bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Framework for Understanding Uncertainty in Seismic Risk Assessment
Authors: Foulser‐Piggott Roxane , Bowman Gary , Hughes Martin 
Published: October 2017

AbstractA better understanding of the uncertainty that exists in models used for seismic risk assessment is critical to improving risk‐based decisions pertaining to earthquake safety. Current models estimating the probability of collapse of a building do not consider comprehensively the nature and impact of uncertainty. This article presents a model framework to enhance seismic risk assessment and thus gives decisionmakers a fuller understanding of the nature and limitations of the estimates. This can help ensure that risks are not over‐ or underestimated and the value of acquiring accurate data is appreciated fully. The methodology presented provides a novel treatment of uncertainties in input variables, their propagation through the model, and their effect on the results. The study presents ranges of possible annual collapse probabilities for different case studies on buildings in different parts of the world, exposed to different levels of seismicity, and with different vulnerabilities. A global sensitivity analysis was conducted to determine the significance of uncertain variables. Two key outcomes are (1) that the uncertainty in ground‐motion conversion equations has the largest effect on the uncertainty in the calculation of annual collapse probability; and (2) the vulnerability of a building appears to have an effect on the range of annual collapse probabilities produced, i.e., the level of uncertainty in the estimate of annual collapse probability, with less vulnerable buildings having a smaller uncertainty.
Mound‐forming cold‐water corals and bryozoans in the Early Palaeocene of Denmark
Authors: Bjerager Morten , Sheldon Emma , Lauridsen Bodil W. 
Published: October 2017

AbstractThe Faxe Quarry in south‐east Denmark offers excellent exposures of Early Palaeocene, Danian deep‐water intercalated coral and bryozoan mounds that form complexes at least 40 m thick and a few kilometres wide along and over submarine highs. The coexisting coral and bryozoan mounds represent two different biogenic carbonate factories with a highly dynamic interplay during growth. The sedimentary facies, mound geometries and the density, diversity and palaeoecology of the associated benthic invertebrates and nannofossils allow recognition of six successive growth units. Unit 1 represents an outer shelf bryozoan mound belt characterized by an oligotrophic cool‐water nannofossil assemblage. Unit 2 comprises a mixed faunal assemblage of bryozoans and octocorals with an initial sparse colonization of hexacorals. The nannofossil assemblage records a decrease in diversity and an increase in warm water forms. Unit 3 marks the onset of dense colonization of the scleractinian coral Dendrophyllia candelabrum with associated low‐diversity macrofauna and nannofossil assemblages. Unit 4 represents the main coral build‐up phase with frame‐building hexacorals of Dendrophyllia and Faxephyllia associated with a high‐diversity invertebrate fauna, and relatively low‐diversity nannofossil assemblages. Unit 5 represents the late coral mound phase showing extensive lateral distribution and finally death and erosion of the coral mounds. This event was contemporaneous with a warming trend in the pelagic environment. The succeeding Unit 6 marks the burial and overgrowth of the coral mound complex by bryozoan‐rich sediments. The coral mound complex in the Faxe Quarry initiated and terminated in global nannofossil zone NP3 and regional nannofossil zones NNTp2G–3 suggesting a mound growth duration of ca 300 kyr and a mean vertical accretion of the coral mound of 13 cm kyr−1. The mound complex probably serves as the best‐exposed analogue to modern deep and cold‐water coral mounds in the North Atlantic.
RiceSUMOproteaseOverly Tolerant to Salt 1targets the transcription factor, OsbZIP23 to promote drought tolerance in rice
Authors: Srivastava Anjil Kumar , Zhang Cunjin , Caine Robert S , Gray Julie , Sadanandom Ari 
Published: October 2017

