bluuebunny/crossref_metadata_2025_split huggingface dataset:
Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project
Authors: Shaffer H Bradley , Toffelmier Erin , Corbett-Detig Russ B , Escalona Merly , Erickson Bjorn , Fiedler Peggy , Gold Mark , Harrigan Ryan J , Hodges Scott , Luckau Tara K , Miller Courtney , Oliveira Daniel R , Shaffer Kevin E , Shapiro Beth , Sork Victoria L , Wang Ian J 
Published: April 2022

AbstractThe California Conservation Genomics Project (CCGP) is a unique, critically important step forward in the use of comprehensive landscape genetic data to modernize natural resource management at a regional scale. We describe the CCGP, including all aspects of project administration, data collection, current progress, and future challenges. The CCGP will generate, analyze, and curate a single high-quality reference genome and 100–150 resequenced genomes for each of 153 species projects (representing 235 individual species) that span the ecological and phylogenetic breadth of California’s marine, freshwater, and terrestrial ecosystems. The resulting portfolio of roughly 20 000 resequenced genomes will be analyzed with identical informatic and landscape genomic pipelines, providing a comprehensive overview of hotspots of within-species genomic diversity, potential and realized corridors connecting these hotspots, regions of reduced diversity requiring genetic rescue, and the distribution of variation critical for rapid climate adaptation. After 2 years of concerted effort, full funding ($12M USD) has been secured, species identified, and funds distributed to 68 laboratories and 114 investigators drawn from all 10 University of California campuses. The remaining phases of the CCGP include completion of data collection and analyses, and delivery of the resulting genomic data and inferences to state and federal regulatory agencies to help stabilize species declines. The aspirational goals of the CCGP are to identify geographic regions that are critical to long-term preservation of California biodiversity, prioritize those regions based on defensible genomic criteria, and provide foundational knowledge that informs management strategies at both the individual species and ecosystem levels.
Role of resection for extrahepatopulmonary metastases of colon cancer
Authors: Mishina Takuya , Uehara Kay , Ogura Atsushi , Murata Yuki , Aiba Toshisada , Mizuno Takashi , Yokoyama Yukihiro , Ebata Tomoki 
Published: April 2022

Abstract

Background
Although surgical resection for liver or lung metastases of colorectal cancer has been widely accepted, the use of this approach for extrahepatopulmonary metastases remains debatable due to the systemic nature of the disease. The aim of this study was to clarify the utility of resection along with perioperative chemotherapy for patients with extrahepatopulmonary metastases of colon cancer.

Methods
This is a retrospective single-arm study at a single institution. Forty-two patients with resectable extrahepatopulmonary metastases who underwent metastasectomy with curative intent between 2009 and 2018 at Nagoya University Hospital were retrospectively analyzed. The primary outcomes measured were overall and relapse-free survival.

Results
The most common metastatic site was the peritoneum (n = 31), followed by the distant lymph nodes (n = 10), ovary (n = 1) and spleen (n = 1), with overlaps. Preoperative and postoperative chemotherapies were administered to 22 and 8 patients, respectively; the remaining 14 patients received surgery alone. R0 resection was achieved in 36 patients (85.7%). The 5-year overall survival and 3-year relapse-free survival rates were 58.6% and 33.8%, respectively. In the univariate analysis, R1 resection was associated with a poor relapse-free survival rate (P = 0.02). In the multivariate analysis, the absence of perioperative chemotherapy was an independent risk factor for poor overall survival rates (P = 0.02).

Conclusions
Surgical resection benefited selected patients with extrahepatopulmonary metastases with favorable long-term survival outcomes. Surgery alone without systemic chemotherapy is likely to bring poor outcome; therefore, preoperative induction might be promising to keep up with chemotherapy.
Liverwort oil bodies: diversity, biochemistry, and molecular cell biology of the earliest secretory structure of land plants
Authors: Romani Facundo , Flores Jorge R , Tolopka Juan Ignacio , Suárez Guillermo , He Xiaolan , Moreno Javier E 
Published: April 2022

