Miracle-dz/UniFAR-FTUs huggingface dataset:
Is the Prevalence of Leishmania infantum Linked to Breeds in Dogs? Characterization of Seropositive Dogs in Ibiza

Simple Summary Leishmaniosis is an important zoonotic protozoan disease. Leishmania infantum is a protozoan species that accounts for the majority of cases in the Mediterranean. In this study, we analyzed the prevalence of infection in different dog breeds from Ibizan Island. Our results showed that the Doberman Pinscher and Boxer breeds present a higher prevalence of infection, and the relationship between antibodies’ serum titer and staging of disease was confirmed. Differences between age and sex were not found. Abstract Leishmaniosis is an important zoonotic protozoan disease primarily spread to the Mediterranean region by Leishmania infantum, the predominant protozoan species, which accounts for the majority of cases. Development of disease depends on the immune response of the definitive host and, predictably, their genetic background. Recent studies have revealed breed-typical haplotypes that are susceptible to the spread of the protozoan parasite. The objective of this study was to analyze the prevalence of leishmaniosis on a Mediterranean island and determine the relationship between disease prevalence and breed. In addition, information on seropositive animals was recorded to characterize animals affected by the disease. To study the prevalence, a total of 3141 dogs were analyzed. Of these, the 149 infected animals were examined for age, sex, antibody titer, and disease stage. We observed a prevalence of 4.74%, which varied between breeds (p < 0.05). The Doberman Pinscher and Boxer breeds had the highest prevalence of leishmaniosis. Significant differences were observed between breeds with common ancestors, emphasizing the important genetic component. Finally, regarding the characterization of seropositive animals, the distribution is similar to other studies. We discovered a relationship (p < 0.05) between the number of antibody titers and the clinical disease stage, which was also present in Leishmania infantum, suggesting that the development of the disease depends on the humoral or Th2 immune response with ineffective antibodies.
Age and Sex Modulate SARS-CoV-2 Viral Load Kinetics: A Longitudinal Analysis of 1735 Subjects

The COVID-19 pandemic caused by SARS-CoV-2 represents a public health emergency, which became even more challenging since the detection of highly transmissible variants and strategies against COVID-19 were indistinctly established. We characterized the temporal viral load kinetics in individuals infected by original and variant strains. Naso-oropharyngeal swabs from 33,000 individuals (admitted to the IRCCS Santa Lucia Foundation Drive-in, healthcare professionals and hospitalized patients who underwent routinary screening) from November 2020 to June 2021 were analyzed. Of them, 1735 subjects were selected and grouped according to the viral strain. Diagnostic analyses were performed by CE-IVD RT-PCR-based kits. The subgenomic-RNA component was assessed in 36 subjects using digital PCR. Infection duration, viral load decay speed, effects of age and sex were assessed and compared by extensive statistical analyses. Overall, infection duration and viral load differed between the groups (p < 0.05). Male sex was more present among both original and variant carriers affected with high viral load and showing fast decay speed, whereas original strain carriers with slow decay speed resulted in older (p < 0.05). Subgenomic-RNA was detected in the positive samples, including those with low viral load. This study provides a picture of the viral load kinetics, identifying individuals with similar patterns and showing differential effects of age and sex, thus providing potentially useful information for personalized management of infected subjects.
Learn to Train: Improving Training Data for a Neural Network to Detect Pecking Injuries in Turkeys

