bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Decision Aid for Genital Surgery in Transmen
Authors: Mokken Sterre E. , Özer Müjde , van de Grift Tim C. , Pigot Garry L. , Bouman Mark-Bram , Mullender Margriet 
Published: August 2020

Abstract

Background
Multiple options of genital gender-affirming surgery are available to transmen. The transman should be able to weigh these options based on the outcomes, risks, and consequences that are most important to him. For this reason, a decision aid for genital surgery in transmen (DA-GST) was developed. It aims to support the transman in making thoughtful choices among treatment options and facilitate shared decision-making between the healthcare professionals and the transindividual.

Aim
The aim of this study was to evaluate the newly developed DA-GST.

Methods
This was a cross-sectional study using mixed methods. Transmen considering to undergo genital surgery were eligible to partake in the study. The questionnaires used in this study were developed by adapting the validated Dutch translation of the “Decisional Conflict Scale,” the “Measures of Informed Choice,” and the “Ottawa Preparation for Decision-Making Scale.” Qualitative interviews were conducted querying their subjective experience with the DA-GST. The data from the questionnaires were statistically analyzed, and the data from the interviews were thematically analyzed.

Outcomes
The main outcome measures were decisional conflict and decisional confidence measured via self-report items and qualitative data regarding the use of the DA-GST via interviews.

Results
In total, 51 transmen participated in the questionnaires study, 99 questionnaires were analyzed, and 15 interviews were conducted. Although confident in their decision, most transmen felt responsible to collect the necessary information themselves. The ability to go through the decision aid independently aided the decision-making process by providing information and highlighting their subjective priorities. Suggested additions are pictures of postoperational outcomes and personal statements from experienced transmen.

Clinical Translation
The DA-GST could be implemented as an integral part of transgender health care. Clinicians could take the individual personal values into account and use it to accurately tailor their consult. This would ultimately improve the doctor-patient relationship and decrease decisional regret by enhancing effective shared decision-making.

Strengths & Limitations
This mixed-method design study confirmed the use of the DA-GST while taking a broad range of decisional factors into account. Limitations include the absence of a baseline analysis and the limited power for the comparison of treatment groups.

Conclusions
This study suggests that the DA-GST helped transmen feel more prepared for their personal consult with the surgeon, reduced decisional conflict, and increased their decisional confidence.
A New Statistical Test Based on the WR for Detecting Offsets in GPS Experiment
Authors: Tehranchi Ramin , Moghtased‐Azar Khosro , Safari Abdolreza 
Published: August 2020

AbstractDetecting the probable offsets is a crucial step in the preprocessing of the Global Positioning System (GPS) coordinate time series. Undetected offsets lead to the biased estimation of time series parameters and their uncertainties resulting in data misinterpretation. In the current research, a DIA (detection, identification, and adaptation)‐based procedure in maximal overlap discrete wavelet transform (MODWT) rough space has been introduced to address the location of offsets in long GPS time series without a priori information of the functional or stochastic models. A remarkable property of a wavelet rough (WR) at lower‐scale (j ≤ 5) details is to reflect the local regularity of the time series, being large where the signal is irregular and small where it is smooth. Performance and effectiveness of the proposed approach have been shown with DOGEx (Detection of Offsets in GPS Experiment) data set, which was a simulated time series that mimicked realistic GPS data consisting of a velocity component, seasonal cycle, offsets, and white and flicker noises composed in an additive model. The results showed that the fifth percentile range (5% to 95%) in velocity biases was equal to 1.24 mm/yr, which was smaller than all tested automatic solutions. Furthermore, the offsets detected by this method were split into 34.3% of true positive (TP), 36.5% of false positive (FP), and 29.2% of the false negative (FN), offering the proposed method as the best automatic solution.
Reconstruction of Sea Ice Concentration in Northern Baffin Bay Using Deuterium Excess in a Coastal Ice Core From the Northwestern Greenland Ice Sheet
Authors: Kurosaki Yutaka , Matoba Sumito , Iizuka Yoshinori , Niwano Masashi , Tanikawa Tomonori , Ando Takuto , Hori Akira , Miyamoto Atsushi , Fujita Shuji , Aoki Teruo 
Published: August 2020

