bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polyoxin D and Other Biopesticides Reduce Gummy Stem Blight But Not Anthracnose on Melon Seedlings
Authors: Keinath Anthony P. 
Published: September 2016

Biopesticides may be useful to prevent fungal foliar diseases on cucurbit seedlings in greenhouses because of the short re-entry intervals, normally 4 h. Bacillus subtilis QST 713 (Serenade ASO), root extract of Reynoutria sachalinensis (Regalia), hydrogen dioxide (Oxidate), paraffinic oil (JMS Stylet Oil), polyoxin D (Oso), and 92% edible fish oil + 5% sesame oil (Organocide) were evaluated against gummy stem blight on muskmelon seedlings and anthracnose on watermelon seedlings. Polyoxin D applied alone, B. subtilis QST 713 followed by polyoxin D, and R. sachalinensis extract followed by B. subtilis QST 713 reduced the severity of gummy stem blight and were as effective as mancozeb. None of the biopesticides applied alone or sequentially were effective against anthracnose. Polyoxin D could be used to prevent outbreaks of gummy stem blight on watermelon and muskmelon seedlings grown for use as transplants. Accepted for publication 1 July 2016. Published 4 August 2016.
Comparison of Two Soil Sampling Methods for Estimating Population Densities of Heterodera glycines Cysts
Authors: Smrtnik Ethan , Niblack Terry , Paul Pierce , Dorrance Anne , Bruns Dain 
Published: September 2016

Soybean cyst nematode (SCN) is a significant economic pest of soybean in Ohio and the Midwest, in which yield losses are directly linked to the population density and distribution of cysts within a field. Advances in automation technology have been used to expedite soil fertility sampling for large-scale and high-density field maps. In this study, we explored the use of this technology as an option for sampling for SCN. There was a significant positive correlation for the number of SCN cysts between soil samples collected with an Automated Precision Soil Sampler and those collected using the traditional soil sampling method from three separate fields (P < 0.05, r values of 0.79 to 0.93). These results suggest that expedited soil sampling in fields with high population densities could be an added benefit for soybean farmers to encourage more sampling for SCN to monitor population levels as part of their overall management program. Accepted for publication 18 July 2016. Published 12 August 2016.
Influence of a Therapeutic Soft Contact Lens on Epithelial Healing, Visual Recovery, Haze, and Pain After Photorefractive Keratectomy
Authors: Taneri Suphi , Oehler Saskia , MacRae Scott , Dick H. Burkhard 
Published: September 2016

Objectives:
To examine the influence of a therapeutic soft contact lens (TSCL) after alcohol-assisted photorefractive keratectomy (PRK) on visual recovery, epithelial closure, pain perception, and haze formation.

Methods:
Prospective, randomized, single-center, contralateral eye, patient-masked study. Same surgeon treated 15 patients with bilateral PRK using a Vidaurri Fluid Retention Ring (Katena) with 8.7 mm inner diameter to apply ethanol 18% for 30 sec. Each patient received a TSCL (Balafilcon A, PureVision, Bausch & Lomb) in a randomized fashion in one eye only.

Results:
Without knowing which eye had a contact lens, four patients preferred the eye with TSCL so much that these patients wanted a TSCL inserted in the second eye as well. Uncorrected distance visual acuity improved postoperatively from day 1 to 3 months from 0.61 to 1.18 with TSCL and from 0.21 to 1.04 without TSCL. Uncorrected distance visual acuity was statistically significantly better on days 1 and 2 with TSCL. Epithelial defect was on average smaller with TSCL. Epithelium was closed at day 4 in all eyes except one without TSCL. Pain perception was significantly lower with TSCL on days 1 and 2. Haze levels after 3 months were significantly lower with TSCL (with 0.09/without 0.45, respectively). One eye without TSCL had haze grade 2 (Fantes).

