bluuebunny/crossref_metadata_2025_split huggingface dataset:
A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina
Authors: Friis Guillermo , Vizueta Joel , Smith Edward G , Nelson David R , Khraiwesh Basel , Qudeimat Enas , Salehi-Ashtiani Kourosh , Ortega Alejandra , Marshell Alyssa , Duarte Carlos M , Burt John A 
Published: February 2021

Abstract
The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied, especially across populations of the West Indian Ocean. High-quality genomic resources accounting for such variability are also sparse. Here we report the first chromosome-level assembly of the genome of A. marina. We used a previously release draft assembly and proximity ligation libraries Chicago and Dovetail HiC for scaffolding, producing a 456,526,188-bp long genome. The largest 32 scaffolds (22.4–10.5 Mb) accounted for 98% of the genome assembly, with the remaining 2% distributed among much shorter 3,759 scaffolds (62.4–1 kb). We annotated 45,032 protein-coding genes using tissue-specific RNA-seq data in combination with de novo gene prediction, from which 34,442 were associated to GO terms. Genome assembly and annotated set of genes yield a 96.7% and 95.1% completeness score, respectively, when compared with the eudicots BUSCO dataset. Furthermore, an FST survey based on resequencing data successfully identified a set of candidate genes potentially involved in local adaptation and revealed patterns of adaptive variability correlating with a temperature gradient in Arabian mangrove populations. Our A. marina genomic assembly provides a highly valuable resource for genome evolution analysis, as well as for identifying functional genes involved in adaptive processes and speciation.
Diploid chromosome-scale assembly of theMuscadinia rotundifoliagenome supports chromosome fusion and disease resistance gene expansion duringVitisandMuscadiniadivergence
Authors: Cochetel Noé , Minio Andrea , Massonnet Mélanie , Vondras Amanda M , Figueroa-Balderas Rosa , Cantu Dario 
Published: February 2021

AbstractMuscadinia rotundifolia, the muscadine grape, has been cultivated for centuries in the southeastern United States. M. rotundifolia is resistant to many of the pathogens that detrimentally affect Vitis vinifera, the grape species commonly used for winemaking. For this reason, M. rotundifolia is a valuable genetic resource for breeding. Single-molecule real-time reads were combined with optical maps to reconstruct the two haplotypes of each of the 20 M. rotundifolia cv. Trayshed chromosomes. The completeness and accuracy of the assembly were confirmed using a high-density linkage map. Protein-coding genes were annotated using an integrated and comprehensive approach. This included using full-length cDNA sequencing (Iso-Seq) to improve gene structure and hypothetical spliced variant predictions. Our data strongly support that Muscadinia chromosomes 7 and 20 are fused in Vitis and pinpoint the location of the fusion in Cabernet Sauvignon and PN40024 chromosome 7. Disease-related gene numbers in Trayshed and Cabernet Sauvignon were similar, but their clustering locations were different. A dramatic expansion of the Toll/Interleukin-1 Receptor-like Nucleotide-Binding Site Leucine-Rich Repeat (TIR-NBS-LRR) class was detected on Trayshed chromosome 12 at the Resistance to Uncinula necator 1 (RUN1)/Resistance to Plasmopara viticola 1 (RPV1) locus, which confers strong dominant resistance to powdery and downy mildews. A genome browser, annotation, and Blast tool for Trayshed are available at www.grapegenomics.com.
Divergent Anabolic Response to Exercise in Young and Older Adult Men-Dependency on Time Frame of Measurement
Authors: Reitelseder Søren , Bülow Jacob , Holm Lars 
Published: February 2021

