Circadian Transcriptome Oscillations In Human Adipose Tissue Depend On Napping Status And Link To Metabolic And Inflammatory Pathways.

STUDY OBJECTIVES: Napping is a common habit in many countries. Nevertheless, studies about the chronic effects of napping on obesity are contradictory, and the molecular link between napping and metabolic alterations has yet to be studied. We aim to identify molecular mechanisms in adipose tissue (AT) that may connect napping and abdominal obesity. METHODS: In this cross-sectional study, we extracted the RNA repeatedly across 24h from cultured AT explants and performed RNA sequencing. Circadian rhythms were analyzed using 6 consecutive time points across 24 hours. We also assessed global gene expression in each group (nappers vs. non-nappers). RESULTS: With napping, there was a loss of rhythmicity in 88% of genes that showed circadian rhythmicity among non-nappers, a reduction in rhythm amplitudes of 29%, and significant phase changes from a coherent unimodal acrophase in non-nappers, towards a scattered and bimodal acrophase in nappers. Those genes that lost rhythmicity with napping were mainly involved in pathways of glucose and lipid metabolism, and of the circadian clock. Additionally, we found differential global gene expression between nappers and non-nappers with 34 genes down- and 32 genes up-regulated in nappers. The top up-regulated gene (IER3) and top down-regulated pseudogene (VDAC2P2) in nappers have been previously shown to be involved in inflammation. CONCLUSION: These new findings may have implications for our understanding of napping's effects on obesity and metabolic disorders.

Ultrasound Therapy With High-Pressure Pulses Is Effective to Reduce the Effects of Collagenase-Induced Tendinopathy in Rat's Achilles Tendon.

OBJECTIVE: We propose an ultrasonic treatment for collagenase-induced tendinopathy in rat's Achilles tendon using pulses with a low number of cycles, high acoustic pressure and very low duty cycle. METHODS: Twenty rats were used to perform the experiment. Four experimental groups of calcaneal tendons were studied: control (n = 6), sham (n = 4), collagenase-induced tendinopathy (n = 8) and ultrasound-treated collagenase-induced tendinopathy (n = 8). Surgical intervention was performed to expose the tendons prior to collagenase injection. A 1 MHz ultrasonic tansducer with a focusing lens was used. Ultrasonic treatments were used with an average total treatment time of 2.5 min, 20-cycle pulses, pressure amplitude p = 7 MPa, and 0.02% duty cycle. Histopathology of the samples was performed to evaluate nuclear density, acute inflammation, and signs of neovascularization. Collagen (types I and III), elastic fibers, and glycosaminoglycans were also analyzed. RESULTS: No tendon involvement was found by the surgical process. Ultrasonic treatment is safe, as it does not affect healthy tendons. When collagenase infiltrated animals were treated with US, a clear predominance of type I collagen fibers and a similar collagen ratio profile to that observed in the control and sham groups was observed, with a higher density of elastic fibers compared to the control and sham groups and a significant increase in the density of glycosaminoglycans. CONCLUSION: The ultrasound treatment proposed reduces the effects of the artificial collagenase lesion to reach the basal level after 45 d.

Melatonin decreases human adipose tissue insulin sensitivity.

Melatonin is a pineal hormone that modulates the circadian system and exerts soporific and phase-shifting effects. It is also involved in many other physiological processes, such as those implicated in cardiovascular, endocrine, immune, and metabolic functions. However, the role of melatonin in glucose metabolism remains contradictory, and its action on human adipose tissue (AT) explants has not been demonstrated. We aimed to assess whether melatonin (a pharmacological dose) influences insulin sensitivity in human AT. This will help better understand melatonin administration's effect on glucose metabolism. Abdominal AT (subcutaneous and visceral) biopsies were obtained from 19 participants with severe obesity (age: 42.84 ± 12.48 years; body mass index: 43.14 ± 8.26 kg/m2) who underwent a laparoscopic gastric bypass. AT biopsies were exposed to four different treatments: control (C), insulin alone (I) (10 nM), melatonin alone (M) (5000 pg/mL), and insulin plus melatonin combined (I + M). All four conditions were repeated in both subcutaneous and visceral AT, and all were performed in the morning at 8 a.m. (n = 19) and the evening at 8 p.m. (in a subsample of n = 12). We used western blot analysis to determine insulin signaling (using the pAKT/tAKT ratio). Furthermore, RNAseq analyses were performed to better understand the metabolic pathways involved in the effect of melatonin on insulin signaling. As expected, insulin treatment (I) increased the pAKT/tAKT ratio compared with control (p < .0001). Furthermore, the addition of melatonin (I + M) resulted in a decrease in insulin signaling as compared with insulin alone (I); this effect was significant only during the evening time (not in the morning time). Further, RNAseq analyses in visceral AT during the evening condition (at 8 p.m.) showed that melatonin resulted in a prompt transcriptome response (around 1 h after melatonin addition), particularly by downregulating the insulin signaling pathway. Our results show that melatonin reduces insulin sensitivity in human AT during the evening. These results may partly explain the previous studies showing a decrease in glucose tolerance after oral melatonin administration in the evening or when eating late when endogenous melatonin is present.

