bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maize domestication and gene interaction
Authors: Stitzer Michelle C. , Ross‐Ibarra Jeffrey 
Published: July 2018

Contents

Summary
395

I.
Introduction
395

II.
The genetic basis of maize domestication
396

III.
The tempo of maize domestication
401

IV.
Genetic interactions and selection during maize domestication
401

V.
Gene networks of maize domestication alleles
404

VI.
Implications of gene interactions on evolution and selection404

VII.
Conclusions
405

Acknowledgements
405

References
405

SummaryDomestication is a tractable system for following evolutionary change. Under domestication, wild populations respond to shifting selective pressures, resulting in adaptation to the new ecological niche of cultivation. Owing to the important role of domesticated crops in human nutrition and agriculture, the ancestry and selection pressures transforming a wild plant into a domesticate have been extensively studied. In Zea mays, morphological, genetic and genomic studies have elucidated how a wild plant, the teosinte Z. mays subsp. parviglumis, was transformed into the domesticate Z. mays subsp. mays. Five major morphological differences distinguish these two subspecies, and careful genetic dissection has pinpointed the molecular changes responsible for several of these traits. But maize domestication was a consequence of more than just five genes, and regions throughout the genome contribute. The impacts of these additional regions are contingent on genetic background, both the interactions between alleles of a single gene and among alleles of the multiple genes that modulate phenotypes. Key genetic interactions include dominance relationships, epistatic interactions and pleiotropic constraint, including how these variants are connected in gene networks. Here, we review the role of gene interactions in generating the dramatic phenotypic evolution seen in the transition from teosinte to maize.
Combining Model‐Based Near‐Term GDP Forecasts and Judgmental Forecasts: A Real‐Time Exercise for the G7 Countries
Authors: Jansen W. Jos , de Winter Jasper M. 
Published: July 2018

AbstractWe investigate the effects of combining model‐based near‐term GDP forecasts and judgmental (quarterly) forecasts by professional analysts (Consensus forecasts) in a real‐time setting for the G7 countries over the years 1999–2013. Model‐based forecasts are produced by a dynamic factor model (DFM). We consider as combination schemes the weighted average and the linear combination. Combining with subjective information delivers sizable gains in forecasting ability of statistical models for all countries except Japan, even when subjective forecasts are somewhat dated. Accuracy gains are much more pronounced in the volatile period after 2008 due to a marked improvement in predictive power of Consensus forecasts relative to the DFM. A possible explanation is that mechanical models may be more vulnerable to extreme observations in estimation samples. Consensus forecasts are superior at the moment of publication for most countries since 2008. For some countries forecast combinations can improve upon Consensus forecasts in between the quarterly release dates of the Consensus survey.
Control of AHPND by phages: a promising biotechnological approach
Authors: Angulo Carlos , Loera‐Muro Abraham , Trujillo Edgar , Luna‐González Antonio 
Published: July 2018

AbstractVibrio parahaemolyticus, V. campbellii, V. owensii and V. harveyi are causative agents of Acute Hepatopancreatic Necrosis Disease (AHPND) in shrimp. AHPND is recently one of the most important diseases worldwide because of the high mortality and huge economic losses in shrimp farms. Antibiotic resistance has caused concern into finding other options to fight against pathogenic bacterial diseases. Currently, the use of lytic phages has reemerged as a promising strategy to combat bacterial pathogens. Likewise, modern molecular tools have been applied to modify phages by genetic engineering to express specific antigens and antibodies. This study reviewed recent research reports in the development of phages to control Vibrio spp. infections in shrimp and discusses different specific strategies, placing them in perspective to combat AHPND.
Household coping behavior and its contribution to resilience to global macroeconomic shocks in Vanuatu and Solomon Islands
Authors: McDonald Lachlan 
Published: July 2018

