bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeny and lipid profiles of snow-algae isolated from Norwegian red-snow microbiomes
Authors: Suzuki Hirono , Détain Alexandre , Park Youngjin , Viswanath Kiron , Wijffels René H , Leborgne-Castel Nathalie , Procházková Lenka , Hulatt Chris J 
Published: May 2023

Abstract
Snow algae blooms often form green or red coloured patches in melting alpine and polar snowfields worldwide, yet little is known about their biology, biogeography, and species diversity. We investigated eight isolates collected from red snow in northern Norway, using a combination of morphology, 18S rRNA gene and internal transcribed spacer 2 (ITS2) genetic markers. Phylogenetic and ITS2 rRNA secondary structure analyses assigned six isolates to the species Raphidonema nivale, Deuterostichococcus epilithicus, Chloromonas reticulata, and Xanthonema bristolianum. Two novel isolates belonging to the family Stichococcaceae (ARK-S05-19) and the genus Chloromonas (ARK-S08-19) were identified as potentially new species. In laboratory cultivation, differences in the growth rate and fatty acid profiles were observed between the strains. Chlorophyta were characterized by abundant C18:3n-3 fatty-acids with increases in C18:1n-9 in the stationary phase, whilst Xanthonema (Ochrophyta) was characterized by a large proportion of C20:5n-3, with increases in C16:1n-7 in the stationary phase. In a further experiment, lipid droplet formation was studied in C. reticulata at the single-cell level using imaging flow cytometry. Our study establishes new cultures of snow algae, reveals novel data on their biodiversity and biogeography, and provides an initial characterization of physiological traits that shape natural communities and their ecophysiological properties.
Insights into the Genomics of Clownfish Adaptive Radiation: The Genomic Substrate of the Diversification
Authors: Marcionetti Anna , Salamin Nicolas 
Published: May 2023

Abstract
Clownfishes are an iconic group of coral reef fishes that evolved a mutualistic interaction with sea anemones, which triggered the rapid diversification of the group. Following the emergence of this mutualism, clownfishes diversified into different ecological niches and developed convergent phenotypes associated with their host use. The genetic basis of the initial acquisition of the mutualism with host anemones has been described, but the genomic architecture underlying clownfish diversification once the mutualism was established and the extent to which clownfish phenotypic convergence originated through shared genetic mechanisms are still unknown. Here, we investigated these questions by performing comparative genomic analyses on the available genomic data of five pairs of closely related but ecologically divergent clownfish species. We found that clownfish diversification was characterized by bursts of transposable elements, an overall accelerated coding evolution, incomplete lineage sorting, and ancestral hybridization events. Additionally, we detected a signature of positive selection in 5.4% of the clownfish genes. Among them, five presented functions associated with social behavior and ecology, and they represent candidate genes involved in the evolution of the size-based hierarchical social structure so particular to clownfishes. Finally, we found genes with patterns of either relaxation or intensification of purifying selection and signals of positive selection linked with clownfish ecological divergence, suggesting some level of parallel evolution during the diversification of the group. Altogether, this work provides the first insights into the genomic substrate of clownfish adaptive radiation and integrates the growing collection of studies investigating the genomic mechanisms governing species diversification.
Sarcopenia Definition and Outcomes Consortium 2020 Definition: Association and Discriminatory Accuracy of Sarcopenia With Disability in the Canadian Longitudinal Study on Aging
Authors: Mayhew Alexandra J , Sohel Nazmul , Beauchamp Marla K , Phillips Stuart , Raina Parminder 
Published: May 2023

Abstract

Background
Previous sarcopenia definitions have poor discriminatory accuracy for identifying people with/without relevant health outcomes, and poor agreement between methods of operationalizing sarcopenia criterion. The 2020 Sarcopenia Definitions and Outcomes Consortium (SDOC) definition recommends grip strength (absolute, or standardized to body mass index, total body fat, lean arm mass, or weight), and gait speed. The agreement between methods of operationalizing grip strength and discriminatory accuracy of the SDOC definition for health outcomes such as activities of daily living (ADL) disability is unknown.

Methods
Cross-sectional analyses of 27 924 Canadian Longitudinal Study on Aging participants aged 45–85 at baseline (2012–2015) stratified by sex. The associations of the SDOC definitions with ADL disability were assessed using logistic regression. Area under the curve (AUC) analyses were conducted to assess discriminatory accuracy. Agreement between methods of operationalizing grip strength was measured using Cohen’s kappa.

