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The construction of large-scale structure catalogs for the Dark Energy Spectroscopic Instrument
No full textA.J. Ross et al. -- Dark energy spectroscopic instrument (DESI) survey year 1 resultsWe present the technical details on how large-scale structure (LSS) catalogs are constructed from redshifts measured from spectra observed by the Dark Energy Spectroscopic Instrument (DESI). The LSS catalogs provide the information needed to determine the relative number density of DESI tracers as a function of redshift and celestial coordinates and, e.g., determine clustering statistics. We produce catalogs that are weighted subsamples of the observed data, each matched to a weighted `random' catalog that forms an unclustered sampling of the probability density that DESI could have observed those data at each location. Precise knowledge of the DESI observing history and associated hardware performance allows for a determination of the DESI footprint and the number of times DESI has covered it at sub-arcsecond level precision. This enables the completeness of any DESI sample to be modeled at this same resolution. The pipeline developed to create LSS catalogs has been designed to easily allow robustness tests and enable future improvements. We describe how it allows ongoing work improving the match between galaxy and random catalogs, such as including further information when assigning redshifts to randoms, accounting for fluctuations in target density, accounting for variation in the redshift success rate, and accommodating blinding schemes.This material is based upon work supported by the U.S. Department of Energy (DOE), Office of Science, Office of High-Energy Physics, under Contract No. DE-AC02-05CH11231, and by the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility under the same contract. Additional support for DESI was provided by the U.S. National Science Foundation (NSF), Division of Astronomical Sciences under Contract No. AST-0950945 to the NSF’s National Optical-Infrared Astronomy Research Laboratory; the Science and Technology Facilities Council of the United Kingdom; the Gordon and Betty Moore Foundation; the Heising-Simons Foundation; the French Alternative Energies and Atomic Energy Commission (CEA); the National Council of Humanities, Science and Technology of Mexico (CONAHCYT); the Ministry of Science and Innovation of Spain (MICINN), and by the DESI Member Institutions: https://www.desi.lbl.gov/collaborating-institutions. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the U.S. National Science Foundation, the U.S. Department of Energy, or any of the listed funding agencies. The DESI Legacy Imaging Surveys consist of three individual and complementary projects: the Dark Energy Camera Legacy Survey (DECaLS), the Beijing-Arizona Sky Survey (BASS), and the Mayall z-band Legacy Survey (MzLS). DECaLS, BASS and MzLS together include data obtained, respectively, at the Blanco telescope, Cerro Tololo Inter-American Observatory, NSF’s NOIRLab; the Bok telescope, Steward Observatory, University of Arizona; and the Mayall telescope, Kitt Peak National Observatory, NOIRLab. NOIRLab is operated by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation. Pipeline processing and analyses of the data were supported by NOIRLab and the Lawrence Berkeley National Laboratory. Legacy Surveys also uses data products from the Near-Earth Object Wide-field Infrared Survey Explorer (NEOWISE), a project of the Jet Propulsion Laboratory/California Institute of Technology, funded by the National Aeronautics and Space Administration. Legacy Surveys was supported by: the Director, Office of Science, Office of High Energy Physics of the U.S. Department of Energy; the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility; the U.S. National Science Foundation, Division of Astronomical Sciences; the National Astronomical Observatories of China, the Chinese Academy of Sciences and the Chinese National Natural Science Foundation. LBNL is managed by the Regents of the University of California under contract to the U.S. Department of Energy. The complete acknowledgments can be found at https://www.legacysurvey.org/. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the U.S. National Science Foundation, the U.S. Department of Energy, or any of the listed funding agencies. The authors are honored to be permitted to conduct scientific research on Iolkam Du’ag (Kitt Peak), a mountain with particular significance to the Tohono O’odham Nation.Peer reviewe
Evolutionary accumulation modeling in AMR: machine learning to infer and predict evolutionary dynamics of multi-drug resistance
