bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Autophagy Gene
BcATG8
Regulates the Vegetative Differentiation and Pathogenicity of Botrytis cinerea
Authors: Ren Weichao , Liu Na , Sang Chengwei , Shi Dongya , Zhou Mingguo , Chen Changjun , Qin Qingming , Chen Wenchan 
Published: March 2018

ABSTRACT

Autophagy is a conserved degradation process that maintains intracellular homeostasis to ensure normal cell differentiation and development in eukaryotes.
ATG8
is one of the key molecular components of the autophagy pathway. In this study, we identified and characterized
BcATG8
, a homologue of
Saccharomyces cerevisiae
(yeast)
ATG8
in the necrotrophic plant pathogen
Botrytis cinerea
. Yeast complementation experiments demonstrated that
BcATG8
can functionally complement the defects of the yeast
ATG8
null mutant. Direct physical interaction between BcAtg8 and BcAtg4 was detected in the yeast two-hybrid system. Subcellular localization assays showed that green fluorescent protein-tagged BcAtg8 (GFP-BcAtg8) localized in the cytoplasm as preautophagosomal structures (PAS) under general conditions but mainly accumulated in the lumen of vacuoles in the case of autophagy induction. Deletion of
BcATG8
(Δ
BcAtg8
mutant) blocked autophagy and significantly impaired mycelial growth, conidiation, sclerotial formation, and virulence. In addition, the conidia of the Δ
BcAtg8
mutant contained fewer lipid droplets (LDs), and quantitative real-time PCR (qRT-PCR) assays revealed that the basal expression levels of the LD metabolism-related genes in the mutant were significantly different from those in the wild-type (WT) strain. All of these phenotypic defects were restored by gene complementation. These results indicate that
BcATG8
is essential for autophagy to regulate fungal development, pathogenesis, and lipid metabolism in
B. cinerea
.

IMPORTANCE
The gray mold fungus
Botrytis cinerea
is an economically important plant pathogen with a broad host range. Although there are fungicides for its control, many classes of fungicides have failed due to its genetic plasticity. Exploring the fundamental biology of
B. cinerea
can provide the theoretical basis for sustainable and long-term disease management. Autophagy is an intracellular process for degradation and recycling of cytosolic materials in eukaryotes and is now known to be vital for fungal life. Here, we report studies of the biological role of the autophagy gene
BcATG8
in
B. cinerea
. The results suggest that autophagy plays a crucial role in vegetative differentiation and virulence of
B. cinerea
.
Homologous Recombination in Core Genomes Facilitates Marine Bacterial Adaptation
Authors: Sun Ying , Luo Haiwei 
Published: March 2018

ABSTRACT

Acquisition of ecologically relevant genes is common among ocean bacteria, but whether it has a major impact on genome evolution in marine environments remains unknown. Here, we analyzed the core genomes of 16 phylogenetically diverse and ecologically relevant bacterioplankton lineages, each consisting of up to five genomes varying at the strain level. Statistical approaches identified from each lineage up to ∼50 loci showing anomalously high divergence at synonymous sites, which is best explained by recombination with distantly related organisms. The enriched gene categories in these outlier loci match well with the characteristics previously identified as the key phenotypes of these lineages. Examples are antibiotic synthesis and detoxification in
Phaeobacter inhibens
, exopolysaccharide production in
Alteromonas macleodii
, hydrocarbon degradation in
Marinobacter hydrocarbonoclasticus
, and cold adaptation in
Pseudoalteromonas haloplanktis
. Intriguingly, the outlier loci feature polysaccharide catabolism in
Cellulophaga baltica
but not in
Cellulophaga lytica
, consistent with their primary habitat preferences in macroalgae and beach sands, respectively. Likewise, analysis of
Prochlorococcus
showed that photosynthesis-related genes listed in the outlier loci are found only in the high-light-adapted ecotype and not in the low-light adapted ecotype. These observations strongly suggest that recombination with distant relatives is a key mechanism driving the ecological diversification among marine bacterial lineages.

