bluuebunny/crossref_metadata_2025_split huggingface dataset:
Registered nurses’ perceptions of new nursing graduates’ clinical competence: A systematic integrative review
Authors: Missen Karen , McKenna Lisa , Beauchamp Alison 
Published: November 2015

AbstractOver the past decade, many questions have been raised about graduates’ clinical competence and fitness for practice upon completion of their undergraduate education. Despite the significance of this issue, the perspectives of registered nurses have rarely been examined. This systematic review explores the perceptions of experienced registered nurses regarding the clinical competence of new nursing graduates. Original research studies published between 2004–2014 were identified using electronic databases, reference lists, and by searching “grey literature.” Papers were critically reviewed and relevant data extracted and synthesized using an approach based on Preferred Reporting Items for Systematic Reviews and Meta‐Analysis. From 153 studies initially identified, 15 original research papers were included. Four main research themes were identified: clinical/technical skills, critical thinking, interaction/communication, and overall readiness for practice. Areas of concern in relation to the clinical competence of new nursing graduates specifically related to two themes: critical thinking and clinical/technical skills. Further research is required on strategies identified within the literature with the ultimate aim of ensuring new nursing graduates are safe and competent practitioners.
A game of hide and seek between avirulence genes AvrLm4‐7 and AvrLm3 in Leptosphaeria maculans
Authors: Plissonneau Clémence , Daverdin Guillaume , Ollivier Bénédicte , Blaise Françoise , Degrave Alexandre , Fudal Isabelle , Rouxel Thierry , Balesdent Marie‐Hélène 
Published: November 2015

Summary

Extending the durability of plant resistance genes towards fungal pathogens is a major challenge. We identified and investigated the relationship between two avirulence genes of Leptosphaeria maculans, AvrLm3 and AvrLm4‐7. When an isolate possesses both genes, the Rlm3‐mediated resistance of oilseed rape (Brassica napus) is not expressed due to the presence of AvrLm4‐7 but virulent isolates toward Rlm7 recover the AvrLm3 phenotype.

Combining genetic and genomic approaches (genetic mapping, RNA‐seq, BAC (bacterial artificial chromosome) clone sequencing and de novo assembly) we cloned AvrLm3, a telomeric avirulence gene of L. maculans. AvrLm3 is located in a gap of the L. maculans reference genome assembly, is surrounded by repeated elements, encodes for a small secreted cysteine‐rich protein and is highly expressed at early infection stages.

Complementation and silencing assays validated the masking effect of AvrLm4‐7 on AvrLm3 recognition by Rlm3 and we showed that the presence of AvrLm4‐7 does not impede AvrLm3 expression in planta. Y2H assays suggest the absence of physical interaction between the two avirulence proteins.

This unusual interaction is the basis for field experiments aiming to evaluate strategies that increase Rlm7 durability.
Testing the large genome constraint hypothesis: plant traits, habitat and climate seasonality inLiliaceae
Authors: Carta Angelino , Peruzzi Lorenzo 
Published: November 2015

SummaryThe factors driving genome size evolution in Liliaceae were examined. In particular, we investigated whether species with larger genomes are confined to less stressful environments with a longer vegetative season.We tested our hypotheses by correlating the genome size with other plant traits and environmental variables. To determine the adaptive nature of the genome size, we also compared the performances of Brownian motion (BM) processes with those inferred by Ornstein–Uhlenbeck (OU) models of trait evolution.A positive correlation of genome size with plant size, mean temperature and habitat moisture and a negative correlation with altitude and precipitation seasonality were found. Models of trait evolution revealed a deviation from a drift process orBM. Instead, changes in genome size were significantly associated with precipitation regimes according to anOUprocess. Specifically, the evolutionary optima towards which the genome size evolves were higher for humid climates and lower for drier ones.Taken together, our results indicate that the genome size increase in Liliaceae is constrained by climate seasonality.
Improving the safety of oral immunotherapy for food allergy
Authors: Vazquez‐Ortiz Marta , Turner Paul J. 
Published: November 2015

