bluuebunny/crossref_metadata_2025 huggingface dataset:
A new fossil psyllid, Cacopsylla trigona sp. nov. (Hemiptera: Psylloidea: Psyllidae), from the Miocene of China

Authors: ZHANG TINGYING , LUO XINYU , YAO YUNZHI , REN DONG
Published: October 2019

Psyllinae, a subfamily of Psyllidae, currently includes 29 genera (Burckhardt & Ouvrard, 2012; Ouvrard, 2018), of which Cacopsylla Ossiannilsson, 1970 is the most species-rich genus, distributed mainly in the Northern Hemisphere (Li, 2011; Ouvrard, 2018). In China, more than 300 extant species of Cacopsylla have been reported (Yang et al., 2004; Li, 2011; Luo et al., 2012, 2016). Based on recent molecular phylogenetic analyses, Cacopsylla in its current sense is a polyphyletic genus (Percy et al., 2018; Cho et al., 2019).
Aspidistra micrantha (Asparagaceae, Nolinoideae), a new species from Vietnam with unusually small flowers

Authors: VISLOBOKOV NIKOLAY A. , NURALIEV MAXIM S. , KUZNETSOV ANDREY N. , KUZNETSOVA SVETLANA P.
Published: October 2019

Aspidistra micrantha is described and illustrated as a new species from southern Vietnam (Quang Nam province, Song Thanh Nature Reserve). The new species has globoid flowers, which are the smallest within the genus Aspidistra. In floral structure, the closest species to A. micrantha is A. urceolata, which is endemic to the Guizhou province of China, but strongly differs from the latter in some morphological features of the rhizome, leaves and position of anthers.
A new Neotropical emerald moth genus based on some unusual “artefacts” (Lepidoptera: Geometridae, Geometrinae)
Authors: VIIDALEPP JAAN , LINDT AARE
Published: October 2019

We describe a nemoriine emerald moth genus, Vallichlora gen. nov., with modified male genitalia, including two new species: Vallichlora rara sp. n.—the type species—and Vallichlora selva, sp. n. The genus is characterised by the presence of two long, thumb-shaped processes of the tegumen.
The systematic position of Pamera noctuabunda Bergroth, 1907 (Hemiptera: Heteroptera: Rhyparochromidae), with a revised key to the species of Stalaria Harrington, 1980
Authors: SCUDDER G.G.E.
Published: October 2019

The rhyparochromid Pamera noctuabunda Bergroth, 1907 is shown to belong in the genus Stalaria Harrington, 1980, not in the genus Remaudiereana Hoberlandt, 1954, where it was placed by Harrington (1980). Stalaria nysias (Linnavouri, 1978) is synonymized with S. noctuabunda. The four species described in Stalaria are confined to Africa: their distribution is outlined. Specimens examined are listed, and a revised key to the species of Stalaria is appended.
Three new species of the genus Paradoxecia Hampson, 1919 (Lepidoptera: Sesiidae) from China
Authors: YU TIANTIAN , ARITA YUTAKA , KALLIES AXEL , WANG MIN
Published: October 2019

Three new species of the genus Paradoxecia Hampson, 1919 (Lepidoptera: Sesiidae) are described from China: Paradoxecia kishidai Yu & Arita sp. nov., Paradoxecia polyzona Yu & Kallies sp. nov. and Paradoxecia beibengensis Yu & Kallies sp. nov. Illustrations of the holotypes and the male genitalia are provided along with a key to all currently known species of the genus. DNA barcodes of the new species are deposited in Genbank.
Taxonomic review and distribution of the genus Vespula Thomson, 1869 (Hymenoptera: Vespidae: Vespinae) from Vietnam
Authors: NGUYEN LIEN THI PHUONG , VU THUONG THI , DAGLIO ANTHONY , WIŚNIOWSKI BOGDAN
Published: October 2019

A taxonomic review of the genus Vespula Thomson in Vietnam is reported. Three species are recorded: V. flaviceps (Smith, 1870), V. koreensis (Radoszkowski, 1887), and V. orbata (Buysson, 1902). Of these, V. flaviceps is newly recorded from Vietnam. Distribution records of all three species and an identification key to species based on morphological characters are presented. Vespula koreensis is distributed from high (Cao Bang, Vinh Phuc, Quang Tri) to lower areas (Thai Nguyen, Tuyen Quang, Lang Son, Bac Giang), while the other two species are distributed in high mountainous areas of the northern and central regions of Vietnam such as in Cao Bang, Lao Cai, Son La, Phu Tho, Vinh Phuc, Quang Tri and Quang Nam provinces.
Spatial Distribution and Seasonality of Halocline Structures in the Subarctic North Pacific
Authors: Katsura Shota , Ueno Hiromichi , Mitsudera Humio , Kouketsu Shinya
Published: October 2019