Abstract
Older adults’ skeletal muscle has shown to be less responsive to anabolic stimuli as compared to young both in vitro, in short and controlled in vivo settings and in long-term training studies. However, to translate controlled mechanistic findings to long-term adaptations intermediate measures allowing daily life routines with regard to activity and diet would be useful to evaluate physiological interventions. The purpose of this study was to investigate the exercise effect in young and older adults with 2 independent methods to measure muscle protein synthesis rate. Healthy young and old men were recruited to the study protocol where myofibrillar fractional synthesis rate was measured during 2 days allowing normal activities of daily living with D2O-labeled alanine and during 4 hours in the overnight fasted state with [13C6]phenylalanine infusion. During this period 1 leg completed an exercise session every day (exercise leg) while the contralateral leg was kept inactive (normal leg). Both legs were used for activities of daily living. Two-day myofibrillar fractional synthesis rate was significantly higher in the exercise leg in both young and old as compared to normal leg with no age difference. The 4-hour overnight fasted myofibrillar fractional synthesis rate showed that only young exercise leg was significantly higher than normal leg. The present findings support the notion that anabolic resistance exists in the skeletal muscle of healthy older men when evaluated in controlled settings. However, this response is not as clear when measured during daily life where variance is greater, which calls for further investigations in larger cohorts.
Core transcriptional networks in Williams syndrome: IGF1-PI3K-AKT-mTOR, MAPK and actin signaling at the synapse echo autism
Authors: Dai Li , Weiss Robert B , Dunn Diane M , Ramirez Anna , Paul Sharan , Korenberg Julie R 
Published: February 2021

AbstractGene networks for disorders of social behavior provide the mechanisms critical for identifying therapeutic targets and biomarkers. Large behavioral phenotypic effects of small human deletions make the positive sociality of Williams syndrome (WS) ideal for determining transcriptional networks for social dysfunction currently based on DNA variations for disorders such as autistic spectrum disorder (ASD) and schizophrenia (SCHZ). Consensus on WS networks has been elusive due to the need for larger cohort size, sensitive genome-wide detection and analytic tools. We report a core set of WS network perturbations in a cohort of 58 individuals (34 with typical, 6 atypical deletions and 18 controls). Genome-wide exon-level expression arrays robustly detected changes in differentially expressed gene (DEG) transcripts from WS deleted genes that ranked in the top 11 of 12 122 transcripts, validated by quantitative reverse transcription PCR, RNASeq and western blots. WS DEG’s were strictly dosed in the full but not the atypical deletions that revealed a breakpoint position effect on non-deleted CLIP2, a caveat for current phenotypic mapping based on copy number variants. Network analyses tested the top WS DEG’s role in the dendritic spine, employing GeneMANIA to harmonize WS DEGs with comparable query gene-sets. The results indicate perturbed actin cytoskeletal signaling analogous to the excitatory dendritic spines. Independent protein–protein interaction analyses of top WS DEGs generated a 100-node graph annotated topologically revealing three interacting pathways, MAPK, IGF1-PI3K-AKT-mTOR/insulin and actin signaling at the synapse. The results indicate striking similarity of WS transcriptional networks to genome-wide association study-based ASD and SCHZ risk suggesting common network dysfunction for these disorders of divergent sociality.
A Global Synthesis of the Correspondence Between Epizoic Barnacles and Their Sea Turtle Hosts
Authors: Zardus John D 
Published: February 2021

SynopsisBarnacles that are obligate epizoites of sea turtles are not parasites in the traditional sense. However, they can impair their hosts in some instances, disqualifying the association as strictly commensal. Characterizing these interactions requires knowing which epibionts pair with which hosts, but records of barnacles from sea turtles are scattered and symbiont/host match-ups remain equivocal. The objective of this study was to collate global records on the occurrence of barnacles with sea turtles and describe each species pair quantitatively. Records reporting barnacles with sea turtles were searched spanning the last 167 years, including grey literature, and findings were enumerated for 30,580 individual turtles to evaluate prevalence. The data were summarized globally as well as subdivided across six geographic regions to assess constancy of the affiliations. Patterns of partnering were visualized by hierarchical clustering analysis of percent occurrence values for each barnacle/turtle pair and the relative selectivity of each symbiont and susceptibility of each host were evaluated. After adjusting for synonymies and taxonomic inaccuracies, the occurrence of 16 nominal species of barnacles was recorded from all 7 extant sea turtle species. Mostly, barnacles were not specific to single turtle species, partnering on average with three hosts each. Neither were barnacles entirely host-consistent among regions. Three barnacles were common to all sea turtles except leatherbacks. The most common, widespread, and least selective barnacle was Chelonibia testudinaria, the only symbiont of all turtles. Excluding single-record occurrences, the barnacle Stomatolepas transversa was the only single-host associate of any hard-shell sea turtle (the green sea turtle) and Platylepas coriacea and Stomatolepas dermochelys were exclusive associates of leatherback sea turtles. Green sea turtles were the most vulnerable to epibiosis, hosting 13 barnacle species and Kemp’s ridley sea turtles were the least, hosting three. Geographically, there was an average of nine barnacle species per world region, with diversity highest in the Pacific Ocean (12 species) and lowest in the Mediterranean Sea (6 species). It is paradoxical that the flexibility of barnacles for multiple host species contrasts with their overall strict specificity for sea turtles, with each symbiont occupying a virtually unique suite of turtle hosts.
Application of Critical Care Scores in Severely Burned Patients
Authors: Dastagir Khaled , Krezdorn Nicco , Bingoel Alperen Sabri , Mett Tobias R , Radtke Christine , Jokuszies Andreas , Vogt Peter M 
Published: February 2021