Salivary biomarkers as pioneering indicators for diagnosis and severity stratification of pediatric long COVID.

Introduction: Long COVID, or post-acute sequelae of SARS-CoV-2 infection (PASC), manifests as persistent and often debilitating symptoms enduring well beyond the initial COVID-19 infection. This disease is especially worrying in children since it can seriously alter their development. Presently, a specific diagnostic test or definitive biomarker set for confirming long COVID is lacking, relying instead on the protracted presence of symptoms post-acute infection. Methods: We measured the levels of 13 biomarkers in 105 saliva samples (49 from children with long COVID and 56 controls), and the Pearson correlation coefficient was used to analyse the correlations between the levels of the different salivary biomarkers. Multivariate logistic regression analyses were performed to determine which of the 13 analysed salivary biomarkers were useful to discriminate between children with long COVID and controls, as well as between children with mild and severe long COVID symptoms. Results: Pediatric long COVID exhibited increased oxidant biomarkers and decreased antioxidant, immune response, and stress-related biomarkers. Correlation analyses unveiled distinct patterns between biomarkers in long COVID and controls. Notably, a multivariate logistic regression pinpointed TOS, ADA2, total proteins, and AOPP as pivotal variables, culminating in a remarkably accurate predictive model distinguishing long COVID from controls. Furthermore, total proteins and ADA1 were instrumental in discerning between mild and severe long COVID symptoms. Discussion: This research sheds light on the potential clinical utility of salivary biomarkers in diagnosing and categorizing the severity of pediatric long COVID. It also lays the groundwork for future investigations aimed at unravelling the prognostic value of these biomarkers in predicting the trajectory of long COVID in affected individuals.

Comparative analysis of patellar tendon, achilles tendon and plantar fascia structure in indoor and outdoor football players: a novel cross-sectional pilot study.

Different sport modalities were associate with tendon adaptation or even tendon disturbances, such as volleyball, soccer or basketball. Purpose: the aim of the present study was to determine de difference between indoor and outdoor football players on patellar tendon (PT), Achilles tendon (AT), plantar fascia (FP) and Hoffa's fat pad thickness assessed with ultrasound imaging (USI). A cross-sectional study was developed with a total sample of 30 soccer players divided in two groups: outdoor group (n = 15) and indoor group (n = 15). The thickness of PT, AT, PF and Hoffa's fat pad has been assessed with USI. Hoffa's fat pad reported significant differences for the left side between groups (P = 0.026). The rest of variables did not show any significant difference (P < 0.05). The ultrasonography assessment of the thickness of the PT, AT and PF did not show differences between outdoor and indoor football players. Hoffa's fat pad resulted showed a significant decrease for outdoor soccer players with respect futsal players. Thus, it can be considered that the load stimuli received in both soccer players were not enough to produce structural adaptations in PT, AT and PF tissues.

Is ankle taping effective to limit the ankle dorsiflexion in a single-training session? An observational study in semi-professional basketball players

