bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exome association analysis sheds light onto leaf rust (Puccinia triticina) resistance genes currently used in wheat breeding (Triticum aestivum L.)
Authors: Liu Fang , Zhao Yusheng , Beier Sebastian , Jiang Yong , Thorwarth Patrick , H. Longin C. Friedrich , Ganal Martin , Himmelbach Axel , Reif Jochen C. , Schulthess Albert W. 
Published: November 2019

SummaryResistance breeding is crucial for a sustainable control of leaf rust (Puccinia triticina) in wheat (Triticum aestivum L.) while directly targeting functional variants is the Holy Grail for efficient marker‐assisted selection and map‐based cloning. We assessed the limits and prospects of exome association analysis for severity of leaf rust in a large hybrid wheat population of 1574 single‐crosses plus their 133 parents. After imputation and quality control, exome sequencing revealed 202 875 single‐nucleotide polymorphisms (SNPs) covering 19.7% of the high‐confidence annotated gene space. We performed intensive data mining and found significant associations for 2171 SNPs corresponding to 50 different loci. Some of these associations mapped in the proximity of the already known resistance genes Lr21, Lr34‐B, Lr1 and Lr10, while other associated genomic regions, such as those on chromosomes 1A and 3D, harboured several annotated genes putatively involved in resistance. Validation with an independent population helped to narrow down the list of putative resistance genes that should be targeted by fine‐mapping. We expect that the proposed strategy of intensive data mining coupled with validation will significantly influence research in plant genetics and breeding.
Cytokinin dehydrogenase: a genetic target for yield improvement in wheat
Authors: Chen Lei , Zhao Jiqiang , Song Jiancheng , Jameson Paula E. 
Published: November 2019

SummaryThe plant hormone group, the cytokinins, is implicated in both qualitative and quantitative components of yield. Cytokinins have opposing actions in shoot and root growth—actions shown to involve cytokinin dehydrogenase (CKX), the enzyme that inactivates cytokinin. We revise and provide unambiguous names for the CKX gene family members in wheat, based on the most recently released wheat genome database, IWGSC RefSeq v1.0 & v2.0. We review expression data of CKX gene family members in wheat, revealing tissue‐specific gene family member expression as well as sub‐genome‐specific expression. Manipulation of CKX in cereals shows clear impacts on yield, root growth and orientation, and Zn nutrition, but this also emphasizes the necessity to unlink promotive effects on grain yield from negative effects of cytokinin on root growth and uptake of mineral nutrients, particularly Zn and Fe. Wheat is the most widely grown cereal crop globally, yet is under‐research compared with rice and maize. We highlight gaps in our knowledge of the involvement of CKX for wheat. We also highlight the necessity for accurate analysis of endogenous cytokinins, acknowledging why this is challenging, and provide examples where inadequate analyses of endogenous cytokinins have led to unjustified conclusions. We acknowledge that the allohexaploid nature of bread wheat poses challenges in terms of uncovering useful mutations. However, we predict TILLING followed by whole‐exome sequencing will uncover informative mutations and we indicate the potential for stacking mutations within the three genomes to modify yield components. We model a wheat ideotype based on CKX manipulation.
Epidemiology and microevolution of Phytophthora ramorum during a controlled disease outbreak in a simulated plant production facility
Authors: Serrano M. S. , Eyre C. , Garbelotto M. 
Published: November 2019

Phytophthora ramorum outbreaks have been documented to occur in natural settings during favourable environmental conditions, and to be caused by the overdominance of highly infectious genotypes. However, little is known about the dynamics of outbreaks in nursery settings. Through the description and quantification of symptoms, as well as through systematic pathogen isolation and genotyping, this study examines the scale and dynamic of spread of four different genotypes of P. ramorum in soil, water and leaves among Rhododendron plants in a nursery setting. Phytophthora ramorum isolation success was highest from leaves and intermediate from soil, reaching peak values at the end of the wet‐warm season. The observed disease outbreak was of moderate intensity, and abundance among the four genotypes used as inoculum varied, depending on substrate and isolation time. The spread mechanism of the disease was mostly through leaf‐to‐leaf contagion, followed by leaf‐to‐soil, and the scale of pathogen spread was less than 2 m in the 20 months of the experiment. Surprisingly, a large number of novel genotypes were detected during the experiment, and all were clearly derived from the four used as inoculum. The frequency of two such novel genotypes in the post‐outbreak phase was comparable to the frequency of some of the original four genotypes, suggesting they may be competitive. The creation of new genotypes in a nursery setting poses a threat to the industry itself, as well as to wildlands, due to the increase in pathogen adaptability often associated with new genetic variation.
Changes to the functional traits of phosphoenolpyruvate carboxylase following hybridization in C‐4 halophytes
Authors: Gallego‐Tévar Blanca , Peinado‐Torrubia Procopio , Álvarez Rosario , Gandullo Jacinto , Grewell Brenda J. , Figueroa Enrique , Castillo Jesús M. 
Published: November 2019

