bluuebunny/crossref_metadata_2025 huggingface dataset:
The Prognostic Value of BRCA1 and PARP Expression in Epithelial Ovarian Carcinoma: Immunohistochemical Detection
Authors: Hjortkjær Mette , Waldstrøm Marianne , Jakobsen Anders , Kanstrup Hanne , Søgaard-Andersen Erik , Dahl Steffensen Karina
Published: July 2016

BRCA1/2 mutation status in epithelial ovarian cancer (EOC) presently relies on genetic testing which is resource consuming. Immunohistochemistry is cheap, fairly reproducible, and may identify gene product alterations due to both germline and somatic mutations and other defects along the BRCA gene pathway (BRCAness phenomenon), which is important when treatment with poly (adenosine-diphosphate-ribose) polymerase (PARP) inhibitors is considered. The aim of this study was to investigate immunohistochemical detection of BRCA1 and PARP expression in EOC and their possible prognostic relevance. Tumor tissue from 170 patients with EOC was stained immunohistochemically with BRCA1 and PARP antibodies. Semiquantitative analyses were performed to determine loss of, equivocal, and retained BRCA1 and high versus low PARP protein expression. These parameters were analyzed for relation with patient and clinicopathologic characteristics and overall survival. BRCA1 expression was reduced in 21.2 % of the tumors and 36.5% showed high PARP expression. No correlation between the 2 parameters or between PARP and clinicopathologic features was found. Overall survival was significantly increased in the BRCA1-reduced and equivocal groups [median survival 2.4 y (95% CI, 1.6–6.6) and 4.9 y (95 % CI, 2.3–6.7) vs. 1.5 y (95% CI, 1.3–1.9); P=0.0002]. Multivariate analysis confirmed these findings; hazard ratio=0.53 (95% CI, 0.34–0.81; P=0.0037; loss of BRCA1 expression). In conclusion, immunohistochemical BRCA1 expression in EOC holds considerable prognostic information, whereas PARP expression did not influence the outcome. The results call for validation in prospective trials.
Kynurenine and Tryptophan Levels in Patients With Schizophrenia and Elevated Antigliadin Immunoglobulin G Antibodies
Authors: Okusaga Olaoluwa , Fuchs Dietmar , Reeves Gloria , Giegling Ina , Hartmann Annette M. , Konte Bettina , Friedl Marion , Groer Maureen , Cook Thomas B. , Stearns-Yoder Kelly A. , Pandey Janardan P. , Kelly Deanna L. , Hoisington Andrew J. , Lowry Christopher A. , Eaton William W. , Brenner Lisa A. , Rujescu Dan , Postolache Teodor T.
Published: July 2016

Objective

Several studies have reported an association between nonceliac gluten sensitivity and schizophrenia. Immune and kynurenine (KYN) pathways have also been implicated in the pathophysiology of schizophrenia, and certain proinflammatory immune mediators may increase KYN and reduce tryptophan (TRP) levels.

Methods

We measured serum antigliadin immunoglobulin G (IgG), KYN, and TRP in 950 patients with schizophrenia. Patients with antibody level at the 90th percentile or higher of control participants (21.9% of all patients) were classified as having elevated antigliadin IgG. Independent t tests and linear regression models were used to compare TRP, KYN, and KYN-TRP ratio (indicator of TRP metabolism) between patients with and those without elevated antigliadin IgG. The correlation between antigliadin IgG and TRP, KYN, and the ratio was also evaluated in the patients.

Results

KYN and KYN-TRP ratio were higher in patients with elevated antigliadin IgG (geometric mean [standard deviation {SD}] = 2.65 [0.25] µmol/L versus 2.25 [0.23] µmol/L [p < .001] and 0.05 [0.26] versus 0.04 [0.25; p = .001] respectively), findings robust to adjustment for potential demographic and clinical confounders. Antigliadin IgG positively correlated with KYN and KYN-TRP ratio (r = 0.12, p < .001; r = 0.11, p = .002). TRP did not differ between the two groups and did not correlate with antigliadin IgG.