AbstractFood allergy is a major public health problem in children, impacting upon the affected individual, their families and others charged with their care, for example educational establishments, and the food industry. In contrast to most other paediatric diseases, there is no established cure: current management is based upon dietary avoidance and the provision of rescue medication in the event of accidental reactions, which are common. This strategy has significant limitations and impacts adversely on health‐related quality of life. In the last decade, research into disease‐modifying treatments for food allergy has emerged, predominantly for peanut, egg and cow's milk. Most studies have used the oral route (oral immunotherapy, OIT), in which increasing amounts of allergen are given over weeks–months. OIT has proven effective to induce immune modulation and ‘desensitization’ – that is, an increase in the amount of food allergen that can be consumed, so long as regular (typically daily) doses are continued. However, its ability to induce permanent tolerance once ongoing exposure has stopped seems limited. Additionally, the short‐ and long‐term safety of OIT is often poorly reported, raising concerns about its implementation in routine practice. Most patients experience allergic reactions and, although generally mild, severe reactions have occurred. Long‐term adherence is unclear, which rises concerns given the low rates of long‐term tolerance induction. Current research focuses on improving current limitations, especially safety. Strategies include alternative routes (sublingual, epicutaneous), modified hypoallergenic products and adjuvants (anti‐IgE, pre‐/probiotics). Biomarkers of safe/successful OIT are also under investigation.
Towards plant pangenomics
Authors: Golicz Agnieszka A. , Batley Jacqueline , Edwards David 
Published: November 2015

SummaryAs an increasing number of genome sequences become available for a wide range of species, there is a growing understanding that the genome of a single individual is insufficient to represent the gene diversity within a whole species. Many studies examine the sequence diversity within genes, and this allelic variation is an important source of phenotypic variation which can be selected for by man or nature. However, the significant gene presence/absence variation that has been observed within species and the impact of this variation on traits is only now being studied in detail. The sum of the genes for a species is termed the pangenome, and the determination and characterization of the pangenome is a requirement to understand variation within a species. In this review, we explore the current progress in pangenomics as well as methods and approaches for the characterization of pangenomes for a wide range of plant species.
Idiopathic pulmonary fibrosis: Diagnosis, epidemiology and natural history
Authors: Sgalla Giacomo , Biffi Alice , Richeldi Luca 
Published: November 2015

AbstractIdiopathic pulmonary fibrosis (IPF) is a chronic, progressive fibrosing lung disorder of unknown aetiology whose diagnosis involves the careful exclusion of secondary causes for pulmonary fibrosis and the presence of a pattern of usual interstitial pneumonia (UIP) at either high‐resolution computed tomography (HRCT) scan or surgical lung biopsy. Despite great efforts made in establishing precise, universally acknowledged diagnostic criteria for IPF, its ascertainment remains a challenge, especially in those individuals presenting with atypical HRCT patterns. With new drugs emerging, establishing a precise diagnosis is becoming a clinically relevant issue. Although regarded as a rare disease, IPF epidemiology is controversial due to studies relying on old data and adopting mixed, incomparable methodologies for cases definition. Overall, the prevalence and incidence appear to be increasing over the last decades, suggesting that in earlier studies they might have been underestimated because of diagnostic uncertainty. IPF is invariably progressive, although its clinical course might greatly vary on an individual basis, with episodes of severe acute respiratory deterioration (acute exacerbations) being unpredictable. A deeper understanding of the mechanisms responsible for an accelerated course of the disease and the identification of biomarkers of progression would lead to a better stratification of the disease, essential for delivering individualized therapeutic strategies.
Fitting Cox Models with Doubly Censored Data Using Spline‐Based Sieve Marginal Likelihood
Authors: Li Zhiguo , Owzar Kouros 
Published: November 2015