The spatial distribution and seasonality of halocline structures in the subarctic North Pacific (SNP) were investigated using Argo profiling float data and various surface flux data collected in 2003–17. The permanent halocline (PH) showed zonal patterns in the spatial distributions of its depth and intensity and tended to be shallow and strong in the eastern SNP but deep and weak in the west. Mean distributions of PH depth and intensity corresponded to the winter mixed layer depth and sea surface salinity, respectively, indicating that it forms in association with the development of the winter mixed layer. In the Western Subarctic Gyre and Alaskan Gyre, where a relatively strong PH formed, PH intensity and depth showed clear seasonal variations, and deepening of the mixed layer compressed the underlying PH during the cooling period, resulting in intensification and development of the PH in late winter. In both regions, upwelling of high-salinity water also contributed to PH intensification. The summer seasonal halocline (SH) showed distinct zonal differences in frequency and intensity, which were opposite to the PH distribution. While an SH formed in the western and central SNP and coastal regions, it was seldom present in the eastern area. This zonal contrast of SH corresponded to freshening of the mixed layer during the warming period, primarily reflecting freshwater flux. Geostrophic and Ekman advection play important roles in spatial differences in SH intensity and depth. SH development contributed to PH intensification in the following winter, by decreasing salinity above the PH through entrainment.
Tree-Ring Reconstruction of Single-Day Precipitation Totals over Eastern Colorado
Authors: Howard Ian M. , Stahle David W.
Published: October 2019

Mean daily to monthly precipitation averages peak in late July over eastern Colorado and some of the most damaging Front Range flash floods have occurred because of extreme 1-day rainfall events during this period. Tree-ring chronologies of adjusted latewood width in ponderosa pine from eastern Colorado are highly correlated with the highest 1-day rainfall totals occurring during this 2-week precipitation maximum in late July. A regional average of four adjusted latewood chronologies from eastern Colorado was used to reconstruct the single wettest day observed during the last two weeks of July. The regional chronology was calibrated with the CPC 0.25° × 0.25° Daily U.S. Unified Gauge-Based Analysis of Precipitation dataset and explains 65% of the variance in the highest 1-day late July precipitation totals in the instrumental data from 1948 to 1997. The reconstruction and instrumental data extend fully from 1779 to 2019 and indicate that the frequency of 1-day rainfall extremes in late July has increased since the late eighteenth century. The largest instrumental and reconstructed 1-day precipitation extremes are most commonly associated with the intrusion of a major frontal system into a deep layer of atmospheric moisture across eastern Colorado. These general synoptic conditions have been previously linked to extreme localized rainfall totals and widespread thunderstorm activity over Colorado during the summer season. Chronologies of adjusted latewood width in semiarid eastern Colorado constitute a proxy of weather time-scale rainfall events useful for investigations of long-term variability and for framing natural and potential anthropogenic forcing of precipitation extremes during this 2-week precipitation maximum in a long historical perspective.
Maintaining Stable Macroeconomic Conditions
Authors: Jones Russell , Llewellyn John
Published: October 2019

Executive Summary

The UK economy faces more than usually uncertain times. Outside the European Union, and in an increasingly challenging global environment characterised by ageing populations, climate change, populism, protectionism, and more, the country needs to chart a new course. This may well require policymakers to consider unconventional approaches to monetary and fiscal policy and, at the very least argues for important modifications of the current policy regime, including the autonomous mandate of the Bank of England.

At some point, there will be a major slowdown in economic activity. Yet the Bank of England has very little leeway to respond by cutting interest rates, and it has already adopted an armoury of unorthodox tools that may be decreasing in effectiveness. More radical monetary approaches would be likely to be politically controversial; and are not without risks. In these circumstances it would be a mistake to rely solely, or even largely, on monetary policy to maintain demand. It would be better to conduct monetary and fiscal policy in tandem, and for discretionary fiscal policy to be required to play a much more active role in demand management than hitherto. This would, for example, imply major extension of the automatic stabilisers and efforts better to calibrate discretionary initiatives with the business cycle.

But given the long-term pressures on the public finances, more fundamental changes in the structure of spending and taxation are needed, along with a redrawing of fiscal rules and targets, under independent budgetary oversight. The current, historically low, share in GDP of public spending is itself unsustainable in light of the demand for services of an ageing population; plans should be made to raise it closer to the European average. In the most extreme circumstances it might become necessary to waive the fiscal rules entirely and for the Bank of England directly to underwrite fiscal stimulus in order to sustain aggregate demand. It would be wise for the authorities to consider the options in detail now, while the environment is still relatively stable.
Reorienting Foreign Policy
Authors: Greenstock Jeremy
Published: October 2019

Executive Summary

After Brexit, the UK must show that it has a voice. It will need to re-earn international respect, and in particular establish the concept of a ‘global Britain’ on the basis of performance, not rhetoric. That means re-establishing a strong network of relationships around the world in support of its security and economic health, but also continuing to play a leading role in support of the international rules-based order. For example, it should make the most of its continuing status as a Permanent Member of the UN Security Council to act as a problem-solver and system-enhancer in the collective interest.

An early, first-order priority will be establishing a new, mutually beneficial partnership with the European Union, which continues to form our economic and political neighbourhood. Reconstructing a modern relationship with the United States is not secondary to that, but cannot substitute for it and must be undertaken in recognition of the differing interests and instincts of the two sides. A further challenge is building the right relationship with China based on mutual interest in trade, peace, and international respect and on confronting expansionist or opportunistic practices. With Russia, too, it is possible to design a predictable set of behaviours on either side, and with both countries good communication channels will need to be maintained.

Brexit gives the UK the scope to construct a more deliberate diplomatic approach to the rest of the English-speaking world than was explicitly possible as an EU member – notably in working with Canada, Australia and New Zealand to promote the international rules-based order. But this should be complemented by more effective outreach to non-English-speaking countries, notably in support of trade and investment opportunities with emerging nations. But with them as with all the UK's interlocutors, the need to earn its place, and to show that it realises that, will be vital.