AbstractThis paper examines the resilience of households in Vanuatu and Solomon Islands—two small island developing states in Melanesia renowned for their vulnerabilities—to the adverse effects of global macroeconomic shocks. The focus is on the spike in international food and fuel prices in 2008 and the subsequent shock to global demand, known as the Global Economic Crisis (GEC). Using a unique retrospective cross‐section survey, the results show that experience of these shocks was widespread across urban and rural areas. Households with more education, access to income‐generating activities—particularly in the informal sector—and greater wealth were best placed to withstand a deterioration in their well‐being, measured as a fall in self‐reported disposable income. Households also employed a variety of coping strategies in response to the shocks. Local food gardens and informal insurance are seen as key safety nets in times of stress, yet neither provided full insurance from the shocks. Some households, particularly in urban areas, employed harmful coping strategies, such as reducing spending on health, education, and food. While potentially effective in withstanding a temporary fall in disposable income, these responses are likely to weaken overall resilience and leave households vulnerable to future shocks.
A Comparative Perspective on the Role of Acoustic Cues in Detecting Language Structure
Authors: Mueller Jutta L. , Cate Carel ten , Toro Juan M. 
Published: July 2018

AbstractMost human language learners acquire language primarily via the auditory modality. This is one reason why auditory artificial grammars play a prominent role in the investigation of the development and evolutionary roots of human syntax. The present position paper brings together findings from human and non‐human research on the impact of auditory cues on learning about linguistic structures with a special focus on how different types of cues and biases in auditory cognition may contribute to success and failure in artificial grammar learning (AGL). The basis of our argument is the link between auditory cues and syntactic structure across languages and development. Cross‐species comparison suggests that many aspects of auditory cognition that are relevant for language are not human specific and are present even in rather distantly related species. Furthermore, auditory cues and biases impact on learning, which we will discuss in the example of auditory perception and AGL studies. This observation, together with the significant role of auditory cues in language processing, supports the idea that auditory cues served as a bootstrap to syntax during language evolution. Yet this also means that potentially human‐specific syntactic abilities are not due to basic auditory differences between humans and non‐human animals but are based upon more advanced cognitive processes.
l‐lysine metabolism to N‐hydroxypipecolic acid: an integral immune‐activating pathway in plants
Authors: Hartmann Michael , Zeier Jürgen 
Published: July 2018

Summaryl‐lysine catabolic routes in plants include the saccharopine pathway to α‐aminoadipate and decarboxylation of lysine to cadaverine. The current review will cover a third l‐lysine metabolic pathway having a major role in plant systemic acquired resistance (SAR) to pathogen infection that was recently discovered in Arabidopsis thaliana. In this pathway, the aminotransferase AGD2‐like defense response protein (ALD1) α‐transaminates l‐lysine and generates cyclic dehydropipecolic (DP) intermediates that are subsequently reduced to pipecolic acid (Pip) by the reductase SAR‐deficient 4 (SARD4). l‐pipecolic acid, which occurs ubiquitously in the plant kingdom, is further N‐hydroxylated to the systemic acquired resistance (SAR)‐activating metabolite N‐hydroxypipecolic acid (NHP) by flavin‐dependent monooxygenase1 (FMO1). N‐hydroxypipecolic acid induces the expression of a set of major plant immune genes to enhance defense readiness, amplifies resistance responses, acts synergistically with the defense hormone salicylic acid, promotes the hypersensitive cell death response and primes plants for effective immune mobilization in cases of future pathogen challenge. This pathogen‐inducible NHP biosynthetic pathway is activated at the transcriptional level and involves feedback amplification. Apart from FMO1, some cytochrome P450 monooxygenases involved in secondary metabolism catalyze N‐hydroxylation reactions in plants. In specific taxa, pipecolic acid might also serve as a precursor in the biosynthesis of specialized natural products, leading to C‐hydroxylated and otherwise modified piperidine derivatives, including indolizidine alkaloids. Finally, we show that NHP is glycosylated in Arabidopsis to form a hexose‐conjugate, and then discuss open questions in Pip/NHP‐related research.
THE PLANFORM STABILITY OF EMBAYED BEACHES ON THE WEST COAST OF PENINSULAR MALAYSIA
Authors: Ab Razak Mohd Shahrizal , Jamaludin Nurhamizah , Mohd Nor Nur Ariffah Zaimah 
Published: July 2018

