Illuminati: a form of gene expression plasticity in Drosophila neural stem cells.

While testing for genome instability in Drosophila as reported by unscheduled upregulation of UAS-GFP in cells that co-express GAL80 and GAL4, we noticed that, as expected, background levels were low in most developing tissues. However, GFP-positive clones were frequent in the larval brain. Most of these clones originated from central brain neural stem cells. Using imaging-based approaches and genome sequencing, we show that these unscheduled clones do not result from chromosome loss or mutations in GAL80. We have named this phenomenon 'Illuminati'. Illuminati is strongly enhanced in brat tumors and is also sensitive to environmental conditions such as food content and temperature. Illuminati is suppressed by Su(var)2-10, but it is not significantly affected by several modifiers of position effect variegation or Gal4::UAS variegation. We conclude that Illuminati identifies a previously unknown type of functional instability that may have important implications in development and disease.

Classification of tumor types using XGBoost machine learning model: a vector space transformation of genomic alterations.

BACKGROUND: Machine learning (ML) represents a powerful tool to capture relationships between molecular alterations and cancer types and to extract biological information. Here, we developed a plain ML model aimed at distinguishing cancer types based on genetic lesions, providing an additional tool to improve cancer diagnosis, particularly for tumors of unknown origin. METHODS: TCGA data from 9,927 samples spanning 32 different cancer types were downloaded from cBioportal. A vector space model type data transformation technique was designed to build consistently homogeneous new datasets containing, as predictive features, calls for somatic point mutations and copy number variations at chromosome arm-level, thus allowing the use of the XGBoost classifier models. Considering the imbalance in the dataset, due to large difference in the number of cases for each tumor, two preprocessing strategies were considered: i) setting a percentage cut-off threshold to remove less represented cancer types, ii) dividing cancer types into different groups based on biological criteria and training a specific XGBoost model for each of them. The performance of all trained models was mainly assessed by the out-of-sample balanced accuracy (BACC) and the AUC scores. RESULTS: The XGBoost classifier achieved the best performance (BACC 77%; AUC 97%) on a dataset containing the 10 most represented tumor types. Moreover, dividing the 18 most represented cancers into three different groups (endocrine-related carcinomas, other carcinomas and other cancers),such analysis models achieved 78%, 71% and 86% BACC, respectively, with AUC scores greater than 96%. In addition, the model capable of linking each group to a specific cancer type reached 81% BACC and 94% AUC. Overall, the diagnostic potential of our model was comparable/higher with respect to others already described in literature and based on similar molecular data and ML approaches. CONCLUSIONS: A boosted ML approach able to accurately discriminate different cancer types was developed. The methodology builds datasets simpler and more interpretable than the original data, while keeping enough information to accurately train standard ML models without resorting to sophisticated Deep Learning architectures. In combination with histopathological examinations, this approach could improve cancer diagnosis by using specific DNA alterations, processed by a replicable and easy-to-use automated technology. The study encourages new investigations which could further increase the classifier's performance, for example by considering more features and dividing tumors into their main molecular subtypes.

Do stock markets love misery? Evidence from the COVID-19.

This study examines the impact of the change in the Barro Misery Index (BMI) and the novel coronavirus (COVID-19) cases and deaths on the stock markets' returns and volatility. Based on a sample of 76 different countries, we find that an increase in BMI adversely affects the stock returns and increases stock volatility. We also find that an increase in BMI coupled with an increase in percentage cases of COVID-19 adversely affect stock returns and increases volatility. We find that the impacts of BMI on stock returns and volatility are driven by real GDP changes, unemployment rate, and long-term interest rate instead of inflation rates, especially for the developed countries. Our findings are consistent with Barro (1999), which indicates that the BMI represents a better measure relative to the original misery index in predicting the economic outcome, especially during the COVID-19 pandemic. We also find that the impacts of BMI components on stock returns and volatility for the developed countries are different from the emerging markets.

How do equity markets react to COVID-19? Evidence from emerging and developed countries.

