bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Analyses of the RsmY and RsmZ Small Noncoding Regulatory RNAs in Pseudomonas aeruginosa
Authors: Janssen Kayley H. , Diaz Manisha R. , Golden Matthew , Graham Justin W. , Sanders Wes , Wolfgang Matthew C. , Yahr Timothy L. 
Published: February 2018

ABSTRACT

Pseudomonas aeruginosa
is a Gram-negative opportunistic pathogen with distinct acute and chronic virulence phenotypes. Whereas acute virulence is typically associated with expression of a type III secretion system (T3SS), chronic virulence is characterized by biofilm formation. Many of the phenotypes associated with acute and chronic virulence are inversely regulated by RsmA and RsmF. RsmA and RsmF are both members of the CsrA family of RNA-binding proteins and regulate protein synthesis at the posttranscriptional level. RsmA activity is controlled by two small noncoding regulatory RNAs (RsmY and RsmZ). Bioinformatic analyses suggest that RsmY and RsmZ each have 3 or 4 putative RsmA binding sites. Each predicted binding site contains a GGA sequence presented in the loop portion of a stem-loop structure. RsmY and RsmZ regulate RsmA, and possibly RsmF, by sequestering these proteins from target mRNAs. In this study, we used selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) chemistry to determine the secondary structures of RsmY and RsmZ and functional assays to characterize the contribution of each GGA site to RsmY/RsmZ activity. Our data indicate that RsmA has two preferential binding sites on RsmY and RsmZ, while RsmF has one preferential binding site on RsmY and two sites on RsmZ. Despite RsmF and RsmA sharing a common consensus site, RsmF binding properties are more restrictive than those of RsmA.

IMPORTANCE
CsrA homologs are present in many bacteria. The opportunistic pathogen
Pseudomonas aeruginosa
uses RsmA and RsmF to inversely regulate factors associated with acute and chronic virulence phenotypes. RsmA has an affinity for RsmY and RsmZ higher than that of RsmF. The goal of this study was to understand the differential binding properties of RsmA and RsmF by using the RsmY and RsmZ regulatory small RNAs (sRNAs) as a model. Mutagenesis of the predicted RsmA/RsmF binding sites on RsmY and RsmZ revealed similarities in the sites required to control RsmA and RsmF activity
in vivo
. Whereas binding by RsmA was relatively tolerant of binding site mutations, RsmF was sensitive to disruption to all but two of the sites, further demonstrating that the requirements for RsmF binding activity
in vivo
and
in vitro
are more stringent than those for RsmA.
qSOFA, SIRS and NEWS for predicting inhospital mortality and ICU admission in emergency admissions treated as sepsis
Authors: Goulden Robert , Hoyle Marie-Claire , Monis Jessie , Railton Darran , Riley Victoria , Martin Paul , Martina Reynaldo , Nsutebu Emmanuel 
Published: February 2018

BackgroundThe third international consensus definition for sepsis recommended use of a new prognostic tool, the quick Sequential Organ Failure Assessment (qSOFA), based on its ability to predict inhospital mortality and prolonged intensive care unit (ICU) stay in patients with suspected infection. While several studies have compared the prognostic accuracy of qSOFA to the Systemic Inflammatory Response Syndrome (SIRS) criteria in suspected sepsis, few have compared qSOFA and SIRS to the widely used National Early Warning Score (NEWS).MethodsThis was a retrospective cohort study carried out in a UK tertiary centre. The study population comprised emergency admissions in whom sepsis was suspected and treated. The accuracy for predicting inhospital mortality and ICU admission was calculated and compared for qSOFA, SIRS and NEWS.ResultsAmong 1818 patients, 53 were admitted to ICU (3%) and 265 died in hospital (15%). For predicting inhospital mortality, the area under the receiver operating characteristics curve for NEWS (0.65, 95% CI 0.61 to 0.68) was similar to qSOFA (0.62, 95% CI 0.59 to 0.66) (test for difference, P=0.18) and superior to SIRS (P<0.001), which was not predictive. The sensitivity of NEWS≥5 (74%, 95% CI 68% to 79%) was similar to SIRS≥2 (80%, 95% CI 74% to 84%) and higher than qSOFA≥2 (37%, 95% CI 31% to 43%). The specificity of NEWS≥5 (43%, 95% CI 41% to 46%) was higher than SIRS≥2 (21%, 95% CI 19% to 23%) and lower than qSOFA≥2 (79%, 95% CI 77% to 81%). The negative predictive value was 88% (86%–90%) for qSOFA, 86% (82%–89%) for SIRS and 91% (88%–93%) for NEWS. Results were similar for the secondary outcome of ICU admission.ConclusionNEWS has equivalent or superior value for most test characteristics relative to SIRS and qSOFA, calling into question the rationale of adopting qSOFA in institutions where NEWS is already in use.
Polarised epithelial monolayers of the gastric mucosa reveal insights into mucosal homeostasis and defence against infection
Authors: Boccellato Francesco , Woelffling Sarah , Imai-Matsushima Aki , Sanchez Gabriela , Goosmann Christian , Schmid Monika , Berger Hilmar , Morey Pau , Denecke Christian , Ordemann Juergen , Meyer Thomas F 
Published: February 2018