Embayed beaches can be found along the West coast of Peninsular Malaysia and they are subject to beach’s dynamic changes. Some part of the coast along the West coasts have experienced severe erosion for several decades, in spite of the construction of various coastal defence structures. Therefore, it is crucial to predict the stability of embayed beaches along the West coast of Peninsular Malaysia. The planform stability of embayed beaches was established by applying the MEPBAY model. It was found that the total number of embayed beaches along the West coast of Peninsular Malaysia is 139 with 73 % were natural embayed beaches and 27 % were artificial embayed beaches. From the analyses, out of the 139 embayed beaches; 82 % were in static equilibrium and 18 % were in dynamic state. The causes of the instability of embayed beaches are the topography of the embayed beach, discrepancies in the design of previous coastal structures, influenced by wave climate as well as human intervenes without prior investigation of the biological and physical effects towards the beach. Furthermore, the applicability of engineering solutions applied on embayed beaches that are in either dynamic equilibrium can be predicted using MEPBAY programme.
A Useful Equation for Gas Turbine Design
Authors: Langston Lee S. 
Published: July 2018

Abstract
This article presents three different gas turbine phenomena and design cases. The sketch in the article shows a schematic of a combined cycle powerplant consisting of a Brayton cycle (gas turbine) whose exhaust provides energy to a Rankine cycle (steam turbine). Frequently, one can use simple but exact one-dimensional (1D) heat conduction solutions to estimate the heat loss or gain of gas turbine components under transient conditions. These easy-to-use solutions are found in most undergraduate heat transfer texts. The article suggests that those three widely different gas turbine phenomena and design cases all have the simple, nonlinear superposition form.
Virus Control of Trafficking from Sorting Endosomes
Authors: Zeltzer Sebastian , Zeltzer Carol A. , Igarashi Suzu , Wilson Jean , Donaldson Julie G. , Goodrum Felicia 
Published: July 2018

ABSTRACT
The maintenance of cell surface proteins is critical to the ability of a cell to sense and respond to information in its environment. As such, modulation of cell surface composition and receptor trafficking is a potentially important target of control in virus infection. Sorting endosomes (SEs) are control stations regulating the recycling or degradation of internalized plasma membrane proteins. Here we report that human cytomegalovirus (HCMV), a ubiquitous betaherpesvirus, alters the fate of internalized clathrin-independent endocytosis (CIE) cargo proteins, retaining them in virally reprogrammed SEs. We show that the small G protein ARF6 (ADP ribosylation factor 6), a regulator of CIE trafficking, is highly associated with SE membranes relative to uninfected cells. Combined with the observation of accumulated CIE cargo at the SE, these results suggest that infection diminishes the egress of ARF6 and its cargo from the SE. Expression of ubiquitin-specific protease 6 (USP6), also known as TRE17, was sufficient to restore ARF6 and some ARF6 cargo trafficking to the cell surface in infected cells. The USP activity of TRE17 was required to rescue both ARF6 and associated cargo from SE retention in infection. The finding that TRE17 expression does not rescue the trafficking of all CIE cargos retained at SEs in infection suggests that HCMV hijacks the normal sorting machinery and selectively sorts specific cargos into endocytic microdomains that are subject to alternative sorting fates.

IMPORTANCE
Cells maintain their surface composition, take up nutrients, and respond to their environment through the internalization and recycling of cargo at the cell surface through endocytic trafficking pathways. During infection with human cytomegalovirus (HCMV), host endocytic membranes are reorganized into a juxtanuclear structure associated with viral assembly and egress. Less appreciated is the effect of this reorganization on the trafficking of host proteins through the endocytic pathway. We show that HCMV retains internalized cargo and the effector of clathrin-independent endocytosis at sorting endosomes. The retention of some cargo, but not all, was reversed by overexpression of a ubiquitin-specific protease, TRE17. Our results demonstrate that HCMV induces profound reprogramming of endocytic trafficking and influences cargo sorting decisions. Further, our work suggests the presence of a novel ubiquitin-regulated checkpoint for the recycling of cargo from sorting endosome. These findings have important implications for host signaling and immune pathways in the context of HCMV infection.
The Pseudomonas aeruginosa PilSR Two-Component System Regulates Both Twitching and Swimming Motilities
Authors: Kilmury Sara L. N. , Burrows Lori L. 
Published: July 2018