AbstractIn some applications, the failure time of interest is the time from an originating event to a failure event while both event times are interval censored. We propose fitting Cox proportional hazards models to this type of data using a spline‐based sieve maximum marginal likelihood, where the time to the originating event is integrated out in the empirical likelihood function of the failure time of interest. This greatly reduces the complexity of the objective function compared with the fully semiparametric likelihood. The dependence of the time of interest on time to the originating event is induced by including the latter as a covariate in the proportional hazards model for the failure time of interest. The use of splines results in a higher rate of convergence of the estimator of the baseline hazard function compared with the usual non‐parametric estimator. The computation of the estimator is facilitated by a multiple imputation approach. Asymptotic theory is established and a simulation study is conducted to assess its finite sample performance. It is also applied to analyzing a real data set on AIDS incubation time.
Estimating Abundance from Presence–Absence Maps via a Paired Negative‐Binomial Model
Authors: Hwang Wen‐Han , Huggins Richard 
Published: November 2015

AbstractThe estimation of abundance from presence–absence data is an intriguing problem in applied statistics. The classical Poisson model makes strong independence and homogeneity assumptions and in practice generally underestimates the true abundance. A controversialad hocmethod based on negative‐binomial counts (Am. Nat.) has been empirically successful but lacks theoretical justification. We first present an alternative estimator of abundance based on a paired negative binomial model that is consistent and asymptotically normally distributed. A quadruple negative binomial extension is also developed, which yields the previousad hocapproach and resolves the controversy in the literature. We examine the performance of the estimators in a simulation study and estimate the abundance of 44 tree species in a permanent forest plot.
A Necessary Condition for the Strong Oracle Property
Authors: Kim Yongdai , Jeon Jong‐June , Han Sangmi 
Published: November 2015

AbstractA problem of using a non‐convex penalty for sparse regression is that there are multiple local minima of the penalized sum of squared residuals, and it is not known which one is a good estimator. The aim of this paper is to give a guide to design a non‐convex penalty that has the strong oracle property. Here, the strong oracle property means that the oracle estimator is the unique local minimum of the objective function. We summarize three definitions of the oracle property – the global, weak and strong oracle properties. Then, we give sufficient conditions for the weak oracle property, which means that the oracle estimator becomes a local minimum. We give an example of non‐convex penalties that possess the weak oracle property but not the strong oracle property. Finally, we give a necessary condition for the strong oracle property.
Sample acceptance time criteria, electronic issue and alloimmunisation in thalassaemia
Authors: Trompeter S. , Baxter L. , McBrearty M. , Zatkya E. , Porter J. 
Published: November 2015

SUMMARYObjectivesTo determine the safety of a 1‐week acceptance criteria of sample receipt in laboratory to transfusion commencement in transfusion dependent thalassaemia with respect to alloimmunisation. To determine the safety of electronic issue of blood components in such a setting.MethodsRetrospective audit of alloimmunisation (1999–2012) and blood exposure in registered thalassaemia patients at a central London thalassaemia centre where the acceptance criteria for the group and save sample from arrival in the laboratory to the time of issue of blood for transfusion for someone who has been transfused in the last 28 days was 1 week, and there was electronic issue protocol for patients who have always had a negative antibody screen (other than temporary positivity in pregnant women receiving prophylactic anti‐D or anti Le‐a, Anti Le‐b and Anti P1 that are no longer detectable).ResultsThere were 133 patients with thalassemia variants regularly attending UCLH for review. A total of 105 patients had transfusion dependent thalassaemia (TDT) (7 E‐beta thalassaemia, 98 beta thalassaemia major). Ten of the 84 patients who received their transfusions at UCLH were alloimmunised. Seven of them had been alloimmunised prior to arrival at UCLH. Only two patients developed antibodies at UCLH during this period.ConclusionThe prevalence of alloantibody formation of 2% in UCLH transfused patients, with presumptive incidence of 0·01 alloantibodies per 100 units or 0·001 immunisations per person per year compares favourably with other reported series and suggests that 1 week interval with appropriate electronic issue is acceptable practice.
Hypokalemia and suspected renal tubular acidosis associated with topical carbonic anhydrase inhibitor therapy in a cat
Authors: Thiessen Charlotte E. , Tofflemire Kyle L. , Makielski Kelly M. , Ben‐Shlomo Gil , Whitley R. David , Allbaugh Rachel A. 
Published: November 2015

