PP2A Controls Genome Integrity by Integrating Nutrient-Sensing and Metabolic Pathways with the DNA Damage Response.

Mec1ATR mediates the DNA damage response (DDR), integrating chromosomal signals and mechanical stimuli. We show that the PP2A phosphatases, ceramide-activated enzymes, couple cell metabolism with the DDR. Using genomic screens, metabolic analysis, and genetic and pharmacological studies, we found that PP2A attenuates the DDR and that three metabolic circuits influence the DDR by modulating PP2A activity. Irc21, a putative cytochrome b5 reductase that promotes the condensation reaction generating dihydroceramides (DHCs), and Ppm1, a PP2A methyltransferase, counteract the DDR by activating PP2A; conversely, the nutrient-sensing TORC1-Tap42 axis sustains DDR activation by inhibiting PP2A. Loss-of-function mutations in IRC21, PPM1, and PP2A and hyperactive tap42 alleles rescue mec1 mutants. Ceramides synergize with rapamycin, a TORC1 inhibitor, in counteracting the DDR. Hence, PP2A integrates nutrient-sensing and metabolic pathways to attenuate the Mec1ATR response. Our observations imply that metabolic changes affect genome integrity and may help with exploiting therapeutic options and repositioning known drugs.

RNAseq Analysis of Brain Aging in Wild Specimens of Short-Lived Turquoise Killifish: Commonalities and Differences With Aging Under Laboratory Conditions.

A vast body of studies is available that describe age-dependent gene expression in relation to aging in a number of different model species. These data were obtained from animals kept in conditions with reduced environmental challenges, abundant food, and deprivation of natural sensory stimulation. Here, we compared wild- and captive aging in the short-lived turquoise killifish (Nothobranchius furzeri). These fish inhabit temporary ponds in the African savannah. When the ponds are flooded, eggs hatch synchronously, enabling a precise timing of their individual and population age. We collected the brains of wild fish of different ages and quantified the global age-dependent regulation of transcripts using RNAseq. A major difference between captive and wild populations is that wild populations had unlimited access to food and hence grew to larger sizes and reached asymptotic size more rapidly, enabling the analysis of age-dependent gene expression without the confounding effect of adult brain growth. We found that the majority of differentially expressed genes show the same direction of regulation in wild and captive populations. However, a number of genes were regulated in opposite direction. Genes downregulated in the wild and upregulated in captivity were enriched for terms related to neuronal communication. Genes upregulated in the wild and downregulated in captive conditions were enriched in terms related to DNA replication. Finally, the rate of age-dependent gene regulation was higher in wild animals, suggesting a phenomenon of accelerated aging.

Impact of systemic and tumor lipid metabolism on everolimus efficacy in advanced pancreatic neuroendocrine tumors (pNETs).

The mTOR inhibitor everolimus is effective against advanced pancreatic neuroendocrine tumors (pNETs). However, it can cause metabolic adverse events, such as hyperglycemia, hypertriglyceridemia and hypercholesterolemia. In this work we aimed at evaluating the impact of systemic and tumor lipid metabolism on everolimus efficacy. We carried out a monocentric, retrospective study to correlate plasma triglyceride and cholesterol levels with the progression free survival (PFS) of advanced pNET patients treated with everolimus. In formalin fixed, paraffin embedded (FFPE) tumor specimens, we also assessed by mRNA quantification and immunohistochemistry the expression of acetyl-CoA carboxylase 1 (ACC1) and fatty acid synthase (FASN), two enzymes crucially involved in fatty acid biosynthesis, and we analyzed their impact on PFS. We evaluated 58 consecutive pNET patients who started everolimus between December 2006 and January 2015. Patients with higher plasma triglycerides during the first 3 months of treatment had an increased risk of disease progression (aHR 3.08, 95% CIs 1.15-8.21; p = 0.025). In 23 FFPE tumor specimens amenable for IHC evaluations, we found a positive correlation between ACC1 and FASN at both mRNA (r = 0.87, p = 0.00045) and protein (r = 0.68, p = 0.0004) level. Patients with higher ACC1 protein expression in metastatic lesions had significantly lower PFS when compared to patients with lower ACC1 levels (5.5 vs. 36 months; aHR 4.49, 95% CIs 1.08-18.72; p = 0.039). In conclusion, systemic and tumor lipid metabolism are associated with the PFS of everolimus-treated patients with advanced pNETs; based on these findings, dietary and pharmacological interventions targeting lipid metabolism could improve everolimus efficacy in this patient population.

