bluuebunny/crossref_metadata_2025_split huggingface dataset:
Delimiting 33 Carpinus (Betulaceae) species with a further phylogenetic inference
Authors: Dong Congcong , Lu Zhiqiang , Zhang Han , Liu Jianquan , Li Minjie 
Published: February 2022

Abstract
Carpinus (Betulaceae) has approximately 52 species distributed in the Northern Hemisphere, with many species of Carpinus found in China. However, the species boundaries and phylogenetic relationships remain poorly understood. This study reported ITS sequences for 225 individuals of 33 Carpinus species, mainly from China. We also included eight Ostrya species in our analyses, the closely related sister group of Carpinus. We aimed to delimit these species based on ITS sequences and clarify their phylogenetic relationships by constructing tree-like topology and networks at population level. We found that only 17 of 33 species could be delimited from the closely related ones based on species-specific mutations in ITS sequence variation, including all species of sect. Distegocarpus, and sect. Carpinus subsect. Carpinus. Carpinus subsect. Carpinus contained two endangered species, although one seemed to be a recently originated allopolyploid species with genetic additivity from two likely parents in the ITS sequence variation. Sixteen species of sect. Carpinus subsect. Polyneurae were classified into three species complexes, in each of which two or more could be not distinguished from each other. The closely related species of these complexes may still diverge at the early stage without genetic distinction in the nuclear ITS sequences because of too short of divergence time and frequent gene flow. Otherwise, some species may be established based on the intraspecific variations without genetic bases for an independently evolving unit.
TWO-SIGMA-G: a new competitive gene set testing framework for scRNA-seq data accounting for inter-gene and cell–cell correlation
Authors: Van Buren Eric , Hu Ming , Cheng Liang , Wrobel John , Wilhelmsen Kirk , Su Lishan , Li Yun , Wu Di 
Published: February 2022

Abstract
We propose TWO-SIGMA-G, a competitive gene set test for scRNA-seq data. TWO-SIGMA-G uses a mixed-effects regression model based on our previously published TWO-SIGMA to test for differential expression at the gene-level. This regression-based model provides flexibility and rigor at the gene-level in (1) handling complex experimental designs, (2) accounting for the correlation between biological replicates and (3) accommodating the distribution of scRNA-seq data to improve statistical inference. Moreover, TWO-SIGMA-G uses a novel approach to adjust for inter-gene-correlation (IGC) at the set-level to control the set-level false positive rate. Simulations demonstrate that TWO-SIGMA-G preserves type-I error and increases power in the presence of IGC compared with other methods. Application to two datasets identified HIV-associated interferon pathways in xenograft mice and pathways associated with Alzheimer’s disease progression in humans.
seqgra: principled selection of neural network architectures for genomics prediction tasks
Authors: Krismer Konstantin , Hammelman Jennifer , Gifford David K 
Published: February 2022

AbstractMotivationSequence models based on deep neural networks have achieved state-of-the-art performance on regulatory genomics prediction tasks, such as chromatin accessibility and transcription factor binding. But despite their high accuracy, their contributions to a mechanistic understanding of the biology of regulatory elements is often hindered by the complexity of the predictive model and thus poor interpretability of its decision boundaries. To address this, we introduce seqgra, a deep learning pipeline that incorporates the rule-based simulation of biological sequence data and the training and evaluation of models, whose decision boundaries mirror the rules from the simulation process.ResultsWe show that seqgra can be used to (i) generate data under the assumption of a hypothesized model of genome regulation, (ii) identify neural network architectures capable of recovering the rules of said model and (iii) analyze a model’s predictive performance as a function of training set size and the complexity of the rules behind the simulated data.Availability and implementationThe source code of the seqgra package is hosted on GitHub (https://github.com/gifford-lab/seqgra). seqgra is a pip-installable Python package. Extensive documentation can be found at https://kkrismer.github.io/seqgra.Supplementary informationSupplementary data are available at Bioinformatics online.
Investigation of phase-change materials for interior temperature regulation in public transport
Authors: Islam Md Nahidul , Hossain Md Nahid , Ahmed Dewan Hasan 
Published: February 2022