AbstractVariations in the conditions of sea ice in the northern part of Baffin Bay and North Open Water polynya influence human activity in northwestern Greenland through oceanic circulation and heat balance between air and sea. To evaluate the impact of variations in sea ice conditions on the surrounding environment, it is important to understand the mechanism of sea ice variations over long periods. In this study, we estimated the age of the SIGMA‐A ice core collected northwestern Greenland Ice Sheet and researched the relationship between annual or seasonal deuterium excess (d‐excess) and seasonal sea ice concentration. We found that a temporal variation in the spring d‐excess in the ice core negatively correlated significantly with that of sea ice concentration in February–April in northern Baffin Bay from 1979–2005 (r = −0.61,p < 0.001). Using this relationship, we reconstructed the temporal variations in sea ice concentrations for 100 years from the ice core drilled in the northwestern Greenland Ice Sheet. The sea ice concentration in the early twentieth century was lower than that in the present. The decrease in sea ice concentration was consistent with analytical results for marine sediments obtained from Baffin Bay. We also suggested that the sea ice concentration was controlled by atmospheric conditions from the 1920s to 1940s based on examinations of correlations with the North Atlantic Oscillation index and air temperature in Ilulissat and by oceanographic conditions from 1945–1955, 1959–1969, and 1982–1992 based on the Atlantic Multidecadal Oscillation index and meridional heat transport to western Greenland.
Geneses of Two Contrasting Antigorite Crystal Preferred Orientations and Their Implications for Seismic Anisotropy in the Forearc Mantle
Authors: Liu Wenlong , Zhang Junfeng , Cao Yi , Jin Zhenmin 
Published: August 2020

AbstractCrystal preferred orientation (CPO) of antigorite is an important parameter for the interpretation of seismic anisotropies and related geodynamic processes in subduction zones. However, mechanisms for the development of various antigorite CPOs and their effects on seismic anisotropies in the forearc mantle still remain to be constrained. In this study, we investigated olivine and antigorite CPOs and calculated seismic anisotropies of the serpentinized peridotites from Val Malenco, Central Alps. The results show that antigorite in the olivine‐rich (weakly serpentinized) layer displays an L‐type CPO (i.e., (h0l) plane//foliation and [010] axis//lineation), whereas antigorite in the antigorite‐rich (highly serpentinized) layer develops an LS‐b‐type CPO (i.e., (001) plane//foliation and [010] axis//lineation). The antigorite L‐type CPO is most likely formed by diffusion and dislocation creep accommodated phase boundary sliding and substantial grain rotation at a higher temperature and smaller strain regime. In contrast, the development of an antigorite LS‐b‐type CPO requires diffusion and dislocation creep accommodated grain boundary sliding, smaller contribution of grain rotation, and significant role of dissolution‐precipitation creep at a lower temperature and larger strain regime. In this context, we propose an antigorite CPO distribution model in the forearc mantle. Based on this model and under vertically incident teleseismic waves, if significant serpentinization and asymmetric shearing do indeed occur within serpentinized layers, then strong and weak trench‐parallel seismic anisotropies can be expected for cold and warm moderate‐angle subduction zones, respectively. This model may provide an alternative interpretation on the seismic anisotropy observations in some modern subduction systems.
Rise of Great Lakes Surface Water, Sinking of the Upper Midwest of the United States, and Viscous Collapse of the Forebulge of the Former Laurentide Ice Sheet
Authors: Argus Donald F. , Ratliff Benjamin , DeMets Charles , Borsa Adrian A. , Wiese David N. , Blewitt Geoffrey , Crowley John W. , Martens Hilary R. , Kreemer Corné , Landerer Felix W. 
Published: August 2020