An Ex Vivo Test of Complement Activation on Endothelium for Individualized Eculizumab Therapy in Hemolytic Uremic Syndrome.

RATIONALE & OBJECTIVE: Although primary atypical hemolytic uremic syndrome (aHUS) is associated with abnormalities in complement genes and antibodies to complement factor H, the role of complement in secondary aHUS remains debatable. We evaluated the usefulness of an ex vivo test to: (1) detect complement activation within the endothelium in primary and secondary aHUS, (2) differentiate active disease from remission, (3) monitor the effectiveness of eculizumab therapy, and (4) identify relapses during eculizumab dosage tapering and after discontinuation of treatment. STUDY DESIGN: Case series. SETTING & PARTICIPANTS: 121 patients with primary aHUS and 28 with secondary aHUS. Serum samples were collected during acute episodes, following remission, and during eculizumab treatment and were assessed using a serum-induced ex vivo C5b-9 endothelial deposition test. RESULTS: Serum-induced C5b-9 deposition on cultured microvascular endothelium was quantified by calculating the endothelial area covered by C5b-9 staining; values were expressed as percentage of C5b-9 deposits induced by a serum pool from healthy controls. Testing with adenosine diphosphate-activated endothelium demonstrated elevated C5b-9 deposits for all untreated patients with aHUS independent of disease activity, while testing with unstimulated endothelium demonstrated deposits only in active disease. Similar findings were observed in secondary aHUS. Serum-induced C5b-9 deposits on activated and unstimulated endothelium normalized during eculizumab treatment. 96% (22/23) of patients receiving eculizumab at extended 3- or 4-week dosing intervals demonstrated normal C5b-9 deposits on activated endothelium, despite most patients having CH50Eq (serum complement activity) > 20 UEq/mL, indicating that adequate complement control was achieved even with incomplete blockade of circulating C5. During eculizumab dosage tapering or after treatment discontinuation, all patients experiencing relapses versus only 6% (1/17) of those in stable remission had elevated C5b-9 deposits on unstimulated endothelium. LIMITATIONS: The C5b-9 endothelial deposition test can be performed in only specialized laboratories. Findings on eculizumab dosage tapering need to be confirmed with longitudinal monitoring of C5b-9 deposition. CONCLUSIONS: The C5b-9 endothelial deposition assay may represent an advance in our ability to monitor aHUS activity and individualize therapy.

Flexible Juvenile Flat Foot Surgical Correction: A Comparison Between Two Techniques After Ten Years' Experience.

The aim of our study is a retrospective analysis of the 2 most common surgical treatments of symptomatic juvenile flat foot: different arthroereisis techniques. Exosinotarsal arthroereisis with metallic screw and endosinotarsal with bioabsorbable devices were compared. In total, 402 feet were examined for a median follow-up of 130 months. Only symptomatic (plantar or calcaneus pain), flexible, and idiopathic flat feet were included in our study. Congenital (fibrous/bone tarsal coalitions), neurologic, and posttraumatic flat feet were excluded. During clinical examination, the feet were categorized according to the Viladot classification, which took into consideration the plantar impression: only grades 3 and 4 were included (complete medial longitudinal arch collapse). Evaluation was determined by taking into consideration 3 parameters: clinical evaluation, pain, and variation of the radiologic angles. No statistical differences were found between the 2 techniques; the choice can be determined mostly by the surgeon's preference.

Sch9S6K controls DNA repair and DNA damage response efficiency in aging cells.

