract This article presents a technique to integrate two dynamical models, a four-wing spherical chaotic oscillator and the elliptical path described by the planet Earth during its translation movement around the sun. Four application cases are derived from the system by varying the dynamics of the chaotic oscillator and these can be applied in information encryption to transmit RGB and grayscale images modulated by CSK. Consequently, the three main contributions of this work are (1) the emulation of the trajectories of the planet Earth with chaotic interference, (2) the CSK modulation and image encryption in a master-slave synchronization topology, and (3) the CSK demodulation for decryption without loss of information with respect to the original information. The three contributions are based on VHDL code implementation. The results of the synchronization, encryption and decryption technique were verified by means of time series and the encrypted images showed a correlation less than − 0.000142 and − 0.0003439 for RGB and grayscale format, respectively, while the retrieved image shows a complete correlation with the image original. In this work, the co-simulations were performed between MATLAB/Simulink and Vivado, using the VHDL language on two FPGA boards from different manufacturers, namely, Xilinx Artix-7 AC701 and Intel Cyclone IV.

Abstract Prognostic scales may help to optimize the use of hospital resources, which may be of prime interest in the context of a fast spreading pandemics. Nonetheless, such tools are underdeveloped in the context of COVID-19. In the present article we asked whether accurate prognostic scales could be developed to optimize the use of hospital resources. We retrospectively studied 467 files of hospitalized patients after COVID-19. The odds ratios for 16 different biomarkers were calculated, those that were significantly associated were screened by a Pearson’s correlation, and such index was used to establish the mathematical function for each marker. The scales to predict the need for hospitalization, intensive-care requirement and mortality had enhanced sensitivities (0.91 CI 0.87–0.94; 0.96 CI 0.94–0.98; 0.96 CI 0.94–0.98; all with p

Abstract For the past thirty years, hemoglobin-based oxygen carriers (HBOCs) have been under development as a red blood cell substitute. Side-effects such as vasoconstriction, oxidative injury, and cardiac toxicity have prevented clinical approval of HBOCs. Recently, high molecular weight (MW) polymerized human hemoglobin (PolyhHb) has shown positive results in rats. Studies have demonstrated that high MW PolyhHb increased O2 delivery, with minimal effects on blood pressure, without vasoconstriction, and devoid of toxicity. In this study, we used guinea pigs to evaluate the efficacy and safety of high MW PolyhHb, since like humans guinea pigs cannot produce endogenous ascorbic acid, which limits the capacity of both species to deal with oxidative stress. Hence, this study evaluated the efficacy and safety of resuscitation from severe hemorrhagic shock with high MW PolyhHb, fresh blood, and blood stored for 2 weeks. Animals were randomly assigned to each experimental group, and hemorrhage was induced by the withdrawal of 40% of the blood volume (BV, estimated as 7.5% of body weight) from the carotid artery catheter. Hypovolemic shock was maintained for 50 min. Resuscitation was implemented by infusing 25% of the animal’s BV with the different treatments. Hemodynamics, blood gases, total hemoglobin, and lactate were not different before hemorrhage and during shock between groups. The hematocrit was lower for the PolyhHb group compared to the fresh and stored blood groups after resuscitation. Resuscitation with stored blood had lower blood pressure compared to fresh blood at 2 h. There was no difference in mean arterial pressure between groups at 24 h. Resuscitation with PolyhHb was not different from fresh blood for most parameters. Resuscitation with PolyhHb did not show any remarkable change in liver injury, inflammation, or cardiac damage. Resuscitation with stored blood showed changes in liver function and inflammation, but no kidney injury or systemic inflammation. Resuscitation with stored blood after 24 h displayed sympathetic hyper-activation and signs of cardiac injury. These results suggest that PolyhHb is an effective resuscitation alternative to blood. The decreased toxicities in terms of cardiac injury markers, vital organ function, and inflammation following PolyhHb resuscitation in guinea pigs indicate a favorable safety profile. These results are promising and support future studies with this new generation of PolyhHb as alternative to blood when blood is unavailable.

Abstract In humans, disruptions in the heme biosynthetic pathway are associated with various types of porphyrias, including variegate porphyria that results from the decreased activity of protoporphyrinogen oxidase IX (PPO; E.C.1.3.3.4), the enzyme catalyzing the penultimate step of the heme biosynthesis. Here we report the generation and characterization of human cell lines, in which PPO was inactivated using the CRISPR/Cas9 system. The PPO knock-out (PPO-KO) cell lines are viable with the normal proliferation rate and show massive accumulation of protoporphyrinogen IX, the PPO substrate. Observed low heme levels trigger a decrease in the amount of functional heme containing respiratory complexes III and IV and overall reduced oxygen consumption rates. Untargeted proteomics further revealed dysregulation of 22 cellular proteins, including strong upregulation of 5-aminolevulinic acid synthase, the major regulatory protein of the heme biosynthesis, as well as additional ten targets with unknown association to heme metabolism. Importantly, knock-in of PPO into PPO-KO cells rescued their wild-type phenotype, confirming the specificity of our model. Overall, our model system exploiting a non-erythroid human U-2 OS cell line reveals physiological consequences of the PPO ablation at the cellular level and can serve as a tool to study various aspects of dysregulated heme metabolism associated with variegate porphyria.