Simple Summary Injurious pecking against conspecifics in turkey husbandry is a widespread, serious problem for animal welfare. Evidence suggests that bloody injuries act as a trigger mechanism to induce pecking. Thus, continuous monitoring of the herd should be ensured to allow timely intervention in this type of behavior. The aim of the present study was therefore to develop a camera-based warning system using a neural network to detect injuries in the flock. The data for the network were provided by images on which human observers marked existing pecking injuries. Then, a network was trained with these human-labeled images in order to learn to detect pecking injuries on other unknown images from the same domain. As the initial agreement on the injuries detected by human observers and the trained network was unacceptable, various work steps were initiated to improve the data that were used to train the network. Finally, the aim of this process was for the network to achieve at least a similar ability to mark injuries in the images as a trained human observer. Abstract This study aimed to develop a camera-based system using artificial intelligence for automated detection of pecking injuries in turkeys. Videos were recorded and split into individual images for further processing. Using specifically developed software, the injuries visible on these images were marked by humans, and a neural network was trained with these annotations. Due to unacceptable agreement between the annotations of humans and the network, several work steps were initiated to improve the training data. First, a costly work step was used to create high-quality annotations (HQA) for which multiple observers evaluated already annotated injuries. Therefore, each labeled detection had to be validated by three observers before it was saved as “finished”, and for each image, all detections had to be verified three times. Then, a network was trained with these HQA to assist observers in annotating more data. Finally, the benefit of the work step generating HQA was tested, and it was shown that the value of the agreement between the annotations of humans and the network could be doubled. Although the system is not yet capable of ensuring adequate detection of pecking injuries, the study demonstrated the importance of such validation steps in order to obtain good training data.
Targeted Nanoparticle Photodynamic Diagnosis and Therapy of Colorectal Cancer

Colorectal cancer (CRC) is an aggressive cancer that remains a challenge to diagnose and treat. Photodynamic diagnosis (PDD) and therapy (PDT) are novel alternative techniques, which can enhance early diagnosis, as well as elicit tumor cell death. This is accomplished through photosensitizer (PS) mediated fluorescence and cytotoxic reactive oxygen species activation upon laser light irradiation excitation at specific low and high range wavelengths, respectively. However, the lack of PS target tumor tissue specificity often hampers these techniques. This study successfully fabricated a bioactive nanoconjugate, ZnPcS4-AuNP-S-PEG5000-NH2-Anti-GCC mAb (BNC), based upon a polyethylene glycol-gold nanoparticle, which was multi-functionalized with a fluorescent PDT metalated zinc phthalocyanine PS, and specific anti-GCC targeting antibodies, to overcome CRC PDD and PDT challenges. The BNC was found to be stable and showed selectively improved subcellular accumulation within targeted CRC for improved PDD and PDT outcomes in comparison to healthy in vitro cultured cells. Additionally, the BNC reported significantly higher late apoptotic PDT-induced CRC cell death rates (34% ***) when compared to PDT PS administration alone (15% *). These results indicated that the improved PDD and PDT outcomes were due to the specific PS accumulation in CRC cells through nanoparticle carriage and bioactive anti-GCC targeting.
Epigenetic Mechanisms Underlying COVID-19 Pathogenesis

In 2019, a novel severe acute respiratory syndrome called coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was reported and was declared a pandemic by the World Health Organization (WHO) in March 2020. With the advancing development of COVID-19 vaccines and their administration globally, it is expected that COVID-19 will converge in the future; however, the situation remains unpredictable because of a series of reports regarding SARS-CoV-2 variants. Currently, there are still few specific effective treatments for COVID-19, as many unanswered questions remain regarding the pathogenic mechanism of COVID-19. Continued elucidation of COVID-19 pathogenic mechanisms is a matter of global importance. In this regard, recent reports have suggested that epigenetics plays an important role; for instance, the expression of angiotensin I converting enzyme 2 (ACE2) receptor, an important factor in human infection with SARS-CoV-2, is epigenetically regulated; further, DNA methylation status is reported to be unique to patients with COVID-19. In this review, we focus on epigenetic mechanisms to provide a new molecular framework for elucidating the pathogenesis of SARS-CoV-2 infection in humans and of COVID-19, along with the possibility of new diagnostic and therapeutic strategies.
Population Diversity and Genetic Structure Reveal Patterns of Host Association and Anthropogenic Impact for the Globally Important Fungal Tree Pathogen Ceratocystis manginecans