Survival from UV-induced DNA lesions relies on nucleotide excision repair (NER) and the Mec1ATR DNA damage response (DDR). We study DDR and NER in aging cells and find that old cells struggle to repair DNA and activate Mec1ATR. We employ pharmacological and genetic approaches to rescue DDR and NER during aging. Conditions activating Snf1AMPK rescue DDR functionality, but not NER, while inhibition of the TORC1-Sch9S6K axis restores NER and enhances DDR by tuning PP2A activity, specifically in aging cells. Age-related repair deficiency depends on Snf1AMPK-mediated phosphorylation of Sch9S6K on Ser160 and Ser163. PP2A activity in old cells is detrimental for DDR and influences NER by modulating Snf1AMPK and Sch9S6K. Hence, the DDR and repair pathways in aging cells are influenced by the metabolic tuning of opposing AMPK and TORC1 networks and by PP2A activity. Specific Sch9S6K phospho-isoforms control DDR and NER efficiency, specifically during aging.

Rad5-dependent DNA repair functions of the Saccharomyces cerevisiae FANCM protein homolog Mph1.

Interstrand cross-links (ICLs) covalently link complementary DNA strands, block DNA replication, and transcription and must be removed to allow cell survival. Several pathways, including the Fanconi anemia (FA) pathway, can faithfully repair ICLs and maintain genomic integrity; however, the precise mechanisms of most ICL repair processes remain enigmatic. In this study we genetically characterized a conserved yeast ICL repair pathway composed of the yeast homologs (Mph1, Chl1, Mhf1, Mhf2) of four FA proteins (FANCM, FANCJ, MHF1, MHF2). This pathway is epistatic with Rad5-mediated DNA damage bypass and distinct from the ICL repair pathways mediated by Rad18 and Pso2. In addition, consistent with the FANCM role in stabilizing ICL-stalled replication forks, we present evidence that Mph1 prevents ICL-stalled replication forks from collapsing into double-strand breaks. This unique repair function of Mph1 is specific for ICL damage and does not extend to other types of damage. These studies reveal the functional conservation of the FA pathway and validate the yeast model for future studies to further elucidate the mechanism of the FA pathway.

Morphological characteristics of professional ballet dancers of the Bolshoi theater company.

The objective of this study was to describe the morphological profile ofprofessional dancers compared with university physical education students. Thirty-five subjects were evaluated as follows: 13 professional ballet dancers of the Bolshoi Theater Company, six males and seven females, and 22 university physical education students, 11 males and 11 females. Body mass, height, skinfold (triceps, biceps, subscapular, chest, axilla, supraspinale, Iliac crest, abdominal, Front thigh, medial calf) girth (Arm flexed and tensed, forearm, waist, gluteal girth, Mid-thigh girth and calf) and breadth (wrist, ankle, Biepicondylar humerus and femur) were evaluated and somatotype, body fat percentage (BF%) body mass index (BMI), Sigma7 Skinfolds lean body mass, bone, residual and muscle mass were calculated. Dancers showed lower values for BMI, sum of seven skinfolds, BF%, body fat percentage, fat mass, residual mass (p<0.05). For females, lean body mass was also lower in the group of dancers. Body muscle values were lower for university physical education students of both sexes (p<0.05). When assessing differences between male and female dancers and male and female university physical education students, dancers appeared to be more homogeneous than students. As for somatotype, male dancers showed predominance of mesomorphy over the other components and female dancers showed predominance of ectomorphy. The intense training in classical ballet interfered in body composition components, changing them significantly.

First report of oral cryptococcal osteomyelitis in a cat.

Cryptococcosis is a worldwide-distributed fungal disease affecting humans and animals and is considered the most common systemic mycosis in cats. Classically, the clinical presentation of cryptococcal infection in cats consists of solitary or multiple nodules located on the planum nasale or the bridge of the nose. Bone involvement as cryptococcal osteomyelitis is a rare clinical entity of cryptococcosis. Herein, this case report describes a domestic shorthair cat with osteomyelitis of the mandibular bone resulting from Cryptococcus spp. infection. During the physical examination, a subcutaneous mass measuring approximately 6 cm in diameter was identified at the mandibular region. Cytological evaluation revealed numerous encapsulated yeasts resembling Cryptococcus spp. Histopathological examination revealed multifocal to coalescent subcutaneous granulomatous inflammation with a large number of spherical yeasts surrounded by a clear capsule. These yeasts were positive for periodic acid-Schiff (PAS) staining. The cat was successfully treated with a combination of itraconazole therapy and surgical management. To the author's knowledge, this is the first clinical report of oral cryptococcal osteomyelitis in a cat.