Results
Sarcopenia was associated with 1.60 (1.42–1.80) to 5.80 (4.89–6.88) greater odds of ADL disability with AUC values between 0.60 and 0.81. Agreement between methods of operationalizing grip strength was between 0.10–0.80 for grip strength alone and 0.45–0.91 when combined with gait speed.

Conclusions
The SDOC-suggested criteria of grip strength and gait speed are significantly associated with ADL disability and have high discriminatory accuracy. However, the agreement between methods of operationalizing grip strength tended to be modest, and AUC, sensitivity, and specificity differed depending on the definition. We suggest a single measure of grip strength be considered and age-stratified cutoff values to improve AUC values.
Developmental dynamics of chromatin accessibility during post-implantation development of monkey embryos
Authors: Dai Xi , Shao Honglian , Sun Nianqin , Ci Baiquan , Wu Jun , Liu Chuanyu , Wu Liang , Yuan Yue , Wei Xiaoyu , Yang Huanming , Liu Longqi , Ji Weizhi , Bai Bing , Shang Zhouchun , Tan Tao 
Published: May 2023

Abstract

Background
Early post-implantation development, especially gastrulation in primates, is accompanied by extensive drastic chromatin reorganization, which remains largely elusive.

Results
To delineate the global chromatin landscape and understand the molecular dynamics during this period, a single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) was applied to in vitro cultured cynomolgus monkey (Macaca fascicularis, hereafter referred to as monkey) embryos to investigate the chromatin status. First, we delineated the cis-regulatory interactions and identified the regulatory networks and critical transcription factors involved in the epiblast (EPI), hypoblast, and trophectoderm/trophoblast (TE) lineage specification. Second, we observed that the chromatin opening of some genome regions preceded the gene expression during EPI and trophoblast specification. Third, we identified the opposing roles of FGF and BMP signaling in pluripotency regulation during EPI specification. Finally, we revealed the similarity between EPI and TE in gene expression profiles and demonstrated that PATZ1 and NR2F2 were involved in EPI and trophoblast specification during monkey post-implantation development.

Conclusions
Our findings provide a useful resource and insights into dissecting the transcriptional regulatory machinery during primate post-implantation development.
3-D crustal shear wave velocity model derived from full-waveform tomography for Central Honshu Island, Japan
Authors: Mukumoto Kota , Tsuji Takeshi 
Published: May 2023

SUMMARY
We present a crustal shear wave (S-wave) velocity model for central Japan that accurately captures the previously mapped geology and lithology of the region. We perform a full-waveform tomographic inversion using a large seismic data volume that was recorded by the dense, permanent seismic monitoring network that spans the Japan Islands to resolve the seismic structure beneath central Honshu Island. The inversion reduces the time–frequency phase misfit by 16.4 and 6.7 per cent in the 20–50-s and 10–30-s period ranges, respectively. We infer that the resolved seismic velocity anomalies in our inversion reflect a range of subsurface features, including volcanic fluids, dehydration fluids from the subducted crust and sedimentary basins. In contrast to previous S-wave velocity models of the same region, which have been based primarily on first-arrival tomography, our S-wave velocity model is based on the explicit computation of the full seismic wavefield. This approach makes our model more suitable for modelling seismic wavefields in the 10–50-s period range and enables high-resolution imaging of the subsurface.
Instantaneous 3D tomography-based convection beneath the Rungwe Volcanic Province, East Africa: implications for melt generation
Authors: Njinju Emmanuel A , Stamps D Sarah , Atekwana Estella A , Rooney Tyrone O , Rajaonarison Tahiry A 
Published: May 2023

