A conceptual taxonomy of adaptation in evolutionary biology

The concept of adaptation is employed in many fields such as biology, psychology, cognitive sciences, robotics, social sciences, even literacy and art,1 and its meaning varies quite evidently according to the particular research context in which it is applied. We expect to find a particularly rich catalogue of meanings within evolutionary biology, where adaptation has held a particularly central role since Darwin’s The Origin of Species (1859) throughout important epistemological shifts and scientific findings that enriched and diversified the concept. Accordingly, a conceptual taxonomy of adaptation in evolutionary biology may help to disambiguate it. Interdisciplinary researches focused on adaptation would benefit from such a result. In the present work we recognize and define seven different meanings of adaptation: (1) individual fitness; (2) adaptation of a population; (3) adaptation as the process of natural selection; (4) adaptive traits; (5) molecular adaptation; (6) adaptation as structural tinkering; (7) plasticity. For convenience here, we refer to them as W-, P-, NS-, T-, M-, S- and PL-ADAPTATION. We present the seven meanings in some detail, hinting at their respective origins and conceptual developments in the history of evolutionary thought (references are offered for further deepening). However, it is important to point out that evolution researchers seldom if ever refer to a single meaning purified from the others. This applies also to the authors we cite as representatives of one of the seven meanings. In Discussion and Conclusion draw from our work some future perspectives for adaptation within evolutionary biology

Explaining cognitive behaviour : a neurocomputational perspective

While the search for models and explanations of cognitive phenomena is a growing area of research, there is no consensus on what counts as a good explanation in cognitive science. This Ph.D. thesis offers a philosophical exploration of the different frameworks adopted to explain cognitive behaviour. It then builds on this systematic exploration to offer a new understanding of the explanatory standards employed in the construction and justification of models and modelling frameworks in cognitive science. Sub-goals of the project include a better understanding of some theoretical terms adopted in cognitive science and a deep analysis of the role of representation in explanations of cognitive phenomena. Results of this project can advance the debate on issues in general philosophy of cognitive science and be valuable for guiding future scientific and cognitive research. In particular, the goals of the thesis are twofold: (i) to provide some necessary desiderata that genuine explanations in cognitive science need to meet; (ii) to identify the framework that is most apt to generate such good explanations. With reference to the first goal, I claim that a good explanation needs to provide predictions and descriptions of mechanisms. With regards to the second goal, I argue that the neurocomputational framework can meet these two desiderata. In order to articulate the first claim, I discuss various possible desiderata of good explanations and I motivate why the ability to predict and to identify mechanisms are necessary features of good explanations in cognitive science. In particular, I claim that a good explanation should advance our understanding of the cognitive phenomenon under study, together with providing a clear specification of the components and their interactions that regularly bring the phenomenon about. I motivate the second claim by examining various frameworks employed to explain cognitive phenomena: the folk-psychological, the anti-representational, the solely subpersonal and the neurocomputational frameworks. I criticise the folk-psychological framework for meeting only the predictive criterion and I stress the inadequacy of its account of cause and causal explanation by engaging with James Woodward’s manipulationist theory of causation and causal explanation. By examining the anti-representational framework, I claim that the notion of representation is necessary to predict and to generalise cognitive phenomena. I reach the same conclusion by engaging with William Ramsey (2007) and Jose Luis Bermudez (2003). I then analyse the solely subpersonal framework and I argue that certain personal-level concepts are indeed required to successfully explain cognitive behaviour. Finally, I introduce the neurocomputational framework as more promising than the alternatives in explaining cognitive behaviour. I support this claim by assessing the framework’s ability to: (i) meet the two necessary criteria for good explanations; (ii) overcome some of the other frameworks’ explanatory limits. In particular, via an analysis of one of its family of models — Bayesian models — I argue that the neurocomputational framework can suggest a more adequate notion of representation, shed new light on the problem of how to bridge personal and subpersonal explanations, successfully meet the prediction criterion (it values predictions as a means to evaluate the goodness of an explanation) and can meet the mechanistic criterion (its model-based methodology opens up the possibility to study the nature of internal and unobservable components of cognitive phenomena)

What is the role of the placebo effect for pain relief in neurorehabilitation? Clinical implications from the Italian consensus conference on pain in neurorehabilitation

