Scuola Superiore Sant'Anna

This paper reports the genome sequence of domesticated tomato, a major crop plant, and a draft sequence for its closest wild relative; comparative genomics reveal very little divergence between the two genomes but some important differences with the potato genome, another important food crop in the genus Solanum. Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

OBJECTIVE: Colorectal cancer (CRC) is the third most common cancer worldwide. The geographical and temporal burden of this cancer provides insights into risk factor prevalence and progress in cancer control strategies. We examine the current and future burden of CRC in 185 countries in 2020 and 2040. METHODS: Data on CRC cases and deaths were extracted from the GLOBOCAN database for the year 2020. Age-standardised incidence and mortality rates were calculated by sex, country, world region and Human Development Index (HDI) for 185 countries. Age-specific rates were also estimated. The predicted number of cases and deaths in 2040 were calculated based on global demographic projections by HDI. RESULTS: Over 1.9 million new CRC cases and 930 000 deaths were estimated in 2020. Incidence rates were highest in Australia/ New Zealand and European regions (40.6 per 100 000, males) and lowest in several African regions and Southern Asia (4.4 per 100 000, females). Similar patterns were observed for mortality rates, with the highest observed in Eastern Europe (20.2 per 100 000, males) and the lowest in Southern Asia (2.5 per 100 000, females). The burden of CRC is projected to increase to 3.2 million new cases and 1.6 million deaths by 2040 with most cases predicted to occur in high or very high HDI countries. CONCLUSIONS: CRC is a highly frequent cancer worldwide, and largely preventable through changes in modifiable risk factors, alongside the detection and removal of precancerous lesions. With increasing rates in transitioning countries and younger adults, there is a pressing need to better understand and act on findings to avert future cases and deaths from the disease.

The alterations in myocardial energy substrate metabolism that occur in heart failure, and the causes and consequences of these abnormalities, are poorly understood. There is evidence to suggest that impaired substrate metabolism contributes to contractile dysfunction and to the progressive left ventricular remodeling that are characteristic of the heart failure state. The general concept that has recently emerged is that myocardial substrate selection is relatively normal during the early stages of heart failure; however, in the advanced stages there is a downregulation in fatty acid oxidation, increased glycolysis and glucose oxidation, reduced respiratory chain activity, and an impaired reserve for mitochondrial oxidative flux. This review discusses 1) the metabolic changes that occur in chronic heart failure, with emphasis on the mechanisms that regulate the changes in the expression of metabolic genes and the function of metabolic pathways; 2) the consequences of these metabolic changes on cardiac function; 3) the role of changes in myocardial substrate metabolism on ventricular remodeling and disease progression; and 4) the therapeutic potential of acute and long-term manipulation of cardiac substrate metabolism in heart failure.

Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding. The draft genome of the Norway spruce (P. abies) is presented; this is the first gymnosperm genome to be sequenced and reveals a large genome size (20 Gb) resulting from the accumulation of transposable elements, and comparative sequencing of five other gymnosperm genomes provides insights into conifer genome evolution. The first draft gymnosperm genome, that of a Norway spruce (Picea abies), is published this week by the Spruce Genome Project consortium. The genome is from a tree originally collected in 1959 in eastern Jämtland, central Sweden. At 20 gigabases, the genome is more than a hundred times larger than that of the model plant species Arabidopsis, but the two contain a similar number of genes. The large genome size is the result of an accumulation of transposable elements. Comparative sequencing of five further gymnosperm genomes suggests that transposable element diversity is shared among extant conifers. The sequence data are available for public access from the ConGenIE website ( http://congenie.org/ ).