SUMMARY
Within the Western Branch of the East African Rift (EAR), volcanism is highly localized, which is distinct from the voluminous magmatism seen throughout the Eastern Branch of the EAR. A possible mechanism for the source of melt beneath the EAR is decompression melting in response to lithospheric stretching. However, the presence of pre-rift magmatism in both branches of the EAR suggest an important role of plume-lithosphere interactions, which validates the presence of voluminous magmatism in the Eastern Branch, but not the localized magmatism in the Western Branch. We hypothesize that the interaction of a thermally heterogeneous asthenosphere (plume material) with the base of the lithosphere enables localization of deep melt sources beneath the Western Branch where there are sharp variations in lithospheric thickness. To test our hypothesis, we investigate sublithospheric mantle flow beneath the Rungwe Volcanic Province (RVP), which is the southernmost volcanic center in the Western Branch. We use seismically constrained lithospheric thickness and sublithospheric mantle structure to develop an instantaneous 3D thermomechanical model of tomography-based convection (TBC) with melt generation beneath the RVP using ASPECT. Shear wave velocity anomalies suggest excess temperatures reach ∼250 K beneath the RVP. We use the excess temperatures to constrain parameters for melt generation beneath the RVP and find that melt generation occurs at a maximum depth of ∼140 km. The TBC models reveal mantle flow patterns not evident in lithospheric modulated convection (LMC) that do not incorporate upper mantle constraints. The LMC model indicates lateral mantle flow at the base of the lithosphere over a longer interval than the TBC model, which suggests that mantle tractions from LMC might be overestimated. The TBC model provides higher melt fractions with a slightly displaced melting region when compared to LMC models. Our results suggest that upwellings from a thermally heterogeneous asthenosphere distribute and localize deep melt sources beneath the Western Branch in locations where there are sharp variations in lithospheric thickness. Even in the presence of a uniform lithospheric thickness in our TBC models, we still find a characteristic upwelling and melt localization beneath the RVP, which suggest that sublithospheric heterogeneities exert a dominant control on upper mantle flow and melt localization than lithospheric thickness variations. Our TBC models demonstrate the need to incorporate upper mantle constraints in mantle convection models and have global implications in that small-scale convection models without upper mantle constraints should be interpreted with caution.
Graph-based approximate message passing iterations
Authors: Gerbelot Cédric , Berthier Raphaël 
Published: May 2023

Abstract
Approximate message passing (AMP) algorithms have become an important element of high-dimensional statistical inference, mostly due to their adaptability and concentration properties, the state evolution (SE) equations. This is demonstrated by the growing number of new iterations proposed for increasingly complex problems, ranging from multi-layer inference to low-rank matrix estimation with elaborate priors. In this paper, we address the following questions: is there a structure underlying all AMP iterations that unifies them in a common framework? Can we use such a structure to give a modular proof of state evolution equations, adaptable to new AMP iterations without reproducing each time the full argument? We propose an answer to both questions, showing that AMP instances can be generically indexed by an oriented graph. This enables to give a unified interpretation of these iterations, independent from the problem they solve, and a way of composing them arbitrarily. We then show that all AMP iterations indexed by such a graph verify rigorous SE equations, extending the reach of previous proofs and proving a number of recent heuristic derivations of those equations. Our proof naturally includes non-separable functions and we show how existing refinements, such as spatial coupling or matrix-valued variables, can be combined with our framework.
Memory B cell differentiation from germinal centers
Authors: Inoue Takeshi 
Published: May 2023

Abstract
Establishment of humoral immune memory depends on two layers of defense: pre-existing antibodies secreted by long-lived plasma cells; and the antibodies produced by antigen-reactivated memory B cells. Memory B cells can now be considered as a second layer of defense upon re-infection by variant pathogens that have not been cleared by the long-lived plasma cell-mediated defense. Affinity-matured memory B cells are derived from the germinal center (GC) reaction, but the selection mechanism of GC B cells into the memory compartment is still incompletely understood. Recent studies have revealed the critical determinants of cellular and molecular factors for memory B cell differentiation from the GC reaction. In addition, the contribution of antibody-mediated feedback regulation to B cell selection, as exemplified by the B cell response upon COVID-19 mRNA vaccination, has now garnered considerable attention, which may provide valuable implications for future vaccine design.
Towards optimizing carbapenem selection in stewardship strategies: a prospective propensity score-matched study of ertapenem versus class 2 carbapenems for empirical treatment of third-generation cephalosporin-resistant Enterobacterales bacteraemia
Authors: Vasikasin Vasin , Panuvatvanich Bawornnan , Rawson Timothy M , Holmes Alison H , Nasomsong Worapong 
Published: May 2023