ObjectiveHelicobacter pylori causes life-long colonisation of the gastric mucosa, leading to chronic inflammation with increased risk of gastric cancer. Research on the pathogenesis of this infection would strongly benefit from an authentic human in vitro model.DesignAntrum-derived gastric glands from surgery specimens served to establish polarised epithelial monolayers via a transient air–liquid interface culture stage to study cross-talk with H. pylori and the adjacent stroma.ResultsThe resulting ‘mucosoid cultures’, so named because they recapitulate key characteristics of the gastric mucosa, represent normal stem cell-driven cultures that can be passaged for months. These highly polarised columnar epithelial layers encompass the various gastric antral cell types and secrete mucus at the apical surface. By default, they differentiate towards a foveolar, MUC5AC-producing phenotype, whereas Wnt signalling stimulates proliferation of MUC6-producing cells and preserves stemness—reminiscent of the gland base. Stromal cells from the lamina propria secrete Wnt inhibitors, antagonising stem-cell niche signalling and inducing differentiation. On infection with H. pylori, a strong inflammatory response is induced preferentially in the undifferentiated basal cell phenotype. Infection of cultures for several weeks produces foci of viable bacteria and a persistent inflammatory condition, while the secreted mucus establishes a barrier that only few bacteria manage to overcome.ConclusionGastric mucosoid cultures faithfully reproduce the features of normal human gastric epithelium, enabling new approaches for investigating the interaction of H. pylori with the epithelial surface and the cross-talk with the basolateral stromal compartment. Our observations provide striking insights in the regulatory circuits of inflammation and defence.
Content analysis of requests for religious exemptions from a mandatory influenza vaccination program for healthcare personnel
Authors: Antommaria Armand H , Prows Cynthia A 
Published: February 2018

ObjectiveHaving failed to achieve adequate influenza vaccination rates among employees through voluntary programmes, healthcare organisations have adopted mandatory ones. Some programmes permit religious exemptions, but little is known about who requests religious objections or why.MethodsContent analysis of applications for religious exemptions from influenza vaccination at a free-standing children’s hospital in Cincinnati, Ohio, USA during the 2014–2015 influenza season.ResultsTwelve of 15 260 (0.08%) employees submitted applications requesting religious exemptions. Requestors included both clinical and non-clinical employees. All requestors voluntarily identified their religious affiliation, and most were Christian (n=9). Content analysis identified six categories of reasons used to justify an exemption: risks/benefits, ethical/political, lack of direct patient contact, providence, purity and sanctity of life. Individuals articulated reasons in 1–5 (mean 2.6) categories. The most frequently cited category (n=9) was purity; the vaccine and/or its mode of administration were impure, or receiving the vaccine would make the individual impure. Two individuals asserted that the vaccine contained cells derived from aborted human fetuses. Individuals (n=6) also volunteered information supporting the sincerity of their beliefs including distress over previous vaccination and examples of behaviour consistent with their specific objection or their general religious commitment. All requests were approved.ConclusionsLess than 0.1% of employees requested religious exemptions. Partnering with religious leaders and carefully correcting erroneous information may help address requestors’ concerns.
Learned rather than online relative weighting of visual-proprioceptive sensory cues
Authors: Mikula Laura , Gaveau Valérie , Pisella Laure , Khan Aarlenne Z. , Blohm Gunnar 
Published: February 2018