BACKGROUND: Tracking progress and providing timely evidence is a fundamental step forward for countries to remain aligned with the targets set by WHO to eliminate cervical cancer as a public health problem (ie, to reduce the incidence of the disease below a threshold of 4 cases per 100 000 women-years). We aimed to assess the extent of global inequalities in cervical cancer incidence and mortality, based on The Global Cancer Observatory (GLOBOCAN) 2020 estimates, including geographical and socioeconomic development, and temporal aspects. METHODS: For this analysis, we used the GLOBOCAN 2020 database to estimate the age-specific and age-standardised incidence and mortality rates of cervical cancer per 100 000 women-years for 185 countries or territories aggregated across the 20 UN-defined world regions, and by four-tier levels of the Human Development Index (HDI). Time trends (1988-2017) in incidence were extracted from the Cancer Incidence in Five Continents (CI5) plus database. Mortality estimates were obtained using the most recent national vital registration data from WHO. FINDINGS: Globally in 2020, there were an estimated 604 127 cervical cancer cases and 341 831 deaths, with a corresponding age-standardised incidence of 13·3 cases per 100 000 women-years (95% CI 13·3-13·3) and mortality rate of 7·2 deaths per 100 000 women-years (95% CI 7·2-7·3). Cervical cancer incidence ranged from 2·2 (1·9-2·4) in Iraq to 84·6 (74·8-94·3) in Eswatini. Mortality rates ranged from 1·0 (0·8-1·2) in Switzerland to 55·7 (47·7-63·7) in Eswatini. Age-standardised incidence was highest in Malawi (67·9 [95% CI 65·7 -70·1]) and Zambia (65·5 [63·0-67·9]) in Africa, Bolivia (36·6 [35·0-38·2]) and Paraguay (34·1 [32·1-36·1]) in Latin America, Maldives (24·5 [17·0-32·0]) and Indonesia (24·4 [24·2-24·7]) in Asia, and Fiji (29·8 [24·7-35·0]) and Papua New Guinea (29·2 [27·3-31·0]) in Melanesia. A clear socioeconomic gradient exists in cervical cancer, with decreasing rates as HDI increased. Incidence was three times higher in countries with low HDI than countries with very high HDI, whereas mortality rates were six times higher in low HDI countries versus very high HDI countries. In 2020 estimates, a general decline in incidence was observed in most countries of the world with representative trend data, with incidence becoming stable at relatively low levels around 2005 in several high-income countries. By contrast, in the same period incidence increased in some countries in eastern Africa and eastern Europe. We observed different patterns of age-specific incidence between countries with well developed population-based screening and treatment services (eg, Sweden, Australia, and the UK) and countries with insufficient and opportunistic services (eg, Colombia, India, and Uganda). INTERPRETATION: The burden of cervical cancer remains high in many parts of the world, and in most countries, the incidence and mortality of the disease remain much higher than the threshold set by the WHO initiative on cervical cancer elimination. We identified substantial geographical and socioeconomic inequalities in cervical cancer globally, with a clear gradient of increasing rates for countries with lower levels of human development. Our study provides timely evidence and impetus for future strategies that prioritise and accelerate progress towards the WHO elimination targets and, in so doing, address the marked variations in the global cervical cancer landscape today. FUNDING: French Institut National du Cancer, Horizon 2020 Framework Programme for Research and Innovation of the European Commission; and EU4Health Programme.

The proliferation of soft robotics research worldwide has brought substantial achievements in terms of principles, models, technologies, techniques, and prototypes of soft robots. Such achievements are reviewed here in terms of the abilities that they provide robots that were not possible before. An analysis of the evolution of this field shows how, after a few pioneering works in the years 2009 to 2012, breakthrough results were obtained by taking seminal technological and scientific challenges related to soft robotics from actuation and sensing to modeling and control. Further progress in soft robotics research has produced achievements that are important in terms of robot abilities-that is, from the viewpoint of what robots can do today thanks to the soft robotics approach. Abilities such as squeezing, stretching, climbing, growing, and morphing would not be possible with an approach based only on rigid links. The challenge ahead for soft robotics is to further develop the abilities for robots to grow, evolve, self-heal, develop, and biodegrade, which are the ways that robots can adapt their morphology to the environment.

The International Peach Genome Initiative reports the high quality draft genome sequence of peach (Prunus persica). They also resequenced ten additional P. persica accessions, as well as those of Prunus ferganensis, Prunus kansuensis, Prunus davidiana and Prunus mira. Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.

The mechanical mismatch between soft neural tissues and stiff neural implants hinders the long-term performance of implantable neuroprostheses. Here, we designed and fabricated soft neural implants with the shape and elasticity of dura mater, the protective membrane of the brain and spinal cord. The electronic dura mater, which we call e-dura, embeds interconnects, electrodes, and chemotrodes that sustain millions of mechanical stretch cycles, electrical stimulation pulses, and chemical injections. These integrated modalities enable multiple neuroprosthetic applications. The soft implants extracted cortical states in freely behaving animals for brain-machine interface and delivered electrochemical spinal neuromodulation that restored locomotion after paralyzing spinal cord injury.

Transcription factors belonging to the APETALA2/Ethylene Responsive Factor (AP2/ERF) family are conservatively widespread in the plant kingdom. These regulatory proteins are involved in the control of primary and secondary metabolism, growth and developmental programs, as well as responses to environmental stimuli. Due to their plasticity and to the specificity of individual members of this family, AP2/ERF transcription factors represent valuable targets for genetic engineering and breeding of crops. In this review, we integrate the evidence collected from functional and structural studies to describe their different mechanisms of action and the regulatory pathways that affect their activity.