ABSTRACT

Motility is an important virulence trait for many bacterial pathogens, allowing them to position themselves in appropriate locations at appropriate times. The motility structures type IV pili and flagella are also involved in sensing surface contact, which modulates pathogenicity. In
Pseudomonas aeruginosa
, the PilS-PilR two-component system (TCS) regulates expression of the type IV pilus (T4P) major subunit PilA, while biosynthesis of the single polar flagellum is regulated by a hierarchical system that includes the FleSR TCS. Previous studies of
Geobacter sulfurreducens
and
Dichelobacter nodosus
implicated PilR in regulation of non-T4P-related genes, including some involved in flagellar biosynthesis. Here we used transcriptome sequencing (RNA-seq) analysis to identify genes in addition to
pilA
with changes in expression in the absence of
pilR
. Among the genes identified were 10 genes whose transcription increased in the
pilA
mutant but decreased in the
pilR
mutant, despite both mutants lacking T4P and pilus-related phenotypes. The products of these inversely dysregulated genes, many of which were hypothetical, may be important for virulence and surface-associated behaviors, as mutants had altered swarming motility, biofilm formation, type VI secretion system expression, and pathogenicity in a nematode model. Further, the PilSR TCS positively regulated transcription of
fleSR
, and thus many genes in the FleSR regulon. As a result,
pilSR
deletion mutants had defects in swimming motility that were independent of the loss of PilA. Together, these data suggest that in addition to controlling T4P expression, PilSR could have a broader role in the regulation of
P. aeruginosa
motility and surface sensing behaviors.

IMPORTANCE
Surface appendages such as type IV pili and flagella are important for establishing surface attachment and infection in a host in response to appropriate cues. The PilSR regulatory system that controls type IV pilus expression in
Pseudomonas aeruginosa
has an established role in expression of the major pilin PilA. Here we provide evidence supporting a new role for PilSR in regulating flagellum-dependent swimming motility in addition to pilus-dependent twitching motility. Further, even though both
pilA
and
pilR
mutants lack PilA and pili, we identified sets of genes downregulated in the
pilR
mutant and upregulated in a
pilA
mutant as well as genes downregulated only in a
pilR
mutant, independent of pilus expression. This finding suggests that change in the inner membrane levels of PilA is only one of the cues to which PilR responds to modulate gene expression. Identification of PilR as a regulator of multiple motility pathways may make it an interesting therapeutic target for antivirulence compounds.
Low-Level Antimicrobials in the Medicinal Leech Select for Resistant Pathogens That Spread to Patients
Authors: Beka Lidia , Fullmer Matthew S. , Colston Sophie M. , Nelson Michael C. , Talagrand-Reboul Emilie , Walker Paul , Ford Bradley , Whitaker Iain S. , Lamy Brigitte , Gogarten Johann Peter , Graf Joerg 
Published: July 2018