ABSTRACT BACKGROUND: Ankle taping (AT) is effective in preventing ankle sprain injuries in most common sports and is employed in rehabilitation and prevention sports. OBJECTIVE: This study aimed to investigate the effectiveness of AT to restricting excessive frontal plane ankle movements in semi-professional basketball players throughout the training session. DESIGN AND SETTING: A cross-sectional study was performed at the Universidad Europea de Madrid. METHODS: Forty male and female semi-professional basketball players were divided into two groups. The ankle dorsiflexion range of motion (ROM) and interlimb asymmetries in a weight-bearing lunge position were evaluated at four time points: 1) with no tape, 2) before practice, at 30 min of practice, and 3) immediately after practice. RESULTS: In male basketball players, no differences were observed in the right and left ankles between the baseline and 30 min and between baseline and 90 min of assessment. In female athletes, significant differences were reported between baseline and pre-training assessments for the right ankle and also significant differences between baseline and 90 min in both ankles. CONCLUSIONS: Ankle taping effectively decreased the ankle dorsiflexion ROM in male and female basketball players immediately after application. However, ROM restriction was very low after 30 and 90 min, as assessed in a single basketball practice. Therefore, the classic taping method should be revised to develop new prophylactic approaches, such as the implementation of semi-rigid bracing techniques or the addition of active stripes during training or game pauses.

Glenohumeral internal rotation deficit in general population with shoulder pain: A descriptive observational study.

Glenohumeral internal rotation deficit (GIRD) is one of the most important factors influencing injury risk in the arm of overhead athletes. Some studies have shown that the GIRD of athletes with shoulder pain was higher than those without shoulder pain, establishing a relation between shoulder pain and GIRD. However, there are no studies that relate to GIRD and shoulder pain or the risk factors that affect GIRD in the population with this ailment. This study aimed to: determine if GIRD could be found clinically and between which values it oscillates in patients with shoulder pain, and explore if there are any potential associations between GIRD and some sociodemographic data, and orthopedic or radiological findings. A descriptive observational study design was adopted to determine if GIRD could be found clinically in patients with shoulder pain and to gain further evidence in the potential associations between GIRD and sociodemographic data, and orthopedic or radiological findings. All those patients without exclusion criteria between October 1,2020 and March 31,2021 were included. Exclusion criteria consisted of being under 18 years old but younger than 80 years old, showing shoulder pain in both shoulders and having a joint prosthesis in at least one of the 2 shoulders, tumor, or infection. A total of 67 patients aged between 25 and 75 years (52.7 ±â€…11.8 years, 36 male and 31 female). More than 82% of patients with shoulder pain showed a GIRD higher than 20º. The mean GIRD was 37.6 ±â€…17.09º. The 95th percentile was 66.22º. From sociodemographic data could be extracted that: patients who have children showed a lower GIRD, patients with right shoulder pain, or whose dominance coincided with a painful shoulder showed a higher GIRD. The orthopedic findings revealed that patients with a positive Jobe test showed a lower GIRD. The linear model considering both sociodemographic and orthopedic findings showed that GIRD was reduced by having children and by BMI. GIRD shows a high incidence in patients with shoulder pain. The descendant, BMI, and positive Jobe test were negatively associated with the GIRD.

Treatment of glenohumeral internal rotation deficit in the general population with shoulder pain: An open single-arm clinical trial.

BACKGROUND: Maladaptation can provoke important alterations in the arthrokinematics such as an internal rotation reduction in the dominant shoulder compared with the nondominant shoulder known as glenohumeral internal rotation deficit (GIRD). Though the number of studies investigating GIRD in athletic population, there are not studies reporting the efficacy of the GIRD treatment in the nonathlete population, a kind of study required to improve our understanding of patient care with this pathology. This study aimed to describe the efficacy of the GIRD treatment in nonathlete population with shoulder pain. METHODS: An open single-arm trial with 35 patients was adopted for evaluating the efficacy of GIRD treatment in patients with shoulder pain. All patients with shoulder pain who attended the consultation, accepted, and agreed to participate in the study between October 2020 and March 2021 were included. A treatment sequence including joint manual therapy techniques and soft tissue release techniques was applied in the consultation. Then, patients were instructed to adapt the daily active biological stimulus at home. The IR before (IR0) and after (IR1) the treatment was considered the outcome measure. The GIRD was calculated as the difference between the IR of the non-painful shoulder and the IR of the painful shoulder before (GIRD0) and after treatment (GIRD1). A paired Student t test was used to compare the GIRD of each patient before and after the treatment. RESULTS: Treatment of the patients significantly increased the IR of the painful shoulder in all the patients (P-value < .0001) So, the mean IR0 was 26.09 ± 14.46º (23.64-28.53), and after the treatment the mean IR1 was 67.98 ± 15.03º (65.48-70.52). The mean difference after the treatment (IR1-IR0) was 41.89 ± 14.74º (39.4-44.39). The treatment also significantly reduced GIRD (P-value < .0001). So, the mean GIRD0 was 42.95 ± 16.26º (40.2-45.7), and after the treatment the mean GIRD1 was -1.05 ± 17.18º (-3.96 to 1.85). CONCLUSIONS: The treatment administrated in this study significantly increased the internal rotation of the treated and painful shoulder and reduced the GIRD from the first consultation. LEVEL OF EVIDENCE: Level 3.

