bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assembly of the non‐heading pak choi genome and comparison with the genomes of heading Chinese cabbage and the oilseed yellow sarson
Authors: Li Peirong , Su Tongbing , Zhao Xiuyun , Wang Weihong , Zhang Deshuang , Yu Yangjun , Bayer Philipp E. , Edwards David , Yu Shuancang , Zhang Fenglan 
Published: December 2020

SummaryBrassica rapa displays a wide range of morphological diversity which is exploited for a variety of food crops. Here we present a high‐quality genome assembly for pak choi (Brassica rapa L. subsp. chinensis), an important non‐heading leafy vegetable, and comparison with the genomes of heading type Chinese cabbage and the oilseed form, yellow sarson. Gene presence–absence variation (PAV) and genomic structural variations (SV) were identified, together with single nucleotide polymorphisms (SNPs). The structure and expression of genes for leaf morphology and flowering were compared between the three morphotypes revealing candidate genes for these traits in B. rapa. The pak choi genome assembly and its comparison with other B. rapa genome assemblies provides a valuable resource for the genetic improvement of this important vegetable crop and as a model to understand the diversity of morphological variation across Brassica species.
Citrus miraculin‐like protein hijacks a viral movement‐related p33 protein and induces cellular oxidative stress in defence against Citrus tristeza virus
Authors: Sun Yong‐Duo , Zhang Lei , Folimonova Svetlana Y. 
Published: December 2020

SummaryTo defend against pathogens, plants have developed a complex immune system, which recognizes the pathogen effectors and mounts defence responses. In this study, the p33 protein of Citrus tristeza virus (CTV), a viral membrane‐associated effector, was used as a molecular bait to explore virus interactions with host immunity. We discovered that Citrus macrophylla miraculin‐like protein 2 (CmMLP2), a member of the soybean Kunitz‐type trypsin inhibitor family, targets the viral p33 protein. The expression of CmMLP2 was up‐regulated by p33 in the citrus phloem‐associated cells. Knock‐down of the MLP2 expression in citrus plants resulted in a higher virus accumulation, while the overexpression of CmMLP2 reduced the infectivity of CTV in the plant hosts. Further investigation revealed that, on the one hand, binding of CmMLP2 interrupts the cellular distribution of p33 whose proper function is necessary for the effective virus movement throughout the host. On the other hand, the ability of CmMLP2 to reorganize the endomembrane system, amalgamating the endoplasmic reticulum and the Golgi apparatus, induces cellular stress and accumulation of the reactive oxygen species, which inhibits the replication of CTV. Altogether, our data suggest that CmMLP2 employs a two‐way strategy in defence against CTV infection.
Acclimation of leaf photosynthesis and respiration to warming in field‐grown wheat
Authors: Coast Onoriode , Posch Bradley C. , Bramley Helen , Gaju Oorbessy , Richards Richard A. , Lu Meiqin , Ruan Yong‐Ling , Trethowan Richard , Atkin Owen K. 
Published: December 2020

AbstractClimate change and future warming will significantly affect crop yield. The capacity of crops to dynamically adjust physiological processes (i.e., acclimate) to warming might improve overall performance. Understanding and quantifying the degree of acclimation in field crops could ensure better parameterization of crop and Earth System models and predictions of crop performance. We hypothesized that for field‐grown wheat, when measured at a common temperature (25°C), crops grown under warmer conditions would exhibit acclimation, leading to enhanced crop performance and yield. Acclimation was defined as (a) decreased rates of net photosynthesis at 25°C (A25) coupled with lower maximum carboxylation capacity (Vcmax25), (b) reduced leaf dark respiration at 25°C (both in terms of O2 consumption Rdark_O225 and CO2 efflux Rdark_CO225) and (c) lower Rdark_CO225 to Vcmax25 ratio. Field experiments were conducted over two seasons with 20 wheat genotypes, sown at three different planting dates, to test these hypotheses. Leaf‐level CO2‐based traits (A25, Rdark_CO225 and Vcmax25) did not show the classic acclimation responses that we hypothesized; by contrast, the hypothesized changes in Rdark_O2 were observed. These findings have implications for predictive crop models that assume similar temperature response among these physiological processes and for predictions of crop performance in a future warmer world.
Making a melanoma: Molecular and cellular changes underlying melanoma initiation
Authors: Darp Revati , Ceol Craig 
Published: December 2020

