bluuebunny/crossref_metadata_2025_split huggingface dataset:
Purification and characterization of Arabidopsis thaliana oligosaccharyltransferase complexes from the native host: a protein super‐expression system for structural studies
Authors: Jeong In Sil , Lee Sangmin , Bonkhofer Florian , Tolley Jordan , Fukudome Akihito , Nagashima Yukihiro , May Kimberly , Rips Stephan , Lee Sang Y. , Gallois Patrick , Russell William K. , Jung Hyun Suk , von Schaewen Antje , Koiwa Hisashi 
Published: February 2018

SummaryThe oligosaccharyltransferase (OT) complex catalyzes N‐glycosylation of nascent secretory polypeptides in the lumen of the endoplasmic reticulum. Despite their importance, little is known about the structure and function of plant OT complexes, mainly due to lack of efficient recombinant protein production systems suitable for studies on large plant protein complexes. Here, we purified Arabidopsis OT complexes using the tandem affinity‐tagged OT subunit STAUROSPORINE AND TEMPERATURE SENSITIVE3a (STT3a) expressed by an Arabidopsis protein super‐expression platform. Mass‐spectrometry analysis of the purified complexes identified three essential OT subunits, OLIGOSACCHARYLTRANSFERASE1 (OST1), HAPLESS6 (HAP6), DEFECTIVE GLYCOSYLATION1 (DGL1), and a number of ribosomal subunits. Transmission‐electron microscopy showed that STT3a becomes incorporated into OT–ribosome super‐complexes formed in vivo, demonstrating that this expression/purification platform is suitable for analysis of large protein complexes. Pairwise in planta interaction analyses of individual OT subunits demonstrated that all subunits identified in animal OT complexes are conserved in Arabidopsis and physically interact with STT3a. Genetic analysis of newly established OT subunit mutants for OST1 and DEFENDER AGAINST APOTOTIC DEATH (DAD) family genes revealed that OST1 and DAD1/2 subunits are essential for the plant life cycle. However, mutations in these individual isoforms produced much milder growth/underglycosylation phenotypes than previously reported for mutations in DGL1, OST3/6 and STT3a.
Cellular distribution of secretory pathway markers in the haploid synergid cells of Arabidopsis thaliana
Authors: Jones Daniel S. , Liu Xunliang , Willoughby Andrew C. , Smith Benjamin E. , Palanivelu Ravishankar , Kessler Sharon A. 
Published: February 2018

SummaryIn flowering plants, cell–cell communication plays a key role in reproductive success, as both pollination and fertilization require pathways that regulate interactions between many different cell types. Some of the most critical of these interactions are those between the pollen tube (PT) and the embryo sac, which ensure the delivery of sperm cells required for double fertilization. Synergid cells function to attract the PT through secretion of small peptides and in PT reception via membrane‐bound proteins associated with the endomembrane system and the cell surface. While many synergid‐expressed components regulating PT attraction and reception have been identified, few tools exist to study the localization of membrane‐bound proteins and the components of the endomembrane system in this cell type. In this study, we describe the localization and distribution of seven fluorescent markers that labelled components of the secretory pathway in synergid cells of Arabidopsis thaliana. These markers were used in co‐localization experiments to investigate the subcellular distribution of the two PT reception components LORELEI, a GPI‐anchored surface protein, and NORTIA, a MILDEW RESISTANCE LOCUS O protein, both found within the endomembrane system of the synergid cell. These secretory markers are useful tools for both reproductive and cell biologists, enabling the analysis of membrane‐associated trafficking within a haploid cell actively involved in polar transport.
Transfusion‐associated circulatory overload in a pediatric intensive care unit: different incidences with different diagnostic criteria
Authors: De Cloedt Lise , Emeriaud Guillaume , Lefebvre Émilie , Kleiber Niina , Robitaille Nancy , Jarlot Christine , Lacroix Jacques , Gauvin France 
Published: February 2018