Abstract
Early detection of sepsis is of crucial importance in patients with severe burn injuries. However, according to the S1-guideline, based on systemic inflammatory response syndrome (SIRS) criteria, the early diagnosis of sepsis in severely burned patients is difficult. The value of the new definition of sepsis based on sequential organ failure assessment (SOFA) according to S3-guidelines for patients with severe burn injuries is not described in detail in the literature. We analyzed retrospectively all data during the period 2014 to 2018 from the electronic patient information system. Using the receiver operating characteristic curve, the area under the curve was calculated for the diagnostic value of procalcitonin, SIRS, and SOFA score according to the burned total body surface area. Six hundred fifty-one patients with burn injuries were admitted to our burn unit, 315 of them had burn injuries affecting more than 10% body surface area with partial- to full-thickness burns (grade 2–4). In this group, 59 patients showed one or more septic events in the course of the intensive care treatment, defined by positive bloodstream infection. Both S1- and S3-guidelines were inappropriate to diagnose sepsis in patients with severe burn injuries. Due to pathophysiological changes of the body function in severely burned patients, which show features of both SIRS and pathological SOFA scores (&gt;2 points) at the outset of burn injury, the diagnosis of sepsis associated with burns is intricate in this patient group. Assessing data for potential hallmarks of sepsis in burn patients we found procalcitonin to show a significant correlation with sepsis.
Undeliverable Sapien 3 prosthesis in transaortic transcatheter aortic valve implantation
Authors: Shirasaka Tomonori , Kunioka Shingo , Kitani Yuya , Kamiya Hiroyuki 
Published: February 2021

Abstract
In transaortic (TAo) trasncatheter aortic valve implantation (TAVI), direct transmission of forces to the stenotic aortic valve is possible. Therefore, the need of balloon aortic valvoplasty in TAo-TAVI may be very limited regarding the deliverability of TAVI prosthesis. However, if the TAVI prosthesis becomes undeliverable, it becomes seriously problematic. Herein, we present a case of TAo-TAVI in which the TAVI prosthesis was undeliverable, and it was forcefully pushed together with the introducer system into the aortic valve as a bailout technique.
Molecular interplay between phytohormones and geminiviruses: a saga of a never-ending arms race
Authors: Ghosh Dibyendu , Chakraborty Supriya 
Published: February 2021

AbstractGeminiviruses can infect a wide range of plant hosts worldwide and have hence become an emerging global agroeconomic threat. The association of these viruses with satellite molecules and highly efficient insect vectors such as whiteflies further prime their devastating impacts. Plants elicit a strong antiviral immune response to restrict the invasion of these destructive pathogens. Phytohormones help plants to mount this response and occupy a key position in combating these biotrophs. These defense hormones not only inhibit geminiviral propagation but also hamper viral transmission by compromising the performance of their insect vectors. Nonetheless, geminiviruses have co-evolved to have a few multitasking virulence factors that readily remodel host cellular machineries to circumvent the phytohormone-mediated manifestation of the immune response. Furthermore, these obligate parasites exploit plant growth hormones to produce a cellular environment permissive for virus replication. In this review, we outline the current understanding of the roles and regulation of phytohormones in geminiviral pathogenesis.
The Influence of a 14-Week Infantry Commanders Courses on the Achilles Tendon and Patellar Tendon Structure
Authors: Steinberg Nili , Funk Shany , Svorai-Band Shani , Yavnai Nirit , Pantanowitz Michal , Zeev Aviva , Dar Gali 
Published: February 2021

ABSTRACT

Introduction
Alternated tendon structure may raise stress to the musculoskeletal structures and may increase the potential for overuse injury. Screening the tendon structure of soldiers pre- and post-participation in a strenuous combat course is essential. The aim of the present study was to investigate the influence of a 14-week infantry commanders courses on the Achilles tendon (AT) structure and patellar tendon (PT) structure in combat soldiers.