Hemicalcaneal reconstruction with a 3D printed custom-made prosthesis after partial calcanectomy due to a malignant bone tumor.

The malignant bone tumors of the calcaneus are extremely uncommon lesions. Surgical approach can consist in either an amputation or in a limb sparing procedure, depending on the width and the location of the neoplasm. Although several reconstructive options have been proposed to fulfill the bone defect in those cases that received a selective resection, to this date a consensus reconstructive approach is far from being established. Among the alternatives described in literature, 3D printed custom-made prostheses represent one of the most intriguing and promising reconstructive options. Herein, we report our experience of a spindle cell bone sarcoma of the calcaneus treated with selective resection of the anterior segment of the calcaneus and further reconstruction with a 3D printed custom-made prosthesis, based on patients' own anatomy. The posterior calcaneus and the insertion of the Achilles tendon were preserved. The resection was performed with wide margins and no major complication occurred through the intra-operative or post-operative intercourse. At her latest follow-up, our patient showed good functional results and was continuously disease free. Our outcomes therefore suggest that a partial prosthetic replacement of the anterior calcaneus with preservation of the Achilles insertion site may represent a safe and effective solution for cases that required the resection of the anterior calcaneus due to a malignant bone tumor.

Anthropometric profiles of elite older triathletes in the Ironman Brazil compared with those of young Portuguese triathletes and older Brazilians.

The objective of this study was to describe the anthropometric profiles of elite older triathletes participating in the 2009 Ironman Brazil and to compare their somatotype, anthropometric and body composition characteristics with those of elite young triathletes and older non-athletes. The sample consisted of 64 males, divided into three groups: (1) older triathletes (n = 17), (2) young triathletes (n = 24), and (3) older non-athletes (n = 23). Somatotype was analysed according to the Carter and Heath ( 1990 ) method. Body mass index, sum of four skinfolds, percentage body fat, body fat mass, and fat-free mass were also estimated. Older non-athletes had higher endomorphy, sum of four skinfolds, fat percentage, and body fat mass than the athletes. Older athletes who participated in the Ironman and elite young triathletes had higher fat-free mass than older non-athletes. Older triathletes and older non-athletes were considered mainly endomorphic mesomorphs and young triathletes mainly ectomorphic mesomorphs. The findings that characterize the anthropometric profile of athletes in this sports modality could be used as a reference.

A causal learning framework for the analysis and interpretation of COVID-19 clinical data.

We present a workflow for clinical data analysis that relies on Bayesian Structure Learning (BSL), an unsupervised learning approach, robust to noise and biases, that allows to incorporate prior medical knowledge into the learning process and that provides explainable results in the form of a graph showing the causal connections among the analyzed features. The workflow consists in a multi-step approach that goes from identifying the main causes of patient's outcome through BSL, to the realization of a tool suitable for clinical practice, based on a Binary Decision Tree (BDT), to recognize patients at high-risk with information available already at hospital admission time. We evaluate our approach on a feature-rich dataset of Coronavirus disease (COVID-19), showing that the proposed framework provides a schematic overview of the multi-factorial processes that jointly contribute to the outcome. We compare our findings with current literature on COVID-19, showing that this approach allows to re-discover established cause-effect relationships about the disease. Further, our approach yields to a highly interpretable tool correctly predicting the outcome of 85% of subjects based exclusively on 3 features: age, a previous history of chronic obstructive pulmonary disease and the PaO2/FiO2 ratio at the time of arrival to the hospital. The inclusion of additional information from 4 routine blood tests (Creatinine, Glucose, pO2 and Sodium) increases predictive accuracy to 94.5%.

Results from Brazil's 2022 Report Card on Physical Activity for Children and Adolescents.