Abstract The muscle fiber ultrastructure in Idiopathic Inflammatory Myopathies (IIM) has been scarcely explored, especially in Inclusion Body Myositis. The aim of this study was to implement the Scanning Electron Microscopy (SEM) in a small cohort of IIM patients, together with the characterization of immunological profile for a better understanding of the pathophysiology. For immunological profile characterization, we identified the presence of autoantibodies (Ro-52, OJ, EJ, PL7, PL12, SRP, Jo-1, PMScl75, PMScl100, Ku, SAE1, NXP2, MDA5, TIF1γ, Mi-2α, Mi-2β) and quantified cytokines (IL-1β, IFN-α2, IFN-γ, TNF-α, IL-6, IL-10, IL-12p70, IL-17A, IL-18, IL-23, IL-33) and chemokines (CCL2, CXCL8). The histological analysis was made by hematoxylin–eosin staining while the muscle fiber ultrastructure was characterized by SEM. We observed changes in the morphology and structure of the muscle fiber according to muscle strength and muscle enzymes. We were able to find and describe muscle fiber ultrastructure with marked irregularities, porosities, disruption in the linearity and integrity of the fascicle, more evident in patients with increased serum levels of muscle enzymes and diminished muscle strength. Despite the scarce reports about the use of SEM as a tool in all clinical phenotypes of IIM, our work provides an excellent opportunity to discuss and reframe the clinical usefulness of SEM in the diagnostic approach of IIM.

Abstract Dietary changes are the major variation cause in the composition of the gut microbiota. The short lactation phase in phocids provides an exceptional opportunity to explore the microbiota's response to a quick transition from a milk-based to a solid diet. We investigated the effects of age and sex on the gut microbiota of harbor seals in Mexico using rectal and fecal samples from pups and adults. 16S gene sequencing revealed age explains most of the observed variations in microbial composition. Individuals with frequent contact (pups—female adults) have major microbial similarities than those with little or no contact (pups—male adults). Overall, adults and females (regardless of sex and age, respectively) have a greater microbial richness; as seals grow, the core microbiome shrinks, and microbial diversity increases. We found pathways related to milk and chitin digestion in pups' microbiomes, indicating pups were transitioning to a solid diet. An enrichment of routes related to dramatic weight loss and body mass indicated higher metabolic stress in pups in late breeding season, when they are weaned and start intermittent fasting. Our findings highlight the host-microbiome interaction in harbor seals during late breeding season in response to food shifts and metabolic stress.

Abstract Mobile screening units can help close tuberculosis case detection gaps. Placing screening units where people at high risk for undiagnosed tuberculosis preferentially spend time could make screening more resource-effective. We conducted a case–control study in Lima, Peru to identify locations where people with tuberculosis were more likely to spend time than community controls. We surveyed participants about activity locations over the past 6 months. We used density-based clustering to assess how patient and control activity locations differed, and logistic regression to compare location-based exposures. We included 109 tuberculosis patients and 79 controls. In density-based clustering analysis, the two groups had similar patterns of living locations, but their work locations clustered in distinct areas. Both groups were similarly likely to use public transit, but patients predominantly used buses and were less likely to use rapid transit (adjusted odds ratio [aOR] 0.31, 95% confidence interval [CI] 0.10–0.96) or taxis (aOR 0.42, 95% CI 0.21–0.85). Patients were more likely to have spent time in prison (aOR 11.55, 95% CI 1.48–90.13). Placing mobile screening units at bus terminals serving locations where tuberculosis patients have worked and within and around prisons could help reach people with undiagnosed tuberculosis.

Abstract Autophagy is a housekeeping mechanism tasked with eliminating misfolded proteins and damaged organelles to maintain cellular homeostasis. Autophagy deficiency results in increased oxidative stress, DNA damage and chronic cellular injury. Among the core genes in the autophagy machinery, ATG7 is required for autophagy initiation and autophagosome formation. Based on the analysis of an extended pedigree of familial cholangiocarcinoma, we determined that all affected family members had a novel germline mutation (c.2000C>T p.Arg659* (p.R659*)) in ATG7. Somatic deletions of ATG7 were identified in the tumors of affected individuals. We applied linked-read sequencing to one tumor sample and demonstrated that the ATG7 somatic deletion and germline mutation were located on distinct alleles, resulting in two hits to ATG7. From a parallel population genetic study, we identified a germline polymorphism of ATG7 (c.1591C>G p.Asp522Glu (p.D522E)) associated with increased risk of cholangiocarcinoma. To characterize the impact of these germline ATG7 variants on autophagy activity, we developed an ATG7-null cell line derived from the human bile duct. The mutant p.R659* ATG7 protein lacked the ability to lipidate its LC3 substrate, leading to complete loss of autophagy and increased p62 levels. Our findings indicate that germline ATG7 variants have the potential to impact autophagy function with implications for cholangiocarcinoma development.