BACKGROUNDThe incidence of transfusion‐associated circulatory overload (TACO) is not well known in children, especially in pediatric intensive care unit (PICU) patients.STUDY DESIGN AND METHODSAll consecutive patients admitted over 1 year to the PICU of CHU Sainte‐Justine were included after they received their first red blood cell transfusion. TACO was diagnosed using the criteria of the International Society of Blood Transfusion, with two different ways of defining abnormal values: 1) using normal pediatric values published in the Nelson Textbook of Pediatrics and 2) by using the patient as its own control and comparing pre‐ and posttransfusion values with either 10 or 20% difference threshold. We monitored for TACO up to 24 hours posttransfusion.RESULTSA total of 136 patients were included. Using the “normal pediatric values” definition, we diagnosed 63, 88, and 104 patients with TACO at 6, 12, and 24 hours posttransfusion, respectively. Using the “10% threshold” definition we detected 4, 15, and 27 TACO cases in the same periods, respectively; using the “20% threshold” definition, the number of TACO cases was 2, 6, and 17, respectively. Chest radiograph was the most frequent missing item, especially at 6 and 12 hours posttransfusion. Overall, the incidence of TACO varied from 1.5% to 76% depending on the definition.CONCLUSIONA more operational definition of TACO is needed in PICU patients. Using a threshold could be more optimal but more studies are needed to confirm the best threshold.
Differential sensitivity of Atriplex patula and Chenopodium album to sugar beet herbicides: a possible cause for the upsurge of A. patula in sugar beet fields
Authors: De Cauwer B , Cardinael A , Claerhout S , Manderyck B , Reheul D 
Published: February 2018

SummaryIn the last decade, the prevalence of Atriplex patula as a weed in the Belgian sugar beet area has increased. Possible reasons for its expansion in sugar beet fields, besides a poor implementation of the low‐dose phenmedipham/activator/soil‐acting herbicide (FAR) system, might be low sensitivity or evolved resistance to one or more herbicides used in sugar beet. Dose–response pot bioassays were conducted in the glasshouse to evaluate the effectiveness of five foliar‐applied sugar beet herbicides (metamitron, phenmedipham, desmedipham, ethofumesate and triallate) and three pre‐plant‐incorporated herbicides (metamitron, lenacil, dimethenamid‐P) for controlling five Belgian A. patula populations. Local metamitron‐susceptible and metamitron‐resistant populations of Chenopodium album were used as reference populations. Effective dosages and resistance indices were calculated. DNA sequence analysis of the photosystem II psbA gene was performed on putative resistant A. patula populations. Overall, A. patula exhibited large intraspecific variation in herbicide sensitivity. In general, A. patula populations were less susceptible to phenmedipham, desmedipham, ethofumesate and triallate relative to C. album populations. Two A. patula populations bear the leucine‐218 to valine mutation on the chloroplast psbA gene conferring low level to high level cross‐resistance to the photosystem II inhibitors phenmedipham, desmedipham, metamitron and lenacil. In order to avoid insufficient A. patula control and further spread, seedlings should preferentially be treated with FAR mixtures containing higher‐than‐standard doses of metamitron and phenmedipham/desmedipham and no later than the cotyledon stage.
Phrenic motor neuron adenosine 2A receptors elicit phrenic motor facilitation
Authors: Seven Yasin B. , Perim Raphael R. , Hobson Orinda R. , Simon Alec K. , Tadjalli Arash , Mitchell Gordon S. 
Published: February 2018