SummaryConjugation ofSUMO(Small Ubiquitin‐like Modifier) protein to cellular targets is emerging as a very influential protein modification system. Once covalently bound,SUMOconjugation can change the stability or functionality of its cognate target proteins.SUMOprotease can rapidly reverseSUMOconjugation making this modification system highly dynamic. A major factor in the variation ofSUMO‐target function is the balance between the conjugated/de‐conjugated forms. The mechanistic role of these regulatorySUMOproteases in mediating stress responses has not been defined in any crops. In this study, we reveal the role of theSUMOprotease, OsOTS1 in mediating tolerance to drought in rice.OsOTS1depleted transgenic plants accumulate moreABAand exhibit more productive agronomic traits during drought whileOsOTS1overexpressing lines are drought sensitive butABAinsensitive. Drought andABAtreatment stimulates the degradation of OsOTS1 protein indicating thatSUMOconjugation is an important response to drought stress in rice achieved through down‐regulation ofOTS1/2 activity. We reveal that OsOTS1SUMOprotease directly targets theABAand drought responsive transcription factor OsbZIP23 for de‐SUMOylation affecting its stability.OsOTS‐RNAi lines show increased abundance of OsbZIP23 and increased drought responsive gene expression whileOsOTS1overexpressing lines show reduced levels of OsbZIP23 leading to suppressed drought responsive gene expression. Our data reveal a mechanism in which rice plants governABA‐dependant drought responsive gene expression by controlling the stability of OsbZIP23 bySUMOconjugation through manipulating specificSUMOprotease levels.
Root transcriptional dynamics induced by beneficial rhizobacteria and microbial immune elicitors reveal signatures of adaptation to mutualists
Authors: Stringlis Ioannis A. , Proietti Silvia , Hickman Richard , Van Verk Marcel C. , Zamioudis Christos , Pieterse Corné M. J. 
Published: October 2017

SummaryBelow ground, microbe‐associated molecular patterns (MAMPs) of root‐associated microbiota can trigger costly defenses at the expense of plant growth. However, beneficial rhizobacteria, such as Pseudomonas simiae WCS417, promote plant growth and induce systemic resistance without being warded off by local root immune responses. To investigate early root responses that facilitate WCS417 to exert its plant‐beneficial functions, we performed time series RNA‐Seq of Arabidopsis roots in response to live WCS417 and compared it with MAMPs flg22417 (from WCS417), flg22Pa (from pathogenic Pseudomonas aeruginosa) and fungal chitin. The MAMP transcriptional responses differed in timing, but displayed a large overlap in gene identity. MAMP‐upregulated genes are enriched for genes with functions in immunity, while downregulated genes are enriched for genes related to growth and development. Although 74% of the transcriptional changes inflicted by live WCS417 overlapped with the flg22417 profile, WCS417 actively suppressed more than half of the MAMP‐triggered transcriptional responses, possibly to allow the establishment of a mutually beneficial interaction with the host root. Interestingly, the sector of the flg22417‐repressed transcriptional network that is not affected by WCS417 has a strong auxin signature. Using auxin response mutant tir1afb2afb3, we demonstrate a dual role for auxin signaling in finely balancing growth‐promoting and defense‐eliciting activities of beneficial microbes in plant roots.
On the Popov–Pommerening conjecture for linear algebraic groups
Authors: Bérczi Gergely 
Published: October 2017

Let $G$ be a reductive group over an algebraically closed subfield $k$ of $\mathbb{C}$ of characteristic zero, $H\subseteq G$ an observable subgroup normalised by a maximal torus of $G$ and $X$ an affine $k$-variety acted on by $G$. Popov and Pommerening conjectured in the late 1970s that the invariant algebra $k[X]^{H}$ is finitely generated. We prove the conjecture for: (1) subgroups of $\operatorname{SL}_{n}(k)$ closed under left (or right) Borel action and for: (2) a class of Borel regular subgroups of classical groups. We give a partial affirmative answer to the conjecture for general regular subgroups of $\operatorname{SL}_{n}(k)$.
Kaposi’s Sarcoma-Associated Herpesvirus Increases PD-L1 and Proinflammatory Cytokine Expression in Human Monocytes
Authors: Host Kurtis M. , Jacobs Sarah R. , West John A. , Zhang Zhigang , Costantini Lindsey M. , Stopford Charles M. , Dittmer Dirk P. , Damania Blossom 
Published: October 2017

ABSTRACT

Kaposi’s sarcoma-associated herpesvirus (KSHV) is associated with the human malignancy Kaposi’s sarcoma and the lymphoproliferative disorders primary effusion lymphoma and multicentric Castleman’s disease. KSHV establishes lytic infection of monocytes
in vivo
, which may represent an important cellular reservoir during KS disease progression. KS tumors consist of latently infected endothelial cells; however, lytic phase gene products are important for KS onset. Early KS lesion progression is driven by proinflammatory cytokines supplied by immune cell infiltrates including T cells and monocytes. KSHV-infected monocytes may supply the lytic viral products and the inflammatory milieu conducive to KS tumor progression. To establish successful infection, KSHV extensively modulates the host immune system. KSHV antigens activate both innate and adaptive immune responses including KSHV-specific T cells, but lifelong infection is still established. Programmed death ligand 1 (PD-L1) is a prosurvival cell surface protein that suppresses T-cell-mediated killing. PD-L1 is variably present on various tumor cells and is a targetable marker for cancer treatment. We show that KSHV infection of human monocytes increases PD-L1 expression and transcription in a dose-dependent manner. We also saw evidence of lytic gene expression in the KSHV-infected monocytes. Intact KSHV is needed for full PD-L1 response in human monocytes. KSHV induces a general proinflammatory cytokine milieu including interleukins 1α, 1β, and 6, which have been implicated in early KS lesion progression. KSHV-mediated PD-L1 increase may represent a novel mechanism of KSHV-mediated immune modulation to allow for virus survival and eventually malignant progression.