Many aquatic organisms utilize suction-based organs to adhere to diverse substrates in unpredictable environments. For multiple fish species, these adhesive discs include a softer disc margin consisting of surface structures called papillae, which stabilize and seal on variable substrates. The size, arrangement, and density of these papillae are quite diverse among different species, generating complex disc patterns produced by these structures. Considering papillae arrangements in three fish species, the Northern Clingfish (Gobiesox maeandricus), Tidepool Snailfish (Liparis florae), and Chilean Clingfish (Sicyases sanguineus), we fabricated physical disc models that tested relevant surface pattern parameters under shear loading conditions. Parameters of interest included the area of papillae-like structures, the spacing between adjacent structures (channel spacing), and the percent coverage of elements relative to the total disc area. To create our models, a soft silicone elastomer was added to a stiff circular suction cup, which was then "stamped" using a laser-etched and thermoformed mold base to create the desired surface patterning. Discs were tested using a robotic arm equipped with a force sensor, which sheared them across smooth and rough surfaces at a fixed speed and distance. The arm was also used to vary the initial compression to test performance under both suction-dominant and friction-dominant preloads. For our designs, patterns with smaller papillae-like structures and channel spacing often produced higher peak forces than those with larger features. However, the design that withstood the highest shear load featured an intermediate pad size and channel spacing, potentially highlighting a balance between overall surface area and fluid channeling. Additionally, discs with surface patterns often outperformed the control discs (no pattern) on both smooth and rough surfaces, but performance was highly dependent on preload, with patterned discs exhibiting benefits with the higher "friction-dominant" preloads. [ABSTRACT FROM AUTHOR]

Abstract Gene flow in birds can be affected by urbanization depending on natural history traits and adaptability to habitat change. Contrasting results can be expected when comparing species with opposite resilience to urbanization. In this study, we assessed genetic diversity and structure for two bird species, the urban avoider white-eared ground-sparrow, Melozone leucotis, and the urban dweller house wren Troglodytes aedon. We used seven microsatellite loci and sampled five locations with differing levels of urbanization in Costa Rica. We found considerably higher genetic structure in white-eared ground-sparrows than in house wrens. Circuit theory analyses proved a higher isolation from urban resistance for the white-eared ground-sparrow than for house wrens. These results support that urbanization is a significant barrier for gene flow in urban avoiders, in contrast to urban dweller species that showed little to no impact. Differences could be attributed to a higher plasticity in habitat and nesting site preferences in the house wren, and significant dispersal limitation for the white-eared ground-sparrow. These results emphasize the need for conservation strategies towards white-eared ground-sparrows and other urban avoider species whose habitat and connectivity have been reduced by the recent urban expansion.

Abstract Bone morphogenetic protein 1 (BMP1) belongs to the astacin/BMP1/tolloid-like family of zinc metalloproteinases, which play a fundamental role in the development and formation of extracellular matrix (ECM). BMP1 mediates the cleavage of carboxyl terminal (C-term) propeptides from procollagens, a crucial step in fibrillar collagen fiber formation. Blocking BMP1 by small molecule or antibody inhibitors has been linked to anti-fibrotic activity in the preclinical models of skin, kidney and liver fibrosis. Therefore, we reason that BMP1 may be important for the pathogenesis of lung fibrosis and BMP1 could be a potential therapeutic target for progressive fibrotic disease such as idiopathic pulmonary fibrosis (IPF). Here, we observed the increased expression of BMP1 in both human IPF lungs and mouse fibrotic lungs induced by bleomycin. Furthermore, we developed an inducible Bmp1 conditional knockout (cKO) mouse strain. We found that Bmp1 deletion does not protect mice from lung fibrosis triggered by bleomycin. Moreover, we found no significant impact of BMP1 deficiency upon C-term propeptide of type I procollagen (CICP) production in the fibrotic mouse lungs. Based on these results, we propose that BMP1 is not required for lung fibrosis in mice and BMP1 may not be considered a candidate therapeutic target for IPF.

Abstract Gender captures social components beyond biological sex and can add valuable insight to health studies in populations. However, assessment of gender typically relies on questionnaires which may not be available. The aim of this study is to construct a gender metric using available variables in the UK Biobank and to apply it to the study of angina diagnosis. Proxy variables for femininity characteristics were identified in the UK Biobank and regressed on sex to construct a composite femininity score (FS) validated using tenfold cross-validation. The FS was assessed as a predictor of angina diagnosis before incident myocardial infarction (MI) events. The FS was derived for 315,937 UK Biobank participants. In 3059 individuals with no history of MI at study entry who had an incident MI event, the FS was a significant predictor of angina diagnosis prior to MI (OR 1.24, 95% CI 1.10–1.39, P