Species in the Ceratocystis manginecans complex are important fungal pathogens of plantation trees globally. The most important hosts include species of Eucalyptus, Acacia, Mangifera, and Punica. Despite their relevance and widespread occurrence, little is known regarding their population genetics and how this might relate to their host associations or geographic regions in which they occur. A global collection of 491 isolates representing the C. manginecans complex, from four different plant hosts and nine countries, were genotyped using microsatellite markers. Population genetic analyses using numerous tools were conducted to interrogate how their genetic diversity and structure might be affected by host or areas of occurrence. Results of genetic diversity studies showed that when grouping isolates into populations based on their host associations, the population on Eucalyptus was most diverse, and it also has a broad global distribution. When considering countries of origin as a basis for defining populations, the gene and genotypic diversity were highest in populations from China, Indonesia, and Brazil. In contrast, populations from Oman and Pakistan collected from Mangifera had the lowest genetic diversity and were clonal. Molecular variance, population differentiation, and network and structure analyses showed that the genetic structure of isolates in the C. manginecans complex is influenced by both host association as well as geographical isolation. Furthermore, the results reflected the movement of genotypes between plant hosts and geographic regions that have implications regarding the broad global distribution of this pathogen.
Disease-Related Malnutrition and Sarcopenia Predict Worse Outcome in Medical Inpatients: A Cohort Study

(1) Background: Both sarcopenia and disease-related malnutrition (DRM) are unfortunately underdiagnosed and undertreated in our Western hospitals, which could lead to worse clinical outcomes. Our objectives included to determine the impact of low muscle mass (MM) and strength, and also DRM and sarcopenia, on clinical outcomes (length of stay, death, readmissions at three months, and quality of life). (2) Methodology: Prospective cohort study in medical inpatients. On admission, MM and hand grip strength (HGS) were assessed. The Global Leadership Initiative on Malnutrition (GLIM) criteria were used to diagnose DRM and EWGSOP2 for sarcopenia. Assessment was repeated after one week and at discharge. Quality of life (EuroQoL-5D), length of stay (LoS), readmissions and mortality are reported. (3) Results: Two hundred medical inpatients, median 76.0 years-old and 68% with high comorbidity. 27.5% met GLIM criteria and 33% sarcopenia on admission, increasing to 38.1% and 52.3% on discharge. Both DRM and sarcopenia were associated with worse QoL. 6.5% died and 32% readmission in 3 months. The odds ratio (OR) of mortality for DRM was 4.36 and for sarcopenia 8.16. Readmissions were significantly associated with sarcopenia (OR = 2.25) but not with DRM. A higher HGS, but not MM, was related to better QoL, less readmissions (OR = 0.947) and lower mortality (OR = 0.848) after adjusting for age, sex, and comorbidity. (4) Conclusions: In medical inpatients, mostly polymorbid, both DRM but specially sarcopenia are associated with poorer quality of life, more readmissions, and higher mortality. Low HGS proved to be a stronger predictor of worse outcomes than MM.
Effects of Betaine-Biotin-Chromium Supplementation and Concentrate to Roughage Ratio on Nutrient Utilization Efficiency in Thai Native Cattle

Simple Summary Feed additives are attracting considerable interest due to the need to effectively improve the level of production, efficiency, and health of animals. A combination of betaine, biotin, and chromium has been developed to enhance nutrient utilization efficiency. Ideally, the addition of a combination of supplements to livestock feed could improve ruminal fermentation, digestibility and nutrient utilization, nitrogen and energy balance, and metabolism. Abstract The objective of this study was to evaluate the effects of supplementation with a feed additive containing a combination of betaine, biotin, and chromium (BBC) and concentrate-to-roughage ratio (C:R ratio) on nutrient digestibility, blood metabolites, ruminal fermentation, nitrogen balance, and energy utilization in Thai native beef cattle. Five Thai feedlot native beef bulls at one year old of age and 87.6 ± 15.7 kg of body weight were assigned in a (2 × 2) + 1 augmented factorial experiment according to a 5 × 5 Latin square design with five periods of 21 days. The two levels of BBC were 3 g/kg DM and 6 g/kg DM, and the two ratios of C:R were 60C:40R and 70C:30R. A C:R ratio of 70C:30R without BBC supplementation was used as a negative control. The cattle were offered feed at 3% BW, which provides sufficient energy and protein to support a weight gain of 500 g/day. The results showed that dry matter intake (DMI) and organic matter intake (OMI) were not different (p > 0.05), but the intake of crude protein (CP) and ether extract (EE) was higher (p < 0.05), whereas neutral detergent fiber (NDF) and acid detergent fiber (ADF) were lower (p < 0.05) in the 70C:30R ratio diets compared to the 60:40R ratio diets. Energy balance and nitrogen balance were not influenced (p > 0.05) by the C:R ratio or the addition of BBC. Rumen pH and ammonia-nitrogen (NH3-N) did not differ (p > 0.05) among treatments groups. Total volatile fatty acid (VFA) production was higher (p < 0.05) in bulls fed with the 70C:30R ratio diet. The addition of BBC resulted in a lower (p < 0.01) glucose-to-insulin ratio compared to cattle fed with the control diet. Energy and protein utilization efficiency did not differ (p > 0.05) among the experimental treatment groups, which were higher (p > 0.05) than the control group. In conclusion, BBC supplementation showed greater growth performance of cattle compared to the control. BBC supplementation appeared to improve glucose uptake and insulin sensitivity and energy and protein utilization efficiency. Whether BBC supplementation increases glucose production in the liver remains to be determined in future studies.
Anchoring the CerEla1.0 Genome Assembly to Red Deer (Cervus elaphus) and Cattle (Bos taurus) Chromosomes and Specification of Evolutionary Chromosome Rearrangements in Cervidae