AbstractObjectiveTo describe the occurrence of hypokalemia, metabolic acidosis, and suspected renal tubular acidosis associated with the administration of topical ophthalmic carbonic anhydrase inhibitor (CAI) in a cat.Case SummaryA 2‐year‐old, 5.3 kg, male, castrated, domestic short‐haired cat developed hyporexia 6 weeks after starting topical ophthalmic dorzolamide 2% therapy for treatment of ocular hypertension. Two weeks later, the cat was evaluated for severe weakness, cervical ventroflexion, and anorexia. Plasma electrolyte and acid–base measurement revealed hypokalemia (K+ = 2.9 mmol/L; reference interval 3.8–5.4 mmol/L) and metabolic acidosis (plasma HCO3− = 9.8 mmol/L; reference interval 15–23 mmol/L) in the presence of a urine pH of 7.5 (reference interval 6.5–7.5). The pH abnormalities were consistent with a renal tubular acidosis. Clinical and biochemical abnormalities resolved with short‐term supportive care, potassium supplementation, and discontinuation of dorzolamide therapy.New or Unique Information ProvidedThis is the first report of hypokalemia and metabolic acidosis associated with topical CAI therapy in a cat.
Downregulation of prostaglandin E2 is involved in hindgut mucosal damage in lactating goats fed a high‐concentrate diet
Authors: Tao Shiyu , Han Zhengqiang , Tian Jing , Cong Rihua , Duanmu Yongqian , Dong Haibo , Ni Yingdong , Zhao Ruqian 
Published: November 2015

New Findings

What is the central question of this study?
A high‐concentrate (HC) diet results in damage to the hindgut mucosa. The aim of the study was to investigate the status of epithelial proliferation in the hindgut mucosa of goats with subacute ruminal acidosis and, simultaneously, to evaluate prostaglandin E2 synthesis and the downstream signalling pathways.

What is the main finding and its importance?
The downregulation of local prostaglandin E2 synthesis and its downstream signalling pathway are involved in the process of inhibiting epithelial proliferation in the hindgut epithelium of HC‐fed goats. Our results provide new insight into the relationship between abnormal fermentation in the hindgut and damage to the intestinal mucosal barrier.

Our previous data demonstrated that feeding a high‐concentrate (HC) diet to lactating goats for a long time causes severe damage to the hindgut mucosa and parallels the activation of cell apoptosis and local oxidative stress. In the present study, changes in production of prostaglandin E2 (PGE2) and its signalling pathway were evaluated in the process of epithelial barrier disruption in the hindgut. Twelve goats in mid‐lactation were randomly assigned to either a HC diet group or a low‐concentrate (LC) diet group for 10 weeks. Cell proliferation markers, cyclooxygenase‐2 activity, PGE2 content and the relative signalling pathway, including CREB and AKT, were analysed by enzyme‐linked immunosorbent assay and Western blot, respectively. The mRNA and protein expressions of MKI67 and CCND2 (two proliferation markers) were significantly decreased in the caecal mucosa of HC‐ compared with LC‐fed goats (P < 0.05). The protein content of interleukin‐10 and β‐defensin in the caecal mucosa was also downregulated in HC‐fed goats (P < 0.05). The HC‐fed goats showed a tendency to a decrease in cyclooxygenase‐2 enzyme activity (P = 0.081) and a significant decrease of local PGE2 content and EP4 (PGE2 receptor) protein expression in caecal mucosa (P < 0.05). Moreover, the protein abundance of p‐CREB (P = 0.069) and p‐AKT (P < 0.05) and the mRNA expression of epidermal growth factor receptor (P < 0.05) were downregulated in caecal mucosa of HC‐ compared with LC‐fed goats. These results indicate that a reduction in epithelial cell proliferation was partly responsible for the damage to the epithelial barrier, which might be associated with the downregulation of PGE2 synthesis and its downstream signalling pathway.
Calcium signalling in salivary gland physiology and dysfunction
Authors: Ambudkar Indu S. 
Published: November 2015