Abstract Severe COVID-19 is associated with a systemic hyperinflammatory response leading to acute respiratory distress syndrome (ARDS), multi-organ failure, and death. Galectin-3 is a ß-galactoside binding lectin known to drive neutrophil infiltration and the release of pro-inflammatory cytokines contributing to airway inflammation. Thus, we aimed to investigate the potential of galectin-3 as a biomarker of severe COVID-19 outcomes. We prospectively included 156 patients with RT-PCR confirmed COVID-19. A severe outcome was defined as the requirement of invasive mechanical ventilation (IMV) and/or in-hospital death. A non-severe outcome was defined as discharge without IMV requirement. We used receiver operating characteristic (ROC) and multivariable logistic regression analysis to determine the prognostic ability of serum galectin-3 for a severe outcome. Galectin-3 levels discriminated well between severe and non-severe outcomes and correlated with markers of COVID-19 severity, (CRP, NLR, D-dimer, and neutrophil count). Using a forward-stepwise logistic regression analysis we identified galectin-3 [odds ratio (OR) 3.68 (95% CI 1.47–9.20), p 50%, had significantly improved ability to predict severe outcomes [AUC 0.85 (95% CI 0.79–0.91, p

It has long been recognized that anatomic location is an important feature for defining distinct subtypes of plaque psoriasis. However, little is known about the molecular differences between scalp, palmoplantar, and conventional plaque psoriasis. To investigate the molecular heterogeneity of these psoriasis subtypes, we performed RNA-seq and flow cytometry on skin samples from individuals with scalp, palmoplantar, and conventional plaque psoriasis, along with samples from healthy control patients. We performed differential expression analysis and network analysis using weighted gene coexpression network analysis (WGCNA). Our analysis revealed a core set of 763 differentially expressed genes common to all sub-types of psoriasis. In contrast, we identified 605, 632, and 262 genes uniquely differentially expressed in conventional, scalp, and palmoplantar psoriasis, respectively. WGCNA and pathway analysis revealed biological processes for the core genes as well as subtype-specific genes. Flow cytometry analysis revealed a shared increase in the percentage of CD4+ T regulatory cells in all psoriasis subtypes relative to controls, whereas distinct psoriasis subtypes displayed differences in IL-17A, IFN-gamma, and IL-22 production. This work reveals the molecular heterogeneity of plaque psoriasis and identifies subtype-specific signaling pathways that will aid in the development of therapy that is appropriate for each subtype of plaque psoriasis.

Abstract Though Switzerland has one of the highest life expectancies in the world, this global indicator may mask significant disparities at a local level. The present study used a spatial cluster detection approach based on individual death records to investigate the geographical footprint of life expectancy inequalities in the state of Geneva, Switzerland. Individual-level mortality data (n = 22,751) were obtained from Geneva’s official death notices (2009–2016). We measured life expectancy inequalities using the years of potential life lost or gained (YPLLG) metric, defined as the difference between an individual’s age at death and their life expectancy at birth. We assessed the spatial dependence of YPLLG across the state of Geneva using spatial autocorrelation statistics (Local Moran’s I). To ensure the robustness of the patterns discovered, we ran the analyses for ten random subsets of 10,000 individuals taken from the 22,751 deceased. We also repeated the spatial analysis for YPLLG before and after controlling for individual-level and neighborhood-level covariates. The results showed that YPLLG was not randomly distributed across the state of Geneva. The ten random subsets revealed no significant difference with the geographic footprint of YPLLG and the population characteristics within Local Moran cluster types, suggesting robustness for the observed spatial structure. The proportion of women, the proportion of Swiss, the neighborhood median income, and the neighborhood median age were all significantly lower for populations in low YPLLG clusters when compared to populations in high YPLLG clusters. After controlling for individual-level and neighborhood-level covariates, we observed a reduction of 43% and 39% in the size of low and high YPLLG clusters, respectively. To our knowledge, this is the first study in Switzerland using spatial cluster detection methods to investigate inequalities in life expectancy at a local scale and based on individual data. We identified clear geographic footprints of YPLLG, which may support further investigations and guide future public health interventions at the local level.

Abstract Gene expression is the primary molecular phenotype and can be estimated in specific organs or tissues at particular times. Here we analyzed genome-wide inheritance of gene expression in fruits of chili pepper (Capsicum annuum L.) in reciprocal crosses between a domesticated and a wild accession, estimating this parameter during fruit development. We defined a general hierarchical schema to classify gene expression inheritance which can be employed for any quantitative trait. We found that inheritance of gene expression is affected by both, the time of fruit development as well as the direction of the cross, and propose that such variations could be common in many developmental processes. We conclude that classification of inheritance patterns is important to have a better understanding of the mechanisms underlying gene expression regulation, and demonstrate that sets of genes with specific inheritance pattern at particular times of fruit development are enriched in different biological processes, molecular functions and cell components. All curated data and functions for analysis and visualization are publicly available as an R package.