IMPORTANCE
KSHV is the etiologic agent of Kaposi’s sarcoma and the lymphoproliferative disorders primary effusion lymphoma and multicentric Castleman’s disease. Programmed death ligand 1 (PD-L1) is an immunosuppressive cell surface marker that inhibits T cell activation. We report that KSHV infection of primary human monocytes upregulates PD-L1 transcription and protein expression. Analysis of the cytokine and chemokine milieu following KSHV infection of monocytes revealed that KSHV induces interleukins 1α, 1β, and 6, all of which have been implicated in KS development. Our work has identified another potential immune evasion strategy for KSHV and a potential target for immunotherapy of KSHV-derived disease.
Reciprocal Prioritization to Dietary Glycans by Gut Bacteria in a Competitive Environment Promotes Stable Coexistence
Authors: Tuncil Yunus E. , Xiao Yao , Porter Nathan T. , Reuhs Bradley L. , Martens Eric C. , Hamaker Bruce R. 
Published: October 2017

ABSTRACT

When presented with nutrient mixtures, several human gut
Bacteroides
species exhibit hierarchical utilization of glycans through a phenomenon that resembles catabolite repression. However, it is unclear how closely these observed physiological changes, often measured by altered transcription of glycan utilization genes, mirror actual glycan depletion. To understand the glycan prioritization strategies of two closely related human gut symbionts,
Bacteroides ovatus
and
Bacteroides thetaiotaomicron
, we performed a series of time course assays in which both species were individually grown in a medium with six different glycans that both species can degrade. Disappearance of the substrates and transcription of the corresponding polysaccharide utilization loci (PULs) were measured. Each species utilized some glycans before others, but with different priorities per species, providing insight into species-specific hierarchical preferences. In general, the presence of highly prioritized glycans repressed transcription of genes involved in utilizing lower-priority nutrients. However, transcriptional sensitivity to some glycans varied relative to the residual concentration in the medium, with some PULs that target high-priority substrates remaining highly expressed even after their target glycan had been mostly depleted. Coculturing of these organisms in the same mixture showed that the hierarchical orders generally remained the same, promoting stable coexistence. Polymer length was found to be a contributing factor for glycan utilization, thereby affecting its place in the hierarchy. Our findings not only elucidate how
B. ovatus
and
B. thetaiotaomicron
strategically access glycans to maintain coexistence but also support the prioritization of carbohydrate utilization based on carbohydrate structure, advancing our understanding of the relationships between diet and the gut microbiome.

IMPORTANCE
The microorganisms that reside in the human colon fulfill their energy requirements mainly from diet- and host-derived complex carbohydrates. Members of this ecosystem possess poorly understood strategies to prioritize and compete for these nutrients. Based on direct carbohydrate measurements and corresponding transcriptional analyses, our findings showed that individual bacterial species exhibit different preferences for the same set of glycans and that this prioritization is maintained in a competitive environment, which may promote stable coexistence. Such understanding of gut bacterial glycan utilization will be essential to eliciting predictable changes in the gut microbiota to improve health through the diet.
Characterization of Inner and Outer Membrane Proteins from
Francisella tularensis
Strains LVS and Schu S4 and Identification of Potential Subunit Vaccine Candidates
Authors: Post Deborah M. B. , Slütter Bram , Schilling Birgit , Chande Aroon T. , Rasmussen Jed A. , Jones Bradley D. , D’Souza Alexandria K. , Reinders Lorri M. , Harty John T. , Gibson Bradford W. , Apicella Michael A. 
Published: October 2017