Simple Summary The red deer (Cervus elaphus) de novo genome assembly (CerEla1.0) has provided a great resource for genetic studies in various deer species. In this study, we used gene order comparisons between C. elaphus CerEla1.0 and B. taurus ARS-UCD1.2 genome assemblies and fluorescence in situ hybridization (FISH) with bovine BAC probes to verify the red deer-bovine chromosome relationships and anchor the CerEla1.0 C-scaffolds to karyotypes of both species. We showed the homology between bovine and deer chromosomes and determined the centromere-telomere orientation of the CerEla1.0 C-scaffolds. Using a set of BAC probes, we were able to narrow the positions of evolutionary chromosome breakpoints defining the family Cervidae. In addition, we revealed several errors in the current CerEla1.0 genome assembly. Finally, we expanded our analysis to other Cervidae and confirmed the locations of the cervid evolutionary fissions and orientation of the fused chromosomes in eight cervid species. Our results can serve as a basis for necessary improvements of the red deer genome assembly and provide support to other genetic studies in Cervidae. Abstract The family Cervidae groups a range of species with an increasing economic significance. Their karyotypes share 35 evolutionary conserved chromosomal segments with cattle (Bos taurus). Recent publication of the annotated red deer (Cervus elaphus) whole genome assembly (CerEla1.0) has provided a basis for advanced genetic studies. In this study, we compared the red deer CerEla1.0 and bovine ARS-UCD1.2 genome assembly and used fluorescence in situ hybridization with bovine BAC probes to verify the homology between bovine and deer chromosomes, determined the centromere-telomere orientation of the CerEla1.0 C-scaffolds and specified positions of the cervid evolutionary chromosome breakpoints. In addition, we revealed several incongruences between the current deer and bovine genome assemblies that were shown to be caused by errors in the CerEla1.0 assembly. Finally, we verified the centromere-to-centromere orientation of evolutionarily fused chromosomes in seven additional deer species, giving a support to previous studies on their chromosome evolution.
Antimalarial Inhibitors Targeting Epigenetics or Mitochondria in Plasmodium falciparum: Recent Survey upon Synthesis and Biological Evaluation of Potential Drugs against Malaria

Despite many efforts, malaria remains among the most problematic infectious diseases worldwide, mainly due to the development of drug resistance by P. falciparum. Over the past decade, new essential pathways have been emerged to fight against malaria. Among them, epigenetic processes and mitochondrial metabolism appear to be important targets. This review will focus on recent evolutions concerning worldwide efforts to conceive, synthesize and evaluate new drug candidates interfering selectively and efficiently with these two targets and pathways. The focus will be on compounds/scaffolds that possess biological/pharmacophoric properties on DNA methyltransferases and HDAC’s for epigenetics, and on cytochrome bc1 and dihydroorotate dehydrogenase for mitochondrion.
Specificity and Redundancy of Profilin 1 and 2 Function in Brain Development and Neuronal Structure