Abstract
Liverworts are known for their large chemical diversity. Much of this diversity is synthesized and enclosed within oil bodies (OBs), a synapomorphy of the lineage. OBs contain the enzymes to biosynthesize and store large quantities of sesquiterpenoids and other compounds while limiting their cytotoxicity. Recent important biochemical and molecular discoveries related to OB formation, diversity, and biochemistry allow comparison with other secretory structures of land plants from an evo-devo perspective. This review addresses and discusses the most recent advances in OB origin, development, and function towards understanding the importance of these organelles in liverwort physiology and adaptation to changing environments. Our mapping of OB types and chemical compounds to the current liverwort phylogeny suggests that OBs were present in the most recent common ancestor of liverworts, supporting that OBs evolved as the first secretory structures in land plants. Yet, we require better sampling to define the macroevolutionary pattern governing the ancestral type of OB. We conclude that current efforts to find molecular mechanisms responsible for the morphological and chemical diversity of secretory structures will help understand the evolution of each major group of land plants, and open new avenues in biochemical research on bioactive compounds in bryophytes and vascular plants.
A single substitution inVacuolar protein sorting 4is responsible for resistance toWatermelon mosaic virusin melon
Authors: Agaoua Aimeric , Rittener Vincent , Troadec Christelle , Desbiez Cécile , Bendahmane Abdelhafid , Moquet Frédéric , Dogimont Catherine 
Published: April 2022

AbstractIn plants, introgression of genetic resistance is a proven strategy for developing new resistant lines. While host proteins involved in genome replication and cell to cell movement are widely studied, other cell mechanisms responsible for virus infection remain under investigated. Endosomal sorting complexes required for transport (ESCRT) play a key role in membrane trafficking in plants and are involved in the replication of several plant RNA viruses. In this work, we describe the role of the ESCRT protein CmVPS4 as a new susceptibility factor to the Potyvirus Watermelon mosaic virus (WMV) in melon. Using a worldwide collection of melons, we identified three different alleles carrying non-synonymous substitutions in CmVps4. Two of these alleles were shown to be associated with WMV resistance. Using a complementation approach, we demonstrated that resistance is due to a single non-synonymous substitution in the allele CmVps4P30R. This work opens up new avenues of research on a new family of host factors required for virus infection and new targets for resistance.
Effect of environmental signals on growth and development in mosses
Authors: Mohanasundaram Boominathan , Pandey Sona 
Published: April 2022

AbstractPlants perceive a multitude of environmental signals and stresses, and integrate their response to them in ways that culminate in modified phenotypes, optimized for plant survival. This ability of plants, known as phenotypic plasticity, is found throughout evolution, in all plant lineages. For any given environment, the specifics of the response to a particular signal may vary depending on the plants’ unique physiology and ecological niche. The bryophyte lineage, including mosses, which diverged from the vascular plants ~450–430 million years ago, represent a unique ecological and phylogenetic group in plant evolution. Several aspects of the moss life cycle, their morphology including the presence of specialized tissue types and distinct anatomical features, gene repertoires and networks, as well as the habitat differ significantly from those of vascular plants. To evaluate the outcomes of these differences, we explore the phenotypic responses of mosses to environmental signals such as light, temperature, CO2, water, nutrients, and gravity, and compare those with what is known in vascular plants. We also outline knowledge gaps and formulate testable hypotheses based on the contribution of anatomical and molecular factors to specific phenotypic responses.
Visualization of in vivo protein–protein interactions in plants
Authors: Strotmann Vivien I , Stahl Yvonne 
Published: April 2022

Abstract
Molecular processes depend on the concerted and dynamic interactions of proteins, either by one-on-one interactions of the same or different proteins or by the assembly of larger protein complexes consisting of many different proteins. Here, not only the protein–protein interaction (PPI) itself, but also the localization and activity of the protein of interest (POI) within the cell is essential. Therefore, in all cell biological experiments, preserving the spatio-temporal state of one POI relative to another is key to understanding the underlying complex and dynamic regulatory mechanisms in vivo. In this review, we examine some of the applicable techniques to measure PPIs in planta as well as recent combinatorial advances of PPI methods to measure the formation of higher order complexes with an emphasis on in vivo imaging techniques. We compare the different methods and discuss their benefits and potential pitfalls to facilitate the selection of appropriate techniques by providing a comprehensive overview of how to measure in vivo PPIs in plants.
Climate and genetic data enhancement using deep learning analytics to improve maize yield predictability
Authors: Sarzaeim Parisa , Muñoz-Arriola Francisco , Jarquín Diego 
Published: April 2022