Based on the supply of stock market returns hypothesis, we argue that the unprecedented adverse shock of COVID-19 on the countries' economic growth translates into a negative shock to the stock markets. According to the institutional theory, we also argue that the impact of COVID-19 in emerging countries is different from developed countries. Based on the overreaction hypothesis, we expect that the market reaction during the stabilizing period of COVID-19 spread is different from the market reaction during the infection period. Using high-frequency daily data across 53 emerging and 23 developed countries from January 14 to August 20, 2020, we find that COVID-19 cases and deaths adversely affect stock returns and increase volatility and trading volume. Cases and deaths affected stock returns and volatility in the emerging markets, while only cases of COVID-19 affected stock returns, volatility, and trading volume in the developed markets. COVID-19 cases and deaths are related to returns, volatility, and trading volume for emerging countries during the rising infection of COVID-19 (pre-April 2020), while cases and mortality rates are related to returns, volatility, and trading volume in developed countries during the stabilizing spread (post-April 2020). Therefore, the emerging markets' investors seem to react to COVID-19 cases and mortality rates differently from those in the developed markets across two different periods of COVID-19 infection.

Synergism between altered cortical polarity and the PI3K/TOR pathway in the suppression of tumour growth.

Loss of function of pins (partner of inscuteable) partially disrupts neuroblast (NB) polarity and asymmetric division, results in fewer and smaller NBs and inhibits Drosophila larval brain growth. Food deprivation also inhibits growth. However, we find that the combination of loss of function of pins and dietary restriction results in loss of NB asymmetry, overproliferation of Miranda-expressing cells, brain overgrowth and increased frequency of tumour growth on allograft transplantation. The same effects are observed in well-fed pins larvae that are mutant for pi3k (phosphatidylinositol 3-kinase) or exposed to the TOR inhibitor rapamycin. Thus, pathways that are sensitive to food deprivation and dependent on PI3K and TOR are essential to suppress tumour growth in Drosophila larval brains with compromised pins function. These results highlight an unexpected crosstalk whereby the normally growth-promoting, nutrient-sensing PI3K/TOR pathway suppresses tumour formation in neural stem cells with compromised cell polarity.

An Integer Linear Programming Model to Optimize Coding DNA Sequences By Joint Control of Transcript Indicators.

A Coding DNA Sequence (CDS) is a fraction of DNA whose nucleotides are grouped into consecutive triplets called codons, each one encoding an amino acid. Because most amino acids can be encoded by more than one codon, the same amino acid chain can be obtained by a very large number of different CDSs. These synonymous CDSs show different features that, also depending on the organism the transcript is expressed in, could affect translational efficiency and yield. The identification of optimal CDSs with respect to given transcript indicators is in general a challenging task, but it has been observed in recent literature that integer linear programming (ILP) can be a very flexible and efficient way to achieve it. In this article, we add evidence to this observation by proposing a new ILP model that simultaneously optimizes different well-grounded indicators. With this model, we efficiently find solutions that dominate those returned by six existing codon optimization heuristics.

Economic growth and health progress in Italy: 30 years of National Health Service.

On December 23 of 1978, during first Italian recession since the end of World War II, Parliament voted for Law 833 that gives birth to the Italian National Public Health Services (SSN) as the new and alternative model of health care system. It was the beginning of the match of Italian health care with the world class level of the public health care. Each crisis requires solidarity and actions. Maintaining levels of health and other social expenditures is critical to protect life and livelihood and to boost productivity. The purpose of the present study is to establish an alternative point of view to demonstrate that Gross Domestic Product, is a function of health care expenditure. The chronology of the events was created by using the laws published on "Gazzetta Ufficiale" (GU). In order to analyze the corporate effectiveness and efficiency, we have divided the SSN into its three main components, namely resources (input), services (output) and performances (outcome). Health services have certainly been pioneers and are still today standard-bearers of a challenge which has borne its fruits. According to the "Organization for Economic Co-operation and Development", SSN ranks second in the world classification of the return on the health care services in 2000. The World Health Organization has published in 2005 the same result: SSN ranks second in the world for ability and quality of the health care in relationship to the resources invested The continuous reforms of health care system introduced stability to the Italian system more than others countries. Success of SSN function rooted in the ability of system to adapt assuring mechanism of positive feed-back correction. In the future SSN, will required new set of reforms, such as redefinition of structures and mechanisms of governance, strategic plans, clinical administrations.