AbstractGreat Lakes water levels rose 0.7–1.5 m from 2013 to 2019, increasing surface water volume by 285 km3. Solid Earth's elastic response to the increased mass load is nearly known: The Great Lakes floor fell 8–23 mm, and the adjacent land fell 3–14 mm. Correcting GPS measurements for this predicted elastic loading (1) straightens position‐time series, making the evolution of position more nearly a constant velocity and (2) reduces estimates of subsidence rate in Wisconsin, Michigan, and southern Ontario by 0.5–2 mm/yr, improving constraints on postglacial rebound. GPS records Wisconsin and Michigan to have subsided at 1–4 mm/yr. We find this sinking to be produced primarily by viscous collapse of the former Laurentide ice sheet forebulge and secondarily by elastic Great Lakes loading. We infer water on land in the Great Lakes watershed to be total water change observed by GRACE minus Great Lakes surface water smeared by a Gaussian distribution. Water stored on land each year reaches a maximum in March, 6 months before Great Lakes water levels peak in September. The seasonal oscillation of water on land in the Great Lakes basin, 100 km3 (0.20 m water thickness), is twice that in a hydrology model. In the seasons, groundwater in the Great Lakes watershed increases by 60 km3 (0.12 m) each autumn and winter and decreases by roughly an equivalent amount each spring and summer. In the long term, groundwater volume remained constant from 2004 to 2012 but increased by 50 km3 (0.10 m) from 2013 to 2019.
On the Interdecadal Change in the Interannual Variation in Autumn Snow Cover Over the Central Eastern Tibetan Plateau in the Mid‐1990s
Authors: Qian Qi Feng , Jia Xiao Jing , Wu Renguang 
Published: August 2020

AbstractThe interdecadal changes in the mechanisms accounting for the interannual variation in autumn snow cover over the central eastern Tibetan Plateau (TP) are investigated in this study. An autumn snow index is constructed by area averaging the snow cover over the central eastern TP. The snow index changed from a predominantly negative phase to a positive phase in 1995. Then, the data were divided into two subperiods, 1979–1994 (P1) and 1995–2017 (P2), and the differences in the mechanisms accounting for the variation in autumn snow cover were compared between P1 and P2. An analysis of the local process shows that the autumn snow cover variations over the central eastern TP are caused by snowfall from both autumn and late summer. The autumn snow cover variation over the central eastern TP imposed more significant atmospheric cooling effects during P1 than P2. During P2, except for the local process, the interannual variation in autumn snow cover in the central eastern TP is also affected by atmospheric circulation anomalies originating from the upstream North Atlantic Ocean. During P2, snow‐related North Atlantic sea surface temperature (SST) anomalies (SSTA) can induce a wave train‐like atmospheric pattern that propagates eastward across the Eurasian continent and reaches the TP. Further analysis shows that this wave train‐like atmospheric pattern over the midlatitude Eurasian continent mainly obtains energy from climatological mean flow through baroclinic energy conversion. In contrast, during P1, the North Atlantic SSTA‐related atmospheric circulation pattern tends to propagate northeastward and cannot contribute to the variation in autumn snow cover over the central eastern TP.
MiR156 regulates anthocyanin biosynthesis through SPL targets and other microRNAs in poplar
Authors: Wang Yamei , Liu Wenwen , Wang Xinwei , Yang Ruijuan , Wu Zhenying , Wang Han , Wang Lei , Hu Zhubing , Guo Siyi , Zhang Hailing , Lin Jinxing , Fu Chunxiang 
Published: August 2020

AbstractAnthocyanins biosynthesized from the flavonoid pathway are types of pigments that are involved in the protection of poplar from biotic and abiotic stresses. Previous researchers studying anthocyanin-related transcription factors and structural genes in poplar have made significant discoveries. However, little is known about the regulatory role of microRNAs in anthocyanin biosynthesis in poplar. Here, we overexpressed miR156 in poplar to study the comprehensive effects of the miR156-SPL module on the biosynthesis of anthocyanins. Small RNA sequencing analysis revealed 228 microRNAs differentially expressed in transgenic poplar plants with dramatically increased miR156 levels. Furthermore, integrated microRNAomic and transcriptomic analysis suggested that two microRNAs, miR160h, and miR858, have the potential to affect anthocyanin accumulation in poplar by regulating auxin response factors and MYB transcription factors, respectively. Additionally, the accumulation of miR160h and miR858 displayed a positive correlation with miR156 levels, suggesting a possible interaction between the miR156-SPL module and these microRNAs in poplar. Last, metabolomics analysis revealed that the levels of anthocyanins, flavones, and flavonols were substantially elevated in transgenic poplar plants overexpressing miR156 compared with the wild type, whereas the total lignin content was reduced in the transgenic plants. Taken together, our results indicate that miR156 can fine tune the anthocyanin biosynthetic pathway via multiple factors, including microRNAs, transcription factors, and the levels of structural genes, in poplar. This provides additional clues for understanding the complex regulatory network of anthocyanin biosynthesis in woody plants.
Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing
Authors: Wang Jiawei , Liu Weizhen , Zhu Dongzi , Hong Po , Zhang Shizhong , Xiao Shijun , Tan Yue , Chen Xin , Xu Li , Zong Xiaojuan , Zhang Lisi , Wei Hairong , Yuan Xiaohui , Liu Qingzhong 
Published: August 2020