AbstractDespite efforts to collect genomics and phenomics (‘omics’) and environmental data, spatiotemporal availability and access to digital resources still limit our ability to predict plants’ response to changes in climate. Our goal is to quantify the improvement in the predictability of maize yields by enhancing climate data. Large-scale experiments such as the Genomes to Fields (G2F) are an opportunity to provide access to ‘omics’ and climate data. Here, the objectives are to: (i) improve the G2F ‘omics’ and environmental database by reducing the gaps of climate data using deep neural networks; (ii) estimate the contribution of climate and genetic database enhancement to the predictability of maize yields via environmental covariance structures in genotype by environment (G×E) modeling; and (iii) quantify the predictability of yields resulting from the enhancement of climate data, the implementation of the G×E model, and the application of three trial selection schemes (i.e. randomization, ranking, and precipitation gradient). The results show a 12.1% increase in predictability due to climate and ‘omics’ database enhancement. The consequent enhancement of covariance structures evidenced in all train–test schemes indicated an increase in maize yield predictability. The largest improvement is observed in the ‘random-based’ approach, which adds environmental variability to the model.
Auxin receptors as integrators of developmental and hormonal signals during reproductive development in pea
Authors: Ozga Jocelyn A , Jayasinghege Charitha P A , Kaur Harleen , Gao Lingchao , Nadeau Courtney D , Reinecke Dennis M 
Published: April 2022

Abstract
Auxins regulate many aspects of plant growth and development. In pea, three of the five TIR1/AFB members (PsTIR1a, PsTIR1b, and PsAFB2) have been implicated in auxin-related responses during fruit/seed development; however, the roles of PsAFB4 and PsAFB6 in these processes are unknown. Using yeast two-hybrid assays, we found that all five pea TIR1/AFB receptor proteins interacted with the pea AUX/IAAs PsIAA6 and/or PsIAA7 in an auxin-dependent manner, a requirement for functional auxin receptors. All five auxin receptors are expressed in young ovaries (pericarps) and rapidly developing seeds, with overlapping and unique developmental and hormone-regulated gene expression patterns. Pericarp PsAFB6 expression was suppressed by seeds and increased in response to deseeding, and exogenous hormone treatments suggest that seed-derived auxin and deseeding-induced ethylene are involved in these responses, respectively. Ethylene-induced elevation of pericarp PsAFB6 expression was associated with 4-Cl-IAA-specific reduction in ethylene responsiveness. In developing seeds, expression of PsTAR2 and PsYUC10 auxin biosynthesis genes was associated with high auxin levels in seed coat and cotyledon tissues, and PsAFB2 dominated the seed tissue transcript pool. Overall, auxin receptors had overlapping and unique developmental and hormone-regulated gene expression patterns during fruit/seed development, suggesting mediation of diverse responses to auxin, with PsAFB6 linking auxin and ethylene signaling.
Usefulness of Sōna Aspergillus Galactomannan LFA with digital readout as diagnostic and as screening tool of COVID-19 associated pulmonary aspergillosis in critically ill patients. Data from a multicenter prospective study performed in Argentina
Authors: Giusiano Gustavo , Fernández Norma B , Vitale Roxana G , Alvarez Christian , Ochiuzzi María Eugenia , Santiso Gabriela , Cabeza Matías Sebastián , Tracogna Fernanda , Farías Luciana , Afeltra Javier , Noblega Luciana María , Giuliano Carla Valeria , Garcia-Effron Guillermo 
Published: April 2022

Abstract

COVID-19-associated pulmonary aspergillosis (CAPA) incidence varies depending on the country. Serum galactomannan quantification is a promising diagnostic tool since samples are easy to obtain with low biosafety issues. A multicenter prospective study was performed to evaluate the CAPA incidence in Argentina and to assess the performance of the lateral flow assay with digital readout (Sōna Aspergillus LFA) as a CAPA diagnostic and screening tool. The correlation between the values obtained with Sōna Aspergillus LFA and Platelia® EIA was evaluated. In total, 578 serum samples were obtained from 185 critically ill COVID patients. CAPA screening was done weekly starting from the first week of ICU stay. Probable CAPA incidence in critically ill patients was 10.27% (19/185 patients when LFA was used as mycological criteria) and 9% (9/100 patients when EIA was used as mycological criteria). We found a very good correlation between the two evaluated galactomannan quantification methods (overall agreement of 92.16% with a Kappa statistic value of 0.721). CAPA diagnosis (&gt;0.5 readouts in LFA) were done during the first week of ICU stay in 94.7% of the probable CAPA patients. The overall mortality was 36.21%. CAPA patients' mortality and length of ICU stay were not statistically different from for COVID (non-CAPA) patients (42.11 vs 33.13% and 29 vs 24 days, respectively). These indicators were lower than in other reports. LFA-IMMY with digital readout is a reliable tool for early diagnosis of CAPA using serum samples in critically ill COVID patients. It has a good agreement with Platelia® EIA.