Colorectal medullary carcinoma: heterogeneous presentations of a rare clinico-pathological entity. Report of two cases.

Colorectal medullary carcinoma (CMC) is a rare subset of minimally differentiated carcinomas. CMC tend to be right-sided and present at an advanced stage. Despite this, distant metastases are rare at presentation. The liver and the regional lymph nodes represent the most common sites of metastases. Most of the time, CMCs exhibit mismatch repair deficiency and a strong association with high-level microsatellite instability. There is no conspicuous data regarding treatment strategies and short-term outcomes. CMC is supposed to be related to better prognosis compared to poorly-differentiated and undifferentiated colonic adenocarcinomas, but reports are controversial.This lesion, with heterogeneous presentations and unclear prognostic significance, may be unfamiliar to histopathologists and can lead to diagnostic uncertainty and overtreatments.Our aim is to renew the attention to this rare histological subtype through the report of two cases.

Awake Major Abdominal Surgeries in the COVID-19 Era.

Background: During the outbreak of coronavirus disease 2019 (COVID-19), allocating intensive care beds to patients needing acute care surgery became a very difficult task. Moreover, since general anesthesia is an aerosol-generating procedure, its use became controversial. This strongly restricted therapeutic strategies. Here, we report a series of undeferrable surgical cases treated with awake surgery under neuraxial anesthesia. Contextual benefits of this approach are deepened. Methods: During the first pandemic surge, thirteen patients (5 men and 8 women) with a mean age of 80 years, needing undelayable surgery due to abdominal emergencies, underwent awake open surgery at our Hospital. Prior to surgery, all patients underwent nasopharyngeal swab tests for COVID-19 diagnosis. In all cases, regional anesthesia (spinal, epidural, or combined spinal-epidural anesthesia) was performed. Intraoperative and postoperative pain intensities have been monitored and regularly assessed. A distinct pathway has been set up to keep patients of uncertain COVID-19 diagnosis separated from all other patients. Postoperative course has been examined. Results: The mean operative time was 87 minutes (minimum 60 minutes; maximum 165 minutes). In one case, conversion to general anesthesia was necessary. Postoperative pain was always well controlled. None of them required postoperative intensive care support. No perioperative major complications (Clavien-Dindo ≥3) occurred. Early readmission after surgery never occurred. All nasopharyngeal swabs resulted negative. Conclusions: In our experience, awake laparotomy under regional anesthesia resulted feasible, safe, painless, and, in specific cases, was the only viable option. This approach allowed prevention of the need of postoperative intensive monitoring during the COVID-19 era. In such a peculiar time, we believe it could become part of an ICU-preserving strategy and could limit viral transmission inside theatres.

The management of "fragile" and suspected COVID-19 surgical patients during pandemic: an Italian single-center experience.

BACKGROUND: During Coronavirus disease (COVID-19) pandemic entire countries rapidly ran out of intensive care beds, occupied by critically ill infected patients. Elective surgery was initially halted and acute non-deferrable surgical care drastically limited. The presence of COVID-19 patients into intensive care units (ICU) is currently decreasing but their congestion have restricted our therapeutic strategies during the last months. METHODS: In the COVID-19 era eighteen patients (8 men, 10 women) with a mean age of 80 years, needing undelayable abdominal surgery underwent awake open surgery at our Department. Prior to surgery, all patients underwent COVID-19 investigation. In all cases locoregional anesthesia (LA) was performed. Intraoperative and postoperative pain has been monitored and regularly assessed. A distinct pathway has been set up to keep patients of uncertain COVID-19 diagnosis separated from all other patients. RESULTS: Mean operative time was 104 minutes. In only one case conversion to general anesthesia was necessary. Postoperative pain was always well controlled. None of them required postoperative intensive care support. Only one perioperative complication occurred. Early readmissions after surgery were never observed. CONCLUSIONS: On the basis of our experience awake laparotomy under LA resulted feasible, safe, painless and, in specific cases, the only viable option. For patients presenting fragile cardiovascular and respiratory, reserves and in whom general anesthesia (GA) would presumably increase morbidity and mortality we encourage LA as an alternative to GA. In the COVID-19 era, it has become part of our ICU-preserving strategy allowing us to carry out undeferrable surgeries.