Conclusions

Our results connect nonceliac gluten sensitivity with the KYN pathway of TRP metabolism in psychotic illness and hint toward potential individualized treatment targets.
Measures of Heart Rate Variability in Individuals With Somatic Symptom Disorder
Authors: Huang Wei-Lieh , Liao Shih-Cheng , Yang Cheryl C.H. , Kuo Terry B.J. , Chen Tzu-Ting , Chen I-Ming , Gau Susan Shur-Fen
Published: July 2016

Objective

Little is known about autonomic nervous system activity in individuals with somatic symptom disorder (SSD) as defined by DSM-V criteria. The aims of this study were to investigate whether individuals with SSD differ from healthy controls in heart rate variability (HRV) measures of autonomic nervous system activity and whether sex has a moderating effect on this association.

Methods

We recruited 168 individuals with SSD (35.1% men) and 106 healthy controls (27.4% men). Demographics, HRV, and psychological factors were measured using the Patient Health Questionnaire-15, Health Anxiety Questionnaire, Beck Depression Inventory-II (BDI-II), and Beck Anxiety Inventory. Multiple regression analysis was used to examine the association of SSD with HRV, adjusting for demographic and psychological measures.

Results

Individuals with SSD had lower levels of total-power HRV and low-frequency HRV, but no differences in high-frequency (HF)-HRV were found. HRV differences between SSD and controls varied by sex and age (triple interaction TP-HRV β = −0.222, p < .001; low-frequency HRV β = −0.332, p < .001; and HF-HRV β = −0.167, p = .006). Whole-sample multiple regression analyses revealed significant sex differences in the magnitudes of the association between BDI-II with HF-HRV (β of sex*BDI-II: 0.761, p = .005) and analyses stratified by sex indicated that HF-HRV was significantly correlated with depression in men with SSD (r = −0.491, p < .001) but not in women with SSD (r = 0.057, p = .558).

Conclusions

These results suggest that patients with SSD demonstrate different patterns of HRV and the patterns of association between HRV indices and psychological factors vary between men and women.
A Simple and Powerful Risk-Adjustment Tool for 30-day Mortality Among Inpatients
Authors: Tremblay Douglas , Arnsten Julia H. , Southern William N.
Published: July 2016

Background:

Risk adjustment for mortality is increasingly important in an era when hospitals and health care systems are being compared with respect to health outcomes and quality. A powerful predictive model has been developed to risk-adjust for 30-day mortality among inpatients, but it is complex and not widely used.

Objective:

To develop and validate a simpler model, with predictive power similar to more complex models.

Research Design:

This was a retrospective split-validation study. In a derivation cohort, a predictive model for 30-day mortality was developed using logistic regression with the Charlson comorbidity score, Laboratory-Based Acute Physiology Score, and age as the predictor variables. In the validation cohort, the performance and calibration of the model to predict 30-day mortality was examined.

Subjects:

All admissions to the medical service of 2 urban university-based teaching hospitals located in Bronx, New York, between July 1, 2002, and April 30, 2008.

Measures:

All-cause mortality was taken from the social security death registry. Predictor variables were constructed from demographic characteristics, laboratory and billing data extracted from a clinical data repository.

Results:

The study sample included 147 991 admissions and overall 30-day mortality was 5.4%. The model had excellent discrimination, with a c-statistics of 0.8585 in the derivation cohort and 0.8484 in the validation cohort. The model accurately predicts 30-day mortality in all risk deciles.

Conclusions:

This simple and powerful predictive model can be used by hospitals and health care systems as a risk-adjustment tool for quality and research purposes.
Shared Medical Appointments: Impact on Clinical and Quality Outcomes in Veterans With Diabetes
Authors: Harris Marianne D. , Kirsh Susan , Higgins Patricia A.
Published: July 2016