Profilin functions have been discussed in numerous cellular processes, including actin polymerization. One puzzling aspect is the concomitant expression of more than one profilin isoform in most tissues. In neuronal precursors and in neurons, profilin 1 and profilin 2 are co-expressed, but their specific and redundant functions in brain morphogenesis are still unclear. Using a conditional knockout mouse model to inactivate both profilins in the developing CNS, we found that threshold levels of profilin are necessary for the maintenance of the neuronal stem-cell compartment and the generation of the differentiated neurons, irrespective of the specific isoform. During embryonic development, profilin 1 is more abundant than profilin 2; consequently, modulation of profilin 1 levels resulted in a more severe phenotype than depletion of profilin 2. Interestingly, the relevance of the isoforms was reversed in the postnatal brain. Morphology of mature neurons showed a stronger dependence on profilin 2, since this is the predominant isoform in neurons. Our data highlight redundant functions of profilins in neuronal precursor expansion and differentiation, as well as in the maintenance of pyramidal neuron dendritic arborization. The specific profilin isoform is less relevant; however, a threshold profilin level is essential. We propose that the common activity of profilin 1 and profilin 2 in actin dynamics is responsible for the observed compensatory effects.
In Vitro Cell Interactions on PVDF Films: Effects of Surface Morphology and Polar Phase Transition

In recent years, several studies have validated the use of piezoelectric materials for in situ biological stimulation, opening new interesting insights for bio-electric therapies. In this work, we investigate the morphological properties of polyvinylidene fluoride (PVDF) in the form of microstructured films after temperature-driven phase transition. The work aims to investigate the correlations between morphology at micrometric (i.e., spherulite size) and sub-micrometric (i.e., phase crystallinity) scale and in vitro cell response to validate their use as bio-functional interfaces for cellular studies. Morphological analyses (SEM, AFM) enabled evidence of the peculiar spherulite-like structure and the dependence of surface properties (i.e., intra-/interdomain roughness) upon process conditions (i.e., temperature). Meanwhile, chemical (i.e., FTIR) and thermal (i.e., DSC) analyses highlighted an influence of casting temperature and polymer solution on apolar to polar phases transition, thus affecting in vitro cell response. Accordingly, in vitro tests confirmed the relationship between micro/sub-microstructural properties and hMSC response in terms of adhesion and viability, thus suggesting a promising use of PVDF films to model, in perspective, in vitro functionalities of cells under electrical stimuli upon mechanical solicitation.
Association between Visceral Adiposity Index, Binge Eating Behavior, and Grey Matter Density in Caudal Anterior Cingulate Cortex in Severe Obesity

Visceral adipose tissue accumulation is an important determinant of metabolic risk and can be estimated by the visceral adiposity index (VAI). Visceral adiposity may impact brain regions involved in eating behavior. We aimed to examine the association between adiposity measurements, binge eating behavior, and grey matter density. In 20 men and 59 women with severe obesity, Grey matter density was measured by voxel-based morphometry for six regions of interest associated with reward, emotion, or self-regulation: insula, orbitofrontal cortex, caudal and rostral anterior cingulate cortex (ACC), ventromedial prefrontal cortex (vmPFC), and dorsolateral prefrontal cortex (DLPFC). Binge eating behavior, depression and impulsivity was assessed by the Binge Eating Scale, Beck Depression Inventory and UPPS Impulsive Behavior Scale, respectively. Men and women were distinctively divided into two subgroups (low-VAI and high-VAI) based on the mean VAI score. Women with high-VAI were characterized by metabolic alterations, higher binge eating score and lower grey matter density in the caudal ACC compared to women with low-VAI. Men with high-VAI were characterized by a higher score for the sensation-seeking subscale of the UPPS–Impulsive Behavior Scale compared to men with low-VAI. Using a moderation–mediation analysis, we found that grey matter density in the caudal ACC mediates the association between VAI and binge eating score. In conclusion, visceral adiposity is associated with higher binge eating severity in women. Decreased grey matter density in the caudal ACC, a region involved in cognition and emotion regulation, may influence this relationship.