Materials and Methods
Ninety-eight participants from an infantry commanders course were screened pre- and post-course for the AT and PT structures, using ultrasonographic tissue characterizaton (UTC) imaging to capture a 3D structure of four echo-type fibers (I-IV).

Results
In both tendons, the mean relative frequency of echo-type I fibers significantly decreased from pre- to post-testing, with a significant increase in the relative frequency of echo-types II, III, and IV fibers. In the AT, 60.2% of the subjects showed positive differences (between pre- and post-testing in the echo-type III + IV fiber (“worsened” tendon structure), whereas in the PT, 92.2% of the subject showed an increased frequency. No significant correlation (r = 0.108; P = .324) was found between the differences of echo-type III + IV fibers of the AT and that of the PT.

Conclusions
Loads to the musculoskeletal structures along the combat course increased the mean relative frequency of the “reduced” echo-type fibers (III + IV) in both the AT structure and the PT structure. Yet, whereas in the AT around 40% of the soldiers showed an improved tendon structure along the course, in the PT less than 10% of the soldiers showed that improvement. Soldiers and commanders should be aware of the different influence of the loading exercises along the course on the AT and on the PT structure, as “reduced” tendons structure might put the soldiers at higher risk for injury in the future.
Baryon acoustic oscillations in the projected cross-correlation function between the eBOSS DR16 quasars and photometric galaxies from the DESI Legacy Imaging Surveys
Authors: Zarrouk Pauline , Rezaie Mehdi , Raichoor Anand , Ross Ashley J , Alam Shadab , Blum Robert , Brookes David , Chuang Chia-Hsun , Cole Shaun , Dawson Kyle S , Eisenstein Daniel J , Kehoe Robert , Landriau Martin , Moustakas John , Myers Adam D , Norberg Peder , Percival Will J , Prada Francisco , Schubnell Michael , Seo Hee-Jong , Tarlé Gregory , Zhao Cheng 
Published: February 2021

ABSTRACT
We search for the baryon acoustic oscillations in the projected cross-correlation function binned into transverse comoving radius between the SDSS-IV DR16 eBOSS quasars and a dense photometric sample of galaxies selected from the DESI Legacy Imaging Surveys. We estimate the density of the photometric sample of galaxies in this redshift range to be about 2900 deg−2, which is deeper than the official DESI emission line galaxy selection, and the density of the spectroscopic sample is about 20 deg−2. In order to mitigate the systematics related to the use of different imaging surveys close to the detection limit, we use a neural network approach that accounts for complex dependences between the imaging attributes and the observed galaxy density. We find that we are limited by the depth of the imaging surveys that affects the density and purity of the photometric sample and its overlap in redshift with the quasar sample, which thus affects the performance of the method. When cross-correlating the photometric galaxies with quasars in the range 0.6 ≤ z ≤ 1.2, the cross-correlation function can provide better constraints on the comoving angular distance DM (6 per cent precision) compared to the constraint on the spherically averaged distance DV (9 per cent precision) obtained from the autocorrelation. Although not yet competitive, this technique will benefit from the arrival of deeper photometric data from upcoming surveys that will enable it to go beyond the current limitations we have identified in this work.
The substructure of the Perseus star-forming region: a survey with Gaia DR2
Authors: Pavlidou Tatiana , Scholz Aleks , Teixeira Paula S 
Published: February 2021