Managing diabetes poses substantial challenges to the over 29.1 million Americans afflicted, and is financially overwhelming to the US health care system. One potential strategy is utilizing a group approach to care delivery or shared medical appointment (SMA). The purpose of this 3-year retrospective VA study was to investigate differences in clinical and quality outcome measures in veterans with type 2 diabetes who used SMAs and those who received only usual care (UC) one-on-one with their doctor. This observational, 2-group cohort study used abstracted medical records from a large Midwestern Veterans Administration hospital. Clinical outcome metrics included hemoglobin A1c (hbA1c), systolic blood pressure, low-density lipoprotein cholesterol, and emergency department (ED) visits. Quality outcomes included Veterans' Administration (VA) Department of Defense clinical practice guidelines for the management of diabetes. A total of 988 total VA cases were examined retrospectively over 3 years: 371 cases had used SMAs and 617 were in the UC cohort, and had never attended a diabetes SMA. The study period used abstracted VA medical records from 2008 to 2010. There were no statistically significant differences in HbA1c, systolic blood pressure, and ED visits between groups; however, hbA1c for individuals who attended SMAs was 8.55 (standard deviation [SD] = 1.72) and UC was 7.49 (SD = 1.28) (P < .001). All clinical outcomes were worse at baseline for the SMA cohort. UC had mean ED visits/3 years (mean = 18.62, SD = 13.53, P < .001) versus SMA participants (mean = 27.97, SD = 14.00, P <. 001), revealing a propensity for high health care utilization. SMA providers had statistically significant differences over UC cases on quality measures, including ordering annual ophthalmology and podiatry examinations (P < .001) and prescribing aspirin and angiotension-converting enzyme inhibitors (ACE-I). SMAs may provide a venue for assessing and delivering quality care for patients with type 2 diabetes. More research is needed to ascertain effective strategies for diabetes disease management in high-risk patients.
Testing the Quality Health Outcomes Model Applied to Infection Prevention in Hospitals
Authors: Gilmartin Heather M. , Sousa Karen H.
Published: July 2016

Objective:

To test the Quality Health Outcomes Model to investigate the relationship between health care-associated infection (HAI) prevention interventions, organizational context, and HAI outcomes using structural equation modeling.

Methods:

Variables for adherence to the central line bundle, organizational context, and central line-associated bloodstream infections (CLABSIs) were selected for this secondary data analysis from 614 US hospitals that participated in the Prevention of Nosocomial Infection and Cost-effectiveness-Refined study. One half of the dataset was used for exploration of the concepts, the second half for confirmation of the measurement models and testing of the structural model.

Results:

The final model resulted in a good fit to the data (χ2 (1215) = 1906.86, P < .00; comparative fit index = 0.94; root mean square of error of approximation = 0.04). A significant relationship was noted between adherence to the central line bundle interventions and organizational context (β = 0.23, P < .01), whereas the relationship between context and CLABSIs was not significant (β = −0.20, P = .78).

Conclusions:

This study supports a relationship between greater adherence to HAI interventions and higher levels of organizational context and highlights the complexity of measuring organizational context. Given the importance of preventing HAIs, ongoing research is needed to reveal the exact aspects of context that influence interventions and outcomes.
Efficacy of Repeated Intraperitoneal Administration of Levobupivacaine in Pain and Opioid Consumption After Elective Laparoscopic Cholecystectomy: A Prospective Randomized Placebo-controlled Trial
Authors: Melidi Eleni , Papadima Artemisia , Pandazi Aggeliki , Zografos George
Published: July 2016

Purpose:

To estimate the effect of intraperitoneal levobupivacaine on postoperative pain and analgesic requirements, during the first 24 hours after elective laparoscopic cholecystectomy (LC).

Materials and Methods:

In this prospective, randomized, placebo-controlled study, 73 consecutive patients scheduled for LC were randomized into 2 groups. In the local anesthetic group 36 patients received 10 mL of 0.5% levobupivacaine intraperitoneally at the end of the LC and at 4 hours postoperatively, whereas in the placebo group 37 patients received 10 mL of 0.9% normal saline. Visual analog scale pain scores, analgesic consumption, side-effects, and vital signs were recorded for 24 hours postoperatively.

Results:

In the local anesthetic group lower visual analog scale pain scores were observed postoperatively, both at rest and at movement (P-values compared with placebo, 0.012 and <0.001, respectively). Fentanyl consumption was greater in the placebo group (P-value <0.001).

Conclusions:

Intraperitoneal administration of 10 mL 0.5% levobupivacaine after LC is effective in reducing postoperative pain and decreasing opioid consumption.
Inspiring change: humanities and social science insights into the experience and management of breathlessness
Authors: Oxley Rebecca , Macnaughton Jane
Published: July 2016

Purpose of review

Breathlessness can be debilitating for those with chronic conditions, requiring continual management. Yet, the meaning of breathlessness for those who live with it is poorly understood in respect of its subjective, cultural, and experiential significance. This article discusses a number of current issues in understanding the experience of breathlessness.

Recent findings

Effective communication concerning the experience of breathlessness is crucial for diagnosis, to identify appropriate treatment, and to provide patients with the capacity to self-manage their condition. However, there is an evident disconnect between the way breathlessness is understood between clinical and lay perspectives, in terms of awareness of breathlessness, the way symptoms are expressed, and acknowledgement of how it affects the daily lives of patients.