Conclusions:
A TSCL had statistically significantly and clinically meaningful beneficial effects in the first days in visual recovery and pain perception and after 3 months in haze formation. Epithelial healing was slightly quicker with the use of TSCLs (not statistically, but clinically significantly).
Towards a neurophysiological signature for fibromyalgia
Authors: López-Solà Marina , Woo Choong-Wan , Pujol Jesus , Deus Joan , Harrison Ben J. , Monfort Jordi , Wager Tor D. 
Published: September 2016

Abstract
Patients with fibromyalgia (FM) show characteristically enhanced unpleasantness to painful and nonpainful sensations accompanied by altered neural responses. The diagnostic potential of such neural alterations, including their sensitivity and specificity to FM (vs healthy controls) is unknown. We identify a brain signature that characterizes FM central pathophysiology at the neural systems level. We included 37 patients with FM and 35 matched healthy controls, and analyzed functional magnetic resonance imaging responses to (1) painful pressure and (2) nonpainful multisensory (visual–auditory–tactile) stimulation. We used machine-learning techniques to identify a brain-based FM signature. When exposed to the same painful stimuli, patients with FM showed greater neurologic pain signature (NPS; Wager et al., 2013. An fMRI-based neurologic signature of physical pain. N Engl J Med 2013;368:1388–97) responses. In addition, a new pain-related classifier (“FM-pain”) revealed augmented responses in sensory integration (insula/operculum) and self-referential (eg, medial prefrontal) regions in FM and reduced responses in the lateral frontal cortex. A “multisensory” classifier trained on nonpainful sensory stimulation revealed augmented responses in the insula/operculum, posterior cingulate, and medial prefrontal regions and reduced responses in the primary/secondary sensory cortices, basal ganglia, and cerebellum. Combined activity in the NPS, FM pain, and multisensory patterns classified patients vs controls with 92% sensitivity and 94% specificity in out-of-sample individuals. Enhanced NPS responses partly mediated mechanical hypersensitivity and correlated with depression and disability (P
uncorrected < 0.05); FM-pain and multisensory responses correlated with clinical pain (P
uncorrected < 0.05). The study provides initial characterization of individual patients with FM based on pathophysiological, symptom-related brain features. If replicated, these brain features may constitute objective neural targets for therapeutic interventions. The results establish a framework for assessing therapeutic mechanisms and predicting treatment response at the individual level.
High GC Content Causes De Novo Created Proteins to be Intrinsically Disordered
Authors: Basile Walter , Sachenkova Oxana , Light Sara , Elofsson Arne 
Published: September 2016

AbstractDe novocreation of protein coding genes involves formation of short ORFs from noncoding regions; some of these ORFs might then become fixed in the population.De novocreated proteins need to, at the bare minimum, not cause serious harm to the organism, meaning that they should for instance not cause aggregation. Therefore, although the creation of the short ORFs could be truly random, but the fixation should be of subject to some selective pressure. The selective forces acting onde novocreated proteins have been elusive and contradictory results have been reported. InDrosophilathey are more disordered, i.e. are enriched in polar residues, than ancient proteins, while the opposite trend is present in yeast. To the best of our knowledge no valid explanation for this difference has been proposed.To solve this riddle we studied structural properties and age of all proteins in 187 eukaryotic species. We find that, on average, there are small differences between proteins of different ages, with the exception that younger proteins are shorter. However, when we take the GC content into account we find that this can explain the opposite trends observed in yeast (low GC) and drosophila (high GC). GC content is correlated with codons coding for disorder-promoting amino acids, and inversely correlated with transmembrane, helix and sheet promoting residues. We find that for the youngest proteins, i.e. the ones that are most likely to bede novocreated, there exists a strong correlation with GC and structural properties. In contrast, this strong relationship is not seen for ancient proteins. This leads us to propose that structural features are not a strong determining factor for fixation ofde novocreated genes. Instead these proteins resemble random proteins given a particular GC level. The dependency on GC content is then gradually weakened during evolution.Author SummaryWe show that the GC content of a genomic area is of great importance for the properties of a protein-codingde novocreated gene. The GC content affects the frequency of the codons and this affects the probability for each amino acid to be included in ade novocreated protein. The codons encoding for Ala, Pro and Glu contain 80% GC, while codons for Lys, Phe, Asn, Tyr and Ile contain 20% or less. Pro and Gly are disorder-promoting, while Phe, Tyr and Ile are order-promoting. Therefore random protein sequences at a high GC will be more disordered than the ones created at a low GC. The structural properties of the youngest (orphan) proteins match to a large degree the properties of random proteins when the GC content is taken into account. In contrast structural properties of ancient proteins only show a weak correlation with GC content. This suggests that even after fixation ofde novocreated proteins largely resemble random proteins given a certain GC content. Thereafter, during evolution the correlation between structural properties and GC weakens.
Paperfuge: An ultra-low cost, hand-powered centrifuge inspired by the mechanics of a whirligig toy
Authors: Bhamla M. Saad , Benson Brandon , Chai Chew , Katsikis Georgios , Johri Aanchal , Prakash Manu 
Published: September 2016