Abstract Bovine tuberculosis (bTB) is an important animal health and economic problem for the cattle industry and a potential zoonotic threat. Wild badgers (Meles meles) play a role on its epidemiology in some areas of high prevalence in cattle, particularly in the UK and Republic of Ireland and increasingly in parts of mainland Europe. However, little is known about the involvement of badgers in areas on the spatial edge of the cattle epidemic, where increasing prevalence in cattle is seen. Here we report the findings of a study of found-dead (mainly road-killed) badgers in six counties on the edge of the English epidemic of bTB in cattle. The overall prevalence of Mycobacterium tuberculosis complex (MTC) infection detected in the study area was 51/610 (8.3%, 95% CI 6.4–11%) with the county-level prevalence ranging from 15 to 4–5%. The MTC spoligotypes of recovered from badgers and cattle varied: in the northern part of the study area spoligotype SB0129 predominated in both cattle and badgers, but elsewhere there was a much wider range of spoligotypes found in badgers than in cattle, in which infection was mostly with the regional cattle spoligotype. The low prevalence of MTC in badgers in much of the study area, and, relative to in cattle, the lower density of sampling, make firm conclusions difficult to draw. However, with the exception of Cheshire (north-west of the study area), little evidence was found to link the expansion of the bTB epidemic in cattle in England to widespread badger infection.

Abstract Malaria is a highly prevalent parasitic disease in regions with tropical and subtropical climates worldwide. Among the species of Plasmodium causing human malaria, P. vivax is the second most prevalent and the most geographically widespread species. A major target of a pre-erythrocytic vaccine is the P. vivax circumsporozoite protein (PvCSP). In previous studies, we fused two recombinant proteins representing three allelic variants of PvCSP (VK210, VK247 and P. vivax-like) to the mumps virus nucleocapsid protein to enhance immune responses against PvCSP. The objective of the present study was to evaluate the protective efficacy of these recombinants in mice challenged with transgenic P. berghei parasites expressing PvCSP allelic variants. Formulations containing Poly (I:C) or Montanide ISA720 as adjuvants elicited high and long-lasting IgG antibody titers specific to each PvCSP allelic variant. Immunized mice were challenged with two existing chimeric P. berghei parasite lines expressing PvCSP-VK210 and PvCSP-VK247. We also developed a novel chimeric line expressing the third allelic variant, PvCSP-P. vivax-like, as a new murine immunization-challenge model. Our formulations conferred partial protection (significant delay in the time to reach 1% parasitemia) against challenge with the three chimeric parasites. Our results provide insights into the development of a vaccine targeting multiple strains of P. vivax.

Abstract RNA-Seq experiments allow genome-wide estimation of relative gene expression. Estimation of gene expression at different time points generates time expression profiles of phenomena of interest, as for example fruit development. However, such profiles can be complex to analyze and interpret. We developed a methodology that transforms original RNA-Seq data from time course experiments into standardized expression profiles, which can be easily interpreted and analyzed. To exemplify this methodology we used RNA-Seq data obtained from 12 accessions of chili pepper (Capsicum annuum L.) during fruit development. All relevant data, as well as functions to perform analyses and interpretations from this experiment, were gathered into a publicly available R package: “Salsa”. Here we explain the rational of the methodology and exemplify the use of the package to obtain valuable insights into the multidimensional time expression changes that occur during chili pepper fruit development. We hope that this tool will be of interest for researchers studying fruit development in chili pepper as well as in other angiosperms.

Abstract The optimal defence hypothesis predicts that increased plant defence capabilities, lower levels of damage, and lower investment in vegetative biomass will occur more frequently in sexual forms with higher resource-demanding tissue production and/or younger plant parts. We aimed to examine the effects of sexual form, cladode, and flower age on growth rate, herbivore damage, and 4-hydroxybenzoic acid (4-HBA), chlorogenic acid, and quercetin (QUE) concentrations in Opuntia robusta plants in central Mexico. Our findings demonstrated that hermaphrodite flowers showed faster growth and lesser damage than female flowers. The effect of cladode sexual forms on 4-HBA and QUE occurrence was consistent with the predictions of the optimal defence hypothesis. However, chlorogenic acid occurrences were not significantly affected by sexual forms. Old cladodes exhibited higher QUE and 4-HBA occurrences than young cladodes, and hermaphrodites exhibited higher 4-HBA concentrations than females. Resource allocation for reproduction and secondary metabolite production, and growth was higher and lower, respectively, in females, compared to hermaphrodites, indicating a trade-off between investment in reproduction, growth, and secondary metabolite production. Secondary metabolite concentrations in O. robusta plants were not negatively correlated with herbivore damage, and the two traits were not accurate predictors of plant reproductive output.

Abstract miRNAs are involved in the development of metabolic associated fatty liver disease (MAFLD) and nonalcoholic steatohepatitis (NASH). We aimed to evaluate modifications by prolonged-release pirfenidone (PR-PFD) on key hepatic miRNAs expression in a MAFLD/NASH model. First, male C57BL/6J mice were randomly assigned into groups and fed with conventional diet (CVD) or high fat and carbohydrate diet (HFD) for 16 weeks. At the end of the eighth week, HFD mice were divided in two and only one half was treated with 300 mg/kg/day of PR-PFD mixed with food. Hepatic expression of miRNAs and target genes that participate in inflammation and lipid metabolism was determined by qRT-PCR and transcriptome by microarrays. Increased hepatic expression of miR-21a-5p, miR-34a-5p, miR-122-5p and miR-103-3p in MAFLD/NASH animals was reduced with PR-PFD. Transcriptome analysis showed that 52 genes involved in lipid and collagen biosynthesis and inflammatory response were downregulated in PR-PFD group. The expression of Il1b, Tnfa, Il6, Tgfb1, Col1a1, and Srebf1 were decreased in PR-PFD treated animals. MAFLD/NASH animals compared to CVD group showed modifications in gene metabolic pathways implicated in lipid metabolic process, inflammatory response and insulin resistance; PR-PFD reversed these modifications.