ABSTRACT

Francisella tularensis
is the causative agent of tularemia and a potential bioterrorism agent. In the present study, we isolated, identified, and quantified the proteins present in the membranes of the virulent type A strain, Schu S4, and the attenuated type B strain, LVS (live vaccine strain). Spectral counting of mass spectrometric data showed enrichment for membrane proteins in both strains. Mice vaccinated with whole LVS membranes encapsulated in poly (lactic-co-glycolic acid) (PLGA) nanoparticles containing the adjuvant polyinosinic-polycytidylic acid [poly(I·C)] showed significant protection against a challenge with LVS compared to the results seen with naive mice or mice vaccinated with either membranes or poly(I·C) alone. The PLGA-encapsulated Schu S4 membranes with poly(I·C) alone did not significantly protect mice from a lethal intraperitoneal challenge with Schu S4; however, this vaccination strategy provided protection from LVS challenge. Mice that received the encapsulated Schu S4 membranes followed by a booster of LVS bacteria showed significant protection with respect to a lethal Schu S4 challenge compared to control mice. Western blot analyses of the sera from the Schu S4-vaccinated mice that received an LVS booster showed four immunoreactive bands. One of these bands from the corresponding one-dimensional (1D) SDS-PAGE experiment represented capsule. The remaining bands were excised, digested with trypsin, and analyzed using mass spectrometry. The most abundant proteins present in these immunoreactive samples were an outer membrane OmpA-like protein, FopA; the type IV pilus fiber building block protein; a hypothetical membrane protein; and lipoproteins LpnA and Lpp3. These proteins should serve as potential targets for future recombinant protein vaccination studies.

IMPORTANCE
The low infectious dose, the high potential mortality/morbidity rates, and the ability to be disseminated as an aerosol make
Francisella tularensis
a potential agent for bioterrorism. These characteristics led the Centers for Disease Control (CDC) to classify
F. tularensis
as a Tier 1 pathogen. Currently, there is no vaccine approved for general use in the United States.
Straight from the Horse’s “Mouth”: Genomic Epidemiology of an Icelandic Equine Epidemic
Authors: Davies Mark R. 
Published: October 2017

ABSTRACT

Despite tight biosecurity measures, an outbreak of respiratory disease rapidly spread across the Icelandic equine population in 2010. Horse transportation was brought to a halt in order to contain the spread of the infectious agent. In a recent article, Björnsdóttir and colleagues (S. Björnsdóttir et al., mBio 8:e00826-17, 2017,
https://doi.org/10.1128/mBio.00826-17
) employ the power and resolution of “genomic epidemiology,” the combination of whole genomic sequencing and epidemiological approaches, to examine the source and spread of the outbreak. Intriguingly, the outbreak was not viral in origin, but linked to a bacterial “commensal”
Streptococcus equi
subsp.
zooepidemicus
infection. A national sampling strategy coupled with population genomics revealed that the outbreak was most likely driven by a
S. equi
subsp.
zooepidemicus
sequence type 209 (ST209) infection that spread nationally from a single source. This retrospective study demonstrates the power of genomics applied on a national scale to unravel the cause of a significant biosecurity threat.
High-sensitivity C reactive protein as a predictor of inhospital mortality in patients with cardiovascular disease at an emergency department: a retrospective cohort study
Authors: Yoshinaga Ryo , Doi Yasufumi , Ayukawa Katsuhiko , Ishikawa Shizukiyo 
Published: October 2017

ObjectiveWe investigated whether serum high-sensitivity C reactive protein (hs-CRP) levels measured in an emergency department (ED) are associated with inhospital mortality in patients with cardiovascular disease (CVD).DesignA retrospective cohort study.SettingED of a teaching hospital in Japan.Participants12 211 patients with CVD aged ≥18 years who presented to the ED by an ambulance between 1 February 2006 and 30 September 2014 were evaluated.Main outcome measuresInhospital mortality.Results1156 patients had died. The inhospital mortality increased significantly with the hs-CRP levels (<3.0 mg/L: 7.0%, 95% CI 6.4 to 7.6; 3.1–5.4 mg/L: 9.6%, 95% CI 7.9 to 11.3: 5.5–11.5 mg/L: 11.2%, 95% CI 9.4 to 13.0; 11.6–33.2 mg/L: 12.3%, 95% CI 10.5 to 14.1 and ≥33.3 mg/L: 19.9%, 95% CI 17.6 to 22.2). The age-adjusted and sex-adjusted HR for total mortality was increased significantly in the three ≥5.5 mg/L groups compared with the <3.0 mg/L group (5.5–11.5 mg/L: HR=1.32, 95% CI 1.09 to 1.60, p=0.005; 11.6–33.2 mg/L: HR=1.38, 95% CI 1.14 to 1.65, p=0.001 and ≥33.3 mg/L: HR=2.15, 95% CI 1.84 to 2.51, p<0.001). Similar findings were observed for the CVD subtypes of acute myocardial infarction, heart failure, cerebral infarction and intracerebral haemorrhage. This association remained unchanged even after adjustment for age, sex and white cell count and withstood Bonferroni adjustment for multiple testing. When the causes of death were divided into primary CVD and non-CVD deaths, the association between initial hs-CRP levels and mortality remained significant, but the influence of hs-CRP levels was greater in non-CVD deaths than CVD deaths. The percentage of non-CVD deaths increased with hs-CRP levels; among the patients with hs-CRP levels ≥33.3 mg/L, non-CVD deaths accounted for 37.5% of total deaths.ConclusionOur findings suggest that increased hs-CRP is a significant risk factor for inhospital mortality among patients with CVD in an ED. Particular attention should be given to our finding that non-CVD death is a major cause of death among patients with CVD with higher hs-CRP levels.
Loneliness and depression among rural empty-nest elderly adults in Liuyang, China: a cross-sectional study
Authors: Wang Guojun , Hu Mi , Xiao Shui-yuan , Zhou Liang 
Published: October 2017