AbstractMelanoma arises from the melanocyte lineage and is the most aggressive and lethal form of skin cancer. There are several genetic, genomic, and cellular changes associated with melanoma initiation. Here, we discuss these alterations and the melanoma cells of origin in which they are proposed to promote melanomagenesis.
Phloem and xylem modifications of Vitis vinifera stems in response to flavescence dorée phytoplasma infection
Authors: Jelmini Luca , Rizzoli Attilio , Jermini Mauro , Schumpp Olivier , Conedera Marco 
Published: December 2020

AbstractAnatomical modifications of xylem and phloem tissues of grapevine (Vitis vinifera) stems of shoots infected by the flavescence dorée phytoplasma (FDp) were first observed and described in the 1960s, but never quantified in detail. In this paper, we describe and quantify the impact of FDp on grapevine stem tissues, and relate it to the level of expression of symptoms and to cultivar‐specific FDp susceptibility. For this purpose, we measured and quantified the anatomical parameters of xylem and phloem tissues of a tolerant (Merlot) and a susceptible (Chardonnay) cultivar. For each cultivar, thin sections of eight shoots with symptoms from FDp‐infected grapevines, eight symptomless shoots from the same FDp‐infected grapevines, and eight symptomless shoots from symptomless grapevines (control) were compared. Results showed general inhibition of xylem growth and proliferation of phloem tissues (hyperplasia) with lack or irregular arrangement of the fibre‐sclereids in the axial phloem of the stems from shoots with symptoms, irrespective of the cultivar. Xylem vessels of infected Merlot shoots were partly occluded by tyloses and a higher number of smaller vessels were produced than in control plants. Thus, the anatomical responses confirmed the detrimental effect of FDp on stems of infected grapevine shoots, including impaired stem development and lack of periderm formation. Statistically significant differences were found between the two cultivars with different levels of susceptibility to FDp infection.
Validation of SOBI‐DANS method for automatic identification of horizontal and vertical eye movement components from EEG
Authors: Sun Rui , Chan Cynthia , H. Hsiao Janet , Tang Akaysha C. 
Published: December 2020

AbstractNeurophysiological investigation of neural processes are hindered by the presence of large artifacts associated with eye movement. Although blind source separation (BSS)‐based hybrid algorithms are useful for separating, identifying, and removing these artifacts from EEG, it remains unexamined to what extent neural signals can remain mixed with these artifact components, potentially resulting in unintended removal of critical neural signals. Here, we present a novel validation approach to quantitatively evaluate to what extent horizontal and vertical saccadic eye movement‐related artifact components (H and V Comps) are indeed ocular in origin. To automate the identification of the H and V Comps recovered by the second‐order blind identification (SOBI), we introduced a novel Discriminant ANd Similarity (DANS)‐based method. Through source localization, we showed that over 95% of variance in the SOBI‐DANS identified H and V Comps’ scalp projections were ocular in origin. Through the analysis of saccade‐related potentials (SRPs), we found that the H and V Comps’ SRP amplitudes were finely modulated by eye movement direction and distance jointly. SOBI‐DANS’ component selection was in 100% agreement with human experts’ selection and was 100% successful in component identification across all participants indicating a high cross‐individual consistency or robustness. These results set the stage for future work to transform the to‐be‐thrown‐away artifacts into signals indicative of gaze position, thereby providing readily co‐registered eye movement and neural signal without using a separate eye tracker.
Central serous chorioretinopathy imaging biomarkers
Authors: Singh Sumit Randhir , Iovino Claudio , Zur Dinah , Masarwa Dua , Iglicki Matias , Gujar Ramkailash , Lupidi Marco , Maltsev Dmitrii S , Bousquet Elodie , Bencheqroun Mehdi , Amoroso Francesca , Lima Luiz H , Padhy Srikanta Kumar , Govindahari Vishal , Chandra Khushboo , Souied Eric H , Rodriguez Francisco J , Daza Laura A , Rios Hernan A , Cagini Carlo , Peiretti Enrico , Behar-Cohen Francine , Chhablani Jay 
Published: December 2020