Key points
Although adenosine 2A (A2A) receptor activation triggers specific cell signalling cascades, the ensuing physiological outcomes depend on the specific cell type expressing these receptors.
Cervical spinal adenosine 2A (A2A) receptor activation elicits a prolonged facilitation in phrenic nerve activity, which was nearly abolished following intrapleural A2A receptor siRNA injections.
A2A receptor siRNA injections selectively knocked down A2A receptors in cholera toxin B‐subunit‐identified phrenic motor neurons, sparing cervical non‐phrenic motor neurons.
Collectively, our results support the hypothesis that phrenic motor neurons express the A2A receptors relevant to A2A receptor‐induced phrenic motor facilitation.
Upregulation of A2A receptor expression in the phrenic motor neurons per se may potentially be a useful approach to increase phrenic motor neuron excitability in conditions such as spinal cord injury.
AbstractCervical spinal adenosine 2A (A2A) receptor activation elicits a prolonged increase in phrenic nerve activity, an effect known as phrenic motor facilitation (pMF). The specific cervical spinal cells expressing the relevant A2A receptors for pMF are unknown. This is an important question since the physiological outcome of A2A receptor activation is highly cell type specific. Thus, we tested the hypothesis that the relevant A2A receptors for pMF are expressed in phrenic motor neurons per se versus non‐phrenic neurons of the cervical spinal cord. A2A receptor immunostaining significantly colocalized with NeuN‐positive neurons (89 ± 2%). Intrapleural siRNA injections were used to selectively knock down A2A receptors in cholera toxin B‐subunit‐labelled phrenic motor neurons. A2A receptor knock‐down was verified by a ∼45% decrease in A2A receptor immunoreactivity within phrenic motor neurons versus non‐targeting siRNAs (siNT; P < 0.05). There was no evidence for knock‐down in cervical non‐phrenic motor neurons. In rats that were anaesthetized, subjected to neuromuscular blockade and ventilated, pMF induced by cervical (C3–4) intrathecal injections of the A2A receptor agonist CGS21680 was greatly attenuated in siA2A (21%) versus siNT treated rats (147%; P < 0.01). There were no significant effects of siA2A on phrenic burst frequency. Collectively, our results support the hypothesis that phrenic motor neurons express the A2A receptors relevant to A2A receptor‐induced pMF.
Climate, ecosystems, and planetary futures: The challenge to predict life in Earth system models
Authors: Bonan Gordon B. , Doney Scott C. 
Published: February 2018

Integrating the biosphere into climate models
High-quality climate predictions are crucial for understanding the impacts of different greenhouse gas emission scenarios and for mitigating and adapting to the resulting climatic changes. Bonan and Doney review advances in Earth system models that include the terrestrial and marine biosphere. Such models capture interactions between physical and biological aspects of the Earth system. This provides insight into climate impacts of societal importance, such as altered crop yields, wildfire risk, and water availability. Further research is needed to better understand model uncertainties, some of which may be unavoidable, and to better translate observations into abstract model representations.

Science
, this issue p.
eaam8328
A Novel Dual-
cre
Motif Enables Two-Way Autoregulation of CcpA in Clostridium acetobutylicum
Authors: Zhang Lu , Liu Yanqiang , Yang Yunpeng , Jiang Weihong , Gu Yang 
Published: February 2018

ABSTRACT

The master regulator CcpA (catabolite control protein A) manages a large and complex regulatory network that is essential for cellular physiology and metabolism in Gram-positive bacteria. Although CcpA can affect the expression of target genes by binding to a
cis
-acting catabolite-responsive element (
cre
), whether and how the expression of CcpA is regulated remain poorly explored. Here, we report a novel dual-
cre
motif that is employed by the CcpA in
Clostridium acetobutylicum
, a typical solventogenic
Clostridium
species, for autoregulation. Two
cre
sites are involved in CcpA autoregulation, and they reside in the promoter and coding regions of CcpA. In this dual-
cre
motif,
cre
P
, in the promoter region, positively regulates
ccpA
transcription, whereas
cre
ORF
, in the coding region, negatively regulates this transcription, thus enabling two-way autoregulation of CcpA. Although CcpA bound
cre
P
more strongly than
cre
ORF
in vitro
, the
in vivo
assay showed that
cre
ORF
-based repression dominates CcpA autoregulation during the entire fermentation. Finally, a synonymous mutation of
cre
ORF
was made within the coding region, achieving an increased intracellular CcpA expression and improved cellular performance. This study provides new insights into the regulatory role of CcpA in
C. acetobutylicum
and, moreover, contributes a new engineering strategy for this industrial strain.