AbstractSample preparation, including separation of plasma from whole blood or isolation of parasites, is an unmet challenge in many point of care (POC) diagnostics and requires centrifugation as the first key step. From the context of global health applications, commercial centrifuges are expensive, bulky and electricity-powered, leading to a critical bottle-neck in the development of decentralized, electricity-free POC diagnostic devices. By uncovering the fundamental mechanics of an ancient whirligig toy (3300 B.C.E), we design an ultra-low cost (20 cents), light-weight (2 g), human-powered centrifuge that is made out of paper (“paperfuge”). To push the operating limits of this unconventional centrifuge, we present an experimentally-validated theoretical model that describes the paperfuge as a non-linear, non-conservative oscillator system. We use this model to inform our design process, achieving speeds of 125,000 rpm and equivalent centrifugal forces of 30,000 g, with theoretical limits predicting one million rpm. We harness these speeds to separate pure plasma in less than 1.5 minutes and isolate malaria parasites in 15 minutes from whole human blood. By expanding the materials used, we implement centrifugal microfluidics using PDMS, plastic and 3D-printed devices, ultimately opening up new opportunities for electricity-free POC diagnostics, especially in resource-poor settings.
Biophysical models of protein evolution: Understanding the patterns of evolutionary sequence divergence
Authors: Echave Julian , Wilke Claus O. 
Published: September 2016

AbstractFor decades, rates of protein evolution have been interpreted in terms of the vague concept of “functional importance”. Slowly evolving proteins or sites within proteins were assumed to be more functionally important and thus subject to stronger selection pressure. More recently, biophysical models of protein evolution, which combine evolutionary theory with protein biophysics, have completely revolutionized our view of the forces that shape sequence divergence. Slowly evolving proteins have been found to evolve slowly because of selection against toxic mis-folding and misinteractions, linking their rate of evolution primarily to their abundance. Similarly, most slowly evolving sites in proteins are not directly involved in function, but mutating them has large impacts on protein structure and stability. Here, we review the studies of the emergent field of biophysical protein evolution that have shaped our current understanding of sequence divergence patterns. We also propose future research directions to develop this nascent field.
Genetic Prediction of Male Pattern Baldness
Authors: Hagenaars Saskia P , Hill W David , Harris Sarah E , Ritchie Stuart J , Davies Gail , Liewald David C , Gale Catharine R , Porteous David J , Deary Ian J , Marioni Riccardo E 
Published: September 2016

AbstractMale pattern baldness can have substantial psychosocial effects, and it has been phenotypically linked to adverse health outcomes such as prostate cancer and cardiovascular disease. We explored the genetic architecture of the trait using data from over 52,000 male participants of UK Biobank, aged 40-69 years. We identified over 250 independent novel genetic loci associated with severe hair loss. By developing a prediction algorithm based entirely on common genetic variants, and applying it to an independent sample, we could discriminate accurately (AUC = 0.82) between those with no hair loss from those with severe hair loss. The results of this study might help identify those at the greatest risk of hair loss and also potential genetic targets for intervention.
mtDNA diversity in human populations highlights the merit of haplotype matching in gene therapies
Authors: Røyrvik E.C. , Burgstaller J.P. , Johnston I.G. 
Published: September 2016

AbstractModern gene therapies aim to prevent the inheritance of mutant mitochondrial DNA (mtDNA) from mother to offspring by using a third-party mtDNA background. Technological limitations mean that these therapies may result in a small amount of maternal mtDNA admixed with a majority of third-party mtDNA. This situation is unstable if the mother’s mtDNA experiences a proliferative advantage over the third-party mtDNA, in which case the efficacy of the therapy may be undermined. Animal models suggest that the likelihood of such a proliferative advantage increases with increasing genetic distance between mother and third-party mtDNA, but in real therapeutic contexts the genetic distance, and so the importance of this effect, remains unclear. Here we harness a large volume of available human mtDNA data to model random sampling of mother and third-party mtDNAs from real human populations. We show that even within the same haplogroup, genetic differences around 20-80 SNPs are common between mtDNAs. These values are sufficient to lead to substantial segregation in murine models, over an organismal lifetime, even given low starting heteroplasmy, inducing increases from 5% to 35% over one year. Randomly pairing mothers and third-party women in clinical contexts thus runs the risk that substantial mtDNA segregation will compromise the beneficial effects of the therapy. We suggest that choices of ‘mtDNA donors’ be based on recent shared maternal ancestry, or, preferentially, explicit haplotype matching, in order to reduce the potential for problems in the implementation of these therapies.
Panpulmonate transcriptomes reveal candidate genes involved in the adaptation to freshwater and terrestrial habitats in gastropods
Authors: Romero Pedro E. , Feldmeyer Barbara , Pfenninger Markus 
Published: September 2016