IMPORTANCE
Acquisition of new metabolic genes has been known as an important mechanism driving bacterial evolution and adaptation in the ocean, but acquisition of novel alleles of existing genes and its potential ecological role have not been examined. Guided by population genetic theories, our genomic analysis showed that divergent allele acquisition is prevalent in phylogenetically diverse marine bacterial lineages and that the affected loci often encode metabolic functions that underlie the known ecological roles of the lineages under study.
Neurocognitive outcomes in children following immersion: a long-term study
Authors: Manglick Maria Patricia , Ross Frank I , Waugh Mary-Clare , Holland Andrew J A , Cass Daniel T , Soundappan Soundappan S V 
Published: March 2018

ObjectiveTo investigate long-term neurocognitive outcomes after a near-drowning incident in children who were deemed neurologically intact on discharge from hospital.DesignA prospective cohort study of near-drowning children.Setting95 drowning and near-drowning admissions, 0–16 years of age, from January 2009 to December 2013, to The Children’s Hospital at Westmead, Sydney, NSW, Australia.Participants23 children both met the criteria and had parental consent for the study.Main outcome measuresIdentification of the long-term deficits in behaviour, executive function, motor skills, communicative skills and well-being over a 5-year period. Assessment was undertaken at 3–6 months, 1 year, 3 years and 5 years after near-drowning at clinic visits. Physical developmental screening and executive function screening were done using Behavior Rating Inventory of Executive Function-Preschool version (BRIEF-P) and BRIEF.Result95 drowning and near-drowning episodes occurred during the study period. 10 (11%) children died, 28 were admitted to the paediatric intensive care unit and 64 directly to a ward. 3 children died in emergency department, 7 children had severe neurological deficit on discharge from the hospital. 23 were subsequently recruited into the study; 5 (22%) of these children had abnormalities in behaviour and/or executive function at some during their follow-up.ConclusionChildren admitted to hospital following a near-drowning event warrant long-term follow-up to identify any subtle sequelae which might be amenable to intervention to ensure optimal patient outcome.
Corneal transplant follow-up study II (CTFS II): a prospective clinical trial to determine the influence of HLA class II matching on corneal transplant rejection: baseline donor and recipient characteristics
Authors: Armitage W John , Winton Helen L , Jones Mark N A , Crewe Julie M , Rogers Chris A , Tole Derek M , Dick Andrew D 
Published: March 2018

PurposeTo describe a study to determine the influence of HLA class II matching on allograft rejection of high-risk, full-thickness corneal transplants.MethodsA prospective, longitudinal, clinical trial (ISRCTN25094892) with a primary outcome measure of time to first clinically determined rejection episode. Tissue typing used DNA-based techniques. Corneas were allocated to patients with ≤2 human leucocyte antigen (HLA) class I antigen mismatches by cohort minimisation to achieve 0, 1 or 2 HLA class II (HLA-DR) antigen mismatches. Transplants were to be followed up at 6 months and then annually on the anniversary of surgery for 5 years. Power calculations estimated a sample size of 856 transplants to detect a 0.1 difference in probability of rejection at 1 year between HLA class II matched and mismatched transplants at the 5% level of significance with 80% power.ResultsTo allow for loss to follow-up, 1133 transplants in 980 patients were accrued to the study between 3 September 1998 and 2 June 2011. 17% of transplants had 0 HLA-DR mismatches. The most frequent indication was bullous keratopathy, accounting for 27% of transplants and 54% of the transplants were regrafts. Median waiting time for a matched graft was 3 months. Donor and recipient characteristics were distributed evenly across the study groups.ConclusionRecruitment to the CFS II has closed with 1077/1133 transplants meeting all the study criteria. Follow-up has been completed and final analysis of the data has started.Trial registration numberISRCTN25094892 andUKCRNID9871, Pre-results.
Diagnostic accuracy of self-administered urine glucose test strips as a diabetes screening tool in a low-resource setting in Cambodia
Authors: Storey Helen, L , van Pelt Maurits H , Bun Socheath , Daily Frances , Neogi Tina , Thompson Matthew , McGuire Helen , Weigl Bernhard H 
Published: March 2018