The emerging field of soft robotics makes use of many classes of materials including metals, low glass transition temperature (Tg) plastics, and high Tg elastomers. Dependent on the specific design, all of these materials may result in extrinsically soft robots. Organic elastomers, however, have elastic moduli ranging from tens of megapascals down to kilopascals; robots composed of such materials are intrinsically soft − they are always compliant independent of their shape. This class of soft machines has been used to reduce control complexity and manufacturing cost of robots, while enabling sophisticated and novel functionalities often in direct contact with humans. This review focuses on a particular type of intrinsically soft, elastomeric robot − those powered via fluidic pressurization.

Hand loss is a highly disabling event that markedly affects the quality of life. To achieve a close to natural replacement for the lost hand, the user should be provided with the rich sensations that we naturally perceive when grasping or manipulating an object. Ideal bidirectional hand prostheses should involve both a reliable decoding of the user's intentions and the delivery of nearly "natural" sensory feedback through remnant afferent pathways, simultaneously and in real time. However, current hand prostheses fail to achieve these requirements, particularly because they lack any sensory feedback. We show that by stimulating the median and ulnar nerve fascicles using transversal multichannel intrafascicular electrodes, according to the information provided by the artificial sensors from a hand prosthesis, physiologically appropriate (near-natural) sensory information can be provided to an amputee during the real-time decoding of different grasping tasks to control a dexterous hand prosthesis. This feedback enabled the participant to effectively modulate the grasping force of the prosthesis with no visual or auditory feedback. Three different force levels were distinguished and consistently used by the subject. The results also demonstrate that a high complexity of perception can be obtained, allowing the subject to identify the stiffness and shape of three different objects by exploiting different characteristics of the elicited sensations. This approach could improve the efficacy and "life-like" quality of hand prostheses, resulting in a keystone strategy for the near-natural replacement of missing hands.

The complex juvenile/maturity transition during a plant's life cycle includes growth, reproduction, and senescence of its fundamental organs: leaves, flowers, and fruits. Growth and senescence of leaves, flowers, and fruits involve several genetic networks where the phytohormone ethylene plays a key role, together with other hormones, integrating different signals and allowing the onset of conditions favorable for stage progression, reproductive success and organ longevity. Changes in ethylene level, its perception, and the hormonal crosstalk directly or indirectly regulate the lifespan of plants. The present review focused on ethylene's role in the development and senescence processes in leaves, flowers and fruits, paying special attention to the complex networks of ethylene crosstalk with other hormones. Moreover, aspects with limited information have been highlighted for future research, extending our understanding on the importance of ethylene during growth and senescence and boosting future research with the aim to improve the qualitative and quantitative traits of crops.

The octopus is a marine animal whose body has no rigid structures. It has eight arms composed of a peculiar muscular structure, named a muscular hydrostat. The octopus arms provide it with both locomotion and grasping capabilities, thanks to the fact that their stiffness can change over a wide range and can be controlled through combined contractions of the muscles. The muscular hydrostat can better be seen as a modifiable skeleton. Furthermore, the morphology the arms and the mechanical characteristics of their tissues are such that the interaction with the environment (i.e., water) is exploited to simplify control. Thanks to this effective mechanism of embodied intelligence, the octopus can control a very high number of degrees of freedom, with relatively limited computing resources. From these considerations, the octopus emerges as a good model for embodied intelligence and for soft robotics. The prototype of a robot arm has been built based on an artificial muscular hydrostat inspired to the muscular hydrostat of the Octopus vulgaris. The prototype presents the morphology of the biological model and the broad arrangement of longitudinal and transverse muscles. Actuation is obtained with cables (longitudinally) and with shape memory alloy springs (transversally). The robot arm combines contractions and it can show the basic movements of the octopus arm, like elongation, shortening and bending, in water.

The current economic crisis illustrates a critical need for new and fundamental understanding of the structure and dynamics of economic networks. Economic systems are increasingly built on interdependencies, implemented through trans-national credit and investment networks, trade relations, or supply chains that have proven difficult to predict and control. We need, therefore, an approach that stresses the systemic complexity of economic networks and that can be used to revise and extend established paradigms in economic theory. This will facilitate the design of policies that reduce conflicts between individual interests and global efficiency, as well as reduce the risk of global failure by making economic networks more robust.