Is ankle taping effective to limit the ankle dorsiflexion in a single-training session? An observational study in semi-professional basketball players.

BACKGROUND: Ankle taping (AT) is effective in preventing ankle sprain injuries in most common sports and is employed in rehabilitation and prevention sports. OBJECTIVE: This study aimed to investigate the effectiveness of AT to restricting excessive frontal plane ankle movements in semi-professional basketball players throughout the training session. DESIGN AND SETTING: A cross-sectional study was performed at the Universidad Europea de Madrid. METHODS: Forty male and female semi-professional basketball players were divided into two groups. The ankle dorsiflexion range of motion (ROM) and interlimb asymmetries in a weight-bearing lunge position were evaluated at four time points: 1) with no tape, 2) before practice, at 30 min of practice, and 3) immediately after practice. RESULTS: In male basketball players, no differences were observed in the right and left ankles between the baseline and 30 min and between baseline and 90 min of assessment. In female athletes, significant differences were reported between baseline and pre-training assessments for the right ankle and also significant differences between baseline and 90 min in both ankles. CONCLUSIONS: Ankle taping effectively decreased the ankle dorsiflexion ROM in male and female basketball players immediately after application. However, ROM restriction was very low after 30 and 90 min, as assessed in a single basketball practice. Therefore, the classic taping method should be revised to develop new prophylactic approaches, such as the implementation of semi-rigid bracing techniques or the addition of active stripes during training or game pauses.

The cerebellum and fear extinction: evidence from rodent and human studies.

The role of the cerebellum in emotional control has gained increasing interest, with studies showing it is involved in fear learning and memory in both humans and rodents. This review will focus on the contributions of the cerebellum to the extinction of learned fear responses. Extinction of fearful memories is critical for adaptive behaviour, and is clinically relevant to anxiety disorders such as post-traumatic stress disorder, in which deficits in extinction processes are thought to occur. We present evidence that supports cerebellar involvement in fear extinction, from rodent studies that investigate molecular mechanisms and functional connectivity with other brain regions of the known fear extinction network, to fMRI studies in humans. This evidence is considered in relation to the theoretical framework that the cerebellum is involved in the formation and updating of internal models of the inner and outer world by detecting errors between predicted and actual outcomes. In the case of fear conditioning, these internal models are thought to predict the occurrence of an aversive unconditioned stimulus (US), and when the aversive US is unexpectedly omitted during extinction learning the cerebellum uses prediction errors to update the internal model. Differences between human and rodent studies are highlighted to help inform future work.

Analysis of 16S rRNA Gene Sequence of Nasopharyngeal Exudate Reveals Changes in Key Microbial Communities Associated with Aging.

Functional or compositional perturbations of the microbiome can occur at different sites, of the body and this dysbiosis has been linked to various diseases. Changes in the nasopharyngeal microbiome are associated to patient's susceptibility to multiple viral infections, supporting the idea that the nasopharynx may be playing an important role in health and disease. Most studies on the nasopharyngeal microbiome have focused on a specific period in the lifespan, such as infancy or the old age, or have other limitations such as low sample size. Therefore, detailed studies analyzing the age- and sex-associated changes in the nasopharyngeal microbiome of healthy people across their whole life are essential to understand the relevance of the nasopharynx in the pathogenesis of multiple diseases, particularly viral infections. One hundred twenty nasopharyngeal samples from healthy subjects of all ages and both sexes were analyzed by 16S rRNA sequencing. Nasopharyngeal bacterial alpha diversity did not vary in any case between age or sex groups. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the predominant phyla in all the age groups, with several sex-associated. Acinetobacter, Brevundimonas, Dolosigranulum, Finegoldia, Haemophilus, Leptotrichia, Moraxella, Peptoniphilus, Pseudomonas, Rothia, and Staphylococcus were the only 11 bacterial genera that presented significant age-associated differences. Other bacterial genera such as Anaerococcus, Burkholderia, Campylobacter, Delftia, Prevotella, Neisseria, Propionibacterium, Streptococcus, Ralstonia, Sphingomonas, and Corynebacterium appeared in the population with a very high frequency, suggesting that their presence might be biologically relevant. Therefore, in contrast to other anatomical areas such as the gut, bacterial diversity in the nasopharynx of healthy subjects remains stable and resistant to perturbations throughout the whole life and in both sexes. Age-associated abundance changes were observed at phylum, family, and genus levels, as well as several sex-associated changes probably due to the different levels of sex hormones present in both sexes at certain ages. Our results provide a complete and valuable dataset that will be useful for future research aiming for studying the relationship between changes in the nasopharyngeal microbiome and susceptibility to or severity of multiple diseases.