IMPORTANCE
CcpA is known to be a key transcription factor in Gram-positive bacteria. However, it is still unclear whether and how the intracellular CcpA level is regulated, which may be essential for maintaining normal cell physiology and metabolism. We discovered here that CcpA employs a dual-
cre
motif to autoregulate, enabling dynamic control of its own expression level during the entire fermentation process. This finding answers the questions above and fills a void in our understanding of the regulatory network of CcpA. Interference in CcpA autoregulation leads to improved cellular performance, providing a new useful strategy in genetic engineering of
C. acetobutylicum
. Since CcpA is widespread in Gram-positive bacteria, including pathogens, this dual-
cre
-based CcpA autoregulation would be valuable for increasing our understanding of CcpA-based global regulation in bacteria.
Social and structural conditions for the avoidance of advance care planning in neuro-oncology: a qualitative study
Authors: Llewellyn Henry , Neerkin Jane , Thorne Lewis , Wilson Elena , Jones Louise , Sampson Elizabeth L , Townsley Emma , Low Joseph T S 
Published: February 2018

BackgroundPrimary brain tumours newly affect >260 000 people each year worldwide. In the UK, every year >10 000 people are diagnosed with a brain tumour while >5000 die annually from the disease. Prognoses are poor, cognitive deterioration common and patients have prolonged palliative needs. Advance care planning (ACP) may enable early discussion of future care decisions. Although a core commitment in the UK healthcare strategy, and the shared responsibility of clinical teams, ACP appears uncommon in practice. Evidence around ACP practice in neuro-oncology is limited.ObjectivesWe aimed to elicit keysocial and structural conditionscontributing to the avoidance of ACP in neuro-oncology.DesignA cross-sectional qualitative study design was used.SettingOne tertiary care hospital in the UK.ParticipantsFifteen healthcare professionals working in neuro-oncology participated in this study, including neuro-oncologists, neurosurgeons, clinical nurse specialists, allied healthcare professionals and a neurologist.MethodSemi-structured interviews were conducted with participants to explore their assumptions and experiences of ACP. Data were analysed thematically using the well-established framework method.ResultsParticipants recognised the importance of ACP but few had ever completed formal ACP documentation. We identified eight key factors, which we suggest comprise three main conditions for avoidance: (1) difficulties being a highly emotive, time-intensive practice requiring the right ‘window of opportunity’ and (2) presence and availability of others; (3) ambiguities in ACP definition, purpose and practice. Combined, these created a ‘culture of shared avoidance’.ConclusionIn busy clinical environments, ‘shared responsibility’ is interpreted as ‘others’ responsibility’ laying the basis for a culture of avoidance. To address this, we suggest a ‘generalists and specialists’ model of ACP, wherein healthcare professionals undertake particular responsibilities. Healthcare professionals are already adopting this model informally, but without formalised structure it is likely to fail given a tendency for people to assume a generalist role.
Investigation of the conditions affecting the joining of Hungarian hospitals to an accreditation programme: a cross-sectional study
Authors: Dombrádi Viktor , Margitai Barnabás , Dózsa Csaba , Bárdos-Csenteri Orsolya Karola , Sándor János , Gáll Tibor , Gődény Sándor 
Published: February 2018

ObjectiveQuantitative studies have shown the various benefits for having accreditation in hospitals. However, neither of these explored the general conditions before applying for an accreditation. To close this gap, this study aimed to investigate the possible association between joining an accreditation programme with various hospital characteristics.DesignA cross-sectional study was implemented using the databases of the 2013 Hungarian hospital survey and of the Hungarian State Treasury.SettingPublic general hospitals in Hungary.ParticipantsThe analysis involved 44 public general hospitals, 14 of which joined the preparatory project for a newly developed accreditation programme.Main outcome measuresThe outcomes included the percentage of compliance in quality management, patient information and identification, internal professional regulation, safe surgery, pressure sore prevention, infection control, the opinions of the heads of quality management regarding the usefulness of quality management and clinical audits, and finally, the total debt of the hospital per bed and per discharged patient.ResultsAccording to our findings, the general hospitals joining the preparatory project of the accreditation programme performed better in four of the six investigated activities, the head of quality management had a better opinion on the usefulness of quality management, and both the debt per bed number and the debt per discharged patient were lower than those who did not join. However, no statistically significant differences between the two groups were found in any of the examined outcomes.ConclusionsThe findings suggest that hospitals applying for an accreditation programme do not differ significantly in characteristics from those which did not apply. This means that if in the future the accredited hospitals become better than other hospitals, then the improvement could be solely contributed to the accreditation.
Predicting prostate cancer progression: protocol for a retrospective cohort study to identify prognostic factors for prostate cancer outcomes using routine primary care data
Authors: Merriel Samuel W D , May Margaret T , Martin Richard M 
Published: February 2018