ABSTRACTFluoroquinolones (FQs) and ciprofloxacin (Cp) are important antimicrobials that pollute the environment in trace amounts. Although Cp has been recommended as prophylaxis for patients undergoing leech therapy to prevent infections by the leech gut symbiontAeromonas, a puzzling rise in Cp-resistant (Cpr)Aeromonasinfections has been reported. We report on the effects of subtherapeutic FQ concentrations on bacteria in an environmental reservoir, the medicinal leech, and describe the presence of multiple antibiotic resistance mutations and a gain-of-function resistance gene. We link the rise of CprAeromonasisolates to exposure of the leech microbiota to very low levels of Cp (0.01 to 0.04 µg/ml), <1/100 of the clinical resistance breakpoint forAeromonas. Using competition experiments and comparative genomics of 37 strains, we determined the mechanisms of resistance in clinical and leech-derivedAeromonasisolates, traced their origin, and determined that the presence of merely 0.01 µg/ml Cp provides a strong competitive advantage for Cprstrains. Deep-sequencing the Cpr-conferring region ofgyrAenabled tracing of the mutation-harboringAeromonaspopulation in archived gut samples, and an increase in the frequency of the Cpr-conferring mutation in 2011 coincides with the initial reports of CprAeromonasinfections in patients receiving leech therapy.IMPORTANCEThe role of subtherapeutic antimicrobial contamination in selecting for resistant strains has received increasing attention and is an important clinical matter. This study describes the relationship of resistant bacteria from the medicinal leech,Hirudo verbana, with patient infections following leech therapy. While our results highlight the need for alternative antibiotic therapies, the rise of Cprbacteria demonstrates the importance of restricting the exposure of animals to antibiotics approved for veterinary use. The shift to a more resistant community and the dispersion of Cpr-conferring mechanisms via mobile elements occurred in a natural setting due to the presence of very low levels of fluoroquinolones, revealing the challenges of controlling the spread of antibiotic-resistant bacteria and highlighting the importance of a holistic approach in the management of antibiotic use.
Responses of the Human Gut
Escherichia coli
Population to Pathogen and Antibiotic Disturbances
Authors: Richter Taylor K. S. , Michalski Jane M. , Zanetti Luke , Tennant Sharon M. , Chen Wilbur H. , Rasko David A. 
Published: July 2018

Research on human-associated
E. coli
tends to focus on pathogens, such as enterotoxigenic
E. coli
(ETEC) strains, which are a leading cause of diarrhea in developing countries. However, the severity of disease caused by these pathogens is thought to be influenced by the microbiome. The nonpathogenic
E. coli
community that resides in the human gastrointestinal tract may play a role in pathogen colonization and disease severity and may become a reservoir for virulence and antibiotic resistance genes. Our study used whole-genome sequencing of
E. coli
before, during, and after challenge with an archetype ETEC isolate, H10407, and antibiotic treatment to explore the diversity and resiliency of the resident
E. coli
population in response to the ecological disturbances caused by pathogen invasion and antibiotic treatment.
Clinical characteristics of young adult cataract patients: a 10-year retrospective study of the Zhongshan Ophthalmic Center
Authors: Lin Duoru , Liu Zhenzhen , Cao Qianzhong , Wu Xiaohang , Liu Jinchao , Chen Jingjing , Lin Zhuoling , Li Xiaoyan , Zhang Li , Long Erping , Zhang Xiayin , Wang Jinghui , Wu Dongxuan , Zhao Xutu , Yu Tongyong , Li Jing , Zhou Xiaojia , Wang Lisha , Lin Haotian , Chen Weirong , Liu Yizhi 
Published: July 2018

AimTo investigate the characteristics of young adult cataract (YAC) patients over a 10-year period.MethodsThis observational study included YAC patients aged 18–49 years who were treated surgically for the first time at the Zhongshan Ophthalmic Center in China. YAC patients were analysed and compared with patients with childhood cataract (CC) in January 2005 to December 2014.ResultsDuring the 10-year period, 515 YAC patients and 2421 inpatients with CC were enrolled. Among the YAC patients, 76.76% (109/142) of unilateral patients had a corrected distance visual acuity (CDVA) better than 20/40 in the healthy eye, whereas only 20.38% (76/373) of bilateral patients had a CDVA better than 20/40 in the eye with better visual acuity. Compared with the CC group, the YAC group had a higher proportion of rural patients (40.40% vs 31.60%, p=0.001). Furthermore, the prevalence of other ocular abnormalities in YAC patients was higher than that in patients with CC (29.71% vs 17.47%, p<0.001).ConclusionsA large proportion coming from rural areas and a high prevalence of complicated ocular abnormalities may be the most salient characteristics of YAC patients. Strengthening the counselling and screening strategy for cataract and health education for young adults are required especially for those in rural areas.