This research aims to summarize the process and results of the 2022 Report Card on Physical Activity for Brazilian children and adolescents. A group of experts led by 10 PhD researchers gathered the best possible evidence on physical activity indicators. The Report Card Brazil 2022 included the top 10 indicators of physical activity and sleep, obesity, and poor mental health variables, which made up four dimensions: (I) Daily Behaviors; (II) Settings and Sources of Influence; (III) Government Strategies and Investments; and (IV) Health Outcomes. Comprehensive searches, including peer-reviewed and gray literature searches, were performed for each indicator. Data were considered from systematic reviews, local and national surveys, websites, and official information from the Brazilian Federal Government. Grades from the indicators ranged from F (Active Play) to B (School). In addition, the results found for each indicator were Overall Physical Activity (D), Organized Sport Participation (C-), Active Transportation (C), Sedentary Behaviors (D), Sleep (C), Family and Peers (C-), Community and Environment (C), Government (D+), Physical Fitness (D+), Obesity (11.7%), and Poor Mental Health (37.8%). Successfully strategies for increasing physical activity among Brazilian children and adolescents should look at the different indicators presented in this report.

Solvent and substrate contributions to the formation of breath figure patterns in polystyrene films.

The generation of ordered porous polymer structures by the breath figures (BFs) method has long been described as a complex phenomenon, in which several parameters combine in a fairly unknown way. The type of polymer and solvent, degree of humidity, and additives are just a few examples of the several parameters that have been described as playing a role in the generation of BFs. This work reports a detailed investigation over the role played by the solvent in the process of BFs generation from polystyrene (PS) solutions spread over different substrates, and discusses the geometrical aspects of the pores via a quantitative point of view by using a purposely developed software for image analysis. Results show that thermodynamic affinity between polymer and solvent is the key parameter for BFs formation, along with other solvent characteristics such as water miscibility, boiling point, and enthalpy. According to our findings, the role played by the substrate is strictly related to the type of solvent used in the generation of BFs.

Instability Severity Index Score Does Not Predict the Risk of Shoulder Dislocation after a First Episode Treated Conservatively.

The first purpose of this study was to verify the association between Instability Severity Index Score (ISIS) and Recurrent Shoulder Dislocation (RSD) after a first episode treated conservatively. The second aim is to identify the risk factors associated with RSD after a primary acute shoulder anterior dislocation treated conservatively. A total of 111 patients with first traumatic anterior shoulder dislocation treated at a single trauma centre between January 2014 and March 2016 were enrolled. The main predictive variables of risk factors and the ISIS score were calculated. Among the 85 patients included, 26 cases of RSD were observed (30.6%). Considering the whole population, no significant association between ISIS and RSD were reported. Regarding other risk factors, high-risk working activities and rotator cuff injury had a significantly higher RSD risk. Sex, dominant limb, familiar history, hyperlaxity, contact or overhead sports, competitive sport, post-reduction physiokinesitherapy, return to sports activity time, Hill-Sachs lesion, bony Bankart lesion and great tuberosity fracture did not seem to influence the risk of RSD. No correlation between ISIS score and RSD in patients treated conservatively after a first episode of shoulder dislocation were reported. The only risk factors with a significant association to RSD were high-risk working activities and rotator cuff injury.

Endosomal trafficking and DNA damage checkpoint kinases dictate survival to replication stress by regulating amino acid uptake and protein synthesis.

Atg6Beclin 1 mediates autophagy and endosomal trafficking. We investigated how Atg6 influences replication stress. Combining genetic, genomic, metabolomic, and proteomic approaches, we found that the Vps34-Vps15-Atg6Beclin 1-Vps38UVRAG-phosphatydilinositol-3 phosphate (PtdIns(3)P) axis sensitizes cells to replication stress by favoring the degradation of plasma membrane amino acid (AA) transporters via endosomal trafficking and ESCRT proteins, while the PtdIns(3)P phosphatases Ymr1 and Inp53 promote survival to replication stress by reversing this process. An impaired AA uptake triggers activation of Gcn2, which attenuates protein synthesis by phosphorylating eIF2α. Mec1Atr-Rad53Chk1/Chk2 activation during replication stress further hinders translation efficiency by counteracting eIF2α dephosphorylation through Glc7PP1. AA shortage-induced hyperphosphorylation of eIF2α inhibits the synthesis of 65 stress response proteins, thus resulting in cell sensitization to replication stress, while TORC1 promotes cell survival. Our findings reveal an integrated network mediated by endosomal trafficking, translational control pathways, and checkpoint kinases linking AA availability to the response to replication stress.