No full text© 2025 Renz et al.Can we understand and predict the evolutionary pathways by which bacteria acquire multi-drug resistance (MDR)? These questions have substantial potential impact in basic biology and in applied approaches to address the global health challenge of antimicrobial resistance (AMR). In this minireview, we discuss how a class of machine-learning approaches called evolutionary accumulation modeling (EvAM) may help reveal these dynamics using genetic and/or phenotypic AMR data sets, without requiring longitudinal sampling. These approaches are well-established in cancer progression and evolutionary biology but currently less used in AMR research. We discuss how EvAM can learn the evolutionary pathways by which drug resistances and other AMR features (for example, mutations driving these resistances) are acquired as pathogens evolve, predict next evolutionary steps, identify influences between AMR features, and explore differences in MDR evolution between regions, demographics, and more. We demonstrate a case study from the literature on MDR evolution in Mycobacterium tuberculosis and discuss the strengths and weaknesses of these approaches, providing links to some approaches for implementation.This work was supported by the Trond Mohn Foundation (project HyperEvol under grant agreement No. TMS2021TMT09 to I.G.J.) through the Centre for Antimicrobial Resistance in Western Norway (CAMRIA) (TMS2020TMT11). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 805046 [EvoConBiO] to I.G.J). This research was supported by grant PID2019-111256RB-I00 funded by MCIN/AEI/10.13039/501100011033 to Ramon Diaz-Uriarte.Peer reviewe
Pedro P. Roxas y de Castro and the Foundation and Development of San Miguel Brewery in the 19th Century Philippines. A Creole Company
No full text[EN] This paper analyzes the creation and development of the San Miguel brewery in the Philippines at the end of the 19th century, driven by the collaboration of two Creoles, Enrique M. Barretto y de Ycaza and Pedro P. Roxas y de Castro. The work focuses its attention especially on the last of the two partners, who ended up becoming the main owner. With this purpose, the paper analyzes Pedro Roxas’s family environment, his career as a businessman, the companies he promoted or in which he participated, and the collaborations that he established. Likewise, it analyzes the emergence of beer manufacturing and consumption on the islands and the success of San Miguel until it became a global company. Finally, it reveals the importance of a Creole elite in the progress of the islands’ economy, always in collaboration with other population groups, beyond ethnic and national boundaries[ES] Este artículo analiza la creación y desarrollo de la fábrica de cervezas San Miguel en las Filipinas de fines del siglo XIX, impulsada por la colaboración de dos criollos: Enrique M. Barretto y de Ycaza y Pedro P. Roxas y de Castro. El trabajo centra su atención en especial en el último de los dos socios, que acabó por convertirse en el propietario principal, y para ello analiza su entorno familiar, su trayectoria como empresario, las compañías que impulsó o en las que participó y las colaboraciones que estableció. De igual forma, analiza la irrupción de la fabricación y consumo de la cerveza en las islas y el éxito de la San Miguel hasta convertirse en una empresa global. Finalmente, revela la importancia de una élite criolla en el progreso de la economía de las islas, siempre en colaboración con otros grupos de población, por encima de fronteras étnicas y nacionales.Peer reviewe
An interkinetic envelope surrounds chromosomes between meiosis I and II in C. elegans oocytes
No full textAt the end of cell division, the nuclear envelope reassembles around the decondensing chromosomes. Female meiosis culminates in two consecutive cell divisions of the oocyte, meiosis I and II, which are separated by a brief transition phase known as interkinesis. Due to the absence of chromosome decondensation and the suppression of genome replication during interkinesis, it has been widely assumed that the nuclear envelope does not reassemble between meiosis I and II. By analyzing interkinesis in C. elegans oocytes, we instead show that an atypical structure made of two lipid bilayers, which we termed the interkinetic envelope, surrounds the surface of the segregating chromosomes. The interkinetic envelope shares common features with the nuclear envelope but also exhibits specific characteristics that distinguish it, including its lack of continuity with the endoplasmic reticulum, unique