IntroductionProstate cancer is the most common cancer in men in the UK, with nearly 40 000 diagnosed in 2014; and it is the second most common cause of male cancer-related mortality. The clinical conundrum is that most men live with prostate cancer rather than die from it, while existing treatments have significant associated morbidity. Recent studies have shown very low mortality rates (1% after a median of 10-year follow-up) and no treatment-related reductions in mortality, in men with localised prostate cancer. This study will identify prognostic factors associated with prostate cancer progression to help differentiate aggressive from more indolent tumours in men with localised disease at diagnosis, and so inform the decision to adopt conservative (active surveillance) or radical (surgery or radiotherapy) management strategies.Methods and analysisThe Clinical Practice Research Datalink (CPRD) contains 57 318 men who were diagnosed with prostate cancer between 1 January 1987 and 31 December 2016. These men will be linked to the Office for National Statistics (ONS) and the National Cancer Registration and Analysis Service registry databases for mortality, TNM stage, Gleason grade and treatment data. Men with a diagnosis date prior to 1 January 1987 and men with lymph node or distant metastases at diagnosis will be excluded. A priori determined prognostic factors potentially associated with prostate cancer mortality, the end point of cancer progression, will be measured at baseline, and the participants followed through to development of cancer progression, death or the end of the follow-up period (31 December 2016). Cox proportional hazards regression will be used to estimate crude and mutually adjusted HRs. Mortality risk will be predicted using flexible parametric survival models that can accurately fit the shape of the hazard function.Ethics and disseminationThis study protocol has approval from the Independent Scientific Advisory Committee for the UK Medicines and Healthcare products Regulatory Agency Database Research (protocol 17_041). The findings will be presented in peer-reviewed journals and local CPRD researcher meetings.
Do police officers and firefighters have a higher risk of disease than other public officers? A 13-year nationwide cohort study in South Korea
Authors: Han Minkyung , Park Sohee , Park Jong Heon , Hwang Seung-sik , Kim Inah 
Published: February 2018

ObjectivesThe work of public officers involves repeated and long-term exposure to heavy workloads, high job strain and workplace violence, all of which negatively impact physical and mental health. This study aimed to evaluate and compare the incidences of diseases among different categories of public officers in Korea, in order to further understand the health risks associated with these occupations.DesignA cohort study using the National Health Insurance data.ParticipantsWe collated claims data between 2002 and 2014 for 860 221 public officers.Primary and secondary outcome measuresAge-standardised rates were calculated using the direct standardisation method, and HRs were calculated using the Cox proportional hazard regression models.ResultsOverall, we found that police officers and firefighters had a higher incidence of a range of diseases when compared with national and regional government officers (NRG). The most prominent HRs were observed among police officers for angina pectoris (HR: 1.52, 95% CI 1.49 to 1.54), acute myocardial infarction (HR: 1.84, 95% CI 1.77 to 1.92) and cerebrovascular disease (HR: 1.36, 95% CI 1.31 to 1.40). Firefighters were more susceptible to physical ailments and were at a significantly higher risk for traumatic stress disorders (HR: 1.40, 95% CI 1.26 to 1.56) than NRGs.ConclusionCompared withNRGs, police officers had higher HRs for all measured diseases, except for traumatic stress disorders. While firefighters had higher HRs for almost all diseases examined, public education officers had a higher HR for traumatic stress disorders, when compared with NRGs.