ObjectiveScreening for diabetes in low-resource countries is a growing challenge, necessitating tests that are resource and context appropriate. The aim of this study was to determine the diagnostic accuracy of a self-administered urine glucose test strip compared with alternative diabetes screening tools in a low-resource setting of Cambodia.DesignProspective cross-sectional study.SettingMembers of the Borey Santepheap Community in Cambodia (Phnom Penh Municipality, District Dangkao, Commune Chom Chao).ParticipantsAll households on randomly selected streets were invited to participate, and adults at least 18 years of age living in the study area were eligible for inclusion.OutcomesThe accuracy of self-administered urine glucose test strip positivity, Hemoglobin A1c (HbA1c)>6.5% and capillary fasting blood glucose (cFBG) measurement ≥126 mg/dL were assessed against a composite reference standard of cFBGmeasurement ≥200 mg/dL or venous blood glucose 2 hours after oral glucose tolerance test (OGTT) ≥200 mg/dL.ResultsOf the 1289 participants, 234 (18%) had diabetes based on either cFBG measurement (74, 32%) or the OGTT (160, 68%). The urine glucose test strip was 14% sensitive and 99% specific and failed to identify 201 individuals with diabetes while falsely identifying 7 without diabetes. Those missed by the urine glucose test strip had lower venous fasting blood glucose, lower venous blood glucose 2 hours after OGTT and lower HbA1c compared with those correctly diagnosed.ConclusionsLow cost, easy to use diabetes tools are essential for low-resource communities with minimal infrastructure. While the urine glucose test strip may identify persons with diabetes that might otherwise go undiagnosed in these settings, its poor sensitivity cannot be ignored. The massive burden of diabetes in low-resource settings demands improvements in test technologies.
Role of Avalonia in the development of tectonic paradigms
Authors: Murphy J. Brendan , Nance R. Damian , Keppie J. Duncan , Dostal Jaroslav 
Published: March 2018

Abstract
The geological evolution of Avalonia was fundamental to the first application of plate tectonic principles to the pre-Mesozoic world. Four tectonic phases have now been identified. The oldest phase (760–660 Ma) produced a series of oceanic arcs, some possibly underlain by thin slivers of Baltica crust, which accreted to the northern margin of Gondwana between 670 and 650 Ma. Their accretion to Gondwana may be geodynamically related to the break-up of Rodinia. After accretion, subduction zones stepped outboard, producing the main phase (640–570 Ma) of arc-related magmatism and basin formation that was coeval with the amalgamation of Gondwana. Arc magmatism terminated diachronously between 600 and 540 Ma by the propagation of a San Andreas style transform fault, followed by the Early Paleozoic platformal succession used by Wilson to define the eastern flank of the proto-Atlantic (Iapetus) Ocean. This implies the ocean outboard from the northern Gondwanan margin survived into the Cambrian. Avalonia is one of several terranes distributed obliquely with respect to the adjacent cratonic provinces of Gondwana and Baltica, implying that these terranes evolved on different cratonic basements. As a result, their ages and differing isotopic signatures can be used to reconstruct their respective locations along the ancient continental margin.
An overlooked play? Structure, stratigraphy and hydrocarbon prospectivity of the Carboniferous in the East Irish Sea–North Channel basin complex
Authors: Pharaoh T. C. , Gent C. M. A. , Hannis S. D. , Kirk K. L. , Monaghan A. A. , Quinn M. F. , Smith N. J. P. , Vane C. H. , Wakefield O. , Waters C. N. 
Published: March 2018

Abstract
Seismic mapping of key Paleozoic surfaces in the East Irish Sea–North Channel region has been incorporated into a review of hydrocarbon prospectivity. The major Carboniferous basinal and inversion elements are identified, allowing an assessment of the principal kitchens for hydrocarbon generation and possible migration paths. A Carboniferous tilt-block is identified beneath the central part of the (Permian–Mesozoic) East Irish Sea Basin (EISB), bounded by carbonate platforms to the south and north. The importance of the Bowland Shale Formation as the key source rock is reaffirmed, the Pennine Coal Measures having been extensively excised following Variscan inversion and pre-Permian erosion. Peak generation from the Bowland source coincided with maximum burial of the system in late Jurassic–early Cretaceous time. Multiphase Variscan inversion generated numerous structural traps whose potential remains underexplored. Leakage of hydrocarbons from these into the overlying Triassic Ormskirk Sandstone reservoirs is likely to have occurred on a number of occasions, but currently unknown is how much resource remains in place below the Base Permian Unconformity. Poor permeability in the Pennsylvanian strata beneath the Triassic fields is a significant risk; the same may not be true in the less deeply buried marginal areas of the EISB, where additional potential plays are present in Mississippian carbonate platforms and latest Pennsylvanian clastic sedimentary rocks. Outside the EISB, the North Channel, Solway and Peel basins also contain Devonian and/or Carboniferous rocks. There have, however, been no discoveries, largely a consequence of the absence of a high-quality source rock and a regional seal comparable to the Mercia Mudstone Group and Permian evaporites of the Cumbrian Coast Group in the EISB.
Processes influencing differences in Arctic and Antarctic trough mouth fan sedimentology
Authors: Gales Jenny , Hillenbrand Claus-Dieter , Larter Rob , Laberg Jan Sverre , Melles Martin , Benetti Sara , Passchier Sandra 
Published: March 2018