ABSTRACT
We use photometric and kinematic data from Gaia DR2 to explore the structure of the star-forming region associated with the molecular cloud of Perseus. Apart from the two well-known clusters, IC 348 and NGC 1333, we present five new clustered groups of young stars, which contain between 30 and 300 members, named Autochthe, Alcaeus, Heleus, Electryon, and Mestor. We demonstrate that these are co-moving groups of young stars, based on how the candidate members are distributed in position, proper motion, parallax, and colour–magnitude space. By comparing their colour–magnitude diagrams to isochrones, we show that they have ages between 1 and 5 Myr. Using 2MASS and WISE colours, we find that the fraction of stars with discs in each group ranges from 10 to ∼50 per cent. The youngest of the new groups is also associated with a reservoir of cold dust, according to the Planck map at 353 GHz. We compare the ages and proper motions of the five new groups to those of IC 348 and NGC 1333. Autochthe is clearly linked with NGC 1333 and may have formed in the same star formation event. The seven groups separate roughly into two sets that share proper motion, parallax, and age: Heleus, Electryon, and Mestor as the older set, and NGC 1333 and Autochthe as the younger set. Alcaeus is kinematically related to the younger set, but at a more advanced age, while the properties of IC 348 overlap with both sets. All older groups in this star-forming region are located at higher galactic latitude.
The likelihood of undiscovered globular clusters in the outskirts of the Milky Way
Authors: Webb Jeremy J , Carlberg Raymond G 
Published: February 2021

ABSTRACT
The currently known Galactic globular cluster population extends out to a maximum galactocentric distance of ∼145 kpc, with the peculiarity that the outermost clusters predominantly have an inward velocity. Orbit averaging finds that this configuration occurs by chance about $6{{\ \rm per\ cent}}$ of the time, suggesting that several globular clusters with positive radial velocities remain undiscovered. We evaluate the expected number of undiscovered clusters at large distances under the assumption that the cluster population has a smooth radial distribution and is in equilibrium within the Milky Way’s virial radius. By comparing the present day kinematic properties of outer clusters to random orbital configurations of the Galactic globular cluster system through orbit averaging, we estimate a likelihood of $73{{\ \rm per\ cent}}$ of there being at least one undiscovered globular cluster within the Milky Way. This estimate assumes the current population is complete out to 50 kpc, and increases to $91{{\ \rm per\ cent}}$ if the population is complete out to 150 kpc. The likelihood of there being two undiscovered clusters is between $60$ and $70{{\ \rm per\ cent}}$, with the likelihood of there being three undiscovered clusters being on the order of $50{{\ \rm per\ cent}}$. The most likely scenario is that the undiscovered clusters are moving outwards, which results in the outer cluster population being consistent with an equilibrium state. Searches for distant and possibly quite low concentration and very low metallicity globular clusters will be enabled with upcoming deep imaging surveys.
Reconstructing three-dimensional densities from two-dimensional observations of molecular gas
Authors: Hu Zipeng , Krumholz Mark R , Federrath Christoph , Pokhrel Riwaj , Gutermuth Robert A 
Published: February 2021

ABSTRACT
Star formation has long been known to be an inefficient process, in the sense that only a small fraction ϵff of the mass of any given gas cloud is converted to stars per cloud free-fall time. However, developing a successful theory of star formation will require measurements of both the mean value of ϵff and its scatter from one molecular cloud to another. Because ϵff is measured relative to the free-fall time, such measurements require accurate determinations of cloud volume densities. Efforts to measure the volume density from two-dimensional projected data, however, have thus far relied on treating molecular clouds as simple uniform spheres, while their real shapes are likely to be filamentary and their density distributions far from uniform. The resulting uncertainty in the true volume density is likely to be one of the major sources of error in observational estimates of ϵff. In this paper, we use a suite of simulations of turbulent, magnetized, radiative, self-gravitating star-forming clouds in order to examine whether it is possible to obtain more accurate volume density estimates and thereby reduce this error. We create mock observations from the simulations, and show that current analysis methods relying on the spherical assumption likely yield ∼0.26 dex underestimations and ∼0.51 dex errors in volume density estimates, corresponding to a ∼0.13 dex overestimation and a ∼0.25 dex scatter in ϵff, comparable to the scatter in observed cloud samples. We build a predictive model that uses information accessible in two-dimensional measurements – most significantly, the Gini coefficient of the surface density distribution – to produce estimates of the volume density with ∼0.3 dex less scatter. We test our method on a recent observation of the Ophiuchus cloud, and show that it successfully reduces the ϵff scatter.