92 research outputs found
The Second Edition of the Integrative Levels Classification: Evolution of a KOS
AbstractPurposeThis paper informs about the publication of the second edition of the Integrative Levels Classification (ILC2), a freely-faceted knowledge organization system (KOS), and reviews the main changes that have been introduced as compared to its first edition (ILC1).Design/methodology/approachThe most relevant changes are illustrated, with special reference to those of interest to general classification theory, by means of examples of notation for individual classes and combinations of them.FindingsChanges introduced in ILC2 include: the names and order of some main classes; the development of subclasses for various phenomena, especially quantities and algebraic structures; the order of facet categories and the new category of Disorder; notation for special facets; distinction of the semantical function of facets (attributes) from their syntactic function. The system can be freely accessed online through a PHP browser as well as in SKOS format.Research limitationsOnly a selection of changed classes is discussed for space reasons.Practical implicationsILC1 has been previously applied to the BARTOC directory of KOSs. Update of BARTOC data to ILC2 and application of ILC2 to further information systems are envisaged. Possible methods for reclassifying BARTOC with ILC2 are discussed.OriginalityILC is a newly developed classification system, based on phenomena instead of traditional disciplines and featuring various innovative devices. This paper is an original account of its most recent evolution
Interface-mediated ferroelectric patterning and Mn valency in nano-structured PbTiO <sub>3</sub> /La <sub>0.7</sub> Sr <sub>0.3</sub> MnO <sub>3</sub>
International audienceWe employed a multitechnique approach using piezo-force response microscopy and photoemission microscopy to investigate a self-organizing polarization domain pattern in PbTiO3/La0.7Sr0.3MnO3 (PTO/LSMO) nanostructures. The polarization is correlated with the nanostructure morphology as well as with the thickness and Mn valence of the LSMO template layer. On the LSMO dots, the PTO is upwards polarized, whereas outside the nanodots, the polarization appears both strain and interface roughness dependent. The results suggest that the electronic structure and strain of the PTO/LSMO interface contribute to determining the internal bias of the ferroelectric layer
IT applications for sharing geoheritage information: the example of the geological and geomorphological trail in the Monviso massif (NW Italy)
The dynamical state of bars in cluster dwarf galaxies: The cases of NGC 4483 and NGC 4516
Dwarf barred galaxies are the perfect candidates for hosting slowly-rotating bars. They are common in dense environments and they have a relatively shallow potential well, making them prone to heating by interactions. When an interaction induces bar formation, the bar should rotate slowly. They reside in massive and centrally-concentrated dark matter halos, which slow down the bar rotation through dynamical friction. While predictions suggest that slow bars should be common, measurements of bar pattern speed, using the Tremaine-Weinberg method, show that bars are mostly fast in the local Universe. We present a photometric and kinematic characterisation of bars hosted by two dwarf galaxies in the Virgo Cluster, NGC 4483 and NGC 4516. We derive the bar length and strength using the Next Generation Virgo Survey imaging and the circular velocity, bar pattern speed, and rotation rate using spectroscopy from the Multi Unit Spectroscopic Explorer. Including the previously studied galaxy IC 3167, we compare the bar properties of the three dwarf galaxies with those of their massive counterparts from literature. Bars in the dwarf galaxies are shorter and weaker, and rotate slightly slower with respect to those in massive galaxies. This could be due to a different bar formation mechanism and/or to a large dark matter fraction in the centre of dwarf galaxies. We show that it is possible to push the application of the Tremaine-Weinberg method to the galaxy low mass regime
New insights into the genetic etiology of Alzheimer's disease and related dementias.
Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele
Colorectal Cancer Stage at Diagnosis Before vs During the COVID-19 Pandemic in Italy
IMPORTANCE Delays in screening programs and the reluctance of patients to seek medical
attention because of the outbreak of SARS-CoV-2 could be associated with the risk of more advanced
colorectal cancers at diagnosis.
OBJECTIVE To evaluate whether the SARS-CoV-2 pandemic was associated with more advanced
oncologic stage and change in clinical presentation for patients with colorectal cancer.
DESIGN, SETTING, AND PARTICIPANTS This retrospective, multicenter cohort study included all
17 938 adult patients who underwent surgery for colorectal cancer from March 1, 2020, to December
31, 2021 (pandemic period), and from January 1, 2018, to February 29, 2020 (prepandemic period),
in 81 participating centers in Italy, including tertiary centers and community hospitals. Follow-up was
30 days from surgery.
EXPOSURES Any type of surgical procedure for colorectal cancer, including explorative surgery,
palliative procedures, and atypical or segmental resections.
MAIN OUTCOMES AND MEASURES The primary outcome was advanced stage of colorectal cancer
at diagnosis. Secondary outcomes were distant metastasis, T4 stage, aggressive biology (defined as
cancer with at least 1 of the following characteristics: signet ring cells, mucinous tumor, budding,
lymphovascular invasion, perineural invasion, and lymphangitis), stenotic lesion, emergency surgery,
and palliative surgery. The independent association between the pandemic period and the outcomes
was assessed using multivariate random-effects logistic regression, with hospital as the cluster
variable.
RESULTS A total of 17 938 patients (10 007 men [55.8%]; mean [SD] age, 70.6 [12.2] years)
underwent surgery for colorectal cancer: 7796 (43.5%) during the pandemic period and 10 142
(56.5%) during the prepandemic period. Logistic regression indicated that the pandemic period was
significantly associated with an increased rate of advanced-stage colorectal cancer (odds ratio [OR],
1.07; 95%CI, 1.01-1.13; P = .03), aggressive biology (OR, 1.32; 95%CI, 1.15-1.53; P < .001), and stenotic
lesions (OR, 1.15; 95%CI, 1.01-1.31; P = .03).
CONCLUSIONS AND RELEVANCE This cohort study suggests a significant association between the
SARS-CoV-2 pandemic and the risk of a more advanced oncologic stage at diagnosis among patients
undergoing surgery for colorectal cancer and might indicate a potential reduction of survival for
these patients
Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)
In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field
New insights into the genetic etiology of Alzheimer's disease and related dementias
Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele
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 366959\,nm at
, or two shorter ranges at . 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
million brighter field and open-cluster stars; (ii) survey 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
neutral-hydrogen-selected galaxies with the IFUs; (v) study properties and
kinematics of stellar populations and ionised gas in cluster galaxies;
(vi) survey stellar populations and kinematics in field galaxies
at ; (vii) study the cosmic evolution of accretion
and star formation using million spectra of LOFAR-selected radio sources;
(viii) trace structures using intergalactic/circumgalactic gas at .
Finally, we describe the WEAVE Operational Rehearsals using the WEAVE
Simulator.Comment: 41 pages, 27 figures, accepted for publication by MNRA
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