When reaching to an object, information about the target location as well as the initial hand position is required to program the motor plan for the arm. The initial hand position can be determined by proprioceptive information as well as visual information, if available. Bayes-optimal integration posits that we utilize all information available, with greater weighting on the sense that is more reliable, thus generally weighting visual information more than the usually less reliable proprioceptive information. The criterion by which information is weighted has not been explicitly investigated; it has been assumed that the weights are based on task- and effector-dependent sensory reliability requiring an explicit neuronal representation of variability. However, the weights could also be determined implicitly through learned modality-specific integration weights and not on effector-dependent reliability. While the former hypothesis predicts different proprioceptive weights for left and right hands, e.g., due to different reliabilities of dominant vs. nondominant hand proprioception, we would expect the same integration weights if the latter hypothesis was true. We found that the proprioceptive weights for the left and right hands were extremely consistent regardless of differences in sensory variability for the two hands as measured in two separate complementary tasks. Thus we propose that proprioceptive weights during reaching are learned across both hands, with high interindividual range but independent of each hand’s specific proprioceptive variability. NEW & NOTEWORTHY How visual and proprioceptive information about the hand are integrated to plan a reaching movement is still debated. The goal of this study was to clarify how the weights assigned to vision and proprioception during multisensory integration are determined. We found evidence that the integration weights are modality specific rather than based on the sensory reliabilities of the effectors.
Changes in Dietary Patterns and the Nutritional Status in Men in the Metallurgical Industry in Poland Over A 21-Year Period
Authors: Charkiewicz Angelika Edyta , Jamiołkowski Jacek , Pędziński Bartosz , Krzyżak Michalina , Maślach Dominik , Szpak Andrzej , Omeljaniuk Wioleta Justyna 
Published: February 2018

<b><i>Background/Aims:</i></b> The study was carried out to evaluate the changes in the eating habits and lipid parameters in a 21-year follow-up on a group of 435 men living in Poland. <b><i>Methods:</i></b> The studied population was composed of the same subjects: a group of men who were first studied in the years 1987–1989 and in 2008–2010. The following data was gathered: body mass, body mass index (BMI), total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglyceride concentration in blood serum. <b><i>Results:</i></b> The changes in the eating habits among the studied men registered throughout the 21-year period were positive since they showed a reduction in the caloric content of their diet (<i>p</i> &#x3c; 0.001), lower total fat content (<i>p</i> &#x3c; 0.001), total amount of carbohydrates (<i>p</i> &#x3c; 0.001), sucrose (<i>p</i> &#x3c; 0.001), iron (<i>p</i> &#x3c; 0.001), and featured more vitamins: A (<i>p</i> &#x3c; 0.002), B1 (<i>p</i> &#x3c; 0.001), and C (<i>p</i> &#x3c; 0.001). An adverse trend was observed in terms of constant calcium shortages in their food portions (ns). A 21-year follow-up of the studied group showed significant differences in terms of weight (<i>p</i> &#x3c; 0.001), BMI (<i>p</i> &#x3c; 0.001), and all cholesterol fractions (<i>p</i> &#x3c; 0.001) in their blood serum, except cholesterol alone (ns). <b><i>Conclusion:</i></b> It is important to continue observing the dietary trends in the studied group, with the focus on the occurrence of potential changes in their bodies.
Simulating Extreme Etesians over the Aegean and Implications for Wind Energy Production in Southeastern Europe
Authors: Dafka Stella , Toreti Andrea , Luterbacher Juerg , Zanis Prodromos , Tyrlis Evangelos , Xoplaki Elena 
Published: February 2018

AbstractEpisodes of extremely strong northerly winds (known as etesians) during boreal summer can cause hazardous conditions over the Aegean Archipelago (Greece) and represent a threat for the safe design, construction, and operation of wind energy turbines. Here, these extremes are characterized by employing a peak-over-threshold approach in the extended summer season (May–September) from 1989 to 2008. Twelve meteorological stations in the Aegean are used, and results are compared with 6-hourly wind speed data from five ERA-Interim–driven regional climate model (RCM) simulations from the European domain of the Coordinated Regional Climate Downscaling Experiment (EURO-CORDEX). The main findings show that, in the range of wind speeds for the maximum power output of the turbine, the most etesian-exposed stations could operate 90% at a hub height of 80 m. The central and northern Aegean are identified as areas prone to wind hazards, where medium- to high-wind (class II or I according to the International Electrotechnical Committee standards) wind turbines could be more suitable. In the central Aegean, turbines with a cutout wind speed > 25 m s−1are recommended. Overall, RCMs can be considered a valuable tool for investigating wind resources at regional scale. Therefore, this study encourages a broader use of climate models for the assessment of future wind energy potential over the Aegean.
Sensitivity of Surface Temperature to Oceanic Forcing via q-Flux Green’s Function Experiments. Part I: Linear Response Function
Authors: Liu Fukai , Lu Jian , Garuba Oluwayemi , Leung L. Ruby , Luo Yiyong , Wan Xiuquan 
Published: February 2018