Lay Summary
The incidence of COVID-associated pulmonary aspergillosis (CAPA) in critically-ill Argentinian patients was established (10.27%). Serum galactomannan quantification was useful as a screening tool for this mycosis. A good agreement between Platelia® EIA and Sōna Aspergillus LFA is reported.
The rotation of planet-hosting stars
Authors: Sibony Yves , Helled Ravit , Feldmann Robert 
Published: April 2022

ABSTRACT
Understanding the distribution of angular momentum during the formation of planetary systems is a key topic in astrophysics. Data from the Kepler and Gaia missions allow to investigate whether stellar rotation is correlated with the presence of planets around Sun-like stars. Here, we perform a statistical analysis of the rotation period of 493 planet-hosting stars. These are matched to a control sample, without detected planets, with similar effective temperatures, masses, radii, metallicities, and ages. We find that planet-hosting stars rotate on average 1.63 ± 0.40 d slower. The difference in rotation is statistically significant both in samples including and not including planets confirmed by radial velocity follow-up observations. We also analyse the dependence of rotation distribution on various stellar and planetary properties. Our results could potentially be explained by planet detection biases depending on the rotation period of their host stars in both RV and transit methods. Alternatively, they could point to a physical link between the existence of planets and stellar rotation, emphasizing the need to understand the role of angular momentum in the formation and evolution planetary systems.
Where outflows meet inflows: gas kinematics in SSA22 Ly α blob 2 decoded by advanced radiative transfer modelling
Authors: Li Zhihui , Steidel Charles C , Gronke Max , Chen Yuguang , Matsuda Yuichi 
Published: April 2022

ABSTRACTWe present new spectroscopic observations of Ly α (Ly α) Blob 2 (z ∼ 3.1). We observed extended Ly α emission in three distinct regions, where the highest Ly α surface brightness (SB) centre is far away from the known continuum sources. We searched through the MOSFIRE slits that cover the high Ly α SB regions, but were unable to detect any significant nebular emission near the highest SB centre. We further mapped the flux ratio of the blue peak to the red peak and found it is anticorrelated with Ly α SB with a power-law index of ∼ –0.4. We used radiative transfer models with both multiphase, clumpy, and shell geometries and successfully reproduced the diverse Ly α morphologies. We found that most spectra suggest outflow-dominated kinematics, while 4/15 spectra imply inflows. A significant correlation exists between parameter pairs, and the multiphase, clumpy model may alleviate previously reported discrepancies. We also modelled Ly α spectra at different positions simultaneously and found that the variation of the inferred clump outflow velocities can be approximately explained by line-of-sight projection effects. Our results support the ‘central powering + scattering’ scenario, i.e. the Ly α photons are generated by a central powering source and then scatter with outflowing, multiphase H  i gas while propagating outwards. The infalling of cool gas near the blob outskirts shapes the observed blue-dominated Ly α profiles, but its energy contribution to the total Ly α luminosity is less than 10 per cent, i.e. minor compared to the photoionization by star-forming galaxies and/or AGNs.
Supernovae and photoionizing feedback in spiral arm molecular clouds
Authors: Bending Thomas J R , Dobbs Clare L , Bate Matthew R 
Published: April 2022