AbstractBackgroundThe conquest of the land from aquatic habitats is a fascinating evolutionary event that happened multiple times in different phyla. Mollusks are among the organisms that successfully invaded the non-marine realm, resulting in the radiation of terrestrial panpulmonate gastropods. We compared transcriptomes from panpulmonates to study the selective pressures that modeled the transitions from marine into freshwater and terrestrial realms in this molluscan lineage.ResultsDe novoassembly of six panpulmonate transcriptomes resulted in 55,000 - 97,000 predicted open reading frames, of which 9 - 14% were functionally annotated. Adding published transcriptomes, we predicted 791 ortholog clusters shared among fifteen panpulmonate species, resulting in 702 amino acid and 736 codon-wise alignments. The branch-site test of positive selection applied to the codon-wise alignments showed twenty-eight genes under positive selection in the freshwater lineages and seven in the terrestrial lineages. Gene ontology categories of these candidate genes include actin assembly, transport of glucose, and the tyrosine metabolism in the terrestrial lineages; and, DNA repair, metabolism of xenobiotics, mitochondrial electron transport, and ribosome biogenesis in the freshwater lineages.ConclusionsWe identified candidate genes representing processes that may have played a key role during the water-to-land transition in Panpulmonata. These genes were involved in energy metabolism and gas-exchange surface development in the terrestrial lineages and in the response to the abiotic stress factors (UV radiation, osmotic pressure, xenobiotics) in the freshwater lineages. Our study expands the knowledge of possible adaptive signatures in genes and metabolic pathways related to the invasion of non-marine habitats in invertebrates.
MoRad6‐mediated ubiquitination pathways are essential for development and pathogenicity inMagnaporthe oryzae
Authors: Shi Huan‐Bin , Chen Guo‐Qing , Chen Ya‐Ping , Dong Bo , Lu Jian‐Ping , Liu Xiao‐Hong , Lin Fu‐Cheng 
Published: September 2016

SummaryThe ubiquitin system modulates protein functions through targeting substrates for ubiquitination. Here, E2 conjugating enzyme MoRad6‐related ubiquitination pathways are identified and analyzed inMagnaporthe oryzae, the causal agent of rice blast disease. Disruption of MoRad6 leads to severe defects in growth, sporulation, conidial germination, appressorium formation, and plant infection. To depict the functions of MoRad6, three putative ubiquitin ligases, MoRad18, MoBre1 and MoUbr1, are also characterized. Deletion of MoRad18 causes minor phenotypic changes, while MoBre1 is required for growth, conidiation and pathogenicity inM. oryzae. Defectsin ΔMobre1likely resulted from the reduction in di‐ and tri‐methylation level of Histone 3 lysine 4 (H3K4). Notably, MoUbr1 is crucial for conidial adhesion and germination, possibly by degrading components of cAMP/PKA and mitogen‐activated protein kinase (MAPK) Pmk1 signaling pathways via the N‐end rule pathway. Germination failure ofΔMoubr1conidia could be rescued by elevation of cAMP level or enhanced Pmk1 phosphorylation resulting from further deletion of MoIra1, theM. oryzaehomolog of yeast Ira1/2. These reveal vital effects of cAMP/PKA and MAPK Pmk1 signaling on conidial germination inM. oryzae. Altogether, our results suggest that MoRad6‐mediated ubiquitination pathways are essential for the infection‐related development and pathogenicity ofM. oryzae.
Oligotrophic lagoons of the South Pacific Ocean are home to a surprising number of novel eukaryotic microorganisms
Authors: Kim Eunsoo , Sprung Ben , Duhamel Solange , Filardi Christopher , Kyoon Shin Mann 
Published: September 2016