In this paper, a quaternion based extended Kalman filter (EKF) is developed for determining the orientation of a rigid body from the outputs of a sensor which is configured as the integration of a tri-axis gyro and an aiding system mechanized using a tri-axis accelerometer and a tri-axis magnetometer. The suggested applications are for studies in the field of human movement. In the proposed EKF, the quaternion associated with the body rotation is included in the state vector together with the bias of the aiding system sensors. Moreover, in addition to the in-line procedure of sensor bias compensation, the measurement noise covariance matrix is adapted, to guard against the effects which body motion and temporary magnetic disturbance may have on the reliability of measurements of gravity and earth's magnetic field, respectively. By computer simulations and experimental validation with human hand orientation motion signals, improvements in the accuracy of orientation estimates are demonstrated for the proposed EKF, as compared with filter implementations where either the in-line calibration procedure, the adaptive mechanism for weighting the measurements of the aiding system sensors, or both are not implemented.

Sugars act as signaling molecules, whose signal transduction pathways may lead to the activation or inactivation of gene expression. Whole-genome transcript profiling reveals that the flavonoid and anthocyanin biosynthetic pathways are strongly up-regulated following sucrose (Suc) treatment. Besides mRNA accumulation, Suc affects both flavonoid and anthocyanin contents. We investigated the effects of sugars (Suc, glucose, and fructose) on genes coding for flavonoid and anthocyanin biosynthetic enzymes in Arabidopsis (Arabidopsis thaliana). The results indicate that the sugar-dependent up-regulation of the anthocyanin synthesis pathway is Suc specific. An altered induction of several anthocyanin biosynthetic genes, consistent with in vivo sugar modulation of mRNA accumulation, is observed in the phosphoglucomutase Arabidopsis mutant accumulating high levels of soluble sugars.

Abstract Considerable scientific and technological efforts have been devoted to develop neuroprostheses and hybrid bionic systems that link the human nervous system with electronic or robotic prostheses, with the main aim of restoring motor and sensory functions in disabled patients. A number of neuroprostheses use interfaces with peripheral nerves or muscles for neuromuscular stimulation and signal recording. Herein, we provide a critical overview of the peripheral interfaces available and trace their use from research to clinical application in controlling artificial and robotic prostheses. The first section reviews the different types of non‐invasive and invasive electrodes, which include surface and muscular electrodes that can record EMG signals from and stimulate the underlying or implanted muscles. Extraneural electrodes, such as cuff and epineurial electrodes, provide simultaneous interface with many axons in the nerve, whereas intrafascicular, penetrating, and regenerative electrodes may contact small groups of axons within a nerve fascicle. Biological, technological, and material science issues are also reviewed relative to the problems of electrode design and tissue injury. The last section reviews different strategies for the use of information recorded from peripheral interfaces and the current state of control neuroprostheses and hybrid bionic systems.

Many empirical networks display an inherent tendency to cluster, i.e., to form circles of connected nodes. This feature is typically measured by the clustering coefficient (CC). The CC, originally introduced for binary, undirected graphs, has been recently generalized to weighted, undirected networks. Here we extend the CC to the case of (binary and weighted) directed networks and we compute its expected value for random graphs. We distinguish between CCs that count all directed triangles in the graph (independently of the direction of their edges) and CCs that only consider particular types of directed triangles (e.g., cycles). The main concepts are illustrated by employing empirical data on world-trade flows.

The use of on-body wearable sensors is widespread in several academic and industrial domains. Of great interest are their applications in ambulatory monitoring and pervasive computing systems; here, some quantitative analysis of human motion and its automatic classification are the main computational tasks to be pursued. In this paper, we discuss how human physical activity can be classified using on-body accelerometers, with a major emphasis devoted to the computational algorithms employed for this purpose. In particular, we motivate our current interest for classifiers based on Hidden Markov Models (HMMs). An example is illustrated and discussed by analysing a dataset of accelerometer time series.

In the last decade, we have witnessed a drastic change in the form factor of audio and vision technologies, from heavy and grounded machines to lightweight devices that naturally fit our bodies. However, only recently, haptic systems have started to be designed with wearability in mind. The wearability of haptic systems enables novel forms of communication, cooperation, and integration between humans and machines. Wearable haptic interfaces are capable of communicating with the human wearers during their interaction with the environment they share, in a natural and yet private way. This paper presents a taxonomy and review of wearable haptic systems for the fingertip and the hand, focusing on those systems directly addressing wearability challenges. The paper also discusses the main technological and design challenges for the development of wearable haptic interfaces, and it reports on the future perspectives of the field. Finally, the paper includes two tables summarizing the characteristics and features of the most representative wearable haptic systems for the fingertip and the hand.