Abstract We conducted a genome-wide association study of time to remission of COVID-19 symptoms in 1723 outpatients with at least one risk factor for disease severity from the COLCORONA clinical trial. We found a significant association at 5p13.3 (rs1173773; P = 4.94 × 10–8) near the natriuretic peptide receptor 3 gene (NPR3). By day 15 of the study, 44%, 54% and 59% of participants with 0, 1, or 2 copies of the effect allele respectively, had symptom remission. In 851 participants not treated with colchicine (placebo), there was a significant association at 9q33.1 (rs62575331; P = 2.95 × 10–8) in interaction with colchicine (P = 1.19 × 10–5) without impact on risk of hospitalisations, highlighting a possibly shared mechanistic pathway. By day 15 of the study, 46%, 62% and 64% of those with 0, 1, or 2 copies of the effect allele respectively, had symptom remission. The findings need to be replicated and could contribute to the biological understanding of COVID-19 symptom remission.

Abstract Mutations in the GBA1 gene encoding glucocerebrosidase (GCase) are linked to Gaucher (GD) and Parkinson’s Disease (PD). Since some GD and PD patients develop ocular phenotypes, we determined whether ocular phenotypes might result from impaired GCase activity and the corresponding accumulation of glucosylceramide (GluCer) and glucosylsphingosine (GluSph) in the Gba1 D409V/D409V knock-in (Gba KI/KI; “KI”) mouse. Gba KI mice developed age-dependent pupil dilation deficits to an anti-muscarinic agent; histologically, the iris covered the anterior part of the lens with adhesions between the iris and the anterior surface of the lens (posterior synechia). This may prevent pupil dilation in general, beyond an un-responsiveness of the iris to anti-muscarinics. Gba KI mice displayed atrophy and pigment dispersion of the iris, and occlusion of the iridocorneal angle by pigment-laden cells, reminiscent of secondary open angle glaucoma. Gba KI mice showed progressive thinning of the retina consistent with retinal degeneration. GluSph levels were increased in the anterior and posterior segments of the eye, suggesting that accumulation of lipids in the eye may contribute to degeneration in this compartment. We conclude that the Gba KI model provides robust and reproducible eye phenotypes which may be used to test for efficacy and establish biomarkers for GBA1-related therapies.

Abstract The larval stages of Carmenta theobromae Busck (1910) and Simplicivalva ampliophilobia Davis, Gentili-Poole and Mitter (2008) attack the subcortical zone and pith in guava trees, respectively, in the first productive nucleus of fruit trees in Colombia: Hoya del Río Suárez (HRS). The presence of pest insects has been reported in 98% of the farms sampled in HRS (n = 124), with up to 96 and 11 simultaneous larvae per tree, respectively. Although the aspects of the basic biology and life cycle of both pests have been resolved, there are no strategies for managing populations in the field. Therefore, the aim of this study was to evaluate different management alternatives under laboratory and field conditions in HRS. In laboratory conditions, a completely randomized design was used in two separate experiments, each with six treatments: T1: Spinosad (a mixture of Spinosad A and D); T2: S-1,2-di(ethoxycarbonyl) ethyl 0,0-dimethylphosphorodithioate (chemical control); T3: Lecanicillium lecanii; T4: Beauveria bassiana; T5: Mix of B. bassiana and B. brongniartii, and T6: distilled water (control). The number of dead larvae per replicate per treatment was evaluated (DL), with experimental units of five and three larvae, respectively. In the field, to the two best alternatives found for each pest in the laboratory, pruning and keeping the area around the plants free of weeds were added as cultural management, in two separate additional experiments, each with three larvae as experimental unit per treatment. For C. theobromae, the best laboratory alternatives were chemical control (DL: 3.78) and L. lecanii (DL: 2.33), followed without statistical differences by B. bassiana (DL: 1.67). In the field, the virulence of B. bassiana improved (DL: 3), and together with pruning and keeping the area around the plants clear of weeds (DL: 3), they stood out as the best alternatives. For S. ampliophilobia under laboratory conditions, the best alternatives were Spinosad (2.74) and chemical control (DL: 2.66), without significant difference. In the field, there were no statistical differences between the alternatives, except for the control. This statistical parity of cultural practices, and biological and chemical management is an argument in favor of the use of the former to the detriment of the third, especially when the harmful effects of the molecule S-1,2 di (ethoxycarbonyl) ethyl 0, 0-dimethyl phosphorodithioate have been proven in air, water and agricultural soils, in addition to its association with thyroid cancer in humans. This is a strong argument to favor the use of synergies of cultural and biological management methods framed in IPM, as opposed to the use of chemical agents whose harmful effects are strongly documented, and whose use is becoming increasingly prohibited.