Collective cell migration and metastases induced by an epithelial-to-mesenchymal transition in Drosophila intestinal tumors.

Metastasis underlies the majority of cancer-related deaths yet remains poorly understood due, in part, to the lack of models in vivo. Here we show that expression of the EMT master inducer Snail in primary adult Drosophila intestinal tumors leads to the dissemination of tumor cells and formation of macrometastases. Snail drives an EMT in tumor cells, which, although retaining some epithelial markers, subsequently break through the basal lamina of the midgut, undergo a collective migration and seed polyclonal metastases. While metastases re-epithelialize over time, we found that early metastases are remarkably mesenchymal, discarding the requirement for a mesenchymal-to-epithelial transition for early stages of metastatic growth. Our results demonstrate the formation of metastases in adult flies, and identify a key role for partial-EMTs in driving it. This model opens the door to investigate the basic mechanisms underlying metastasis, in a powerful in vivo system suited for rapid genetic and drug screens.

Cytogenetic and molecular characterization of heterochromatin gene models in Drosophila melanogaster.

In the past decade, genome-sequencing projects have yielded a great amount of information on DNA sequences in several organisms. The release of the Drosophila melanogaster heterochromatin sequence by the Drosophila Heterochromatin Genome Project (DHGP) has greatly facilitated studies of mapping, molecular organization, and function of genes located in pericentromeric heterochromatin. Surprisingly, genome annotation has predicted at least 450 heterochromatic gene models, a figure 10-fold above that defined by genetic analysis. To gain further insight into the locations and functions of D. melanogaster heterochromatic genes and genome organization, we have FISH mapped 41 gene models relative to the stained bands of mitotic chromosomes and the proximal divisions of polytene chromosomes. These genes are contained in eight large scaffolds, which together account for approximately 1.4 Mb of heterochromatic DNA sequence. Moreover, developmental Northern analysis showed that the expression of 15 heterochromatic gene models tested is similar to that of the vital heterochromatic gene Nipped-A, in that it is not limited to specific stages, but is present throughout all development, despite its location in a supposedly "silent" region of the genome. This result is consistent with the idea that genes resident in heterochromatin can encode essential functions.

Data on empirical estimation of the relationship between agency costs and ownership structure in Italian listed companies (2002-2013).

The data presented in this article are related to the research article entitled "Do shareholder coalitions affect agency costs? Evidence from Italian-listed companies", Research in International Business and Finance, Forthcoming (Rossi et al., 2018) [1]. The study shows an empirical analysis using an extensive balanced panel dataset of 163 Italian listed companies for the period 2002-2013, which is a sample yielding 1956 firm-year observations. The sample consists primarily of manufacturing firms, but also includes some service enterprises. However all financial firms and regulated utilities are excluded. We collected data on ownership structure for the entire study period. Information was acquired from the Consob website and the individual company reports on corporate governance. Data on firm-level indicators (debt-to-capital ratio, firm size, and age of the firm) for all companies in the sample were collected from Datastream, Bloomberg, and Calepino dell'Azionista, as well as obtained manually from the financial statements of the individual companies being studied. Our dataset contains several measures of ownership structure for Italian listed companies.

Drosophila Larval Brain Neoplasms Present Tumour-Type Dependent Genome Instability.