PurposeTo identify the factors predicting the visual and anatomical outcomes in eyes with central serous chorioretinopathy (CSCR) through 12 months.MethodsPatients with diagnosis of CSCR, either acute or chronic, were included in this multicentric, retrospective study. Demographic factors; systemic risk factors; central macular thickness (CMT), subfoveal choroidal thickness (SFCT), linear extent of ellipsoid zone (EZ) and interdigitation zone damage on optical coherence tomography; details of leak on fluorescein angiography and indocyanine green angiography were included as predictors of anatomical and visual outcomes. Regression analysis was performed to correlate the changes in best corrected visual acuity (BCVA) and resolution of disease activity.ResultsA total of 231 eyes of 201 patients with a mean age (49.7±11.8 years) were analysed. A total of 97 and 134 eyes were classified as acute and chronic CSCR. BCVA (0.35±0.31 to 0.24±0.34; p<0.001), baseline optical coherence tomography (OCT) parameters including CMT (p<0.001), subretinal fluid (SRF) height (p<0.001) and SFCT (p=0.05) showed a significant change through 12 months. Multivariate regression analysis showed change in CMT (p≤0.01) and SRF height at baseline (p=0.05) as factors predictive of good visual outcome. Logistic regression analysis revealed changes in both CMT (p=0.009) and SFCT (p=0.01) through 12 months to correlate with the resolution of disease.ConclusionOCT parameters such as changes in both CMT and SFCT along with subfoveal EZ damage can be predictive of disease resolution whereas changes in CMT and baseline SRF height correlate well with changes in BCVA through 12 months.
Feasibility and validity of using death surveillance data and SmartVA for fact and cause of death in clinical trials in rural China: a substudy of the China salt substitute and stroke study (SSaSS)
Authors: Huang Liping , Yu Jie , Neal Bruce , Liu Yishu , Yin Xuejun , Hao Zhixin , Wu Yangfeng , Yan Lijing L , Wu Jason HY , Joshi Rohina , Shi Jingpu , Feng Xiangxian , Zhang Jianxin , Zhang Yuhong , Zhang Ruijuan , Zhou Bo , Li Zhifang , Sun Jixin , Zhao Yi , Yu Yan , Pearson Sallie-Anne , Chen Zhengming , Tian Maoyi 
Published: December 2020

BackgroundIn rural China, mortality surveillance data may be an alternative to primary data collection in clinical trials; SmartVA (verbal autopsy) is also a potential alternative for endpoint adjudication. The feasibility and validity of both need to be assessed.MethodsWe used mortality data from the first 24 months of the China Salt Substitute and Stroke Study (SSaSS) trial and assessed the agreement between (1) mortality surveillance data and face-to-face visits for fact of death; (2) mortality surveillance data and SSaSS adjudication for causes of death; (3) SmartVA and SSaSS adjudication for causes of death; (4) cause-specific mortality fraction of different methods. Face-to-face visits and SSaSS adjudication were taken as reference methods. The agreement was measured by sensitivity, specificity and positive predictive value (PPV) across different 10th Revision of International Statistical Classification of Diseases chapters.ResultsOne thousand three hundred and sixty-five deaths were included. Mortality surveillance data had 82% sensitivity for fact of death and 81% sensitivity for causes of death, with substantial variances across different disease types and reasonable quality for circulatory death (91% sensitivity and 94% PPV). The sensitivity of SmartVA for causes of death was 61%, with reasonable quality for deaths of external causes of morbidity (90% sensitivity). The leading causes of death from different sources were the same with some variances in the fractions.ConclusionUsing mortality surveillance data for fact of death in clinical trials need to account for under-reporting. A face-to-face visit to all participants at the completion of trials may be warranted. Neither mortality surveillance data nor SmartVA provided valid data source for endpoint events.
Observation of marine mammal and bird interactions focused around a commercial fishing vessel in central Baffin Bay, Nunavut
Authors: Johnson Kelsey F. , Hussey Nigel E. , Ferguson Steven H. 
Published: December 2020

A detailed account of a variety of species foraging on Greenland halibut (Reinhardtius hippoglossoides (Walbaum, 1792)) fisheries discards associated with a commercial fishing vessel in central Baffin Bay, Nunavut, Canada is presented. Species observed included three marine mammals: northern bottlenose whales (Hyperoodon ampullatus (Forster, 1770)), sperm whales (Physeter macrocephalus Linnaeus, 1758), and a hooded seal (Cystophora cristata (Erxleben, 1777)), and two marine bird species: northern fulmars (Fulmarus glacialis (Linnaeus, 1761)) and glaucous gulls (Larus hyperboreus Gunnerus, 1767). Interspecies and intraspecies interactions were observed while species were in close proximity to the stern and starboard of a commercial fishing vessel confirming anecdotal reports from boat captains. Improved understanding of marine mammal and bird interactions with fisheries in the Arctic is required to accurately assess financial and ecological (i.e., bycatch) losses, potential for entanglement and to predict the likely impact on energy flow and transport of these resource subsidies throughout the Arctic marine ecosystem.
The Cenozoic volcanic fields in northern Hainan Island and the Leizhou Peninsula, south China: eruption history, magma source and dynamic background
Authors: Wei Feixiang , Wei Wei , Yu Hongmei 
Published: December 2020