The review highlights the need for integrated multidisciplinary work on breathlessness, and suggests that effective understanding and management of breathlessness considers its wider subjective and social significance.
A systematic literature review on the ethics of palliative sedation: an update (2016)
Authors: Henry Blair
Published: July 2016

Purpose of review

Palliative sedation has been the subject of intensive debate since its first appearance in 1990. In a 2010 review of palliative sedation, the following areas were identified as lacking in consensus: inconsistent terminology, its use in nonphysical suffering, the ongoing experience of distress, and concern that the practice of palliative sedation may hasten death. This review looks at the literature over the past 6 years and provides an update on these outstanding concerns.

Recent findings

Good clinical guidelines and policies are still required to address issues of emotional distress and waylay concerns that palliative sedation hastens death.

The empirical evidence suggests some movement toward consensus on the practice of palliative sedation. However, a continued need exists for evidence-informed practice guidelines, education, and research to support the ethical practice of palliative sedation at the end of life. Until that time, clinicians are advised to adopt a framework or guideline that has been expert driven to ensure consistent and ethical use of palliative sedation at the end of life.
No child is an island: ethical considerations in end-of-life care for children and their families
Authors: Rapoport Adam , Morrison Wynne
Published: July 2016

Purpose of review

Ethical challenges are commonly encountered when caring for children with life-threatening conditions.

Recent findings

Controversial end-of-life issues, such as physician-assisted death and medical futility, may also arise in children. The approach to these issues in children may be guided by the ‘adult’ medical literature; the age of the patient should not be a relevant factor in determining the morality of these acts. As such, the focus of this review is on ethical issues unique to children and adolescents by nature of their dependence on their parents. Appreciation that child well-being is best promoted when care aligns with parental beliefs, values and culture has given rise to the practice of family-centred care, which we prefer to call ‘family-partnered’ care. Occasionally, a family-partnered approach may challenge fundamental paediatric ethical principles, including best interests, developing autonomy, and the importance of honesty and truth-telling.

This article explores the challenges that may arise when there is disagreement between the child, the parents, and the healthcare providers about care at the end-of-life and provides suggestions to clinicians about how to help resolve these conflicts.
Tissue Resolved, Gene Structure Refined Equine Transcriptome
Authors: Mansour T. A. , Scott E. Y. , Finno C. J. , Bellone R. R. , Mienaltowski M. J. , Penedo M. C. , Ross P. J. , Valberg S. J. , Murray J. D. , Brown C. T.
Published: July 2016

Background

Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR). We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome.

Results

This equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and isoform resolution while providing considerable tissue-specific information. We utilized four levels of transcript filtration in our pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Our most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome.

Conclusions

We have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date and can serve several types of downstream analyses.
Enhancing performance of oppositional BBO using the current optimum (COOBBO) for TSP problems
Authors: Xu Qingzheng , Wang Na , Wang Lei
Published: July 2016

Purpose

– The purpose of this paper is to examine and compare the entire impact of various execution skills of oppositional biogeography-based optimization using the current optimum (COOBBO) algorithm.

Design/methodology/approach

– The improvement measures tested in this paper include different initialization approaches, crossover approaches, local optimization approaches, and greedy approaches. Eight well-known traveling salesman problems (TSP) are employed for performance verification. Four comparison criteria are recoded and compared to analyze the contribution of each modified method.

Findings

– Experiment results illustrate that the combination model of “25 nearest-neighbor algorithm initialization+inver-over crossover+2-opt+all greedy” may be the best choice of all when considering both the overall algorithm performance and computation overhead.

Originality/value

– When solving TSP with varying scales, these modified methods can enhance the performance and efficiency of COOBBO algorithm in different degrees. And an appropriate combination model may make the fullest possible contribution.
Apply neural network for improving production planning at Samarang petrol mine
Authors: Pham Quoc Trung , Phan Thi Kim Dung
Published: July 2016

Purpose

– Artificial neural network (ANN) is considered a good solution for building non-linear relationship between input and output parameters, which is suitable for solving production back allocation, which is the most important step for production planning of petroleum mine. The purpose of this paper is to suggest a solution for solving production back allocation problem at Samarang petrol mine based on ANN approach.