Single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) are found at different rates in human cancer. To determine if these genetic lesions appear in Drosophila tumors we have sequenced the genomes of 17 malignant neoplasms caused by mutations in l(3)mbt, brat, aurA, or lgl We have found CNVs and SNPs in all the tumors. Tumor-linked CNVs range between 11 and 80 per sample, affecting between 92 and 1546 coding sequences. CNVs are in average less frequent in l(3)mbt than in brat lines. Nearly half of the CNVs fall within the 10 to 100Kb range, all tumor samples contain CNVs larger that 100 Kb and some have CNVs larger than 1Mb. The rates of tumor-linked SNPs change more than 20-fold depending on the tumor type: at late time points brat, l(3)mbt, and aurA and lgl lines present median values of SNPs/Mb of exome of 0.16, 0.48, and 3.6, respectively. Higher SNP rates are mostly accounted for by C > A transversions, which likely reflect enhanced oxidative stress conditions in the affected tumors. Both CNVs and SNPs turn over rapidly. We found no evidence for selection of a gene signature affected by CNVs or SNPs in the cohort. Altogether, our results show that the rates of CNVs and SNPs, as well as the distribution of CNV sizes in this cohort of Drosophila tumors are well within the range of those reported for human cancer. Genome instability is therefore inherent to Drosophila malignant neoplastic growth at a variable extent that is tumor type dependent.

A discrete in continuous mathematical model of cardiac progenitor cells formation and growth as spheroid clusters (Cardiospheres).

We propose a discrete in continuous mathematical model describing the in vitro growth process of biophsy-derived mammalian cardiac progenitor cells growing as clusters in the form of spheres (Cardiospheres). The approach is hybrid: discrete at cellular scale and continuous at molecular level. In the present model, cells are subject to the self-organizing collective dynamics mechanism and, additionally, they can proliferate and differentiate, also depending on stochastic processes. The two latter processes are triggered and regulated by chemical signals present in the environment. Numerical simulations show the structure and the development of the clustered progenitors and are in a good agreement with the results obtained from in vitro experiments.

[Risk factors for mortality during a heat-wave in Bari (Italy), summer 2005.]. / Fattori di rischio per la mortalità durante un'ondata di calore a Bari, estate 2005.

INTRODUCTION: The Italian Heat Health Watch Warning System (HHWWS) was set up following the over 3000 excess deaths which occurred in Italy during the heat wave of 2003, In June 2005 the warning system issued a heat warning in various Italian cities. METHODS: A case control study was performed in one of these cities (Bari) in order to identify individual and environmental risk factors as well as preventive strategies for reducing mortality during future heat waves. Cases were defined as subjects aged <65 years who had died during the heat wave and whose death certificate listed one of the following as the cause of death: heat, cardiovascular or cerebrovascular disorders, neurocognitive disorders, dehydration or fever/infection not otherwise specified. For each case, three age-matched controls were randomly selected among individuals followed by the same general practitioner as the case. All variables significantly associated with mortality (<0.1) in the univariate analysis were entered into a conditional logistic regression model and the population attributable fraction (PAF) was calculated for significant variables (at p<0.05). RESULTS: Twenty cases and sixty controls were included in the study. In 17 cases (89%) death had occurred at home and 11(55%) of these were cardiovascular- related deaths. At the multivariate analysis, the factors significantly associated with mortality risk during the heat wave were: having a functioning air conditioner at home [OR:0.09(95% CI 0.01-1.00)], having an Activities of Daily Living score <2 [OR:21.0(95%CI 1.81-242.47)] and having been hospitalized the year preceding death [OR:18.1(95%CI 2.04-160.51)]. CONCLUSIONS: Public health interventions during heat waves should include the provision of access to an air conditioned environment. Subjects with impaired health (especially if recently hospitalized) and with significant limitations in their activities of daily living are probably at higher risk during heat waves.

An in vivo genetic screen in Drosophila identifies the orthologue of human cancer/testis gene SPO11 among a network of targets to inhibit lethal(3)malignant brain tumour growth.