AbstractSweet cherry (Prunus avium) is an economically significant fruit species in the genus Prunus. However, in contrast to other important fruit trees in this genus, only one draft genome assembly is available for sweet cherry, which was assembled using only Illumina short-read sequences. The incompleteness and low quality of the current sweet cherry draft genome limit its use in genetic and genomic studies. A high-quality chromosome-scale sweet cherry reference genome assembly is therefore needed. A total of 65.05 Gb of Oxford Nanopore long reads and 46.24 Gb of Illumina short reads were generated, representing ~190x and 136x coverage, respectively, of the sweet cherry genome. The final de novo assembly resulted in a phased haplotype assembly of 344.29 Mb with a contig N50 of 3.25 Mb. Hi-C scaffolding of the genome resulted in eight pseudochromosomes containing 99.59% of the bases in the assembled genome. Genome annotation revealed that more than half of the genome (59.40%) was composed of repetitive sequences, and 40,338 protein-coding genes were predicted, 75.40% of which were functionally annotated. With the chromosome-scale assembly, we revealed that gene duplication events contributed to the expansion of gene families for salicylic acid/jasmonic acid carboxyl methyltransferase and ankyrin repeat-containing proteins in the genome of sweet cherry. Four auxin-responsive genes (two GH3s and two SAURs) were induced in the late stage of fruit development, indicating that auxin is crucial for the sweet cherry ripening process. In addition, 772 resistance genes were identified and functionally predicted in the sweet cherry genome. The high-quality genome assembly of sweet cherry obtained in this study will provide valuable genomic resources for sweet cherry improvement and molecular breeding.
The regulatory pathways of distinct flowering characteristics in Chinese jujube
Authors: Meng Xianwei , Li Ying , Yuan Ye , Zhang Yao , Li Hongtai , Zhao Jin , Liu Mengjun 
Published: August 2020

AbstractFlowering is the most important event in higher plants. Compared to most fruit tree species, Chinese jujube (Ziziphus jujuba Mill.), the most important member of the large, diverse Rhamnaceae family and a leading dry fruit-producing species, has unique characteristics that include a short juvenile phase and extremely fast flower bud differentiation. However, the distinct mechanism of flowering regulation in Chinese jujube is still unclear. The morphological and cytological development period of jujube flowering was first investigated, and the crucial developmental stages were defined. Flower bud differentiation in Chinese jujube took only approximately 11–13 days, which is a distinct characteristic of perennial fruit trees. Afterward, 44 genes related to six flowering pathways were identified in the jujube genome and were found to be randomly distributed among 11 of the 12 chromosomes. Tissue-specific and spatiotemporal expression patterns showed that all these genes were expressed in the flowers. Overall, photoperiod-related genes were highly expressed during flower bud differentiation. These genes were also positively responsive to photoperiod regulation and phase change processes, indicating that photoperiod- related genes play crucial roles in jujube flower bud differentiation. Under protected cultivation, ZjPIF4, a temperature-related gene, was expressed in the early stages of flowering and responded to increasing temperatures. Moreover, STRING analysis and yeast two-hybrid screening indicated that photoperiod-related (ZjCO) and temperature-related (ZjPIF4) proteins could interact with ZjFT, the key protein involved in the determination of flowering time, indicating crosstalk between photoperiod-related pathways and ambient temperature-related pathways in jujube. This study is the first report to comprehensively analyze the flowering pathways in Chinese jujube and revealed that photoperiod-related and ambient temperature-related pathways are the main mechanisms regulating the distinct flowering process and that members of the ZjPHY family (ZjPIF4, ZjFT, and ZjCO5) are the key factors involved in the regulatory network. These results will increase our understanding of the molecular and genetic mechanisms of flowering in Chinese jujube and provide meaningful clues for the flowering regulation of other fruit tree species.
Growth monitoring of greenhouse lettuce based on a convolutional neural network
Authors: Zhang Lingxian , Xu Zanyu , Xu Dan , Ma Juncheng , Chen Yingyi , Fu Zetian 
Published: August 2020