In defence and security, the UK will continue in its commitment to the strength of NATO as its essential alliance under US leadership, while also liaising carefully with EU Member States as they seek to improve their own capacities to contribute to European security. But it cannot simply rely on old institutional structures. It needs to lead, for example by playing a stronger role in the control of non-military forms of aggression, such as cyber warfare, economic sanctions, rivalry in space, and commercial espionage.

A strategy for realising the UK's interests in the international arena will require the Prime Minister's constant attention, but also a specific mandate for a very senior minister to supervise the interlinked policy areas of foreign affairs, international development, and international trade within a single government department.
Updating Security and Defence Policy
Authors: Grant Mark Lyall
Published: October 2019

Executive Summary

Threats to the security of the UK are evolving with the changing nature of conflict and balance of power in the world. They are multiple and fragmented, and domestic and online as well as overseas in nature: principally state-based threats such as posed by Russian activity; terrorism; cyber-attacks; and serious organised crime. To respond, the United Kingdom will need flexible capabilities aimed at fostering infrastructural and societal resilience as much as conventional defence. Above all, the UK needs to focus on maintaining, promoting, and defending the international rules-based order, as represented by the UN and NATO among other institutions.

The UK possesses significant assets to these ends, including its continuing status as one of eight acknowledged nuclear powers – a status that it should not abandon unilaterally; permanent membership of the UN Security Council; membership of the ‘Five Eyes' intelligence community; and its internationally respected armed forces.

But effort and resources are required to support these commitments, for example in helping to encourage other European states to spend more on defence; in contributing to UN peace-keeping operations or other collaborative overseas actions; and most of all in ensuring that army and navy manpower is rebuilt. Two per cent of GDP is no longer sufficient for the proper defence of the nation. Even allowing for the demands of other parts of government, the target for defence spending should be raised in the next review to 2.2 per cent.

The principal focus will need to be on efficiency and redeployment of resources as the current equipment-heavy procurement cycle comes to an end. In particular, investment needs to continue to be rebalanced towards new capabilities such as drone technology, offensive and defensive cyber and intelligence manpower.

But, to avoid any weakening of the country's security, priority should be given to negotiating a new agreement on security and intelligence cooperation with its European allies to replace the arrangements it had within the EU.
Redesigning Housing Policy
Authors: Barker Kate
Published: October 2019

Executive Summary

Discussion of the UK's housing crisis is of long date, and tends to focus on a simple story about a mismatch in housing supply and demand and the consequent need to build more homes. Yet the reality is more complex with multiple sub-plots including social housing, stress in the private rented sector, benefits, subsidies and ultimately taxation of home ownership.

At the bottom of the market, the crisis is real and acute, as manifested in a sharp increase in homelessness and rough sleeping. The inescapable answer is to increase the depleted stock of social housing and widen eligibility criteria. An increase of 100,000 social units a year in England would help address this problem, as well as alleviate the financial squeeze on tenants of the private rented sector, whose number has grown sharply in the past 15 years in tandem with a steep rise in the housing benefit bill. Recent efforts to curb housing benefit have further increased distress, so it will be necessary to consider increasing benefits again alongside regulatory interventions with private landlords.

In the home ownership market, recent government intervention has taken the form of the much-criticised Help-to-Buy Equity Loan scheme. This market policy to support new-build homes should be wound down and replaced by a scheme to endow all young people with a capital sum that they could use for second-hand homes as well. More generally, a more sophisticated approach to planning home-building is needed, both for assessing overall numbers and their regional distribution and in financing the supporting infrastructure.

But none of these measures is a panacea for a housing crisis that is in large part a symptom of problems in the wider economy, such as low relative wages for young people, a lack of clarity about environmental issues, and failing places. A successful policy package to address the distorted structure of the housing market must also grasp the most difficult nettle of all – namely the way the tax benefits of owner-occupation incentivise overconsumption of housing and a widening wealth gap between renters and home owners, and between owners in different parts of the country. If we spend more to help those who struggle to afford decent housing, then it is only just to raise more taxation from those who benefit from restrictions on housing supply – whether through reform to council tax, a wider wealth tax or a limited form of Capital Gains Tax on principal residences.
In My Name and the Name of All People Who Live in Misery: Rap in the Wake of Revolution in Tunisia and Egypt
Authors: Sánchez García José , Feixa Pàmpols Carles
Published: October 2019

Rap and mahragan were the sound of youths that demanded freedom and social justice in Tahrir Square and in Tunisia Parliament Square sit-ins during 2011. It may have been, not merely the soundtrack of the revolution, but a motivating factor in bringing people into the streets and reshaping their basic political subjectivity: a core process of any revolutionary change in a country’s social and political structures. On the one hand, rap and mahragan are used by young people as a way of calling into question the processes of marginalization. On the other hand, young people use it as a way of participating in public life. Despite its differences, from a mixed analysis using the data collected in the SAHWA project, both qualitative and quantitative, this article proves how rap and mahragan music scenes (re)produce informal spaces as an alternative to their social marginalization and positioned them into Tunisian and Egyptian political arenas in different places according to environmental political dialectics.
Prediction value of pulmonary hypertension in newly identified left ventricular dysfunction among adult patients after patent ductus arteriosus closure
Authors: Chen Peng‐yuan , Luo Dong‐ling , Li He‐zhi , Fei Hong‐wen , Huang Tao , Huang Yi‐gao , Chen Ji‐mei , Zhuang Jian , He Peng‐cheng , Zhang Cao‐jin
Published: October 2019