Abstract
Regulating the indoor temperature of public transport on hot sunny days is a prime concern, as both the external and internal heat sources play an active role in heat gain. Experimental studies have been carried out on a bus model using sodium sulphate decahydrate as a phase-change material (PCM) that is placed in between the ceiling and the roof. Studies are conducted on a sunny day and also for different cases of external (300-W surface heater) and internal (25-W light bulb) heat sources. The results show that PCM, in the presence of an external heat source, can help to keep the indoor temperature lower and delay the time period for increasing the temperature by absorbing heat during the phase change. On the other hand, the presence of the internal heat source contributes to a detrimental effect on the indoor temperature, which gradually increases with the elapse of time. With the combination of the external and internal heat sources, it is found that the internal heat source plays a dominating factor to raise the indoor temperature. It is revealed from the experimental results that a 12.7-mm single layer and a single PCM are not enough to counter the internal heat of 25 W unless the thickness of the PCM layer is increased to delay the increase in the indoor temperature. An additional PCM layer with a lower melting temperature could be placed at the inner portion of the ceiling to have effective thermal-energy storage by absorbing the substantial heat gain from the internal heat sources.
Long-term results of tricuspid valve repair using three-dimensional versus flexible rings in patients with functional tricuspid regurgitation
Authors: Ram Eilon , Peled Yael , Karni Ehud , Dray Efrat Mazor , Cohen Hillit , Sternik Leonid , Raanani Ehud 
Published: February 2022

Abstract

OBJECTIVES
Significant functional tricuspid regurgitation (TR) should be corrected in patients undergoing surgery for left-sided valvular diseases. We hypothesized that ring type may affect outcomes in tricuspid annuloplasty. Herein, we report our experience with three-dimensional semi-rigid rings compared to open simple-band annuloplasty.

METHODS
This is a retrospective study that included all patients who underwent tricuspid annuloplasty concomitant to left-sided valvular surgery. The study's main outcome measure was long-term recurrent TR probability.

RESULTS
Of the 781 study patients, 611 (78%) underwent annuloplasty using flexible band and 170 (22%) underwent rigid ring implantation. Early mortality did not differ significantly between the rigid and flexible groups (4.4% vs 4.1%, P = 1.000). Long-term mortality was similar between the groups [hazard ratio (HR) 0.97, 95% confidence interval (CI) 0.69–1.36, P = 0.847]. At a mean follow-up of 62 (50) months, freedom from TR grade 3+/4+ was 96.4% and 96.7% in the rigid and flexible groups, respectively (HR 1.41, 95% CI 0.55–3.61, P = 0.476). Furthermore, 2.4% of the rigid and 1.3% of the flexible groups required reoperation (HR 1.01, 95% CI 0.21–4.82, P = 0.988). Multivariable analysis demonstrated that rheumatic valve aetiology (HR 1.92, CI 1.04–2.98, P = 0.042) and mitral stenosis (HR 1.44, CI 1.01–2.2, P = 0.044) were predictors for recurrent TR (3+/4+). Ring type was not associated with recurrence (HR 0.86, 95% CI 0.3–2.47, P = 0.787).

CONCLUSIONS
Open bands performed at least as well as three-dimensional rings. Our results suggest that late clinical results of tricuspid annuloplasty depend on left-sided pathology and patient factors and less on the type of ring used.
MIB-626, an Oral Formulation of a Microcrystalline Unique Polymorph of β-Nicotinamide Mononucleotide, Increases Circulating Nicotinamide Adenine Dinucleotide and its Metabolome in Middle-Aged and Older Adults
Authors: Pencina Karol M , Lavu Siva , dos Santos Marcello , Beleva Yusnie M , Cheng Ming , Livingston David , Bhasin Shalender 
Published: February 2022

Abstract

Background
Nicotinamide adenine dinucleotide (NAD) precursors, nicotinamide mononucleotide (NMN), or nicotinamide riboside (NR) extend healthspan and ameliorate some age-related conditions in model organisms. However, early-phase trials of NAD precursors have yielded varying results and their pharmacokinetics remain incompletely understood. Here, we report the pharmacokinetics and pharmacodynamics of MIB-626, a microcrystalline unique polymorph βNMN formulation.

Methods
In this double-blind, placebo-controlled study, 32 overweight or obese adults, 55–80 years, were block-randomized, stratified by sex, to 1 000-mg MIB-626 once daily, twice daily, or placebo for 14 days. NMN, NAD, and NAD metabolome were measured using liquid chromatography–tandem mass spectrometry.

Results
Participant characteristics were similar across groups. MIB-626 was well tolerated and frequency of adverse events was similar across groups. Blood NMN concentrations on Day 14 in MIB-626-treated groups were significantly higher compared to placebo (1.7-times and 3.7-times increase above baseline in 1 000 mg once-daily and twice-daily groups in mean AUClast, respectively). MIB-626 treatment was associated with substantial dose-related increases in blood NAD levels. Blood levels of NAD metabolites were higher in NMN-treated participants on Days 8 and 14 than at baseline. Changes in NMN or NAD levels were not related to sex, body mass index, or age. Very little unmodified NMN was excreted in the urine.