Abstract

Northern Hainan Island and the Leizhou Peninsula volcanic fields (Leiqiong), the southernmost continental Cenozoic volcanism in China, cover an area of
c.
8000 km
2
with 177 volcanoes recognized. Far from the subduction areas, volcanoes in this area provide an ideal opportunity to study the geodynamics of intraplate volcanoes. Here, we review the geochronological and geochemical data of the volcanic rocks in Leiqiong volcanic fields, and discuss their magma sources and geodynamics on the basis of the geological and geophysical observations. Chronological data (34.78–0.01 Ma) show that the volcanic activities started approximately in the Miocene and continued to the Quaternary. These basalts show typical geochemical characteristics of oceanic island basalts, and tomographic images reveal that a mantle plume is situated beneath Hainan Island and extends down to the core–mantle boundary. Thus, we suggest that the Hainan mantle plume is responsible for the Cenozoic volcanism in Leiqiong volcanic fields and this plume is sourced from the lower mantle with additions of dehydrated slab fragments. These mixed plume materials were brought to the upper mantle and produce solid pyroxenites, which are the major source of Leiqiong magmas. Although there is no documental record of volcanic eruptions in Leiqiong volcanic fields, the volcanic danger cannot be neglected.
Automatic Recommendation of a Distance Measure for Clustering Algorithms
Authors: Zhu Xiaoyan , Li Yingbin , Wang Jiayin , Zheng Tian , Fu Jingwen 
Published: December 2020

With a large number of distance measures, the appropriate choice for clustering a given data set with a specified clustering algorithm becomes an important problem. In this article, an automatic distance measure recommendation method for clustering algorithms is proposed. The recommendation method consists of the following steps: (1) metadata extraction, including meta-feature collection and meta-target identification; (2) recommendation model construction using metadata; and (3) distance measure recommendation for a new data set by the recommendation model. Two different types of meta-targets and meta-learning techniques are utilized considering the possible different requirements of users.
To validate the necessity and effectiveness of the distance measure recommendation method, an empirical study is conducted with 199 publicly available data sets, 9 distance measures, and 2 widely used clustering algorithms. The experimental results indicate that distance measure significantly influences the performance of the clustering algorithm for a given data set. Furthermore, performance analysis of the proposed recommendation method proves its effectiveness.
Computed Tomography Perfusion–Based Machine Learning Model Better Predicts Follow-Up Infarction in Patients With Acute Ischemic Stroke
Authors: Kuang Hulin , Qiu Wu , Boers Anna M. , Brown Scott , Muir Keith , Majoie Charles B.L.M. , Dippel Diederik W.J. , White Phil , Epstein Jonathan , Mitchell Peter J. , Dávalos Antoni , Bracard Serge , Campbell Bruce , Saver Jeffrey L. , Jovin Tudor G. , Rubiera Marta , Khaw Alexander V. , Shankar Jai J. , Fainardi Enrico , Hill Michael D. , Demchuk Andrew M. , Goyal Mayank , Menon Bijoy K. ,   for the PRoveIT and HERMES Collaborators
Published: December 2020

Background and Purpose:
Prediction of infarct extent among patients with acute ischemic stroke using computed tomography perfusion is defined by predefined discrete computed tomography perfusion thresholds. Our objective is to develop a threshold-free computed tomography perfusion–based machine learning (ML) model to predict follow-up infarct in patients with acute ischemic stroke.

Methods:

Sixty-eight patients from the PRoveIT study (Measuring Collaterals With Multi-Phase CT Angiography in Patients With Ischemic Stroke) were used to derive a ML model using random forest to predict follow-up infarction voxel by voxel, and 137 patients from the HERMES study (Highly Effective Reperfusion Evaluated in Multiple Endovascular Stroke Trials) were used to test the derived ML model. Average map, T
max
, cerebral blood flow, cerebral blood volume, and time variables including stroke onset-to-imaging and imaging-to-reperfusion time, were used as features to train the ML model. Spatial and volumetric agreement between the ML model predicted follow-up infarct and actual follow-up infarct were assessed. Relative cerebral blood flow <0.3 threshold using RAPID software and time-dependent T
max
thresholds were compared with the ML model.