Background: It is increasingly acknowledged that the outcomes of medical treatments are influenced by the context of the clinical encounter through the mechanisms of the placebo effect. The phenomenon of placebo analgesia might be exploited to maximize the efficacy of neurorehabilitation treatments. Since its intensity varies across neurological disorders, the Italian Consensus Conference on Pain in Neurorehabilitation (ICCP) summarized the studies on this field to provide guidance on its use. Methods: A review of the existing reviews and meta-analyses was performed to assess the magnitude of the placebo effect in disorders that may undergo neurorehabilitation treatment. The search was performed on Pubmed using placebo, pain, and the names of neurological disorders as keywords. Methodological quality was assessed using a pre-existing checklist. Data about the magnitude of the placebo effect were extracted from the included reviews and were commented in a narrative form. Results: 11 articles were included in this review. Placebo treatments showed weak effects in central neuropathic pain (pain reduction from 0.44 to 0.66 on a 0-10 scale) and moderate effects in postherpetic neuralgia (1.16), in diabetic peripheral neuropathy (1.45), and in pain associated to HIV (1.82). Moderate effects were also found on pain due to fibromyalgia and migraine; only weak short-term effects were found in complex regional pain syndrome. Confounding variables might have influenced these results. Clinical implications: These estimates should be interpreted with caution, but underscore that the placebo effect can be exploited in neurorehabilitation programs. It is not necessary to conceal its use from the patient. Knowledge of placebo mechanisms can be used to shape the doctor-patient relationship, to reduce the use of analgesic drugs and to train the patient to become an active agent of the therapy

The wide-field, multiplexed, spectroscopic facility WEAVE : survey design, overview, and simulated implementation

Funding for the WEAVE facility has been provided by UKRI STFC, the University of Oxford, NOVA, NWO, Instituto de Astrofísica de Canarias (IAC), the Isaac Newton Group partners (STFC, NWO, and Spain, led by the IAC), INAF, CNRS-INSU, the Observatoire de Paris, Région Île-de-France, CONCYT through INAOE, Konkoly Observatory (CSFK), Max-Planck-Institut für Astronomie (MPIA Heidelberg), Lund University, the Leibniz Institute for Astrophysics Potsdam (AIP), the Swedish Research Council, the European Commission, and the University of Pennsylvania.WEAVE, the new wide-field, massively multiplexed spectroscopic survey facility for the William Herschel Telescope, will see first light in late 2022. WEAVE comprises a new 2-degree field-of-view prime-focus corrector system, a nearly 1000-multiplex fibre positioner, 20 individually deployable 'mini' integral field units (IFUs), and a single large IFU. These fibre systems feed a dual-beam spectrograph covering the wavelength range 366-959 nm at R ∼ 5000, or two shorter ranges at R ∼ 20,000. After summarising the design and implementation of WEAVE and its data systems, we present the organisation, science drivers and design of a five- to seven-year programme of eight individual surveys to: (i) study our Galaxy's origins by completing Gaia's phase-space information, providing metallicities to its limiting magnitude for ∼ 3 million stars and detailed abundances for ∼ 1.5 million brighter field and open-cluster stars; (ii) survey ∼ 0.4 million Galactic-plane OBA stars, young stellar objects and nearby gas to understand the evolution of young stars and their environments; (iii) perform an extensive spectral survey of white dwarfs; (iv) survey  ∼ 400 neutral-hydrogen-selected galaxies with the IFUs; (v) study properties and kinematics of stellar populations and ionised gas in z 1 million spectra of LOFAR-selected radio sources; (viii) trace structures using intergalactic/circumgalactic gas at z > 2. Finally, we describe the WEAVE Operational Rehearsals using the WEAVE Simulator.PostprintPeer reviewe

The wide-field, multiplexed, spectroscopic facility WEAVE: Survey design, overview, and simulated implementation