protein composition, assembly mechanism, and function in chromosome segregation. These distinct attributes collectively define the interkinetic envelope as a unique and specialized structure that has been previously overlooked.This work was supported by Centre National de la Recherche Scientifique and University Paris Cité, by National Institutes of Health R01GM117407 and R01GM130764 (J.C. Canman), by a grant from the Spanish Agencia Estatal de Investigación and the European Regional Development Fund PID2019-105069GB-I00 (P. Askjaer), by a fourth-year Ph.D. fellowship from the Ligue Nationale Contre le Cancer RS30J21DOC17_ELMOSSADEQ (L. El Mossadeq), and by a grant from the European Research Council ERC-CoG ChromoSOMe 819179 (J. Dumont).Peer reviewe
«Lo que ves es lo que soy»: El valor de «ser real» de la música rap
No full text[EN] This article aims to contribute to the study of the socio-educational potential of Rap music
by focusing specifically on the idea of “being real” or “keeping it real”, a characteristic of
this musical style that has received little attention from an educational perspective. To reflect
on this idea, we will rely on ethnographic material from four Rap artists’ life stories, from
their adolescence to their youth, two women and two men who lived through violent situations. Analyzing their narratives, we will show how the idea of “keep it real” enables them
to talk about their experiences, evaluate their circumstances, transform their discontent into
politics, improve their self-perception and that of their backgrounds, and claim the diversity of narratives and identities as a value. That is why, in spite of the detriments and challenges presented by this feature of Rap music, we do also show its benefits for adolescents
and youths as a way of communication and protection, and for that reason we claim it could
be useful in socio-educational contexts.[ES] El presente artículo pretende contribuir al estudio del potencial socioeducativo de la música rap centrándonos específicamente en la idea de «ser real» o «mantenerlo real», una característica de este estilo musical que apenas ha recibido atención desde una perspectiva educativa. Para reflexionar acerca del tema nos apoyaremos en el material etnográfico de cuatro historias de vida de artistas de rap que entraron en contacto con este estilo musical durante su adolescencia y siguen usándolo como forma de expresión: dos mujeres y dos hombres que han atravesado distintas situaciones de violencia. A través del relato de las participantes vemos cómo esta idea les permite reivindicar sus experiencias, evaluar sus circunstancias, politizar sus malestares, mejorar su autopercepción y la de su contexto, y reconocer el valor de la diversidad de relatos e identificaciones. Es por ello por lo que, a pesar de los perjuicios y desafíos que presenta esta característica de la música rap, reclamamos que también puede actuar de manera muy beneficiosa como factor de expresión y protección para adolescentes y jóvenes, y que por ello puede tener una gran utilidad en procesos socioeducativos.Peer reviewe
On the Brink of Change? Environmental Drivers of Voluntary Thermal Maximum in South American Pitvipers
No full text[Aim] We test the relationship between the voluntary thermal maximum (VTMax; the temperature at which an individual actively retreats to a colder site) and geographical/environmental features in the distribution of South American pitvipers. Additionally, we explore the evolution of environmental temperatures and VTMax in species' ranges.[Location] South America.[Taxon] South American pitvipers of the genera Bothrops and Bothrocophias.[Methods] We experimentally measured the VTMax of 15 species of South American pitvipers. We explored the relationship between VTMax and geographical/environmental features (e.g., latitude, topographic complexity and temperature) with PGLS regressions. Additionally, we explored the evolution of maximum (TMax) and minimum (TMin) environmental temperatures, as well as the Thermal Niche Breadth (TNB) and VTMax, using ancestral state reconstruction and testing for phylogenetic signal.[Results] Mean VTMax values for South American pitvipers clustered primarily within the 34°C–36°C range, exhibiting little variation among species or clades. No significant correlations were found between VTMax and climatic or geographic variables. Furthermore, our analysis revealed that these snakes are absent from regions where maximum temperatures surpass their preferred thermal tolerances. Ancestral state reconstruction indicated divergent evolutionary pathways for thermal limits among species, independent of phylogenetic relationships.