Results:

In the test cohort (137 patients), median follow-up infarct volume predicted by the ML model was 30.9 mL (interquartile range, 16.4–54.3 mL), compared with a median 29.6 mL (interquartile range, 11.1–70.9 mL) of actual follow-up infarct volume. The Pearson correlation coefficient between 2 measurements was 0.80 (95% CI, 0.74–0.86,
P
<0.001) while the volumetric difference was −3.2 mL (interquartile range, −16.7 to 6.1 mL). Volumetric difference with the ML model was smaller versus the relative cerebral blood flow <0.3 threshold and the time-dependent T
max
threshold (
P
<0.001).

Conclusions:
A ML using computed tomography perfusion data and time estimates follow-up infarction in patients with acute ischemic stroke better than current methods.
Catalogue of oribatid mites (Acari: Oribatida) from Continental Southeast Asia
Authors: CORPUZ-RAROS LEONILA , ERMILOV SERGEY G. 
Published: December 2020

This paper presents a catalogue of oribatid mites (Acari, Oribatida) recorded from Continental Southeast Asia (CSEA) covering a period of 55 years from 1965 to the first half of 2020. This subregion comprises countries that are located on the southeastern coast of the Asian continent, namely, Myanmar, Thailand, Laos, Cambodia and Vietnam. For each species, information is compiled on references to the original description, subsequent re-combinations of specific name with other genera, and junior synonyms used in CSEA literature, if any, as well as type habitat, habitats recorded later, and distribution within outside CSEA. A historical review of explorations and taxonomic studies in the various countries is also provided. A total of 820 valid species including subspecies and seven doubtful species are known so far from CSEA. The valid species belong to 313 genera and subgenera, 94 families and 36 superfamilies in all of the five infraorders and two hyporders of the Suborder Oribatida. The Hyporder Brachypylina is most diverse with 620 species, followed by Mixonomata (88), Enarthronota (65), Nothrina (41), Palaeosomata (5) and Parhyposomata (1). Vietnam whose fauna has been best explored tops the records with 730 species, followed by a low second by Thailand (137), then Cambodia (37) and Myanmar (11) while the oribatid fauna of Laos is still entirely unknown. Altogether, the oribatid fauna of Southeast Asia (SEA), including its two subregions, now totals 1601 species belonging to 477 genera, 109 families and 40 superfamilies. Species that are known so far only from CSEA countries and thus probably endemic is highest at 36.4% for Myanmar, 32,1% for Thailand, 23.7% for Vietnam, 0 for Cambodia, 27.2% for CSEA, 59.0% for the Malay Archipelago, and 48.7% for SEA as a whole. About 7% of the recorded species of Thailand and Vietnam are cosmopolitan or semicosmopolitan in distribution, but their faunal elements are decidedly Oriental, with about half (43–54%) occurring also in other Oriental countries. The same countries also share in common many species with other zoogeographic regions, viz. 12–14% Palaearctic, 8–16% Australian, 8–11% Neotropical, 3–11% Ethiopian, and 1–3% Nearctic.
Two Tropical Routes for the Remote Influence of the Northern Tropical Atlantic on the Indo–Western Pacific Summer Climate
Authors: Takaya Yuhei , Saito Naoaki , Ishikawa Ichiro , Maeda Shuhei 
Published: December 2020

AbstractThis study investigates the influence of sea surface temperature (SST) in the northern tropical Atlantic (NTA) on the Indo–western Pacific summer climate by analyzing record-high NTA SSTs in summer 2010. In that time, a decaying El Niño and developing La Niña were accompanied by widespread anomalous climate conditions in the Indo–western Pacific. These conditions are typical of summers that follow El Niño events and are often explained as being due to the influence of Indian Ocean warming induced by El Niños. Meanwhile, the record-high NTA SSTs that resulted from the influence of El Niño, the negative phase of the North Atlantic Oscillation and the interdecadal-and-longer NTA SST variability are one of the possible causes of anomalous conditions in the Indo–western Pacific. The results of sensitivity experiments using a coupled atmosphere–ocean model clearly indicate that the high NTA SSTs had a considerable influence on the summer weather in the Indo–western Pacific via two tropical routes: an eastbound route that involved a reinforcement of the atmospheric equatorial Kelvin wave and a westbound route that involved altering the Walker circulation over the Atlantic–Pacific region. The altered Walker circulation facilitated the transition to La Niña, amplifying the impact on the western North Pacific monsoon. Further evaluation reveals that both the interannual and interdecadal-and-longer variability of the NTA SST contributed to the anomalous Indo–western Pacific summer. The results highlight the interannual to multidecadal predictability of the Indo–western Pacific summer climate that originates in the NTA.