The present study aimed to propose the pulmonary hypertension for predicting left ventricular dysfunction in adults after patent ductus arteriosus closure. A total of 183 patients (age ≥18 years) after patent ductus arteriosus occlusion were retrospectively collected in this study. In brief, pre‐, post‐procedure and short‐term follow‐up transthoracic echocardiography were performed. Simpson’s method was used to measure the left ventricular ejection fraction (LVEF), and LVEF less than 50% after procedure was utilized as a criterion to identify left ventricular dysfunction. As a result, 36 (19.67%) patients developed newly identified left ventricular dysfunction. The rate of newly identified left ventricular dysfunction was significantly higher in moderate or severe pulmonary hypertension groups compared to the groups of mean pulmonary artery pressure (mPAP) <25 mmHg (P < .001). Logistic regression analysis showed that elevated mPAP ( ≥25 mmHg) was an independent predictive value for newly identified left ventricular dysfunction (OR = 3.584, 95%CI: 1.186–10.832, P = .024) after adjusting confounders. The ROC curve revealed a good discrimination power for predicting newly identified left ventricular dysfunction (AUC = 0.924, 95%CI: 0.885–0.963, P < .001). Taken together, newly identified left ventricular dysfunction after patent ductus arteriosus closure was prevalent in patients with elevated mPAP. The pre‐procedure elevated mPAP is an independent risk factor for the prediction of the newly identified left ventricular dysfunction in adult patients undergoing percutaneous patent ductus arteriosus closure. It is feasible to propose a risk model for predicting post‐procedure left ventricular dysfunction and a heart function monitoring in pulmonary hypertension patients.
National trends in coronary intensive care unit admissions, resource utilization, and outcomes
Authors: Woolridge Sarah , Alemayehu Wendimagegn , Kaul Padma , Fordyce Christopher B , Lawler Patrick R , Lemay Michel , Jentzer Jacob C , Goldfarb Michael , Wong Graham C , Armstrong Paul W , van Diepen Sean
Published: October 2019

Background:

Emerging evidence suggests that coronary intensive care units are evolving into intensive care environments with an increasing burden of non-cardiovascular illness, but previous studies have been limited to older populations or single center experiences.

Methods:

Canadian national health-care data was used to identify all patients ≥18 years admitted to dedicated coronary intensive care units (2005–2015) and admissions were categorized as primary cardiac or non-cardiac. The outcomes of interest included longitudinal trends in admission diagnoses, critical care therapies, and all-cause in-hospital mortality.

Results:

Among the 373,992 patients admitted to a coronary intensive care unit, minimal changes in the proportion of patients admitted with a primary cardiac (88.2% to 86.9%; p<0.001) and non-cardiac diagnoses (11.8% to 13.1%; p<0.001) were observed. Among cardiac admissions, a temporal increase in the proportion of ST-segment elevation myocardial infarction (19.4% to 24.1%, p<0.001), non-ST-segment elevation myocardial infarction (14.6% to 16.2%, p<0.001), heart failure (7.3% to 8.4%, p<0.001), shock (4.9% to 5.7%, p<0.001), and decline in unstable angina (4.9% to 4.0%, p<0.001) and stable coronary diseases (21.3% to 12.4%, p<0.001) was observed. The proportion of patients requiring critical care therapies (57.8% to 63.5%, p<0.001) including mechanical ventilation (9.6% to 13.1%, p<0.001) increased. In-hospital mortality rates for patients with primary cardiac (4.9% to 4.4%; adjusted odds ratio 0.71, 95% confidence interval 0.63–0.79) and non-cardiac (17.8% to 16.1%; adjusted odds ratio 0.84, 0.73–0.97) declined; results were consistent when stratified by academic vs community hospital, and by the presence of on-site percutaneous coronary intervention.

Conclusion:

In a national dataset we observed a changing case-mix among patients admitted to a coronary intensive care unit, though the proportion of patients with a primary cardiac diagnosis remained stable. There was an increase in clinical acuity highlighted by critical care therapies, but in-hospital mortality rates for both primary cardiac and non-cardiac conditions declined across all hospitals. Our findings confirm the changing coronary intensive care unit case-mix and have implications for future coronary intensive care unit training and staffing.
Rational design of a trimeric APRIL-based CAR-binding domain enables efficient targeting of multiple myeloma
Authors: Schmidts Andrea , Ormhøj Maria , Choi Bryan D. , Taylor Allison O. , Bouffard Amanda A. , Scarfò Irene , Larson Rebecca C. , Frigault Matthew J. , Gallagher Kathleen , Castano Ana P. , Riley Lauren S. , Cabral Maria L. , Boroughs Angela C. , Velasco Cárdenas Rubí M.-H. , Schamel Wolfgang , Zhou Jing , Mackay Sean , Tai Yu-Tzu , Anderson Kenneth C. , Maus Marcela V.
Published: October 2019

Key Points

A trimeric extracellular moiety of APRIL has enhanced binding to BCMA and TACI compared with monomeric APRIL when incorporated into a CAR. T cells transduced with a trimeric APRIL-based CAR are a promising approach for the treatment of MM.
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning
Authors: Zhang Haicang , Zhang Qi , Ju Fusong , Zhu Jianwei , Gao Yujuan , Xie Ziwei , Deng Minghua , Sun Shiwei , Zheng Wei-Mou , Bu Dongbo
Published: October 2019

Background

Accurate prediction of inter-residue contacts of a protein is important to calculating its tertiary structure. Analysis of co-evolutionary events among residues has been proved effective in inferring inter-residue contacts. The Markov random field (MRF) technique, although being widely used for contact prediction, suffers from the following dilemma: the actual likelihood function of MRF is accurate but time-consuming to calculate; in contrast, approximations to the actual likelihood, say pseudo-likelihood, are efficient to calculate but inaccurate. Thus, how to achieve both accuracy and efficiency simultaneously remains a challenge.