Abstract
This paper explores the use of the linear response function (LRF) to relate the mean sea surface temperature (SST) response to prescribed ocean heat convergence (q flux) forcings. Two methods for constructing the LRF based on the fluctuation–dissipation theorem (FDT) and Green’s function (GRF) are examined. A 900-yr preindustrial simulation by the Community Earth System Model coupled with a slab ocean model (CESM–SOM) is used to estimate the LRF using FDT. For GRF, 106 pairs of CESM–SOM simulations with warm and cold q-flux patches are performed. FDT is found to have some skill in estimating the SST response to a q-flux forcing when the local SST response is strong, but it fails in inverse estimation of the q-flux forcing for a given SST pattern. In contrast, GRF is shown to be reasonably accurate in estimating both SST response and q-flux forcing. Possible degradation in FDT may be attributed to insufficient data sampling, significant departure of the SST distribution from Gaussianity, and the nonnormality of the constructed operator. The GRF-based LRF is then used to (i) generate a global surface temperature sensitivity map that shows the q-flux forcing in higher latitudes to be 3–4 times more effective than low latitudes in producing global surface warming, and (ii) identify the most excitable SST mode (neutral vector) that shows marked resemblance to the interdecadal Pacific oscillation (IPO). The latter discovery suggests that the IPO-like fluctuation exists in the absence of the coupling to the ocean dynamics. Coupling to the ocean dynamics in CESM, on the other hand, only enhances the spectral power of the IPO at interannual time scales.
Climatological Aspects of Convective Parameters over Europe: A Comparison of ERA-Interim and Sounding Data
Authors: Taszarek Mateusz , Brooks Harold E. , Czernecki Bartosz , Szuster Piotr , Fortuniak Krzysztof 
Published: February 2018

Abstract
We compare over 1 million sounding measurements with ERA-Interim reanalysis for the 38-yr period from 1979 to 2016. The large dataset allows us to provide an improved insight into the spatial and temporal distributions of the prerequisites of deep moist convection across Europe. In addition, ERA-Interim is also evaluated. ERA-Interim estimates parameters describing boundary layer moisture and midtropospheric lapse rates well, with correlation coefficients of 0.94. Mixed-layer CAPE is, on average, underestimated by the reanalysis while the most unstable CAPE is overestimated. Vertical shear parameters in the reanalysis are better correlated with observations than CAPE, but are underestimated by approximately 1–2 m s−1. The underestimation decreases as the depth of the shear layer increases. Compared to radiosonde observations, instability in ERA-Interim is overestimated in southern Europe and underestimated over eastern Europe. High values of instability are observed from May to September, out of phase with the climatological pattern of wind shear, which peaks in winter. From September to April, favorable conditions for thunderstorms occur mainly over southern and western Europe with the peak location and higher frequency shifting to central and eastern Europe from May to August. For southern Europe, the annual cycle peaks in September with high values of inhibition suppressing thunderstorm activity in July and August. The area with the highest annual number of days with environmental conditions favorable for thunderstorms extends from Italy and Austria eastward through the Carpathians and Balkans.
Practice Patterns of Referring Physicians in Management of the Dysphonic Patient
Authors: Holcomb Andrew J. , Hamill Chelsea S. , Irwin Thomas , Sykes Kevin , Garnett James D. , Kraft Shannon 
Published: February 2018