Abstract Neonicotinoids are neurotoxic systemic insecticides applied extensively worldwide. The impacts of common neonicotinoids like imidacloprid on non-target invertebrate pollinators have been widely studied, however effects on vertebrate pollinators have received little attention. Here, we describe the first study evaluating the effects of short-term (3 d) exposure to a range of environmentally relevant concentrations ( $${0.2}\,\upmu \hbox {g g}^{-1}$$ 0.2 μ g g - 1 to $${2.5}\,\upmu \hbox {g g}^{-1}\cdot$$ 2.5 μ g g - 1 · Body Weight) of imidacloprid on wild-caught ruby-throated hummingbirds. Within 2 h of exposure, hummingbirds exhibited a significant depression in energy expenditure (up to $$25\% \pm 11\%$$ 25 % ± 11 % ). We did not observe significant effects on foraging behaviour measured in the subsequent 2 h to 4 h, although the effect size estimate was large (0.29). We also analyzed tissues collected 24 h after the final dose and did not observe significant effects on immune response or cholinesterase activity, although this may be related to our small sample size. We determined that hummingbirds excrete imidacloprid quickly (elimination half-life of $$2.1\hbox { h} \pm 0.1\hbox { h}$$ 2.1 h ± 0.1 h ) relative to other bird species. Hummingbirds have high energetic demands and store relatively little energy, especially during migration and breeding seasons. Therefore, changes in their metabolism following exposures to imidacloprid observed herein could bear important survivorship consequences for hummingbirds.

Abstract Candidatus Liberibacter asiaticus (CLas), a bacterium transmitted by the Asian citrus psyllid, Diaphorina citri, is the causal agent of citrus greening disease, or Huanglongbng (HLB). Currently, vector population suppression with insecticides and tree removal are the most effective strategies for managing the HLB pathosystem. In this study, we assessed the bactericidal capabilities of 2′-deoxy-2′-fluoro-d-arabinonucleic acid antisense oligonucleotides (FANA ASO) both in vitro and in vivo by (1) confirming their capacity to penetrate insect cells, (2) silencing bacterial essential genes, and (3) quantifying reductions in bacterial titer and D. citri transmission. We confirmed that FANA ASO are able to penetrate insect cells without the use of a delivery agent. Expression of an essential gene in the D. citri endosymbiont, Wolbachia (wDi), significantly decreased by 30% following incubation with a wDi-specific FANA ASO. Viability of isolated wDi cells also decreased in response to the FANA ASO treatment. Delivery of a CLas-specific FANA ASO to infected adult D. citri in feeding assays resulted in significant silencing of a CLas essential gene. CLas relative density and transmission were significantly lower among D. citri fed FANA ASO in diet compared to untreated insects. Root infusions of a CLas-specific FANA ASO into infected Citrus trees significantly reduced CLas titer during a 30-day trial. Our results suggest that FANA ASO targeting insect-transmitted plant bacteria or insect endosymbionts may be useful tool for integrated management of agricultural pathogens.

Abstract Inherited retinal diseases (IRDs), defined by dysfunction or progressive loss of photoreceptors, are disorders characterized by elevated heterogeneity, both at the clinical and genetic levels. Our main goal was to address the genetic landscape of IRD in the largest cohort of Spanish patients reported to date. A retrospective hospital-based cross-sectional study was carried out on 6089 IRD affected individuals (from 4403 unrelated families), referred for genetic testing from all the Spanish autonomous communities. Clinical, demographic and familiar data were collected from each patient, including family pedigree, age of appearance of visual symptoms, presence of any systemic findings and geographical origin. Genetic studies were performed to the 3951 families with available DNA using different molecular techniques. Overall, 53.2% (2100/3951) of the studied families were genetically characterized, and 1549 different likely causative variants in 142 genes were identified. The most common phenotype encountered is retinitis pigmentosa (RP) (55.6% of families, 2447/4403). The most recurrently mutated genes were PRPH2, ABCA4 and RS1 in autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL) NON-RP cases, respectively; RHO, USH2A and RPGR in AD, AR and XL for non-syndromic RP; and USH2A and MYO7A in syndromic IRD. Pathogenic variants c.3386G > T (p.Arg1129Leu) in ABCA4 and c.2276G > T (p.Cys759Phe) in USH2A were the most frequent variants identified. Our study provides the general landscape for IRD in Spain, reporting the largest cohort ever presented. Our results have important implications for genetic diagnosis, counselling and new therapeutic strategies to both the Spanish population and other related populations.