AbstractBackgroundThird-generation cephalosporin-resistant Enterobacterales (3GCRE) are increasing in prevalence, leading to greater carbapenem consumption. Selecting ertapenem has been proposed as a strategy to reduce carbapenem resistance development. However, there are limited data for the efficacy of empirical ertapenem for 3GCRE bacteraemia.ObjectivesTo compare the efficacy of empirical ertapenem and class 2 carbapenems for the treatment of 3GCRE bacteraemia.MethodsA prospective non-inferiority observational cohort study was performed from May 2019 to December 2021. Adult patients with monomicrobial 3GCRE bacteraemia receiving carbapenems within 24 h were included at two hospitals in Thailand. Propensity scores were used to control for confounding, and sensitivity analyses were performed in several subgroups. The primary outcome was 30 day mortality. This study is registered with clinicaltrials.gov (NCT03925402).ResultsEmpirical carbapenems were prescribed in 427/1032 (41%) patients with 3GCRE bacteraemia, of whom 221 received ertapenem and 206 received class 2 carbapenems. One-to-one propensity score matching resulted in 94 pairs. Escherichia coli was identified in 151 (80%) of cases. All patients had underlying comorbidities. Septic shock and respiratory failure were the presenting syndromes in 46 (24%) and 33 (18%) patients, respectively. The overall 30 day mortality rate was 26/188 (13.8%). Ertapenem was non-inferior to class 2 carbapenems in 30 day mortality (12.8% versus 14.9%; mean difference −0.02; 95% CI: −0.12 to 0.08). Sensitivity analyses were consistent regardless of aetiological pathogens, septic shock, source of infection, nosocomial acquisition, lactate levels or albumin levels.ConclusionsErtapenem may be of comparable efficacy to class 2 carbapenems in the empirical treatment of 3GCRE bacteraemia.
Genetic parameter analysis of bareness and tail traits in New Zealand sheep
Authors: Johnson Patricia L , Scobie David R , Dodds Ken G , Powdrell Sarah-Jane H , Rowe Suzanne J , McRae Kathryn M 
Published: May 2023

Abstract
Physical traits that improve welfare and disease outcomes for sheep are becoming increasingly important due to both increased climate challenges and societal expectations. Such traits include tail length, the amount of skin (vs. wool) on the underside of the tail, and the area of no-wool (hair) on the belly and breech areas (surrounding the anus) of the animal. An industry dataset consisting of records from individual stud breeders and industry progeny tests was available to estimate the genetic parameters associated with these traits and to investigate the potential for within-breed genetic selection. The heritability estimate for tail length was 0.68 ± 0.01 when breed was not fitted, and 0.63 ± 0.01 when breed was fitted. Similar trends were observed for breech and belly bareness which had heritability estimates around 0.50 (± 0.01). The estimates for these bareness traits are both higher than previous reports from animals of the same age. There was, however, between breed variation in the starting point for these traits, with some breeds having significantly longer tails and a wooly breech and belly, and limited variability. Overall, the results of this study show that flocks exhibiting some variation will be able to make rapid genetic progress in selecting for bareness and tail length traits, and therefore have the potential to make progress towards a sheep that is easier to look after and suffers fewer welfare insults. For those breeds that showed limited within-breed variation, outcrossing may be required to introduce genotypes that exhibit shorter tail length and bareness of belly and breech to increase the rate of genetic gain. Whatever approach is taken by the industry, these results support that genetic improvement can be used to breed “ethically improved sheep”.
Comparison of standardized ileal digestibility of amino acids in faba beans and field peas in broiler chickens and pigs
Authors: Adekoya Abidemi Abosede , Adeola Olayiwola 
Published: May 2023