Hybridization is a relevant evolutionary mechanism linked to the invasiveness of plant species, but little is known about its effect on enzymatic activities in response to stress. We analyzed the effects of salinity on key mechanistic traits of phosphoenolpyruvate carboxylase (PEPC) enzyme for two hybrid taxa derived from nativeSpartina maritima(Curtis) Fernald and invasiveSpartina densifloraBrongn. in comparison with their parental species. Parental species showed contrasted strategies at the PEPC level to cope with salinity.Spartina maritimashowed its physiological optimum at 10 to 40 ppt salinity, with high PEPC activity (per unit leaf soluble protein), in contrast to the lower salinity optimum of 0.5 and 10 ppt forS. densiflora, where highest levels of PEPC apparent specific activity coincided with high light‐induced activation of PEPC. Both hybrids showed constant PEPC apparent specific activity from fresh water to hypersalinity and exhibited higher net photosynthesis rates in fresh water than their parents.Spartina maritima × densiflorapresented three transgressive PEPC‐related traits, being the only taxon able to increase its PEPC activation in darkness at high salinity.Spartina densiflora × maritimashowed most PEPC‐related traits intermediate between its parents. Inheritance types operating differently in reciprocal hybrids determine key functional traits conditioning their ecological performance.
Sexual harassment in contemporary workplaces: Contextualizing structural vulnerabilities
Authors: Minnotte Krista Lynn , Legerski Elizabeth M. 
Published: November 2019

AbstractRecent high‐profile cases of unwanted sexual attention in the workplace and the vibrancy of the associated #MeToo movement have drawn attention to the need to continue to explore workplace sexual harassment. In this article, we review existing literature on workplace sexual harassment, with an emphasis on the roles of power and structural vulnerability—key factors underlying sexual harassment. We argue for the need to contextualize structural vulnerabilities, with an eye towards uncovering how dimensions of power and vulnerability vary across workplaces, creating different mechanisms contributing to sexual harassment in specific contexts. With this backdrop, we then use the restaurant service industry as an example to illustrate the unique structural vulnerabilities workers are exposed to in this environment. We conclude with a discussion of the importance of continuing to investigate the dynamics of sexual harassment, especially with work that takes an intersectional approach.
Lifestyle behaviours, ethnicity and menstruation have little added value in prediction models for low haemoglobin deferral in whole blood donors
Authors: Baart A. Mireille , Timmer Tiffany , de Kort Wim L. A. M. , van den Hurk Katja 
Published: November 2019

SummaryObjectiveTo investigate the added value of questionnaire‐based predictors to existing prediction models for low haemoglobin (Hb) deferral in whole blood donors.BackgroundPrediction models for Hb deferral risk can be applied in the invitation process of donors for a blood donation. Existing prediction models are based on routinely collected data. The model performance might be improved by the addition of predictive factors.MethodsThe added value of food consumption, smoking, physical activity, ethnicity and menstruation in the prediction of Hb deferral was assessed by comparing the existing models with extended models using the following measures: model X2, concordance (c)‐statistic and net reclassification improvement (NRI).ResultsAddition of one candidate predictor to the models did not substantially improve the model performance. Addition of multiple new candidate predictors significantly increased the model X2 (from 137 to 159 for men, and from 157 to 199 for women) and resulted in a non‐significant increase of the c‐statistic (from 0.85 to 0.87 for men, and from 0.78 to 0.81 for women). The NRI for men was 11.4% and for women 1.5% after addition of multiple predictors.ConclusionAddition of lifestyle behaviours, ethnicity or menstruation to prediction models for low Hb deferral in whole blood donors improved the model performance, but not substantially. For easy use in practice, we do not recommend addition of the investigated predictors to the prediction models.
Evidence of a significant role of glutathione reductase in the sulfur assimilation pathway
Authors: Cohen Anner , Hacham Yael , Welfe Yochai , Khatib Soliman , Avice Jean‐Christophe , Amir Rachel 
Published: November 2019