Results

In this study, we present such an approach (called clmDCA) for contact prediction. Unlike plmDCA using pseudo-likelihood, i.e., the product of conditional probability of individual residues, our approach uses composite-likelihood, i.e., the product of conditional probability of all residue pairs. Composite likelihood has been theoretically proved as a better approximation to the actual likelihood function than pseudo-likelihood. Meanwhile, composite likelihood is still efficient to maximize, thus ensuring the efficiency of clmDCA. We present comprehensive experiments on popular benchmark datasets, including PSICOV dataset and CASP-11 dataset, to show that:i) clmDCA alone outperforms the existing MRF-based approaches in prediction accuracy.ii) When equipped with deep learning technique for refinement, the prediction accuracy of clmDCA was further significantly improved, suggesting the suitability of clmDCA for subsequent refinement procedure. We further present a successful application of the predicted contacts to accurately build tertiary structures for proteins in the PSICOV dataset.

Conclusions

Composite likelihood maximization algorithm can efficiently estimate the parameters of Markov Random Fields and can improve the prediction accuracy of protein inter-residue contacts.
Exploring effective approaches for haplotype block phasing
Authors: Al Bkhetan Ziad , Zobel Justin , Kowalczyk Adam , Verspoor Karin , Goudey Benjamin
Published: October 2019

Background

Knowledge of phase, the specific allele sequence on each copy of homologous chromosomes, is increasingly recognized as critical for detecting certain classes of disease-associated mutations. One approach for detecting such mutations is through phased haplotype association analysis. While the accuracy of methods for phasing genotype data has been widely explored, there has been little attention given to phasing accuracy at haplotype block scale. Understanding the combined impact of the accuracy of phasing tool and the method used to determine haplotype blocks on the error rate within the determined blocks is essential to conduct accurate haplotype analyses.

Results

We present a systematic study exploring the relationship between seven widely used phasing methods and two common methods for determining haplotype blocks. The evaluation focuses on the number of haplotype blocks that are incorrectly phased. Insights from these results are used to develop a haplotype estimator based on a consensus of three tools. The consensus estimator achieved the most accurate phasing in all applied tests. Individually, EAGLE2, BEAGLE and SHAPEIT2 alternate in being the best performing tool in different scenarios. Determining haplotype blocks based on linkage disequilibrium leads to more correctly phased blocks compared to a sliding window approach. We find that there is little difference between phasing sections of a genome (e.g. a gene) compared to phasing entire chromosomes. Finally, we show that the location of phasing error varies when the tools are applied to the same data several times, a finding that could be important for downstream analyses.

Conclusions

The choice of phasing and block determination algorithms and their interaction impacts the accuracy of phased haplotype blocks. This work provides guidance and evidence for the different design choices needed for analyses using haplotype blocks. The study highlights a number of issues that may have limited the replicability of previous haplotype analysis.
Comprehensive analysis of genetic and evolutionary features of the hepatitis E virus
Authors: Baha Sarra , Behloul Nouredine , Liu Zhenzhen , Wei Wenjuan , Shi Ruihua , Meng Jihong
Published: October 2019

Background

The hepatitis E virus (HEV) is the causative pathogen of hepatitis E, a global public health concern. HEV comprises 8 genotypes with a wide host range and geographic distribution. This study aims to determine the genetic factors influencing the molecular adaptive changes of HEV open reading frames (ORFs) and estimate the HEV origin and evolutionary history.

Results

Sequences of HEV strains isolated between 1982 and 2017 were retrieved and multiple analyses were performed to determine overall codon usage patterns, effects of natural selection and/or mutation pressure and host influence on the evolution of HEV ORFs. Besides, Bayesian Coalescent Markov Chain Monte Carlo (MCMC) Analysis was performed to estimate the spatial-temporal evolution of HEV. The results indicated an A/C nucleotide bias and ORF-dependent codon usage bias affected mainly by natural selection. The adaptation of HEV ORFs to their hosts was also ORF-dependent, with ORF1 and ORF2 sharing an almost similar adaptation profile to the different hosts. The discriminant analysis based on the adaptation index suggested that ORF1 and ORF3 could play a pivotal role in viral host tropism.