AbstractAn experiment, using the same set of five diets was conducted to determine and compare the standardized ileal digestibility (SID) of amino acids (AA) in faba beans and three cultivars of field peas in broiler chickens and pigs. Four test diets were prepared to contain faba beans, DS-Admiral field peas, Hampton field peas, or 4010 field peas as the sole source of nitrogen. A nitrogen-free diet (NFD), as the fifth diet, was prepared to estimate the basal endogenous losses of AA to determine the SID of AA in the test ingredients. A total of 416 male broiler chickens with an initial body weight (BW) of 951 ± 111 g were allotted to five diets in a randomized complete block design with BW as a blocking factor on day 21 posthatching. There were 8 replicate cages with 10 birds per cage for diets containing test ingredients and 12 birds per cage for NFD. All birds were allowed ad-libitum access to feed for 5 days. On day 26 posthatching, all birds were euthanized by CO2 asphyxiation and digesta contents were collected from the distal two-thirds of the ileum. Twenty barrows with an initial BW of 30.2 ± 1.58 kg, surgically fitted with T-cannulas in the distal ileum, were divided into four blocks according to BW and each block was assigned to a 5 × 2 incomplete Latin Square design that consisted of five dietary treatments and two experimental periods. For each experimental period, there was a 5-day adaptation period followed by a 2-day collection of ileal digesta samples. The data were analyzed as a 2 × 4 factorial treatment arrangement with the effect of species (i.e., broiler chickens and pigs) and test diets (i.e., four test ingredients). For broiler chickens, the SID of Lys in faba beans, DS-Admiral field peas, and Hampton field peas were above 90% but in 4010 field peas, it was 85.1%. The SID of Lys in faba beans, DS-Admiral field peas, and Hampton field peas for pigs was above 80% but was 78.9% in 4010 field peas. The respective SID of Met in faba beans, DS-Admiral field peas, Hampton field peas, and 4010 field peas were 84.1%, 87.3%, 89.8%, and 72.1% for broiler chickens, and 71.5%, 80.4%, 81.8%, and 68.1% for pigs. The SID of AA in 4010 field peas was the least (P &lt; 0.05) for chickens, but in pigs, it was comparable with faba beans. In conclusion, the SID of AA in faba beans and field peas was greater in broiler chickens compared with pigs and there was a cultivar effect.
Impact of dietary analyzed calcium to phosphorus ratios and standardized total tract digestible phosphorus to net energy ratios on growth performance, bone, and carcass characteristics of pigs
Authors: Williams Hadley R , Tokach Mike D , Woodworth Jason C , DeRouchey Joel M , Goodband Robert D , Gebhardt Jordan T , Vier Carine M , Lu Ning , Navales Ron , Spindler Matthew , Orlando Uislei , Zaragoza Luis , Betlach Alyssa M 
Published: May 2023

Abstract
A total of 2,184 pigs (337 × 1,050, PIC; initially 12.4 ± 0.17 kg) were used in a 143-d study to evaluate the effects of feeding varying analyzed calcium to phosphorus ratios (Ca:P) at two standardized total tract digestible (STTD) phosphorus to net energy ratios (STTD P:NE). Pens of pigs (26 pigs per pen) were assigned to 1 of the 6 dietary treatments in a 2 × 3 factorial with main effects of STTD P:NE and Ca:P ratio. Diets consisted of two levels of STTD P:NE; High (1.80, 1.62, 1.43, 1.25, 1.10, and 0.99 g STTD P/Mcal NE from 11 to 22, 22 to 40, 40 to 58, 58 to 81, 81 to 104, and 104 to 129 kg, respectively); or Low (75% of the High levels), and three analyzed Ca:P ratios (0.90:1, 1.30:1, and 1.75:1). There were 14 pens per treatment. Diets were corn-soybean meal-based and contained a constant phytase concentration within each dietary phase with levels decreasing throughout the trial (phases 1 through 3, 500 FTU/kg, assumed release of 0.13% STTD P; phase 4, 400 FTU/kg, assumed release of 0.11% STTD P; phase 5, 290 FTU/kg, assumed release of 0.09% STTD P; and phase 6, 210 FTU/kg, assumed release of 0.07% STTD P). Overall, there was a Ca:P × STTD P:NE interaction (P &lt; 0.05) observed for average daily gain (ADG), feed efficiency (G:F), final body weight (BW), hot carcass weight (HCW), bone mineral density, bone mineral content, and bone-breaking strength. When feeding Low STTD P:NE levels, increasing the analyzed Ca:P ratio decreased (linear, P &lt; 0.001) ADG final BW, HCW, and tended to worsen G:F, bone mineral density, and bone mineral content (linear, P &lt; 0.10). However, when feeding High STTD P:NE levels, increasing the analyzed Ca:P ratio significantly improved bone mineral content and bone mineral density (linear, P &lt; 0.05), and tended to improve ADG and final BW (linear, P &lt; 0.10) and G:F (quadratic P &lt; 0.10). Additionally, increasing the analyzed Ca:P ratio worsened ADG, G:F, and bone mineralization with Low STTD P:NE but had marginal impacts when adequate STTD P:NE was fed.