Abstract Chemotherapy for high-grade astrocytic tumors is mainly based on the use of temozolomide (TMZ), whose efficacy is limited by resistance mechanisms. Despite many investigations pointing to O6-methylguanine-DNA-methyltransferase (MGMT) as being responsible for tumor chemo-resistance, its expression does not predict an accurate response in most gliomas, suggesting that MGMT is not the only determinant of response to treatment. In this sense, several reports indicate that N-methylpurine-DNA-glycosylase (MPG) may be involved in that resistance. With that in mind, we evaluated for the first time the degree of resistance to TMZ treatment in 18 patient-derived glioma cells and its association with MGMT and MPG mRNA levels. Viability cell assays showed that TMZ treatment hardly caused growth inhibition in the patient-derived cells, even in high concentrations, indicating that all primary cultures were chemo-resistant. mRNA expression analyses showed that the TMZ-resistant phenotype displayed by cells is associated with an elevated expression of MPG to a greater extent than it is with transcript levels of MGMT. Our findings suggest that not only is MGMT implicated in resistance to TMZ but MPG, the first enzyme in base excision repair processing, is also involved, supporting its potential role as a target in anti-resistance chemotherapy for astrocytoma and glioblastoma.

Germanium is an extremely important material used for numerous functional applications in many fields of nanotechnology. In this paper, we study the crystallization of amorphous Ge using atomistic simulations of critical nano-metric nuclei at high temperatures. We find that crystallization occurs by the recurrent transfer of atoms via a diffusive process from the amorphous phase into suitably-oriented crystalline layers. We accompany our simulations with a comprehensive thermodynamic and kinetic analysis of the growth process, which explains the energy balance and the interfacial growth velocities governing grain growth. For the 〈111〉 crystallographic orientation, we find a degenerate atomic rearrangement process, with two zero-energy modes corresponding to a perfect crystalline structure and the formation of a Σ3 twin boundary. Continued growth in this direction results in the development a twin network, in contrast with all other growth orientations, where the crystal grows defect-free. This particular mechanism of crystallization from amorphous phases is also observed during solid-phase epitaxial growth of 〈111〉 semiconductor crystals, where growth is restrained to one dimension. We calculate the equivalent X-ray diffraction pattern of the obtained nanotwin networks, providing grounds for experimental validation.

Abstract Mitochondria are organelles that perform major roles in cellular operation. Thus, alterations in mitochondrial genome (mtGenome) may lead to mitochondrial dysfunction and cellular deregulation, influencing carcinogenesis. Gastric cancer (GC) is one of the most incident and mortal types of cancer in Brazil, particularly in the Amazon region. Here, we sequenced and compared the whole mtGenome extracted from FFPE tissue samples of GC patients (tumor and internal control – IC) and cancer-free individuals (external control – EC) from this region. We found 3-fold more variants and up to 9-fold more heteroplasmic regions in tumor when compared to paired IC samples. Moreover, tumor presented more heteroplasmic variants when compared to EC, while IC and EC showed no significant difference when compared to each other. Tumor also presented substantially more variants in the following regions: MT-RNR1, MT-ND5, MT-ND4, MT-ND2, MT-DLOOP1 and MT-CO1. In addition, our haplogroup results indicate an association of Native American ancestry (particularly haplogroup C) to gastric cancer development. To the best of our knowledge, this is the first study to sequence the whole mtGenome from FFPE samples and to apply mtGenome analysis in association to GC in Brazil.

Abstract Aedes aegypti is the primary urban mosquito vector of viruses causing dengue, Zika and chikungunya fevers –for which vaccines and effective pharmaceuticals are still lacking. Current strategies to suppress arbovirus outbreaks include removal of larval-breeding sites and insecticide treatment of larval and adult populations. Insecticidal control of Ae. aegypti is challenging, due to a recent rapid global increase in knockdown-resistance (kdr) to pyrethroid insecticides. Widespread, heavy use of pyrethroid space-sprays has created an immense selection pressure for kdr, which is primarily under the control of the voltage-gated sodium channel gene (vgsc). To date, eleven replacements in vgsc have been discovered, published and shown to be associated with pyrethroid resistance to varying degrees. In Mexico, F1,534C and V1,016I have co-evolved in the last 16 years across Ae. aegypti populations. Recently, a novel replacement V410L was identified in Brazil and its effect on vgsc was confirmed by electrophysiology. Herein, we screened V410L in 25 Ae. aegypti historical collections from Mexico, the first heterozygote appeared in 2002 and frequencies have increased in the last 16 years alongside V1,016I and F1,534C. Knowledge of the specific vgsc replacements and their interaction to confer resistance is essential to predict and to develop strategies for resistance management.

Abstract Graphene, carbon nanotubes, and fullerenes are nanomaterials with outstanding properties such as electrical, thermal, mechanical strength, flexibility, and high surface area. These nanomaterials are used as building blocks for the construction of novel and astonishing 3D-dimensional networks. In the present work, nitrogen-doped carbon belt (N-CB) structures containing wrinkled carbon fibres as building blocks were synthesized under unstable conditions in a chemical vapour deposition experiment. N-CB structures with 0.2–3.0 microns of wide and 350 nm thick were assembled from complex individual wrinkled carbon fibres grown on Co/Cu films. These complex structures have a tubular appearance, showing holed and wrinkled graphite layers. Sulphur and copper atoms drastically affect the catalytic role of cobalt, changing the conventional growth of carbon nanotubes. Chemical functional groups, N-doping, and carbons hybridizations involved in the winkled carbon fibres are investigated. These findings provides a novel material that can be used as an excellent oxygen-reduction reaction catalyst or nano-electronics component.