Conclusion

In this study, we estimate that the common ancestor of the modern HEV strains emerged ~ 6000 years ago, in the period following the domestication of pigs. Then, natural selection played the major role in the evolution of the codon usage of HEV ORFs. The significant adaptation of ORF1 of genotype 1 to humans, makes ORF1 an evolutionary indicator of HEV host speciation, and could explain the epidemic character of genotype 1 strains in humans.
Expression profiles of cell-wall related genes vary broadly between two common maize inbreds during stem development
Authors: Penning Bryan W. , Shiga Tânia M. , Klimek John F. , SanMiguel Philip J. , Shreve Jacob , Thimmapuram Jyothi , Sykes Robert W. , Davis Mark F. , McCann Maureen C. , Carpita Nicholas C.
Published: October 2019

Background

The cellular machinery for cell wall synthesis and metabolism is encoded by members of large multi-gene families. Maize is both a genetic model for grass species and a potential source of lignocellulosic biomass from crop residues. Genetic improvement of maize for its utility as a bioenergy feedstock depends on identification of the specific gene family members expressed during secondary wall development in stems.

Results

High-throughput sequencing of transcripts expressed in developing rind tissues of stem internodes provided a comprehensive inventory of cell wall-related genes in maize (Zea mays, cultivar B73). Of 1239 of these genes, 854 were expressed among the internodes at ≥95 reads per 20 M, and 693 of them at ≥500 reads per 20 M. Grasses have cell wall compositions distinct from non-commelinid species; only one-quarter of maize cell wall-related genes expressed in stems were putatively orthologous with those of the eudicot Arabidopsis. Using a slope-metric algorithm, five distinct patterns for sub-sets of co-expressed genes were defined across a time course of stem development. For the subset of genes associated with secondary wall formation, fifteen sequence motifs were found in promoter regions. The same members of gene families were often expressed in two maize inbreds, B73 and Mo17, but levels of gene expression between them varied, with 30% of all genes exhibiting at least a 5-fold difference at any stage. Although presence-absence and copy-number variation might account for much of these differences, fold-changes of expression of aCADaand aFLA11gene were attributed to polymorphisms in promoter response elements.

Conclusions

Large genetic variation in maize as a species precludes the extrapolation of cell wall-related gene expression networks even from one common inbred line to another. Elucidation of genotype-specific expression patterns and their regulatory controls will be needed for association panels of inbreds and landraces to fully exploit genetic variation in maize and other bioenergy grass species.
RETRACTED ARTICLE: TaWRKY40 transcription factor positively regulate the expression of TaGAPC1 to enhance drought tolerance
Authors: Zhang Lin , Xu Zhiyong , Ji Haikun , Zhou Ye , Yang Shushen
Published: October 2019

Backgrounds

Drought stress is one of the major factors that affects wheat yield. Glyceraldehyde-3-Phosphate dehydrogenase (GAPDH) is a multifunctional enzyme that plays the important role in abiotic stress and plant development. However, in wheat, limited information about drought-responsive GAPC genes has been reported, and the mechanism underlying the regulation of the GAPC protein is unknown.

Results

In this study, we evaluated the potential role of GAPC1 in drought stress in wheat and Arabidopsis. We found that the overexpression of TaGAPC1 could enhance the tolerance to drought stress in transgenic Arabidopsis. Yeast one-hybrid library screening and EMSA showed that TaWRKY40 acts as a direct regulator of the TaGAPC1 gene. A dual luciferase reporter assay indicated that TaWRKY40 improved the TaGAPC1 promoter activity. The results of qRT-PCR in wheat protoplast cells with instantaneous overexpression of TaWRKY40 indicated that the expression level of TaGAPC1 induced by abiotic stress was upregulated by TaWRKY40. Moreover, TaGAPC1 promoted H2O2 detoxification in response to drought.

Conclusion

These results demonstrate that the inducible transcription factor TaWRKY40 could activate the transcription of the TaGAPC1 gene, thereby increasing the tolerance of plants to drought stress.
Comparison of chloroplast genomes of Gynura species: sequence variation, genome rearrangement and divergence studies
Authors: Han Tianyu , Li Mimi , Li Jiawei , Lv Han , Ren Bingru , Chen Jian , Li Weilin
Published: October 2019

Background

SomeGynuraspecies have been reported to be natural anti-diabetic plants. Improvement of their traits towards application relies on hybridization. Clearly, phylogenetic relationships could optimize compatible hybridizations. For flowerings plants, chloroplast genomes have been used to solve many phylogenetic relationships. To date, the chloroplast genome sequences of 4 genera of the tribe Senecioneae have been uploaded to GenBank. The internal relationships within the genusGynuraand the relationship of the genusGynurawith other genera in the tribe Senecioneae need further research.

Results

The chloroplast genomes of 4Gynuraspecies were sequenced, assembled and annotated. In comparison with those of 12 other Senecioneae species, theGynurachloroplast genome features were analysed in detail. Subsequently, differences in the microsatellite and repeat types in the tribe were found. From the comparison, it was found that IR expansion and contraction are conserved in the generaGynura,DendrosenecioandLigularia. Compared to other regions on the chloroplast genome, the region from 25,000 to 50,000 bp was not conserved. Sevenndhgenes in this region are under purifying selection, with small changes in amino acids. The whole chloroplast genome sequences of 16 Senecioneae species were used to build a phylogenetic tree. Based on the oldestArtemisiapollen fossil, the divergence time was estimated.