Conclusion
MIB-626 1 000 mg once-daily or twice-daily regimens were safe and associated with substantial dose-related increases in blood NAD levels and its metabolome. These foundational data that were obtained using a pharmaceutical-grade βNMN, standardized sample collection, and validated liquid chromatography–tandem mass spectrometry assays, should facilitate design of efficacy trials in disease conditions.
The effects of discontinuity topography in the mantle transition zone on global geodynamic observables and mantle heterogeneity
Authors: Glišović Petar , Grand Stephen P , Lu Chang , Forte Alessandro M , Wei S Shawn 
Published: February 2022

SUMMARYDespite progress in tomographic imaging of Earth's interior, a number of critical questions regarding the large-scale structure and dynamics of the mantle remain outstanding. One of those questions is the impact of phase-boundary undulations on global imaging of mantle heterogeneity and on geodynamic (i.e. convection-related) observables. To address this issue, we developed a joint seismic-geodynamic-mineral physical tomographic inversion procedure that incorporates lateral variations in the depths of the 410- and 660-km discontinuities. This inversion includes S-wave traveltimes, SS precursors that are sensitive to transition-zone topography, geodynamic observables/data (free-air gravity, dynamic surface topography, horizontal divergence of tectonic plates and excess core-mantle boundary ellipticity) and mineral physical constraints on thermal heterogeneity. Compared to joint tomography models that do not include data sensitivity to phase-boundary undulations in the transition zone, the inclusion of 410- and 660-km topography strongly influences the inference of volumetric anomalies in a depth interval that encompasses the transition zone and mid-mantle. It is notable that joint tomography inversions, which include constraints on transition-zone discontinuity topography by seismic and geodynamic data, yield more pronounced density anomalies associated with subduction zones and hotspots. We also find that the inclusion of 410- and 660-km topography may improve the fit to the geodynamic observables, depending on the weights applied to seismic and geodynamic data in the inversions. As a consequence, we find that the amplitude of non-thermal density anomalies required to explain the geodynamic data decreases in most of the mantle. These findings underline the sensitivity of the joint inversions to the inclusion of transition-zone complexity (e.g. phase-boundary topography) and the implications for the inferred non-thermal density anomalies in these depth regions. Finally, we underline that our inferences of 410- and 660-km topography avoid a commonly employed approximation that represents the contribution of volumetric heterogeneity to SS-wave precursor data. Our results suggest that this previously employed correction, based on a priori estimates of upper-mantle heterogeneity, might be a significant source of error in estimating the 410- and 660-km topography.
Grapevine rootstock and soil microbiome interactions: Keys for a resilient viticulture
Authors: Darriaut Romain , Lailheugue Vincent , Masneuf-Pomarède Isabelle , Marguerit Elisa , Martins Guilherme , Compant Stéphane , Ballestra Patricia , Upton Steven , Ollat Nathalie , Lauvergeat Virginie 
Published: February 2022

Abstract
Soil microbiota has increasingly been shown to play an integral role in viticulture resilience. The emergence of new metagenomic and culturomic technologies has led to significant advances in the study of microbial biodiversity. In the agricultural sector, soil and plant microbiomes have been found to significantly improve resistance to environmental stressors and diseases, as well as influencing crop yields and fruit quality thus improving sustainability under shifting environments. Grapevines are usually cultivated as a scion grafted on rootstocks, which are selected according to pedoclimatic conditions and cultural practices, known as terroir. The rootstock connects the surrounding soil to the vine’s aerial part and impacts scion growth and berry quality. Understanding rootstock and soil microbiome dynamics is a relevant and important field of study, which may be critical to improve viticulture sustainability and resilience. This review aims to highlight the relationship between grapevine roots and telluric microbiota diversity and activity. In addition, this review explores the concept of core microbiome regarding potential applications of soil microbiome engineering with the goal of enhancing grapevine adaptation to biotic and abiotic stress.
Genetic architecture and genomic predictive ability of apple quantitative traits across environments
Authors: Jung Michaela , Keller Beat , Roth Morgane , Aranzana Maria José , Auwerkerken Annemarie , Guerra Walter , Al-Rifaï Mehdi , Lewandowski Mariusz , Sanin Nadia , Rymenants Marijn , Didelot Frédérique , Dujak Christian , Font i Forcada Carolina , Knauf Andrea , Laurens François , Studer Bruno , Muranty Hélène , Patocchi Andrea 
Published: February 2022

Abstract
Implementation of genomic tools is desirable to increase the efficiency of apple breeding. Recently, the multi-environment apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic predictive ability, and studying genotype by environment interactions (G × E). So far, only two phenological traits were investigated using the apple REFPOP, although the population may be valuable when dissecting genetic architecture and reporting predictive abilities for additional key traits in apple breeding. Here we show contrasting genetic architecture and genomic predictive abilities for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic predictive abilities of 0.18–0.88 were estimated using main-effect univariate, main-effect multivariate, multi-environment univariate, and multi-environment multivariate models. The G × E accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of trait-environment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency.
Physiological, biochemical, and molecular aspects of grafting in fruit trees
Authors: Habibi Fariborz , Liu Tie , Folta Kevin , Sarkhosh Ali 
Published: February 2022