Abstract
Trough mouth fans (TMFs) are sediment depocentres that form along high-latitude continental margins at the mouths of some cross-shelf troughs. They reflect the dynamics of past ice sheets over multiple glacial cycles and processes operating on (formerly) glaciated continental shelves and slopes, such as erosion, reworking, transport and deposition. The similarities and differences in TMF morphology and formation processes in the Arctic and Antarctic regions remain poorly constrained. We analyse the dimensions and geometries of 15 TMFs from Arctic and Antarctic margins and the grain size distribution of 82 sediment cores centred on them. We compare the grain size composition of sub- and proglacial diamictons deposited on the shelves and glacigenic debris flows deposited on the adjacent TMFs and find a significant difference between Arctic and Antarctic margins. Antarctic margins show a coarser grain size composition for both glacigenic debris flows and shelf diamictons. This significant difference provides insight into high-latitude sediment input, transportation and glacial–interglacial regimes. We suggest that surface runoff and river discharge are responsible for enhanced fine-grained sediment input in the Arctic compared with the Antarctic.
Improving MLC PCM Performance through Relaxed Write and Read for Intermediate Resistance Levels
Authors: Rashidi Saeed , Jalili Majid , Sarbazi-Azad Hamid 
Published: March 2018

Phase Change Memory (PCM) is one of the most promising candidates to be used at the main memory level of the memory hierarchy due to poor scalability, considerable leakage power, and high cost/bit of DRAM. PCM is a new resistive memory that is capable of storing data based on resistance values. The wide resistance range of PCM allows for storing multiple bits per cell (MLC) rather than a single bit per cell (SLC). Unfortunately, higher density of MLC PCM comes at the expense of longer read/write latency, higher soft error rate, higher energy consumption, and earlier wearout compared to the SLC PCM. Some studies suggest removing the most error-prone level to mitigate soft error and write latency of MLC PCM, hence introducing a less dense memory called Tri-Level memory. Another scheme, called M-Metric, proposes a new read metric to address the soft error problem in MLC PCM.
In order to deal with the limited lifetime of PCM, some extra storage per memory line is required to correct permanent hard errors (stuck-at faults). Since the extra storage is used only when permanent faults occur, it has a low utilization for a long time before hard errors start to occur. In this article, we utilize the extra storage to improve the read/write latency in a 2-bit MLC PCM using a relaxation scheme for reading and writing the cells for intermediate resistance levels. More specifically, we combine the most time-consuming levels (intermediate resistance levels) to reduce the number of resistance levels (making a Tri-Level PCM) and therefore improve write latency. We then store some error correction metadata in the extra storage section to successfully retrieve the exact data values in the read operation. We also modify the Tri-Level PCM cell to increase its read latency when the M-Metric scheme is used. Evaluation results show that the proposed scheme improves read latency by 57.2%, write latency by 56.1%, and overall system performance (IPC) by 26.9% over the baseline. It is noteworthy that combining the proposed scheme and FPC compression method improves read latency by 75.2%, write latency by 67%, and overall system performance (IPC) by 37.4%.
Placental growth factor reverses decreased vascular and uteroplacental MMP-2 and MMP-9 and increased MMP-1 and MMP-7 and collagen types I and IV in hypertensive pregnancy
Authors: Ren Zongli , Cui Ning , Zhu Minglin , Khalil Raouf A. 
Published: March 2018