Conclusions

Sequencing the chloroplast genomes of 4Gynuraspecies helps us to solve many problems. The phylogenetic relationships and divergence time among 4Gynuraand 16 Senecioneae species were evaluated by comparing their chloroplast genomes. The phylogenetic relationship of the generaGynuraandLigulariawas different from that observed previous work. In a previous phylogenetic tree, the genusLigulariabelonged to the Tussilagininae subtribe, which was in a lineage that diverged earlier than other genera. Further morphology and genome-wide analyses are needed to clarify the genus relationships.
Diet is not the primary driver of bacterial community structure in the gut of litter-feeding cockroaches
Authors: Lampert Niclas , Mikaelyan Aram , Brune Andreas
Published: October 2019

Background

Diet is a major determinant of bacterial community structure in termite guts, but evidence of its importance in the closely related cockroaches is conflicting. Here, we investigated the ecological drivers of the bacterial gut microbiota in cockroaches that feed on lignocellulosic leaf litter.

Results

The physicochemical conditions determined with microsensors in the guts ofErgaula capucina,Pycnoscelus surinamensis, andByrsotria rothiwere similar to those reported for both wood-feeding and omnivorous cockroaches. All gut compartments were anoxic at the center and showed a slightly acidic to neutral pH and variable but slightly reducing conditions. Hydrogen accumulated only in the crop ofB. rothi. High-throughput amplicon sequencing of bacterial 16S rRNA genes documented that community structure in individual gut compartments correlated strongly with the respective microenvironmental conditions. A comparison of the hindgut microbiota of cockroaches and termites from different feeding groups revealed that the vast majority of the core taxa in cockroaches with a lignocellulosic diet were present also in omnivorous cockroaches but absent in wood-feeding higher termites.

Conclusion

Our results indicate that diet is not the primary driver of bacterial community structure in the gut of wood- and litter-feeding cockroaches. The high similarity to the gut microbiota of omnivorous cockroaches suggests that the dietary components that are actually digested do not differ fundamentally between feeding groups.
Mild water stress-induced priming enhance tolerance to Rosellinia necatrix in susceptible avocado rootstocks
Authors: Martínez-Ferri E. , Moreno-Ortega G. , van den Berg N. , Pliego C.
Published: October 2019

Background

White root rot (WRR) disease caused by Rosellinia necatrix is one of the most important threats affecting avocado orchards in temperate regions. The eradication of WRR is a difficult task and environmentally friendly control methods are needed to lessen its impact. Priming plants with a stressor (biotic or abiotic) can be a strategy to enhance plant defense/tolerance against future stress episodes but, despite the known underlying common mechanisms, few studies use abiotic-priming for improving tolerance to forthcoming biotic-stress and vice versa (‘cross-factor priming’). To assess whether cross-factor priming can be a potential method for enhancing avocado tolerance to WRR disease, ‘Dusa’ avocado rootstocks, susceptible to R. necatrix, were subjected to two levels of water stress (mild-WS and severe-WS) and, after drought-recovery, inoculated with R. necatrix. Physiological response and expression of plant defense related genes after drought-priming as well as the disease progression were evaluated.

Results

Water-stressed avocado plants showed lower water potential and stomatal limitations of photosynthesis compared to control plants. In addition, NPQ and qN values increased, indicating the activation of energy dissipating mechanisms closely related to the relief of oxidative stress. This response was proportional to the severity of the water stress and was accompanied by the deregulation of pathogen defense-related genes in the roots. After re-watering, leaf photosynthesis and plant water status recovered rapidly in both treatments, but roots of mild-WS primed plants showed a higher number of overexpressed genes related with plant defense than severe-WS primed plants. Disease progression after inoculating primed plants with R. necatrix was significantly delayed in mild-WS primed plants.

Conclusions

These findings demonstrate that mild-WS can induce a primed state in the WRR susceptible avocado rootstock ‘Dusa’ and reveal that ‘cross-factor priming’ with water stress (abiotic stressor) is effective for increasing avocado tolerance against R. necatrix (biotic stressor), underpinning that plant responses against biotic and abiotic stress rely on common mechanisms. Potential applications of these results may involve an enhancement of WRR tolerance of current avocado groves and optimization of water use via low frequency deficit irrigation strategies.
A lil3 chlp double mutant with exclusive accumulation of geranylgeranyl chlorophyll displays a lethal phenotype in rice
Authors: Li Chunmei , Liu Xin , Pan Jihong , Guo Jia , Wang Qian , Chen Congping , Li Na , Zhang Kuan , Yang Bin , Sun Changhui , Deng Xiaojian , Wang Pingrong
Published: October 2019

Background

Phytyl residues are the common side chains of chlorophyll (Chl) and tocopherols. Geranylgeranyl reductase (GGR), which is encoded byCHLPgene, is responsible for phytyl biosynthesis. The light-harvesting like protein LIL3 was suggested to be required for stability of GGR and protochlorophyllide oxidoreductase in Arabidopsis.

Results

In this study, we isolated a yellow-green leaf mutant,637ys, in rice (Oryza sativa). The mutant accumulated majority of Chls with unsaturated geranylgeraniol side chains and displayed a yellow-green leaf phenotype through the whole growth period. The development of chloroplasts was suppressed, and the major agronomic traits, especially No. of productive panicles per plant and of spikelets per panicle, dramatically decreased in637ys. Besides, the mutant exhibited to be sensitive to light intensity and deficiency of tocopherols without obvious alteration in tocotrienols in leaves and grains. Map-based cloning and complementation experiment demonstrated that a point mutation on theOsLIL3gene accounted for the mutant phenotype of637ys.OsLIL3is mainly expressed in green tissues, and its encoded protein is targeted to the chloroplast. Furthermore, the637ys 502ys(lil3 chlp) double mutant exclusively accumulated geranylgeranyl Chl and exhibited lethality at the three-leaf stage.