SummaryWith the objective of studying the role of glutathione reductase (GR) in the accumulation of cysteine and methionine, we generated transgenic tobacco and Arabidopsis lines overexpressing the cytosolic AtGR1 and the plastidic AtGR2 genes. The transgenic plants had higher contents of cysteine and glutathione. To understand why cysteine levels increased in these plants, we also used gr1 and gr2 mutants. The results showed that the transgenic plants have higher levels of sulfite, cysteine, glutathione and methionine, which are downstream to adenosine 5′ phosphosulfate reductase (APR) activity. However, the mutants had lower levels of these metabolites, while the sulfate content increased. A feeding experiment using 34SO42– also showed that the levels of APR downstream metabolites increased in the transgenic lines and decreased in gr1 compared with their controls. These findings, and the results obtained from the expression levels of several genes related to the sulfur pathway, suggest that GR plays an essential role in the sulfur assimilation pathway by supporting the activity of APR, the key enzyme in this pathway. GR recycles the oxidized form of glutathione (GSSG) back to reduce glutathione (GSH), which serves as an electron donor for APR activity. The phenotypes of the transgenic plants and the mutants are not significantly altered under non‐stress and oxidative stress conditions. However, when germinating on sulfur‐deficient medium, the transgenic plants grew better, while the mutants were more sensitive than the control plants. The results give substantial evidence of the yet unreported function of GR in the sulfur assimilation pathway.
The florigen interactor BdES43 represses flowering in the model temperate grass Brachypodium distachyon
Authors: Cao Shuanghe , Luo Xumei , Xie Li , Gao Caixia , Wang Daowen , Holt Ben F. , Lin Hao , Chu Chengcai , Xia Xianchun 
Published: November 2019

SummaryFLOWERING LOCUS T (FT) protein, physiologically florigen, has been identified as a system integrator of numerous flowering time pathways in many studies, and its homologs are found throughout the plant lineage. It is important to uncover how precisely florigenic homologs contribute to flowering initiation and how these factors interact genetically. Here we dissected the function of Brachypodium FT orthologs BdFTL1 and BdFTL2 using overexpression and gene‐editing experiments. Transgenic assays showed that both BdFTL1 and BdFTL2 could promote flowering, whereas BdFTL2 was essential for flowering initiation. Notably, BdFTL1 is subject to alternative splicing (AS), and its transcriptional level and AS are significantly affected by BdFTL2. Additionally, BdFTL2 could bind with the PHD‐containing protein BdES43, an H3K4me3 reader. Furthermore, BdES43 was antagonistic to BdFTL2 in flowering initiation in a transcription‐dependent manner and significantly affected BdFTL1 expression. BdFTL2, BdES43 and H3K4me3 also had highly similar distribution patterns within the BdFTL1 locus, indicating their interplay in regulating target genes. Taken together, florigen BdFTL2 functions as a potential epigenetic effector of BdFTL1 by interacting with a BdES43‐H3K4me3 complex. This finding provides an additional insight for the regulatory mechanism underlying the multifaceted roles of florigen.
Factors associated with non-active retinal capillary density as measured with Confocal Scanning Laser Doppler Flowmetry in an elderly population: the Thessaloniki Eye Study (TES)
Authors: Dervenis Nikolaos , Harris Alon , Coleman Anne L , Wilson M Roy , Founti Panayiota , Yu Fei , Siesky Brent , Anastasopoulos Eleftherios , Pappas Theofanis , Koskosas Archimidis , Kilintzis Vassilis , Topouzis Fotis 
Published: November 2019

Purpose
To identify factors associated with retinal capillary density as measured with Confocal Scanning Laser Doppler Flowmetry (Heidelberg retina flowmeter (HRF)) in the Thessaloniki Eye Study (TES).