[Main Conclusions] South American pitvipers unexpectedly exhibit similar voluntary thermal maximum values across a wide range of habitats and despite distinct phylogenetic relationships. Our results indicate that there is no strong climatic niche conservatism for South American pitvipers, with a likely weak selective pressure of VTMax.This study benefited from grants from the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP; 2023/14087-2, 2015/20215-7, 2018/14091-1, and 2020/12658-4); the H2020 MSCA (897901) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brazil (CAPES)—Finance Code 001. MM thanks Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for a fellowship and a grant (309772/2021-4).Peer reviewe
Overgrazing triggers cascading effects on a top avian scavenger: long-term changes in diet and breeding success
No full textWildlife feeding and nutrition are key drivers of several demographic parameters, such as breeding success and survival, influencing long-term population viability. To comply with the diet requirements that ensure offspring survival, parents adapt their forage strategies to the environmental conditions and resource availability. This is especially important for central-place foragers like raptors, where prey availability in the surroundings of nest and livestock carcasses significantly impact both foraging efforts and breeding success. Here we take advantage of 20 years extensive monitoring (2001–2020) of the Canarian Egyptian vulture (Neophron percnopterus majorensis) on the Fuerteventura Island (Canary Islands, Spain) to assess (1) what factors drive vulture diet diversity and, (2) how the number of livestock and diet diversity coupled together with environmental conditions affect breeding success and, ultimately, the conservation of vulture populations. We identified 3,787 prey items belonging to 37 different species. Diet diversity was positively related to the number of wild prey and to low livestock grazing pressure periods. Breeding success was positively related to the number of wild prey, low herbivory pressure and, to a lesser extent, to diet diversity. These results demonstrate the importance of wild prey on Canarian Egyptian vulture’s diet, albeit livestock carcasses are the most abundant feeding resource. We argue that livestock have controversial conservation implications for this species because it provides a stable feeding resource, but, in turn, is one of the major ecosystem disruptors. Overgrazing by livestock can negatively affect wild primary consumers, which are essential for this endemic vulture population.Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. J.A. Donázar, T. Sánchez-Zapata and L. Fernández-Gómez were supported by the TRASCAR project (RTI2018-099609-B-C21) from the Spanish Ministry of Science and Innovation. T. Sánchez-Zapata and L. Fernández-Gómez by the European Regional Development Fund and DIGITALPAST (TED2021-130005B-C21) from the Spanish Ministry of Science and Innovation, NextGeneration EU. This study also forms part of the AGROALNEXT (2022/038) programme. It was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and by the Generalitat Valenciana. J. M. Barbosa was supported by the Generalitat Valenciana (CIDEGENT/ 2020/030).Peer reviewe
Protocols for monitoring condensate formation and dynamics between the phase-separating proteins SET/TAF-Iβ and cytochrome c
No full textChemicals and CAS Registry Numbers
cytochrome c 9007-43-6, 9064-84-0The targeting of several nuclear stress-response factors by translocated cytochrome c upon genotoxic stress has been demonstrated in recent years to involve liquid-liquid phase separation. This protocol addresses the need to investigate the mechanisms and features of phase separation of the histone chaperone SET/TAF-Iβ induced by cytochrome c. We provide steps for protein purification and fluorescent labeling, condensate formation, imaging, quantification, and evaluation of their dynamics by fluorescence recovery after photobleaching (FRAP). This protocol can be broadly applied to other protein complexes. For complete details on the use and execution of this protocol, please refer to Casado-Combreras et al.1.This publication is part of the project PID2021-126663NB-I00 funded by MICIU/AEI/10.13039/501100011033 and ERDF/EU, the Andalusian Government (BIO-198), the University of Seville (VI PPIT), and the Ramón Areces Foundation. This work was also supported by the Ministry of Education and Professional Training (FPU18/06577 for M.Á.C.-C.). The authors thank Dr. Paloma Domínguez-Giménez at the CABIMER microscopy facility (Seville), as well as the microscopy and chromatography services from the Institute of Plant Biochemistry and Photosynthesis (Seville). We also thank Dr. Carlos A. Elena-Real for the construction of SET/TAF-Iβ Q69C mutant used for fluorescent labeling.Peer reviewe