Conclusions

We identified theOsLIL3gene through a map-based cloning approach. Meanwhile, we demonstrated that OsLIL3 is of extreme importance to the function of OsGGR, and that the complete replacement of phytyl side chain of chlorophyll by geranylgeranyl chain could be fatal to plant survival in rice.
The long non-coding RNA lncRNA973 is involved in cotton response to salt stress
Authors: Zhang Xiaopei , Dong Jie , Deng Fenni , Wang Wei , Cheng Yingying , Song Lirong , Hu Mengjiao , Shen Jian , Xu Qingjiang , Shen Fafu
Published: October 2019

Background

Long non-coding (lnc) RNAs are a class of functional RNA molecules greater than 200 nucleotides in length, and lncRNAs play important roles in various biological regulatory processes and response to the biotic and abiotic stresses. LncRNAs associated with salt stress in cotton have been identified through RNA sequencing, but the function of lncRNAs has not been reported. We previously identified salt stress-related lncRNAs in cotton (Gossypium spp.), and discovered the salt-related lncRNA-lncRNA973.

Results

In this study, we identified the expression level, localization, function, and preliminary mechanism of action of lncRNA973. LncRNA973, which was localized in the nucleus, was expressed at a low level under nonstress conditions but can be significantly increased by salt treatments. Here lncRNA973 was transformed into Arabidopsis and overexpressed. Along with the increased expression compared with wild type under salt stress conditions in transgenic plants, the seed germination rate, fresh weights and root lengths of the transgenic plants increased. We also knocked down the expression of lncRNA973 using virus-induced gene silencing technology. The lncRNA973 knockdown plants wilted, and the leaves became yellowed and dropped under salt-stress conditions, indicating that the tolerance to salt stress had decreased compared with wild type. LncRNA973 may be involved in the regulation of reactive oxygen species-scavenging genes, transcription factors and genes involved in salt stress-related processes in response to cotton salt stress.

Conclusions

LncRNA973 was localized in the nucleus and its expression was increased by salt treatment. The lncRNA973-overexpression lines had increased salt tolerance compared with the wild type, while the lncRNA973 knockdown plants had reduced salt tolerance. LncRNA973 regulated cotton responses to salt stress by modulating the expression of a series of salt stress-related genes. The data provides a basis for further studies on the mechanisms of lncRNA973-associated responses to salt stress in cotton.
Prevalence and associated anthropometric and lifestyle predictors of hypertension among adults in Kombolcha town and suburbs, Northeast Ethiopia: a community-based cross-sectional study
Authors: Hassen Biniem , Mamo Hassen
Published: October 2019

Background

Hypertension (HTN) is major public health challenge. Data on HTN prevalence and associated risk factors is necessary to better control it. This study aimed at estimating the prevalence of HTN and associated anthropometric and lifestyle predictors in Kombolcha and suburbs, northeast Ethiopia.

Methods

The study followed a community-based cross-sectional sampling design. Adult (≥18) residents of Kombolcha and suburbs in 11 kebeles (villages) formed the target population. Of these kebeles, 5(3 urban and 2 suburban) were selected randomly. Households (HHs) within the selected kebeles and individuals within HHs were similarly recruited in December 2016–May 2017. Anthropometric and blood pressure measurements were done. World Health Organization (WHO) STEPWISE TOOL was used to capture socio-demographic, physical activity, dietary habit, and nutritional status data.

Results

Totally 318 adults participated in the study. However, only 312 (169(54.2%) males and 143(45.8%) females) were with complete information for statistical analysis. The lowest age was 18 years, the highest 65 and the mean 38.29 ± 10.88. The prevalence of HTN was 30.8% (96/312) (95% confidence interval (CI): 25.9–36.1%), 16.4% male and 14.4% female. While 45 and older age (odds ratio (OR) 7.385, 95% CI 3.563–15.306, p < 0.0001), obesity (OR 126.286, 95% CI 34.481–462.514, p < 0.0001) and overweightness (OR 16.105, 95% CI 7.024–36.927, p < 0.0001), ‘substantially high risk’ (> 102 cm in men and > 88 cm in female) waist circumference (OR 1.788, 95% CI 1.008–3.173, p = 047), light occupational physical activity (OR 12.427, 95% CI 2.891–53.410, p = 0.001), walking or riding a bicycle for lower than 5 days/week (OR 13.000, 95% CI 5.140–32.882, p < 0.0001) and lack of sport activity (OR 18.322, 95% CI 2.430–138.169, p = 005), smoking (OR 2.283, 95% CI 1.284–4.060, p = 0.005), khat (OR 17.390, 95% CI 6.167–49.037, p < 0.0001), alcohol (OR 4.005, 95% CI 2.357–6.803, p < 0.0001), HH size of two (OR 2.474, 95% CI 1.250–4.895, p = 0.009) and ≥ 3 (OR 6.889, 95% CI 2.610–18.186, p < 0.0001); and HTN in family history (OR 19.417, 95% CI 10.251–36.778, p < 0.0001) were significant predictors of HTN in the binary logistic regression analysis; none of these were so in the multivariable model.

Conclusion

Although there was a high prevalence of HTN in the study area, its independent significant predictors were not identified.