Methods
Participants of the TES (age ≥60 years, cross-sectional population-based study) were assessed for active capillary density in the superior and inferior peripapillary retina using the HRF. Pixel-by-pixel analysis was performed to quantify the percentage of zero flow pixels (ZFPs; surrogate for % retinal area with non-active capillaries). Multivariable regression analyses were performed to assess the association of non-active vascular density with ophthalmic and systemic variables. Glaucoma, late age-related macular degeneration and diabetic retinopathy subjects were excluded.

Results
1189 subjects were included in the analysis. Older age (per year) was associated with higher percentage of ZFP in both the superior (slope estimate (SE)=0.0020) and the inferior (SE=0.0019) peripapillary retina (p<0.0001). History of migraine was associated with lower percentage of ZFP (SE=−0.0166) compared with no history of migraine in the superior peripapillary retina only (p<0.05). Higher intraocular pressure ((IOP) per mm Hg) and height (per cm) were associated with higher percentage of ZFP in the inferior peripapillary retina only (SE=0.0012, p<0.05 and SE=0.0005, p<0.05, respectively). The group consuming vegetables one to three times per week compared with the group consuming vegetables at least once a day had higher percentage of ZFP only in the inferior peripapillary retina (SE=0.0080, p<0.05).

Conclusion
At a population level, our study revealed associations of older age, higher IOP and taller height with lower active retinal capillary density and of migraine with higher capillary density. Looking further into these associations may provide insight into disease mechanisms.
Method effects associated with negatively and positively worded items on the 12-item General Health Questionnaire (GHQ-12): results from a cross-sectional survey with a representative sample of Catalonian workers
Authors: Rodrigo Maria F , Molina J Gabriel , Losilla Josep-Maria , Vives Jaume , Tomás José M 
Published: November 2019

ObjectiveRecent studies into the factorial structure of the 12-item version of the General Health Questionnaire (GHQ-12) have shown that it was best represented by a single substantive factor when method effects associated with negatively worded (NW) items are considered. The purpose of the present study was to examine the presence of method effects, and their relationships with demographic covariates, associated with positively worded (PW) and/or NW items.DesignA cross-sectional, observational study to compare a comprehensive set of confirmatory factor models, including method effects associated with PW and/or NW items with GHQ-12 responses.SettingRepresentative sample of all employees living in Catalonia (Spain).Participants3050 participants (44.6% women) who responded the Second Catalonian Survey of Working Conditions.ResultsA confirmatory factor analysis showed that the best fitting model was a unidimensional model with two additional uncorrelated method factors associated with PW and NW items. Furthermore, structural equation modelling (SEM) revealed that method effects were differentially related to both the sex and age of the respondents.ConclusionIndividual differences related to sex and age can help to identify respondents who are prone to answering PW and NW items differently. Consequently, it is desirable that both the constructs of interest as well as the effects of method factors are considered in SEM models as a means of avoiding the drawing of inaccurate conclusions about the relationships between the substantive factors.
Anisotropic evolution of D-dimensional FRW spacetime
Authors: Middleton Chad , Brouse Bret A. , Jackson Scott D. 
Published: November 2019

AbstractWe examine the time evolution of the $$D=d+4$$D=d+4 dimensional Einstein field equations subjected to a flat Robertson-Walker metric where the 3D and higher-dimensional scale factors are allowed to evolve at different rates. We find the exact solution to these equations for a single fluid component, which yields two limiting regimes offering the 3D scale factor as a function of the time. The fluid regime solution closely mimics that described by 4D FRW cosmology, offering a late-time behavior for the 3D scale factor after becoming valid in the early universe, and can give rise to a late-time accelerated expansion driven by vacuum energy. This is shown to be preceded by an earlier volume regime solution, which offers a very early-time epoch of accelerated expansion for a radiation-dominated universe for $$d=1$$d=1. The time scales describing these phenomena, including the transition from volume to fluid regime, are shown to fall within a small fraction of the first second when the fundamental constants of the theory are aligned with the Planck time. This model potentially offers a higher-dimensional alternative to scalar-field inflationary theory and a consistent cosmological theory, yielding a unified description of early- and late-time accelerated expansions via a 5D spacetime scenario.
John Dewey and James Baldwin on History, Tragedy, and the Forgetting of Race
Authors: McCall Corey 
Published: November 2019