Measuring the effects of confounders in medical supervised classification problems: the Confounding Index (CI).

Over the years, there has been growing interest in using machine learning techniques for biomedical data processing. When tackling these tasks, one needs to bear in mind that biomedical data depends on a variety of characteristics, such as demographic aspects (age, gender, etc.) or the acquisition technology, which might be unrelated with the target of the analysis. In supervised tasks, failing to match the ground truth targets with respect to such characteristics, called confounders, may lead to very misleading estimates of the predictive performance. Many strategies have been proposed to handle confounders, ranging from data selection, to normalization techniques, up to the use of training algorithm for learning with imbalanced data. However, all these solutions require the confounders to be known a priori. To this aim, we introduce a novel index that is able to measure the confounding effect of a data attribute in a bias-agnostic way. This index can be used to quantitatively compare the confounding effects of different variables and to inform correction methods such as normalization procedures or ad-hoc-prepared learning algorithms. The effectiveness of this index is validated on both simulated data and real-world neuroimaging data.

Exploring C4-CAM plasticity within the Portulaca oleracea complex.

Portulaca oleracea is a C4 herb capable of performing CAM under drought stress. It is distributed worldwide and is either considered a polymorphic species or a complex of subspecies, due to its numerous morphological variations. We evaluated CAM plasticity within P. oleracea genotypes since the complexity surrounding this species may be reflected in intraspecific variations in photosynthetic behavior. Eleven subspecies of P. oleracea from distant geographical locations and one cultivar were morphologically and physiologically characterized. C4 and CAM photosynthesis were monitored in plants exposed to well-watered, droughted and rewatered treatments, and data obtained were compared among individual genotypes. All subspecies expressed CAM in a fully-reversible manner. Transcript abundance of C4-CAM signature genes was shown to be a useful indicator of the C4-CAM-C4 switches in all genotypes. C4-related genes were down-regulated and subsequently fully expressed upon drought and rewatering, respectively. CAM-marker genes followed the opposite pattern. A gradient of morphological traits and drought-induced nighttime malate accumulation was observed across genotypes. Therefore, different combinations of CAM expression levels, plant sizes and shapes are available within the P. oleracea complex, which can be a valuable tool in the context of C4/CAM photosynthesis research.

Dealing with confounders and outliers in classification medical studies: The Autism Spectrum Disorders case study.

Machine learning (ML) approaches have been widely applied to medical data in order to find reliable classifiers to improve diagnosis and detect candidate biomarkers of a disease. However, as a powerful, multivariate, data-driven approach, ML can be misled by biases and outliers in the training set, finding sample-dependent classification patterns. This phenomenon often occurs in biomedical applications in which, due to the scarcity of the data, combined with their heterogeneous nature and complex acquisition process, outliers and biases are very common. In this work we present a new workflow for biomedical research based on ML approaches, that maximizes the generalizability of the classification. This workflow is based on the adoption of two data selection tools: an autoencoder to identify the outliers and the Confounding Index, to understand which characteristics of the sample can mislead classification. As a study-case we adopt the controversial research about extracting brain structural biomarkers of Autism Spectrum Disorders (ASD) from magnetic resonance images. A classifier trained on a dataset composed by 86 subjects, selected using this framework, obtained an area under the receiver operating characteristic curve of 0.79. The feature pattern identified by this classifier is still able to capture the mean differences between the ASD and Typically Developing Control classes on 1460 new subjects in the same age range of the training set, thus providing new insights on the brain characteristics of ASD. In this work, we show that the proposed workflow allows to find generalizable patterns even if the dataset is limited, while skipping the two mentioned steps and using a larger but not well designed training set would have produced a sample-dependent classifier.