ObjectiveTo compare loneliness, depressive symptoms and major depressive episodes between empty-nest and not-empty-nest older adults in rural areas of Liuyang city, Hunan, China.MethodsA cross-sectional multi-stage random cluster survey was conducted from November 2011 to April 2012 in Liuyang, China. A total of 839 rural older residents aged 60 or above completed the survey (response rate 97.6%). In line with the definition of empty nest, 25 participants who had no children were excluded from the study, while the remaining 814 elderly adults with at least one child were included for analysis. Loneliness and depressive symptoms in rural elderly parents were assessed using the short-form UCLA Loneliness Scale (ULS-6) and the Geriatric Depression Scale (GDS). Major depressive episodes were diagnosed using the Structured Clinical Interview for DSM-IV (SCID-I).ResultsSignificant differences were found between empty-nest and not-empty-nest older adults regarding loneliness (16.19±3.90 vs. 12.87±3.02, Cohen’s d=0.97), depressive symptoms (8.50±6.26 vs. 6.92±5.19, Cohen’s d=0.28) and the prevalence of major depressive episodes (10.1% vs. 4.6%) (all p<0.05). After controlling for demographic characteristics and physical disease, the differences in loneliness, depressive symptoms and major depressive episodes remained significant. Path analysis showed that loneliness mediated the relationship between empty-nest syndrome and depressive symptoms and major depressive episodes.ConclusionLoneliness and depression are more severe among empty-nest than not-empty-nest rural elderly adults. Loneliness was a mediating variable between empty-nest syndrome and depression.
The prognostic significance of smoking cessation after acute coronary syndromes: an observational, multicentre study from the Melbourne interventional group registry
Authors: Yudi Matias B , Farouque Omar , Andrianopoulos Nick , Ajani Andrew E , Kalten Katie , Brennan Angela L , Lefkovits Jeffrey , Hiew Chin , Oqueli Ernesto , Reid Christopher M , Duffy Stephen J , Clark David J 
Published: October 2017

ObjectiveWe aim to ascertain the prognostic significance of persistent smoking and smoking cessation after an acute coronary syndrome (ACS) in the era of percutaneous coronary intervention (PCI) and optimal secondary prevention pharmacotherapy.MethodsConsecutive patients from the Melbourne Interventional Group registry (2005–2013) who were alive at 30 days post-ACS presentation were included in our observational cohort study. Patients were divided into four categories based on their smoking status: non-smoker; ex-smoker (quit >1 month before ACS); recent quitter (smoker at presentation but quit by 30 days) and persistent smoker (smoker at presentation and at 30 days). The primary endpoint was survival ascertained through the Australian National Death Index linkage. A Cox-proportional hazards model was used to estimate the adjusted HR and 95% CI for survival.ResultsOf the 9375 patients included, 2728 (29.1%) never smoked, 3712 (39.6%) were ex-smokers, 1612 (17.2%) were recent quitters and 1323 (14.1%) were persistent smokers. Cox-proportional hazard modelling revealed, compared with those who had never smoked, that persistent smoking (HR 1.78, 95% CI 1.36 to 2.32, p<0.001) was an independent predictor of increased hazard (mean follow-up 3.9±2.2 years) while being a recent quitter (HR 1.27, 95% CI 0.96 to 1.68, p=0.10) or an ex-smoker (HR 1.03, 95% CI 0.87 to 1.22, p=0.72) were not.ConclusionsIn a contemporary cohort of patients with ACS, those who continued to smoke had an 80% risk of lower survival while those who quit had comparable survival to lifelong non-smokers. This underscores the importance of smoking cessation in secondary prevention despite the improvement in management of ACS with PCI and pharmacotherapy.