WEAVE, the new wide-field, massively multiplexed spectroscopic survey facility for the William Herschel Telescope, will see first light in late 2022. WEAVE comprises a new 2-degree field-of-view prime-focus corrector system, a nearly 1000-multiplex fibre positioner, 20 individually deployable 'mini' integral field units (IFUs), and a single large IFU. These fibre systems feed a dual-beam spectrograph covering the wavelength range 366$-$959\,nm at $R\sim5000$, or two shorter ranges at $R\sim20\,000$. After summarising the design and implementation of WEAVE and its data systems, we present the organisation, science drivers and design of a five- to seven-year programme of eight individual surveys to: (i) study our Galaxy's origins by completing Gaia's phase-space information, providing metallicities to its limiting magnitude for $\sim$3 million stars and detailed abundances for $\sim1.5$ million brighter field and open-cluster stars; (ii) survey $\sim0.4$ million Galactic-plane OBA stars, young stellar objects and nearby gas to understand the evolution of young stars and their environments; (iii) perform an extensive spectral survey of white dwarfs; (iv) survey $\sim400$ neutral-hydrogen-selected galaxies with the IFUs; (v) study properties and kinematics of stellar populations and ionised gas in $z<0.5$ cluster galaxies; (vi) survey stellar populations and kinematics in $\sim25\,000$ field galaxies at $0.3\lesssim z \lesssim 0.7$; (vii) study the cosmic evolution of accretion and star formation using $>1$ million spectra of LOFAR-selected radio sources; (viii) trace structures using intergalactic/circumgalactic gas at $z>2$. Finally, we describe the WEAVE Operational Rehearsals using the WEAVE Simulator.Comment: 41 pages, 27 figures, accepted for publication by MNRA

The wide-field, multiplexed, spectroscopic facility WEAVE: Survey design, overview, and simulated implementation

WEAVE, the new wide-field, massively multiplexed spectroscopic survey facility for the William Herschel Telescope, will see first light in late 2022. WEAVE comprises a new 2-degree field-of-view prime-focus corrector system, a nearly 1000-multiplex fibre positioner, 20 individually deployable 'mini' integral field units (IFUs), and a single large IFU. These fibre systems feed a dual-beam spectrograph covering the wavelength range 366−959\,nm at R∼5000, or two shorter ranges at R∼20000. After summarising the design and implementation of WEAVE and its data systems, we present the organisation, science drivers and design of a five- to seven-year programme of eight individual surveys to: (i) study our Galaxy's origins by completing Gaia's phase-space information, providing metallicities to its limiting magnitude for ∼3 million stars and detailed abundances for ∼1.5 million brighter field and open-cluster stars; (ii) survey ∼0.4 million Galactic-plane OBA stars, young stellar objects and nearby gas to understand the evolution of young stars and their environments; (iii) perform an extensive spectral survey of white dwarfs; (iv) survey ∼400 neutral-hydrogen-selected galaxies with the IFUs; (v) study properties and kinematics of stellar populations and ionised gas in z1 million spectra of LOFAR-selected radio sources; (viii) trace structures using intergalactic/circumgalactic gas at z>2. Finally, we describe the WEAVE Operational Rehearsals using the WEAVE Simulator

Microalgal cultivation on digestate: Process efficiency and economics

International audienc

Adolescents' resilience during COVID-19 pandemic and its mediating role in the association between SEL and mental health

The main purpose of this paper is to investigate the role of social and emotional learning (SEL) skills and resilience in explaining mental health in male and female adolescents, during the COVID-19 pandemic. Three self-report questionnaires were administered to 778 participants aged between 11 and 16 years (mean age = 12.73 years; SD = 1.73) and recruited from 18 schools in Northern Italy. The SSIS-SELb-S and the CD-RISC 10 assessed SEL and resilience skills respectively, while the Strengths and Difficulties Questionnaire (SDQ) was used to measure mental health in terms of internalizing problems, externalizing problems, and prosocial behavior. We found that SEL and resilience skills were positively and significantly associated with each other, negatively associated with internalizing and externalizing problems, and positively related to prosocial behavior. Three linear regression analyses showed the significant role of resilience, age, and gender in explaining the variance of internalizing problems; the significant role of SEL skills, resilience, age, and gender in explaining the variance of externalizing problems; and the role of SEL skills, age, and gender in explaining prosocial behavior. Importantly, we found that resilience fully mediated the relationship between SEL skills and internalizing problems, partially mediated the relationship between SEL skills and externalizing problems and didn't mediate the relationship between SEL skills and prosocial behavior. The paper concludes with a discussion of the limitations of the study as well as its practical implications.peer-reviewe