Preeclampsia is a complication of pregnancy manifested as maternal hypertension (HTN) and fetal intrauterine growth restriction, with unclear mechanisms. Placental ischemia increases antiangiogenic soluble fms-like tyrosine kinase-1 (sFlt-1) relative to angiogenic placental growth factor (PlGF); however, the molecular targets are unclear. To test the hypothesis that placental ischemia-induced changes in sFlt-1 and PlGF target vascular and uteroplacental matrix metalloproteinases (MMPs), we tested whether raising the sFlt-1-to-PlGF ratio by infusing sFlt-1 (10 µg·kg−1·day−1) in pregnant (Preg) rats increases blood pressure (BP) and alters MMPs and whether correcting sFlt-1/PlGF by infusing PlGF (20 µg·kg−1·day−1) in Preg rats with reduced uterine perfusion pressure (RUPP) improves BP and reverses the changes in MMPs. On gestational day 19, BP was higher and the litter size and uterine, placenta, and pup weight were less in Preg + sFlt-1 and RUPP than Preg rats and restored in RUPP + PlGF versus RUPP rats. Gelatin and casein zymography and Western blots revealed decreases in MMP-2 and MMP-9 and increases in MMP-1 and MMP-7 in the aorta, uterine artery, uterus, and placenta of Preg + sFlt-1 and RUPP versus Preg rats, which were reversed in RUPP + PlGF versus RUPP rats. Collagen types I and IV were more abundant in Preg + sFlt-1 and RUPP versus Preg rats and were reversed in RUPP + PlGF versus RUPP rats. Thus, PlGF reverses decreased vascular and uteroplacental MMP-2 and MMP-9 and increased MMP-1, MMP-7, and collagen types I and IV induced by placental ischemia and sFlt-1 in HTN in pregnancy. Angiogenic factors and MMP modulators could rectify changes in MMPs and collagen, restore vascular and uteroplacental remodeling, and improve HTN and intrauterine growth restriction in preeclampsia. NEW & NOTEWORTHY Understanding the mechanisms of preeclampsia could help in its prevention and management. This study shows that correcting soluble fms-like tyrosine kinase-1 (sFlt-1)/placental growth factor (PlGF) imbalance by infusing PlGF reverses the decreases in vascular and uteroplacental matrix metalloproteinase (MMP)-2 and MMP-9 and the increases in MMP-1, MMP-7, and collagen types I and IV induced by placental ischemia and antiangiogenic sFlt-1 in hypertension in pregnancy. Angiogenic factors and MMP modulators could rectify changes in vascular and uteroplacental MMPs and collagen content and ameliorate hypertension and intrauterine growth restriction in preeclampsia.
Nitrosative stress uncovers potent β2-adrenergic receptor-linked vasodilation further enhanced by blockade of clathrin endosome formation
Authors: Frame Mary D. , Dewar Anthony M. , Calizo Rhodora C. , Qifti Androniqi , Scarlata Suzanne F. 
Published: March 2018

This study investigated the effect of sodium nitroprusside (SNP) preexposure on vasodilation via the β-adrenergic receptor (BAR) system. SNP was used as a nitrosative/oxidative proinflammatory insult. Small arterioles were visualized by intravital microscopy in the hamster cheek pouch tissue (isoflurane, n = 45). Control dilation to isoproterenol (EC50: 10−7 mol/l) became biphasic as a function of concentration after 2 min of exposure to SNP (10−4 M), with increased potency at picomolar dilation uncovered and decreased efficacy at the micromolar dilation. Control dilation to curcumin was likewise altered after SNP, but only the increased potency at a low dose was uncovered, whereas micromolar dilation was eliminated. The picomolar dilations were blocked by the potent BAR-2 inverse agonist carazolol (10−9 mol/l). Dynamin inhibition with dynasore mimicked this effect, suggesting that SNP preexposure prevented BAR agonist internalization. Using HeLa cells transfected with BAR-2 tagged with monomeric red fluorescent protein, exposure to 10−8−10−6 mol/l curcumin resulted in internalization and colocalization of BAR-2 and curcumin (FRET) that was prevented by oxidative stress (10−3 mol/l CoCl2), supporting that stress prevented internalization of the BAR agonist with the micromolar agonist. This study presents novel data supporting that distinct pools of BARs are differentially available after inflammatory insult. NEW & NOTEWORTHY Preexposure to an oxidative/nitrosative proinflammatory insult provides a “protective preconditioning” against future oxidative damage. We examined immediate vasoactive and molecular consequences of a brief preexposure via β-adrenergic receptor signaling in small arterioles. Blocked receptor internalization with elevated reactive oxygen levels coincides with a significant and unexpected vasodilation to β-adrenergic agonists at picomolar doses.