Features of Extrinsic Plantar Muscles in Patients with Plantar Fasciitis by Ultrasound Imaging: A Retrospective Case Control Research.

The present study aimed to compare by ultrasound imaging (USI) the tibial posterior (TP), medial gastrocnemius (MG) and soleus muscle in patients with and without plantar fasciitis (PF). A sample of 42 individuals was recruited and divided into two groups: PF and a healthy group. The thickness, cross-sectional area (CSA), echointensity and echovariation were assessed in both groups by USI. TP, soleus and MG variables did not report differences (p > 0.05) for thickness and CSA. For the echotexture parameters significant differences were found for MG echointensity (p = 0.002), MG echovariation (p = 0.002) and soleus echointensity (p = 0.012). Non-significant differences (p > 0.05) were reported for soleus echovariation, TP echointensity and TP echovariation variables. The thickness and CSA of the TP, GM and soleus muscle did not show significant differences between individuals with and without PF measured by USI. Muscle quality assessment reported an increase of the MG echointensity and echovariation, as well as a decrease of echointensity of the soleus muscle in the PF group with respect to the healthy group. Therefore, the evaluation of the structure and muscle quality of the extrinsic foot muscles may be beneficial for the diagnosis and monitoring the physical therapy interventions.

DEVEA: an interactive shiny application for Differential Expression analysis, data Visualization and Enrichment Analysis of transcriptomics data.

We are at a time of considerable growth in the use and development of transcriptomics studies and subsequent in silico analysis. RNA sequencing is one of the most widely used approaches, now integrated in many studies.  The processing of these data may typically require a noteworthy number of steps, statistical knowledge, and coding skills which is not accessible to all scientists. Despite the undeniable development of software applications over the years to address this concern, it is still possible to improve.  Here we present DEVEA, an R shiny application tool developed to perform differential expression analysis, data visualization and enrichment pathway analysis mainly from transcriptomics data, but also from simpler gene lists with or without statistical values.  Its intuitive and easy-to-manipulate interface facilitates gene expression exploration through numerous interactive figures and tables, statistical comparisons of expression profile levels between groups and further meta-analysis such as enrichment analysis, without bioinformatics expertise. DEVEA performs a thorough analysis from multiple and flexible input data representing distinct analysis stages. From them, it produces dynamic graphs and tables, to explore the expression levels and statistical differential expression analysis results. Moreover, it generates a comprehensive pathway analysis to extend biological insights. Finally, a complete and customizable HTML report can be extracted for further result exploration outside the application. DEVEA is accessible at https://shiny.imib.es/devea/ and the source code is available on our GitHub repository https://github.com/MiriamRiquelmeP/DEVEA.

Impact of the COVID-19 Lockdown on Ophthalmological Assistance in the Emergency Department at a Spanish Primary Level Hospital.

PURPOSE: To analyze the changes in ophthalmological emergencies during the COVID-19 pandemic lockdown at a Spanish primary level hospital. METHODS: The number and type of emergencies attended in the emergency department of Hospital Universitario del Henares between March 10 and August 31, 2020 (COVID-19 cohort) were compared with the emergencies attended during the same period of 2019 (pre-COVID-19 cohort). Data on the diagnosis, patient age, and gender was retrospectively collected from the electronic medical records of the hospital. The different diagnoses were organized into "clusters," which include those conditions that affect the same ocular tissue and that have similar clinical expression. RESULTS: The number of ophthalmological emergencies during the study period was 841, compared to 1343 during the same month of 2019, which represents a reduction of 37.4%. The percentage reduction in each cluster was as follows: conjunctiva (-65.4%), cornea (-35.8%), uveitis (-3.6%), eyelid and orbital and lacrimal (-35.5%), strabismus (-60%), neuro-ophthalmology (-11.8%), retina (-10.6%), cataract (+16.4%), glaucoma (-37%), and miscellaneous (-45.1%). The number of people seen with viral conjunctivitis decreased by -87.1% compared to 2019. Patients with complications due to conjunctivitis also decreased: patients with pseudomembranes dropped from 16 to 4 cases and patients with corneal subepithelial infiltrates from 9 to 3 cases. CONCLUSIONS: Most diagnostic clusters showed a similar decrease. Clusters that included vision-threating conditions (retina, neuro-ophthalmology, and uveitis) remained mostly stable. During the COVID-19 lockdown, the diagnosis of adenoviral conjunctivitis decreased nearly 10 times. This fact may represent a decrease in the transmission of these infections.