Design/methodology/approach

– In this study, well operational parameters’ surveillance was conducted and ANN was used to build relationships between operation parameters and production rates. Experimental method is used for testing and evaluating the possibility of using ANN for supporting production planning at Samarang mine.

Findings

– Consequently, the proposed ANN solution can increase the accuracy of predicted values and could be used for supporting production planning at Samarang mine. Because ANN uses well test data for training and predicting (without adding new devices), it could be a feasible and cheap solution.

Research limitations/implications

– There is a need for applying other methods, such as: support machine vector, non-linear autoregressive models, etc. for better evaluation of ANN solution.

Practical implications

– The ANN models helped operation engineers to understand well production performance and make decision to improve production plan in timely manner. This solution could be generalized for the whole mine or to similar petroleum mines in practice.

Originality/value

– This paper aims to propose a solution based on ANN for solving production back allocation problem of petroleum industry. The solution is tested at Samarang mine.
The determinants of bank profitability: empirical evidence from European banking sector
Authors: Menicucci Elisa , Paolucci Guido
Published: July 2016

Purpose

The purpose of this paper is to investigate the relationship between bank-specific characteristics and profitability in European banking sector to find the role of internal factors in achieving high profitability.

Design/methodology/approach

A regression analysis is built on an unbalanced panel data set comprising 175 observations of 35 top European banks over the period 2009-2013. To this end, the empirical data are collected from Bankscope and a comprehensive set of internal characteristics is examined.

Findings

All the determinant variables included in the model have statistically significant impacts on European banks’ profitability. However, the effects are not uniform across profitability measures. Regression findings reveal that size and capital ratio are significant company-level determinants of bank profitability in Europe, while higher loan loss provisions result in lower profitability levels. Findings also suggest that banks with higher deposits and loans ratio tend to be more profitable but the effects on profitability are statistically insignificant in some cases.

Practical implications

This study has considerable policy implications, as the performance of the European banking sector depends on its efficiency, profitability and competitiveness. In view of these findings, some suggestions may be functional for bank regulatory authorities to intensify and sustain robustness and stability of the banking sector.

Originality/value

The results provide interesting insights into the characteristics and practices of profitable banks in Europe. Few econometric studies have empirically explored the determinants of bank profitability in Europe so far, even though similar studies have been conducted in several developed countries. Therefore, this paper tries to close an important gap in the existing literature improving the understanding of bank profitability in Europe.
Anti-money laundering program and suspicious activity report filing requirements for registered investment advisors: practicalities and implications of FinCEN’s proposed new rule
Authors: Lopez Jonathan A. , Linn Courtney J. , Eisert Edward , Muldoon Lauren
Published: July 2016

Purpose

To provide a summary and analysis of the Proposed Rulemaking published by the Financial Crimes Enforcement Network (FinCEN) on September 1, 2015, which proposes to subject investment advisers to certain requirements of the Bank Secrecy Act of 1970.

Design/methodology/approach

The article discusses the proposed expansion of Bank Secrecy Act regulations to include investment advisers, including the history behind the rulemaking, proposed definition of “investment adviser” under the Act, the comments received in response to the proposed rulemaking, and the potential implications of the rule, should it be finalized.

Findings

This article concludes that FinCEN, in cooperation with the Securities and Exchange Commission (SEC) and other agencies, is nearing completion of the proposed rule. Investment advisers that fall under the proposed definition of those subject to Bank Secrecy Act should prepare to implement anti-money laundering compliance programs.

Originality/value

This article contains valuable information about proposed regulations impacting investment advisers registered or required to be registered with the Securities and Exchange Commission.
AIFMD passport: Europe must try harder
Authors: Sims Stephen , Brandt Patrick , Norman Greg
Published: July 2016

Purpose

To explain two papers published by the European Securities and Marketing Authority (ESMA) covering the application of the mar-keting “passport” under the Alternative Investment Fund Managers Directive (AIFMD).

Design/methodology/approach

Explains ESMA’s first paper, containing an advice to the European Parliament, Council and Commission (collectively the Trilogue) on the potential application of the AIFMD passport to non-EU Alternative Investment Fund Managers (AIFMs) and Alternative in-vestment Funds (AIFs), and a second paper, containing ESMA’s opinion on the current functioning of the AIFMD (currently used by EU AIFMs marketing EU AIFs in the EU) and National Private Placement Regimes (NPPRs, used for marketing by non-EU AIFMs and non-EU AIFs).