Molecular Determinants of Decitabine Response in Chronic Myelomonocytic Leukemia

Abstract The nucleoside analog (na) 5-aza-2’-deoxycytidine (dac) has good, but heterogeneous, efficacy in the therapy of chronic myelomonocytic leukemia (cmml). Given that no standard therapy has been identified so far for cmml, there is urgent need to identify molecular markers that could support the choice of dac therapy and identify patients more prone to respond. Recently, we demonstrated that in mds patients the expression of uck1, involved in the activation of azacitidine, may influence the clinical response to this treatment (valencia et al, leukemia 2013). In the present study, we assessed the role of dac metabolizing enzymes as well as genetic alterations common to cmml patients in response to dac in a uniformly and prospectively treated cohort of cmml patients. Methods: Patients Forty cmml patients were treated with dac 20mg/m2/day for 5 days every 28 d. DNA and rna were extracted from bm mononuclear cells of 19 pts defined as responders to dac (r), and 21 as non-responders (nr). Hematological response was evaluated according to iwg 2006 criteria. Gene mutation. the fifteen most frequently mutated genes in cmml were sequenced at a mean depth of coverage of 520x (range 169–714x). Functional studies. the role of two main genes involved in dac metabolism: dck (dac activation) and dctd (dac deactivation) was evaluated by silencing both genes with sirnas. The experiments were performed in the mds-skm1 cell line and in primary cells of 6 cmml cases exposed in vitro to dac 10um for 48h. Gene expression. the expression level of genes hent1, hent2, dctd, hcnt3, cn-ii, dck and cda, involved in dac metabolism was evaluated by qrt-pcr in 38/40 cmml patients and by rnaseq in 14/40 patients. CDNA libraries were sequenced using the hiseq 2000. The counts of endogenous genes were normalized by ercc spike-in library controls, and differential expression analysis was performed using edger (v3.4.2) glm model. The differentially expressed genes were identified at the fdr cutoff of 0.05 and absolute fold change greater than 2. Results: in skm-1 cells and in cmml primary mononuclear cells, dctd silencing increased dac- induced apoptosis (annexin v-positive cells 20.2%±0.8% vs control 13.8%±0.5%; p=0.01). dck silencing led to a decrease in dac-induced apoptosis (annexin v-positive cells 8.8%±0.1% vs control 13.8%±0.5%; p=0.05). We could not detect by rnaseq a significant difference in the expression levels of na metabolizing enzymes between responders and non responders to dac. qrt-pcr confirmed these observations. The mutational frequencies (figure) in this cohort of cmml cases were: srsf2 50%, tet2 44.7%, asxl1 39.4%, nras 18.4%, runx1 and dnmt3a 10.5%, u2af1 and tp53 7.8%, kras, jak2 and kit 5.2%, ezh2, idh1, idh2 and sf3b1 2.6%. No single genetic alteration was significantly associated with shorter overall survival or resistance to dac. Conclusions: although we could clearly demonstrate that in vitro expression of dac metabolizing enzymes influenced response to dac, clinical resistance does not appear to be directly correlated with the expression of genes involved in dac metabolism nor to specific gene mutations and is likely determined by other clinical/molecular variables that remain to be identified. Figure 1 Figure 1. Disclosures Finelli: Janssen: Speaker, Speaker Other; Novartis: Speaker, Speaker Other; Celgene: Research Funding, Speaker Other

Impaired expression of p66Shc, a novel regulator of B-cell survival, in chronic lymphocytic leukemia

Intrinsic apoptosis defects underlie to a large extent the extended survival of malignant B cells in chronic lymphocytic leukemia (CLL). Here, we show that the Shc family adapter p66Shc uncouples the B-cell receptor (BCR) from the Erk- and Akt-dependent survival pathways, thereby enhancing B-cell apoptosis. p66Shc expression was found to be profoundly impaired in CLL B cells compared with normal peripheral B cells. Moreover, significant differences in p66Shc expression were observed in patients with favorable or unfavorable prognosis, based on the mutational status of IGHV genes, with the lowest expression in the unfavorable prognosis group. Analysis of the expression of genes implicated in apoptosis defects of CLL showed an alteration in the balance of proapoptotic and antiapoptotic members of the Bcl-2 family in patients with CLL. Reconstitution experiments in CLL B cells, together with data obtained on B cells from p66Shc(-/-) mice, showed that p66Shc expression correlates with a bias in the Bcl-2 family toward proapoptotic members. The data identify p66Shc as a novel regulator of B-cell apoptosis which attenuates BCR-dependent survival signals and modulates Bcl-2 family expression. They moreover provide evidence that the p66Shc expression defect in CLL B cells may be causal to the imbalance toward the antiapoptotic Bcl-2 family members in these cells