Abstract
Grafting is a widely used practice for asexual propagation of fruit trees. Many physiological, biochemical, and molecular changes occur upon grafting that can influence important horticultural traits. This technology has many advantages, including avoidance of juvenility, modifying the scion architecture, improving productivity, adapting scion cultivars to unfavourable environmental conditions, and developing traits in resistance to insect pests, bacterial and fungal diseases. A limitation of grafting is scion-rootstock incompatibility. It may be caused by many factors, including insufficient genetic proximity, physiological or biochemical factors, lignification at the graft union, poor graft architecture, insufficient cell recognition between union tissues, and metabolic differences in the scion and the rootstock. Plant hormones, like auxin, ethylene (ET), cytokinin (CK), gibberellin (GA), abscisic acid (ABA), and jasmonic acid (JA) orchestrate several crucial physiological and biochemical processes happening at the site of the graft union. Additionally, epigenetic changes at the union affect chromatin architecture by DNA methylation, histone modification, and the action of small RNA molecules. The mechanism triggering these effects likely is affected by hormonal crosstalk, protein and small molecules movement, nutrients uptake, and transport in the grafted trees. This review provides an overview of the basis of physiological, biochemical, and molecular aspects of fruit tree grafting between scion and rootstock.
Across-population genomic prediction in grapevine opens up promising prospects for breeding
Authors: Brault Charlotte , Segura Vincent , This Patrice , Le Cunff Loïc , Flutre Timothée , François Pierre , Pons Thierry , Péros Jean-Pierre , Doligez Agnès 
Published: February 2022

AbstractCrop breeding involves two selection steps: choosing progenitors and selecting individuals within progenies. Genomic prediction, based on genome-wide marker estimation of genetic values, could facilitate these steps. However, its potential usefulness in grapevine (Vitis vinifera L.) has only been evaluated in non-breeding contexts mainly through cross-validation within a single population. We tested across-population genomic prediction in a more realistic breeding configuration, from a diversity panel to ten bi-parental crosses connected within a half-diallel mating design. Prediction quality was evaluated over 15 traits of interest (related to yield, berry composition, phenology and vigour), for both the average genetic value of each cross (cross mean) and the genetic values of individuals within each cross (individual values). Genomic prediction in these conditions was found useful: for cross mean, average per-trait predictive ability was 0.6, while per-cross predictive ability was halved on average, but reached a maximum of 0.7. Mean predictive ability for individual values within crosses was 0.26, about half the within-half-diallel value taken as a reference. For some traits and/or crosses, these across-population predictive ability values are promising for implementing genomic selection in grapevine breeding. This study also provided key insights on variables affecting predictive ability. Per-cross predictive ability was well predicted by genetic distance between parents and when this predictive ability was below 0.6, it was improved by training set optimization. For individual values, predictive ability mostly depended on trait-related variables (magnitude of the cross effect and heritability). These results will greatly help designing grapevine breeding programs assisted by genomic prediction.
New insights into flowering date in Prunus: fine mapping of a major QTL in sweet cherry
Authors: Branchereau Camille , Quero-García José , Zaracho-Echagüe Nathalia Helena , Lambelin Laurine , Fouché Mathieu , Wenden Bénédicte , Donkpegan Armel , Le Dantec Loïck , Barreneche Teresa , Alletru David , Parmentier Julien , Dirlewanger Elisabeth 
Published: February 2022

Abstract
Flowering date is an important trait in Prunus fruit species, especially for their adaptation in a global warming context. Numerous quantitative trait loci (QTLs) have been identified and a major one was previously located on LG4. The objectives of this study were to fine-map this QTL in sweet cherry, to identify robust candidate genes by using the new sweet cherry genome sequence of the cultivar “Regina” and to define markers usable in marker-assisted selection (MAS). We performed QTL analyses on two populations derived from crosses using cultivars “Regina” and “Garnet” as parents. The first one (n = 117) was phenotyped over ten years, while the second one (n = 1386) was evaluated during three years. Kompetitive allele specific PCR (KASP) markers located within the QTL region on LG4 were developed and mapped within this region, consisting in the first fine mapping in sweet cherry. The QTL interval was narrowed from 380 kb to 68 kb and candidate genes were identified by using the genome sequence of “Regina”. Their expression was analyzed from bud dormancy period to flowering in cultivars “Regina” and “Garnet”. Several genes, such as PavBOI-E3, PavSR45a and PavSAUR71, were differentially expressed in these two cultivars and could be then considered as promising candidate genes. Two KASP markers were validated using a population derived from a cross between cultivars “Regina” and “Lapins” and two collections, including landraces and modern cultivars. Thanks to the high synteny within the Prunus genus, these results give new insights into the control of flowering date in Prunus species and pave the way for the development of molecular breeding strategies.