Findings

The ESMA papers were disappointing because they gave far less guidance and encouragement than anticipated that AIFs located in major jurisdictions such as the US and the Cayman Islands will be any easier to market to EU professional investors in the near future.

Practical implications

AIFMs (both inside and outside the EU) who are already using, or intending to use, the NPPRs should take some comfort that it seems highly unlikely that these regimes will be removed in the near future.

Originality/value

Practical guidance from experienced financial services lawyers.
Interactive decision support for academic advising
Authors: Mohamed Abdallah
Published: July 2016

Purpose

This paper aims to support academic advising, which plays a crucial role in student success and retention. The paper focuses on one of the most challenging tasks involved in academic advising: individual course scheduling. This task includes not only careful planning for different courses over several semesters according to students’ preferences and goals but also must conform to many student constraints and administrative regulations, some of which may rely on student-specific cases..

Design/methodology/approach

This paper introduces a novel approach that tries to provide meaningful support to decision makers involved in the course scheduling problem. The approach uses optimization algorithms to perform a pro-active analysis of the impact of different problem aspects and eventually suggests a balanced study plan that tries to satisfy both student preferences and advisor recommendations without violating any constraints.

Findings

An initial application of the proposed system is used to discuss its benefits.

Originality/value

The paper introduces a novel approach that uses optimization techniques to support making efficient decisions during the academic advising process.
Perceptions of higher education quality at three universities in Vietnam
Authors: Pham Huong Thi , Starkey Louise
Published: July 2016

Purpose

Vietnam is experiencing rapid expansion in the provision of higher education that requires quality assurance appropriate for the Vietnamese-centralised Confucian cultural context. This paper aims to examine the concept of quality from the perspectives of academic leaders, quality assurance members and academics at three higher education institutions in Vietnam.

Design/methodology/approach

Based on an interpretative study, semi-structured interviews were used as a major research instrument augmented with document analysis across three case studies. Interviews were conducted with 35 participants from three groups of stakeholders.

Findings

The concept of quality was found to be under-conceptualised in this Vietnamese context. Quality was conceptualised as meeting societal needs across the case studies underpinned by the belief that the purpose of higher education is to prepare graduates for employment.

Research limitations/implications

The study was conducted in similar disciplines at three state-owned universities in Vietnam in 2011. This provides insight within this context and timeframe that may not be generalised. It is suggested to extend this research to other disciplines, the private sector and other groups of stakeholders.

Practical implications

The paper discusses the necessity of revisiting the philosophy of higher education and re-conceptualising quality in Vietnam that informs quality assurance processes that are relevant to the cultural context.

Originality/value

This paper provides a centralised Confucian perspective to the literature on quality assurance in higher education. How quality is perceived by academic leaders, quality assurance members and, in particular, academic staff can be used to inform policy. In a centralised country such as Vietnam, academic leaders and quality assurance members may indicate their “obedient” attitudes to policies, leading to the same view with what is centrally enacted, while the academic staff have a different perception of quality.
Bridging Ecological Stoichiometry and Nutritional Geometry with homeostasis concepts and integrative models of organism nutrition
Authors: Sperfeld Erik , Wagner Nicole D. , Halvorson Halvor M. , Malishev Matthew , Raubenheimer David
Published: July 2016

The role of nutrition in linking animals with their environment is increasingly seen as fundamental to explain ecological interactions.

The two currently predominant frameworks for exploring questions in nutritional ecology – Nutritional Geometry (NG) and Ecological Stoichiometry (ES) – share common features, but also differ in their goals and origins. NG originates from behavioural ecology using terrestrial insects as model organisms in tightly controlled feeding experiments, while ES originates from biogeochemistry focusing on the transfer of key elements across trophic levels, mainly in aquatic environments.

Here, we review the history of these two complementary frameworks, emphasizing the key concepts defining their respective aims, methodologies and focal taxa to answer questions at different ecological scales.

We identify and explore homeostasis as a shared conceptual cornerstone of each framework that can be used to bridge knowledge gaps and for developing new hypotheses within nutritional ecology.

Expanding on the concept of homeostasis, we introduce dynamic energy budget (DEB) models as a general way to address homeostatic regulation at its fundamental level.