ABSTRACT
We explore the interplay between supernovae and the ionizing radiation of their progenitors in star-forming regions. The relative contributions of these stellar feedback processes are not well understood, particularly on scales greater than a single star-forming cloud. We focus predominantly on how they affect the interstellar medium. We re-simulate a 500 pc2 region from previous work that included photoionization and add supernovae. Over the course of 10 Myr, more than 500 supernovae occur in the region. The supernova remnants cool very quickly in the absence of earlier photoionization, but form much larger and more spherical hot bubbles when photoionization is present. Overall, the photoionization has a significantly greater effect on gas morphology and the sites of star formation. However, the two processes are comparable when looking at their effect on velocity dispersion. When combined, the two feedback processes increase the velocity dispersions by more than the sum of their parts, particularly on scales above 5 pc.
Is Terzan 5 the remnant of a building block of the Galactic bulge? Evidence from APOGEE
Authors: Taylor Dominic J , Mason Andrew C , Schiavon Ricardo P , Horta Danny , Nataf David M , Geisler Doug , Kisku Shobhit , Phillips Siân G , Cohen Roger E , Fernández-Trincado José G , Beers Timothy C , Bizyaev Dmitry , García-Hernández Domingo Aníbal , Lane Richard R , Longa-Peña Penélope , Minniti Dante , Muñoz Cesar , Pan Kaike , Villanova Sandro 
Published: April 2022

ABSTRACT
It has been proposed that the globular cluster-like system Terzan 5 is the surviving remnant of a primordial building block of the Milky Way bulge, mainly due to the age/metallicity spread and the distribution of its stars in the α–Fe plane. We employ Sloan Digital Sky Survey data from the Apache Point Observatory Galactic Evolution Experiment to test this hypothesis. Adopting a random sampling technique, we contrast the abundances of 10 elements in Terzan 5 stars with those of their bulge field counterparts with comparable atmospheric parameters, finding that they differ at statistically significant levels. Abundances between the two groups differ by more than 1σ in Ca, Mn, C, O, and Al, and more than 2σ in Si and Mg. Terzan 5 stars have lower [α/Fe] and higher [Mn/Fe] than their bulge counterparts. Given those differences, we conclude that Terzan 5 is not the remnant of a major building block of the bulge. We also estimate the stellar mass of the Terzan 5 progenitor based on predictions by the Evolution and Assembly of GaLaxies and their Environments suite of cosmological numerical simulations, concluding that it may have been as low as ∼3 × 108 M⊙ so that it was likely unable to significantly influence the mean chemistry of the bulge/inner disc, which is significantly more massive (∼1010 M⊙). We briefly discuss existing scenarios for the nature of Terzan 5 and propose an observational test that may help elucidate its origin.
Distal coronary artery abnormalities in Kawasaki disease: experience on CT coronary angiography in 176 children
Authors: Singhal Manphool , Pilania Rakesh Kumar , Jindal Ankur Kumar , Gupta Aman , Sharma Avinash , Guleria Sandesh , Johnson Nameirakpam , Maralakunte Muniraju , Vignesh Pandiarajan , Suri Deepti , Sandhu Manavjit Singh , Singh Surjit 
Published: April 2022

AbstractObjectivePrecise evaluation of coronary artery abnormalities (CAAs) in Kawasaki disease (KD) is essential. The aim of this study is to determine role of CT coronary angiography (CTCA) for detection of CAAs in distal segments of coronary arteries in patients with KD.MethodsCTCA findings of KD patients with distal coronary artery involvement were compared with those on transthoracic echocardiography (TTE) during the period 2013–21.ResultsAmong 176 patients with KD who underwent CTCA (128-Slice Dual Source scanner), 23 (13.06%) had distal CAAs (right coronary—15/23; left anterior descending—14/23; left circumflex—4/23 patients). CTCA identified 60 aneurysms—37 proximal (36 fusiform; 1 saccular) and 23 distal (17 fusiform; 6 saccular); 11 patients with proximal aneurysms had distal contiguous extension; 9 patients showed non-contiguous aneurysms in both proximal and distal segments; 4 patients showed distal segment aneurysms in absence of proximal involvement of same coronary artery; 4 patients had isolated distal CAAs. On TTE, only 40 aneurysms could be identified. Further, distal CAAs could not be identified on TTE. CTCA also identified complications (thrombosis, mural calcification and stenosis) that were missed on TTE.ConclusionsCAAs can, at times, occur in distal segments in isolation and also in association with, or extension of, proximal CAAs. CTCA demonstrates CAAs in distal segments of coronary arteries, including branches, in a significant number of children with KD—these cannot be detected on TTE. CTCA may therefore be considered as a complimentary imaging modality in children with KD who have CAAs on TTE.