Chromatin Interaction and Histone Mark Signatures Associated With TBXT Expression in Metastatic Lung Cancer
No full text[Background] TBXT, a member of the T-box transcription factor family, drives epithelial-to-mesenchymal transition in the metastasis of some cancers. However, the relationship between the epigenetic regulatory landscape and its expression in lung cancers remains elusive.[Methods] Circularized chromosome capture combined with sequencing (4C-seq) was employed to analyze physical chromatin interactions at the TBXT loci in the lung cancer cell line H460, a high TBXT-expressing cell line, compared to H358 and A549, which do not express TBXT. To define the regulatory landscape, the targeted TBXT chromatin interactions were integrated with histone modification profiles from respective cells, followed with motif analysis.[Results] Our analysis identified distinct patterns of potential cis-regulatory elements (pCREs) associated with the TBXT promoter, with increased near-cis pCRE enrichment in the TBXT-expressing cells. Integration of pCREs with epigenetic histone modification revealed two unique pCREs in TBXT-expressing H460 cells enriched with the active histone mark H3K27ac, harboring binding sites for transcription factors of the forkhead box, zinc finger, and musculoaponeurotic fibrosarcoma families that are linked to cancer metastasis.[Conclusion] Our findings shed light on active chromatin interactions with TBXT expression in lung cancers, pointing to specific DNA elements and regulatory proteins that may be involved. This knowledge paves the way for understanding TBXT expression dynamics at the onset and progression of metastatic cancers.This work was supported by Darwin Trust of Edinburgh and EMBO.Peer reviewe
Metabolic interplays between the tumour and the host shape the tumour macroenvironment
No full textMetabolic reprogramming of cancer cells and the tumour microenvironment are pivotal characteristics of cancers, and studying these processes offer insights and avenues for cancer diagnostics and therapeutics. Recent advancements have underscored the impact of host systemic features, termed macroenvironment, on facilitating cancer progression. During tumorigenesis, these inherent features of the host, such as germline genetics, immune profile and the metabolic status, influence how the body responds to cancer. In parallel, as cancer grows, it induces systemic effects beyond the primary tumour site and affects the macroenvironment, for example, through inflammation, the metabolic end-stage syndrome of cachexia, and metabolic dysregulation. Therefore, understanding the intricate metabolic interplay between the tumour and the host is a growing frontier in advancing cancer diagnosis and therapy. In this Review, we explore the specific contribution of the metabolic fitness of the host to cancer initiation, progression and response to therapy. We then delineate the complex metabolic crosstalk between the tumour, the microenvironment and the host, which promotes disease progression to metastasis and cachexia. The metabolic relationships among the host, cancer pathogenesis and the consequent responsive systemic manifestations during cancer progression provide new perspectives for mechanistic cancer therapy and improved management of patients with cancer.P.A.-M. is supported by the European Research Council Starting Grant (101116912) and the Ramón y Cajal Program. A.D.-F. is funded by Cancer Center Scholar T32 Grant (20910820). T.J. is supported by research grants from the National Institutes of Health (1R37CA286477-01A1, 1OT2CA278690-03), the Cancer Research Institute (CGCATF-2021/100019), the Mark Foundation (20-028-EDV), the STARR Cancer Consortium (I15-0037), and the Simons Foundation (1142664). A.E. is supported by research grants from Minerva, Israel Ministry of Health, the European Research Council (PoC 101111915), the Israel Science Foundation (873/23), and The Israel Cancer Research Fund (837124). A.E. is the incumbent of the Sir Ernst B. Chain Professorial Chair. The Moross Integrated Cancer Center, EKARD Institute for Cancer Diagnosis Research, Abisch-Frenkel RNA Therapeutics Center, G. S. Omenn and M. A. Darling, and the Koret Foundation generously supported the research performed by A.E.’s laboratory. Grammarly and ChatGPT were used for English editingPeer reviewe