ObjectiveDysphonia is commonly encountered by primary care physicians and general otolaryngologists. We examine practice patterns of referring physicians to a tertiary voice clinic, including adherence to evidence‐based guidelines.Study DesignRetrospective case series with chart review.SettingAcademic tertiary care hospital.Subjects and MethodsIn total, 821 charts of patients with voice complaints seen at a tertiary voice clinic between January 2011 and June 2016 were reviewed. Included charts (n = 755) were reviewed for type of referring provider, prior diagnoses, and treatments employed by referring physicians. Additional information regarding findings at the time of laryngoscopy/stroboscopy and diagnoses provided by a laryngologist were also obtained. Statistical analysis was performed to determine significant relationships between variables of interest.ResultsA total of 244 patients (32.2%) received a diagnosis prior to evaluation in the voice clinic, most commonly laryngopharyngeal reflux disease (n = 134). Prior medical treatment was attempted in 221 (29.3%) patients, typically antireflux medications (n = 141). Of the patients treated with proton pump inhibitors by referring physicians, 65.1% lacked symptoms of gastroesophageal reflux disease. Patients with prior treatment had a median duration of symptoms 6 weeks longer than those without prior treatment (P =. 04). Among previously diagnosed patients, 199 (81.6%) of diagnoses changed after evaluation in the voice clinic.ConclusionReferring physicians frequently treat dysphonic patients empirically, often with antireflux medications. Subspecialist evaluation results in changes in diagnosis in many patients. Empiric treatment can delay referral and appropriate treatment.
Utility of DWI with quantitative ADC values in ovarian tumors: a meta-analysis of diagnostic test performance
Authors: Pi Shan , Cao Rong , Qiang Jin Wei , Guo Yan Hui 
Published: February 2018

Background Diffusion-weighted imaging (DWI) and quantitative apparent diffusion coefficient (ADC) values are widely used in the differential diagnosis of ovarian tumors. Purpose To assess the diagnostic performance of quantitative ADC values in ovarian tumors. Material and Methods PubMed, Embase, the Cochrane Library, and local databases were searched for studies assessing ovarian tumors using quantitative ADC values. We quantitatively analyzed the diagnostic performances for two clinical problems: benign vs. malignant tumors and borderline vs. malignant tumors. We evaluated diagnostic performances by the pooled sensitivity and specificity values and by summary receiver operating characteristic (SROC) curves. Subgroup analyses were used to analyze study heterogeneity. Results From the 742 studies identified in the search results, 16 studies met our inclusion criteria. A total of ten studies evaluated malignant vs. benign ovarian tumors and six studies assessed malignant vs. borderline ovarian tumors. Regarding the diagnostic accuracy of quantitative ADC values for distinguishing between malignant and benign ovarian tumors, the pooled sensitivity and specificity values were 0.91 and 0.91, respectively. The area under the SROC curve (AUC) was 0.96. For differentiating borderline from malignant tumors, the pooled sensitivity and specificity values were 0.89 and 0.79, and the AUC was 0.91. The methodological quality of the included studies was moderate. Conclusion Quantitative ADC values could serve as useful preoperative markers for predicting the nature of ovarian tumors. Nevertheless, prospective trials focused on standardized imaging parameters are needed to evaluate the clinical value of quantitative ADC values in ovarian tumors.
Joint Influence of SNPs and DNA Methylation on Lipids in African Americans From Hypertensive Sibships
Authors: Wright Michelle L. , Ware Erin B. , Smith Jennifer A. , Kardia Sharon L. R. , Taylor Jacquelyn Y. 
Published: February 2018

Introduction: Plasma concentrations of lipids (i.e., total cholesterol, high-density cholesterol, low-density cholesterol, and triglycerides) are amenable to therapeutic intervention and remain important factors for assessing risk of cardiovascular diseases. Some of the observed variability in serum lipid concentrations has been associated with genetic and epigenetic variants among cohorts with European ancestry (EA). Serum lipid levels have also been associated with genetic variants in multiethnic populations. Methods: The purpose of this study was to determine whether single-nucleotide polymorphisms (SNPs) and DNA methylation (DNAm) differences contribute to lipid variation among African Americans ([AAs], N = 739) in the Genetic Epidemiology Network of Arteriopathy (GENOA) study. Results: Previous meta-analyses identified 161 SNPs that are associated with lipid traits in populations of EA. We evaluated these SNPs and 66 DNAm sites within the genes containing the SNPs in the GENOA cohort using linear mixed-effects modeling. We did not identify any significant associations of SNPs or DNAm with serum lipid levels. These results suggest that the SNPs identified as being significant for lipid levels through the EA genome-wide association studies may not be significant across AA populations. Conclusions: Reductions in morbidity and mortality due to variation in lipids among AAs may be achieved through a better understanding of the genetic and epigenetic factors associated with serum lipid levels for early and appropriate screening. Further large-scale studies specifically within AA and other non-EA populations are warranted.