Global Methylome Scores Correlate with Histological Subtypes of Colorectal Carcinoma and Show Different Associations with Common Clinical and Molecular Features.

BACKGROUND: The typical methylation patterns associated with cancer are hypermethylation at gene promoters and global genome hypomethylation. Aberrant CpG island hypermethylation at promoter regions and global genome hypomethylation have not been associated with histological colorectal carcinomas (CRC) subsets. Using Illumina's 450 k Infinium Human Methylation beadchip, the methylome of 82 CRCs were analyzed, comprising different histological subtypes: 40 serrated adenocarcinomas (SAC), 32 conventional carcinomas (CC) and 10 CRCs showing histological and molecular features of microsatellite instability (hmMSI-H), and, additionally, 35 normal adjacent mucosae. Scores reflecting the overall methylation at 250 bp, 1 kb and 2 kb from the transcription starting site (TSS) were studied. RESULTS: SAC has an intermediate methylation pattern between CC and hmMSI-H for the three genome locations. In addition, the shift from promoter hypermethylation to genomic hypomethylation occurs at a small sequence between 250 bp and 1 Kb from the gene TSS, and an asymmetric distribution of methylation was observed between both sides of the CpG islands (N vs. S shores). CONCLUSION: These findings show that different histological subtypes of CRC have a particular global methylation pattern depending on sequence distance to TSS and highlight the so far underestimated importance of CpGs aberrantly hypomethylated in the clinical phenotype of CRCs.

Proteomics in Liver Transplantation: A Systematic Review.

Background: Although proteomics has been employed in the study of several models of liver injury, proteomic methods have only recently been applied not only to biomarker discovery and validation but also to improve understanding of the molecular mechanisms involved in transplantation. Methods: The study was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology and the guidelines for performing systematic literature reviews in bioinformatics (BiSLR). The PubMed, ScienceDirect, and Scopus databases were searched for publications through April 2020. Proteomics studies designed to understand liver transplant outcomes, including ischemia-reperfusion injury (IRI), rejection, or operational tolerance in human or rat samples that applied methodologies for differential expression analysis were considered. Results: The analysis included 22 studies after application of the inclusion and exclusion criteria. Among the 497 proteins annotated, 68 were shared between species and 10 were shared between sample sources. Among the types of studies analyzed, IRI and rejection shared a higher number of proteins. The most enriched pathway for liver biopsy samples, IRI, and rejection was metabolism, compared to cytokine-cytokine receptor interactions for tolerance. Conclusions: Proteomics is a promising technique to detect large numbers of proteins. However, our study shows that several technical issues such as the identification of proteoforms or the dynamic range of protein concentration in clinical samples hinder the successful identification of biomarkers in liver transplantation. In addition, there is a need to minimize the experimental variability between studies, increase the sample size and remove high-abundance plasma proteins.

Culture Medium and Sex Drive Epigenetic Reprogramming in Preimplantation Bovine Embryos.

Assisted reproductive technologies impact transcriptome and epigenome of embryos and can result in long-term phenotypic consequences. Whole-genome DNA methylation profiles from individual bovine blastocysts in vivo- and in vitro-derived (using three sources of protein: reproductive fluids, blood serum and bovine serum albumin) were generated. The impact of in vitro culture on DNA methylation was analyzed, and sex-specific methylation differences at blastocyst stage were uncovered. In vivo embryos showed the highest levels of methylation (29.5%), close to those produced in vitro with serum, whilst embryos produced in vitro with reproductive fluids or albumin showed less global methylation (25-25.4%). During repetitive element analysis, the serum group was the most affected. DNA methylation differences between in vivo and in vitro groups were more frequent in the first intron than in CpGi in promoters. Moreover, hierarchical cluster analysis showed that sex produced a stronger bias in the results than embryo origin. For each group, distance between male and female embryos varied, with in vivo blastocyst showing a lesser distance. Between the sexually dimorphic methylated tiles, which were biased to X-chromosome, critical factors for reproduction, developmental process, cell proliferation and DNA methylation machinery were included. These results support the idea that blastocysts show sexually-dimorphic DNA methylation patterns, and the known picture about the blastocyst methylome should be reconsidered.