SummaryThe diversity of microbial eukaryotes was surveyed by environmental sequencing from tropical lagoon sites of the South Pacific, collected through the American Museum of Natural History (AMNH)'s Explore21 expedition to the Solomon Islands in September 2013. The sampled lagoons presented low nutrient concentrations typical of oligotrophic waters, but contained levels of chlorophyll a, a proxy for phytoplankton biomass, characteristic of meso‐ to eutrophic waters. Two 18S rDNA hypervariable sites, the V4 and V8–V9 regions, were amplified from the total of eight lagoon samples and sequenced on the MiSeq system. After assembly, clustering at 97% similarity, and removal of singletons and chimeras, a total of 2741 (V4) and 2606 (V8–V9) operational taxonomic units (OTUs) were identified. Taxonomic annotation of these reads, including phylogeny, was based on a combination of automated pipeline and manual inspection. About 18.4% (V4) and 13.8% (V8–V9) of the OTUs could not be assigned to any of the known eukaryotic groups. Of these, we focused on OTUs that were not divergent and possessed multiple sources of evidence for their existence. Phylogenetic analyses of these sequences revealed more than ten branches that might represent new deeply‐branching lineages of microbial eukaryotes, currently without any cultured representatives or morphological information.
Why Does Australia Have an Affordable Housing Problem and What Can Be Done About It?
Authors: Yates Judith 
Published: September 2016

AbstractAs a result of economic trends in Australia over the past 25 years, a growing proportion of households have faced high housing costs in relation to their income because of a shortage of affordable housing, particularly in areas where there is ready access to well‐paid employment. Problems have been particularly severe for lower income renters. This article provides a proposal to address this shortage, based on encouraging institutional financing of affordable rental housing, suggests more controversial policies that might be needed to address underlying causes and identifies a number of reasons why so little progress has been made.
Ireland—A Remarkable Economic Recovery?
Authors: Ruane Frances 
Published: September 2016

AbstractThe collapse of the Irish economy during the Global Financial Crisis brought a substantial decline in gross domestic product, a trebling of the unemployment rate and a sharp increase in public debt. Key to the scale of Ireland's crisis was the scale of a domestic property bubble. In the Corden Lecture, I explored how Ireland's notable turnaround since 2013 contrasts with the experiences of Spain, Portugal and Greece. This was primarily due to Ireland's large, foreign‐owned, modern, export‐oriented, multinational sector and its early and sustained action to deal with the fiscal deficit that emerged in 2008.
Pregnancy at very advanced maternal age: a UK population‐based cohort study
Authors: Fitzpatrick KE , Tuffnell D , Kurinczuk JJ , Knight M 
Published: September 2016

ObjectivesTo describe the characteristics, management and outcomes of women giving birth at advanced maternal age (≥48 years).DesignPopulation‐based cohort study using the UK Obstetric Surveillance System (UKOSS).SettingAll UK hospitals with obstetrician‐led maternity units.PopulationWomen delivering at advanced maternal age (≥48 years) in the UK between July 2013 and June 2014 (n = 233) and 454 comparison women.MethodsCohort and comparison group identification through the UKOSS monthly mailing.Main outcome measuresPregnancy complications.ResultsOlder women were more likely than comparison women to be overweight (33% versus 23%, P = 0.0011) or obese (23% versus 19%, P = 0.0318), nulliparous (53% versus 44%, P = 0.0299), have pre‐existing medical conditions (44% versus 28%, P < 0.0001), a multiple pregnancy (18% versus 2%, P < 0.0001), and conceived following assisted conception (78% versus 4%, P < 0.0001). Older women appeared more likely than comparison women to have pregnancy complications including gestational hypertensive disorders, gestational diabetes, postpartum haemorrhage, caesarean delivery, iatrogenic and spontaneous preterm delivery on univariable analysis and after adjustment for demographic and medical factors. However, adjustment for multiple pregnancy or use of assisted conception attenuated most effects, with significant associations remaining only with gestational diabetes (adjusted odds ratio [aOR] 4.81, 95% CI 1.93–12.00), caesarean delivery (aOR 2.78, 95% CI 1.44–5.37) and admission to an intensive care unit (aOR 33.53, 95% CI 2.73–412.24).ConclusionsWomen giving birth at advanced maternal age have higher risks of a range of pregnancy complications. Many of the increased risks appear to be explained by multiple pregnancy or use of assisted conception.Tweetable abstractThe pregnancy complications in women giving birth aged 48 or over are mostly explained by multiple pregnancy.