AbstractStudies over the past four decades have established that Ca2+ is a critical factor in control of salivary gland function and have led to identification of the critical components of this process. The major ion transport mechanisms and ion channels that are involved in fluid secretion have also been established. The key event in activation of fluid secretion is an increase in [Ca2+]i triggered by inositol 1,4,5‐trisphosphate (IP3)‐induced release of Ca2+ from ER via the IP3 receptor (IP3R). IP3Rs determine the site of initiation and the pattern of the [Ca2+]i signal in the cell. However, Ca2+ entry into the cell is required to sustain the elevation of [Ca2+]i and fluid secretion and is mediated by the store‐operated Ca2+ entry (SOCE) mechanism. Orai1, TRPC1, TRPC3 and STIM1 have been identified as critical components of SOCE in these cells. Cells finely tune the generation and amplification of [Ca2+]i signals for regulation of cell function. An important emerging area is the concept that unregulated [Ca2+]i signals in cells can directly cause cell damage, dysfunction and disease. Alternatively, aberrant [Ca2+]i signals can also amplify and increase the rates of cell damage. Such defects in Ca2+ signalling have been described in salivary glands in conjunction with radiation‐induced loss of salivary gland function as well as in the salivary defects associated with the autoimmune exocrinopathy Sjögren's syndrome. Such defects have been associated with altered function or expression of key Ca2+ signalling components, such as STIM proteins and TRP channels. These studies offer new avenues for examining the mechanisms underlying the disease and development of novel clinical targets and therapeutic strategies.
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The Feasibility of Using Questionnaires and Accelerometers to Measure Physical Activity and Sedentary Behavior Among Inpatient Adults With Mental Illness
Authors: Fraser Sarah J. , Chapman Justin J. , Brown Wendy J. , Whiteford Harvey A. , Burton Nicola W. 
Published: November 2015

Background:The aim of this study was to assess the feasibility of using questionnaires and accelerometers to measure physical activity and sedentary behavior among inpatient adults with mental illness.Methods:Participants completed a physical activity and sitting time questionnaire and wore an accelerometer for 7 consecutive days. Feasibility was assessed in terms of participant engagement, self-reported ease/difficulty of completing study components, extreme self-report data values and adherence to accelerometer wear time criteria. Ease/difficulty ratings were examined by level of distress.Results:177 inpatients were invited to the study, 101 completed the questionnaires and 36 provided valid accelerometry data. Participants found it more difficult to complete sitting time and physical activity questionnaires than to wear the accelerometer during waking hours (z = 3.787, P < .001; z = 2.824, P = .005 respectively). No significant differences were found in ease/difficulty ratings by level of distress for any of the study components. Extreme values for self-reported sitting time were identified in 27% of participants.Conclusion:Inpatient adults with mental illness can engage with self-report and objective methods of measuring physical activity and sedentary behavior. They were initially less willing to participate in objective measurement, which may however be more feasible than self-report measures.
GI-SVM: A sensitive method for predicting genomic islands based on unannotated sequence of a single genome
Authors: Lu Bingxin , Leong Hon Wai 
Published: November 2015

Genomic islands (GIs) are clusters of functionally related genes acquired by lateral genetic transfer (LGT), and they are present in many bacterial genomes. GIs are extremely important for bacterial research, because they not only promote genome evolution but also contain genes that enhance adaption and enable antibiotic resistance. Many methods have been proposed to predict GI. But most of them rely on either annotations or comparisons with other closely related genomes. Hence these methods cannot be easily applied to new genomes. As the number of newly sequenced bacterial genomes rapidly increases, there is a need for methods to detect GI based solely on sequences of a single genome. In this paper, we propose a novel method, GI-SVM, to predict GIs given only the unannotated genome sequence. GI-SVM is based on one-class support vector machine (SVM), utilizing composition bias in terms of k-mer content. From our evaluations on three real genomes, GI-SVM can achieve higher recall compared with current methods, without much loss of precision. Besides, GI-SVM allows flexible parameter tuning to get optimal results for each genome. In short, GI-SVM provides a more sensitive method for researchers interested in a first-pass detection of GI in newly sequenced genomes.