Influence of Main Ocular Variables in #TheDress Perception: An Ophthalmic Survey.

The objective of this study is to study the influence of ocular variables in the perception of #thedress and to develop a logistic regression model that could help predict it. This is a cross-sectional study on 1,100 subjects. People who did not report one of the two main perceptions were excluded from the study. Dress perception was codified as 0 (white&gold) or 1 (black&blue). The association between dress perception and demographic and main ocular variables (age, gender, binocular visual acuity, grade of nuclear cataract, crystalline lens status [phakic/pseudophakic], spherical equivalent, and ocular health status) was tested using logistic regression. Receiver operation curves were used to test the predictive value of the model. Several variables were found to be related with dress perception. The best model included three variables-Age: adjusted odds ratio (OR) = 1.02 (1.01-1.03), p = 0.08; ocular refraction: adjusted OR = 1.07 (1.02-1.12), p = 0.009; and nuclear cataract grade: adjusted OR = 1.45 (1.05-1.99), p = 0.026. The predictive value of the model was low (area under the curve = 0.62). Older age, nuclear cataract grade, and hyperopia were associated with black&blue perception. The predictive capacity of the developed model was poor. Only a small proportion of the variability in the #thedress perception can be explained by ocular examination.

gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites.

Metabolomes comprise constitutive and non-constitutive metabolites produced due to physiological, genetic or environmental effects. However, finding constitutive metabolites and non-constitutive metabolites in large datasets is technically challenging. We developed gcProfileMakeR, an R package using standard Excel output files from an Agilent Chemstation GC-MS for automatic data analysis using CAS numbers. gcProfileMakeR has two filters for data preprocessing removing contaminants and low-quality peaks. The first function NormalizeWithinFiles, samples assigning retention times to CAS. The second function NormalizeBetweenFiles, reaches a consensus between files where compounds in close retention times are grouped together. The third function getGroups, establishes what is considered as Constitutive Profile, Non-constitutive by Frequency i.e., not present in all samples and Non-constitutive by Quality. Results can be plotted with the plotGroup function. We used it to analyse floral scent emissions in four snapdragon genotypes. These included a wild type, Deficiens nicotianoides and compacta affecting floral identity and RNAi:AmLHY targeting a circadian clock gene. We identified differences in scent constitutive and non-constitutive profiles as well as in timing of emission. gcProfileMakeR is a very useful tool to define constitutive and non-constitutive scent profiles. It also allows to analyse genotypes and circadian datasets to identify differing metabolites.

Efficiency of Machine Learning Algorithms for the Determination of Macrovesicular Steatosis in Frozen Sections Stained with Sudan to Evaluate the Quality of the Graft in Liver Transplantation.

Liver transplantation is the only curative treatment option in patients diagnosed with end-stage liver disease. The low availability of organs demands an accurate selection procedure based on histological analysis, in order to evaluate the allograft. This assessment, traditionally carried out by a pathologist, is not exempt from subjectivity. In this sense, new tools based on machine learning and artificial vision are continuously being developed for the analysis of medical images of different typologies. Accordingly, in this work, we develop a computer vision-based application for the fast and automatic objective quantification of macrovesicular steatosis in histopathological liver section slides stained with Sudan stain. For this purpose, digital microscopy images were used to obtain thousands of feature vectors based on the RGB and CIE L*a*b* pixel values. These vectors, under a supervised process, were labelled as fat vacuole or non-fat vacuole, and a set of classifiers based on different algorithms were trained, accordingly. The results obtained showed an overall high accuracy for all classifiers (>0.99) with a sensitivity between 0.844 and 1, together with a specificity >0.99. In relation to their speed when classifying images, KNN and Naïve Bayes were substantially faster than other classification algorithms. Sudan stain is a convenient technique for evaluating ME in pre-transplant liver biopsies, providing reliable contrast and facilitating fast and accurate quantification through the machine learning algorithms tested.