Abstract
This essay examines various intellectual affinities between Dewey and Baldwin, including their pragmatic and tragic conceptions of history. I argue in the first section that Dewey’s attention to the precarious dimensions of experience and his critique of dominant modes of inquiry that prioritize the stable over the precarious pay insufficient attention to race, though this focus on the precarious over the stable aspects of experience is enough to show that pragmatism does acknowledge the tragic dimension. The subsequent section argues that this insufficiency might be rectified through a reading of Baldwin’s work. While Dewey and Baldwin both acknowledge that existence is finite and precarious (and hence the tragic), Baldwin shows that racism and the promotion of white identity is essentially an attempt to disavow the precariousness of existence. Baldwin’s writings should supplement Dewey’s theory of experience and his account of history because we find in them an acknowledgement of the deep institutional roots of racial oppression and various forms of resistance to this oppression as a key dimension of American history.
“Caught in Its Movement”: Liberalism, Critique, and Dewey’s Implicit Philosophy of History
Authors: Portella Elizabeth 
Published: November 2019

Abstract
“Philosophers,” Dewey writes, “are parts of history, caught in its movement; creators perhaps in some measure of its future, but also assuredly creatures of its past” (Dewey 1927, 2). The question of the philosopher’s embeddedness in either her own or some earlier historical moment constitutes an important theme in Dewey’s account of pragmatism, in particular his account of politics. In lieu of a formal treatise on history, this paper focuses on Dewey’s claims about history as they are enacted in his political analyses. Drawing on texts such as Liberalism and Social Action (1935) and Freedom and Culture (1939) as well “The Role of Philosophy in the History of Civilization” (1927), I hope to elucidate in greater depth the function and meaning of the term “historic relativity” as a central concept in Dewey’s philosophy of history (Dewey 1935, 42). Further, I evaluate Dewey’s criticisms of both classical liberalism and Marxism on historical grounds, where he employs what I call political obsolescence claims. From these texts I reconstruct and critically assess what I refer to as Dewey’s implicit philosophy of history. I conclude that the presuppositions of Dewey’s political reconstruction represent the very mode of uncritical historical reproduction which his philosophy ostensibly cautions against. To suggest one possibility for addressing these tensions, I gesture toward non-coincidence as a critical historical category through which we might articulate the historic present with the hope of transforming it.
Leukoplakia or LPR: The Misdiagnosis of Laryngeal Tuberculosis
Authors: Lou Zheng cai , Li Xiuguo 
Published: November 2019

Objective: The objective is to reduce the rates of misdiagnosis and inappropriate treatment of laryngeal tuberculosis (LTB). Study Design: Retrospective case series. Materials and Methods: Medical records of 3 histopathology-confirmed cases at a tertiary medical center from 2000 to 2018. Results: Seventeen patients with LTB included in this study. Of the 17 patients, 16 patients were male and 1 was female; 11 patients had a history of smoking. Odynophagia was the chief complaint in 6 cases, and 11 patients complained of hoarseness. The appearance of the affected larynx was ranged from diffuse swelling (n = 7, 41.2%), mucosa white lesion (n = 5,29.4%), and granulomatous tumors (n = 2, 11.76%), and these features presented together (n = 2, 11.76%). Seventeen patients with LTB were misdiagnosed as acute epiglottitis in 4 (23.5%) patients, acute laryngitis in 1 (5.9%) patient, leukoplakia in 5 (29.4%) patients, laryngopharyngeal reflux (LPR) in 6 (35.3%) patients, and laryngocarcinoma in 1 (5.9%) patient. Chest computed tomography reported old pulmonary tuberculosis in 2 (11.7%) patients, active pulmonary tuberculosis in 7 (41.2%) patients, and normal lung status in 8 (47.1%) patients. Histopathological examination reported Mycobacterium tuberculosis infection by revealing epithelioid cell granulomas with Langhans-type giant cells in 14 (82.4%) patients and epithelioid cell granulomas with caseous necrosis and Langhans-type giant cells in 3 (17.6%) patients. Conclusions: Laryngeal tuberculosis was easily misdiagnosed as acute epiglottitis or leukoplakia because of diffuse swelling of the epiglottis or white lesions over the true vocal cord, especially patients with increasing LTB were misdiagnosed as LPR with the enhancement of LPR awareness among otolaryngologist. Clinicians should be aware of the possibility of LTB for chronic intractable laryngitis with failure treatment of proton pump inhibitor and recurrent acute epiglottitis with foreign body injury.