Using transgenic RNAi technology, we have screened over 4000 genes to identify targets to inhibit malignant growth caused by the loss of function of lethal(3)malignant brain tumour in Drosophila in vivo We have identified 131 targets, which belong to a wide range of gene ontologies. Most of these target genes are not significantly overexpressed in mbt tumours hence showing that, rather counterintuitively, tumour-linked overexpression is not a good predictor of functional requirement. Moreover, we have found that most of the genes upregulated in mbt tumours remain overexpressed in tumour-suppressed double-mutant conditions, hence revealing that most of the tumour transcriptome signature is not necessarily correlated with malignant growth. One of the identified target genes is meiotic W68 (mei-W68), the Drosophila orthologue of the human cancer/testis gene Sporulation-specific protein 11 (SPO11), the enzyme that catalyses the formation of meiotic double-strand breaks. We show that Drosophila mei-W68/SPO11 drives oncogenesis by causing DNA damage in a somatic tissue, hence providing the first instance in which a SPO11 orthologue is unequivocally shown to have a pro-tumoural role. Altogether, the results from this screen point to the possibility of investigating the function of human cancer relevant genes in a tractable experimental model organism like Drosophila.

Foetal bovine serum-derived exosomes affect yield and phenotype of human cardiac progenitor cell culture.

INTRODUCTION: Cardiac progenitor cells (CPCs) represent a powerful tool in cardiac regenerative medicine. Pre-clinical studies suggest that most of the beneficial effects promoted by the injected cells are due to their paracrine activity exerted on endogenous cells and tissue. Exosomes are candidate mediators of this paracrine effects. According to their potential, many researchers have focused on characterizing exosomes derived from specific cell types, but, up until now, only few studies have analyzed the possible in vitro effects of bovine serum-derived exosomes on cell proliferation or differentiation. METHODS: The aim of this study was to analyse, from a qualitative and quantitative point of view, the in vitro effects of bovine serum exosomes on human CPCs cultured either as cardiospheres or as monolayers of cardiosphere-forming cells. RESULTS: Effects on proliferation, yield and molecular patterning were detected. We show, for the first time, that exogenous bovine exosomes support the proliferation and migration of human cardiosphere-forming cells, and that their depletion affects cardiospheres formation, in terms of size, yield and extra-cellular matrix production. CONCLUSION: These results stress the importance of considering differential biological effects of exogenous cell culture supplements on the final phenotype of primary human cell cultures.

Exosomes isolation protocols: facts and artifacts for cardiac regeneration.

In recent years, exosomes have attracted increasing scientific interest and are no longer considered just as containers for cell waste, but as important mediators of intercellular communication. Among many biomedical research topics, a possible direct role of exosomes in the regenerative medicine field has been underlined in recent studies, including those regarding the so called "paracrine hypothesis". In this perspective, a therapeutic role and/or use of exosomes for tissue regeneration seems to be plausible. However, the majority of the cells isolated and cultured in vitro are exposed to an exogenous exosomes source because of the wide use of foetal bovine serum as cell culture supplement. Bovine serum has been gradually considered as a major biological stimulus, but with still unknown outcome. In this review, we present the state of the art about the role of exosomes in regenerative medicine, particularly for the cardiovascular system. We also analyse the most commonly used exosome isolation techniques that, since their discovery, have undergone continuous development to reach the highest degree of scalability for future clinical translation.

Arl2- and Msps-dependent microtubule growth governs asymmetric division.

Asymmetric division of neural stem cells is a fundamental strategy to balance their self-renewal and differentiation. It is long thought that microtubules are not essential for cell polarity in asymmetrically dividing Drosophila melanogaster neuroblasts (NBs; neural stem cells). Here, we show that Drosophila ADP ribosylation factor like-2 (Arl2) and Msps, a known microtubule-binding protein, control cell polarity and spindle orientation of NBs. Upon arl2 RNA intereference, Arl2-GDP expression, or arl2 deletions, microtubule abnormalities and asymmetric division defects were observed. Conversely, overactivation of Arl2 leads to microtubule overgrowth and depletion of NBs. Arl2 regulates microtubule growth and asymmetric division through localizing Msps to the centrosomes in NBs. Moreover, Arl2 regulates dynein function and in turn centrosomal localization of D-TACC and Msps. Arl2 physically associates with tubulin cofactors C, D, and E. Arl2 functions together with tubulin-binding cofactor D to control microtubule growth, Msps localization, and NB self-renewal. Therefore, Arl2- and Msps-dependent microtubule growth is a new paradigm regulating asymmetric division of neural stem cells.