AbstractGrowth-related traits, such as aboveground biomass and leaf area, are critical indicators to characterize the growth of greenhouse lettuce. Currently, nondestructive methods for estimating growth-related traits are subject to limitations in that the methods are susceptible to noise and heavily rely on manually designed features. In this study, a method for monitoring the growth of greenhouse lettuce was proposed by using digital images and a convolutional neural network (CNN). Taking lettuce images as the input, a CNN model was trained to learn the relationship between images and the corresponding growth-related traits, i.e., leaf fresh weight (LFW), leaf dry weight (LDW), and leaf area (LA). To compare the results of the CNN model, widely adopted methods were also used. The results showed that the values estimated by CNN had good agreement with the actual measurements, with R2 values of 0.8938, 0.8910, and 0.9156 and normalized root mean square error (NRMSE) values of 26.00, 22.07, and 19.94%, outperforming the compared methods for all three growth-related traits. The obtained results showed that the CNN demonstrated superior estimation performance for the flat-type cultivars of Flandria and Tiberius compared with the curled-type cultivar of Locarno. Generalization tests were conducted by using images of Tiberius from another growing season. The results showed that the CNN was still capable of achieving accurate estimation of the growth-related traits, with R2 values of 0.9277, 0.9126, and 0.9251 and NRMSE values of 22.96, 37.29, and 27.60%. The results indicated that a CNN with digital images is a robust tool for the monitoring of the growth of greenhouse lettuce.
Major-effect candidate genes identified in cultivated strawberry (Fragaria × ananassa Duch.) for ellagic acid deoxyhexoside and pelargonidin-3-O-malonylglucoside biosynthesis, key polyphenolic compounds
Authors: Davik Jahn , Aaby Kjersti , Buti Matteo , Alsheikh Muath , Šurbanovski Nada , Martens Stefan , Røen Dag , Sargent Daniel James 
Published: August 2020

AbstractStrawberries are rich in polyphenols which impart health benefits when metabolized by the gut microbiome, including anti-inflammatory, neuroprotective, and antiproliferative effects. In addition, polyphenolic anthocyanins contribute to the attractive color of strawberry fruits. However, the genetic basis of polyphenol biosynthesis has not been extensively studied in strawberry. In this investigation, ripe fruits from three cultivated strawberry populations were characterized for polyphenol content using HPLC-DAD-MSnand genotyped using the iStraw35k array. GWAS and QTL analyses identified genetic loci controlling polyphenol biosynthesis. QTL were identified on four chromosomes for pelargonidin-3-O-malonylglucoside, pelargonidin-3-O-acetylglucoside, cinnamoyl glucose, and ellagic acid deoxyhexoside biosynthesis. Presence/absence of ellagic acid deoxyhexoside and pelargonidin-3-O-malonylglucoside was found to be under the control of major gene loci on LG1X2 and LG6b, respectively, on theF. × ananassalinkage maps. Interrogation of gene predictions in theF. vescareference genome sequence identified a single candidate gene for ellagic acid deoxyhexoside biosynthesis, while seven malonyltransferase genes were identified as candidates for pelargonidin-3-O-malonylglucoside biosynthesis. Homologous malonyltransferase genes were identified in theF. × ananassa‘Camarosa’ genome sequence but the candidate for ellagic acid deoxyhexoside biosynthesis was absent from the ‘Camarosa’ sequence. This study demonstrated that polyphenol biosynthesis in strawberry is, in some cases, under simple genetic control, supporting previous observations of the presence or absence of these compounds in strawberry fruits. It has also shed light on the mechanisms controlling polyphenol biosynthesis and enhanced the knowledge of these biosynthesis pathways in strawberry. The above findings will facilitate breeding for strawberries enriched in compounds with beneficial health effects.