Specifically, we describe how a two‐reserve DEB model can be used to track metabolic pathways of nutrients as well as elements and suggest that multi‐reserve DEB models, when integrated and parameterized with NG and ES concepts, can form powerful components of agent‐based models to predict how animal nutrition influences individual and trophic interactions in food webs.
Spatial and temporal variability of aerobic anoxygenic photoheterotrophic bacteria along the east coast of Australia
Authors: Bibiloni‐Isaksson Jaime , Seymour Justin R. , Ingleton Tim , van de Kamp Jodie , Bodrossy Levente , Brown Mark V.
Published: July 2016

Aerobic Anoxygenic Phototrophic Bacteria (AAnPB) are ecologically important microorganisms, widespread in oceanic photic zones. However, the key environmental drivers underpinning AAnPB abundance and diversity are still largely undefined. The temporal patterns in AAnPB dynamics at three oceanographic reference stations spanning at approximately 15° latitude along the Australian east coast were examined. AAnPB abundance was highly variable, with pufM gene copies ranging from 1.1 × 102 to 1.4 × 105 ml−1 and positively correlated with day length and solar radiation. pufM gene Miseq sequencing revealed that the majority of sequences were closely related to those obtained previously, suggesting that key AAnPB groups are widely distributed across similar environments globally. Temperature was a major structuring factor for AAnPB assemblages across large spatial scales, correlating positively with richness and Gammaproteobacteria (phylogroup K) abundance but negatively with Roseobacter‐clade (phylogroup E) abundance, with temperatures between 16°C and 18°C identified as a potential transition zone between these groups. Network analysis revealed that discrete AAnPB populations exploit specific niches defined by varying temperature, light and nutrient conditions in the Tasman Sea system, with evidence for both niche sharing and partitioning amongst closely related operational taxonomic units.
Petroleum hydrocarbon contamination, plant identity and arbuscular mycorrhizal fungal (AMF) community determine assemblages of the AMF spore‐associated microbes
Authors: Iffis Bachir , St‐Arnaud Marc , Hijri Mohamed
Published: July 2016

The root‐associated microbiome is a key determinant of pollutant degradation, soil nutrient availability and plant biomass productivity, but could not be examined in depth prior to recent advances in high‐throughput sequencing. Arbuscular mycorrhizal fungi (AMF) form symbioses with the majority of vascular plants. They are known to enhance mineral uptake and promote plant growth and are postulated to influence the processes involved in phytoremediation. Amplicon sequencing approaches have previously shown that petroleum hydrocarbon pollutant (PHP) concentration strongly influences AMF community structure in in situ phytoremediation experiments. We examined how AMF communities and their spore‐associated microbiomes were structured within the rhizosphere of three plant species growing spontaneously in three distinct waste decantation basins of a former petrochemical plant. Our results show that the AMF community was only affected by PHP concentrations, while the AMF‐associated fungal and bacterial communities were significantly affected by both PHP concentrations and plant species identity. We also found that some AMF taxa were either positively or negatively correlated with some fungal and bacterial groups. Our results suggest that in addition to PHP concentrations and plant species identity, AMF community composition may also shape the community structure of bacteria and fungi associated with AMF spores.
Antipodean agricultural and resource economics at 60: booming sector economics
Authors: Freebairn John
Published: July 2016

Contributions of Australian economists to understand the effects of a boom export industry are reviewed. Effects are considered on: the real exchange rate; output, prices and factor incomes of the boom industry, other trade‐exposed industries and nontraded industries; and national income and its distribution. Theoretical models and empirical models are reviewed. Different effects are considered for supply‐side‐ versus demand‐side‐driven booms, and then for the price increase, investment increase and production increase phases of the boom. Evaluations of industry and macroeconomic policy options are canvassed.
Antipodean agricultural and resource economics at 60: risk and uncertainty
Authors: Quiggin John C. , Anderson Jock R.
Published: July 2016

Risk and uncertainty issues have been long addressed by members of AARES, reflecting the importance of the issue in agriculture, particularly in Australia. Members have been among the most innovative developers of methods and insights, around the world, as is reflected in the many publications in journals beyond the domestic shores. It seems, given the recent keen attention to such issues in the Australian literature and beyond, that, with high probability, members will continue to make strong contributions to this area of agricultural and resource economics.
Microbial biotechnology for the synthesis of (pro)vitamins, biopigments and antioxidants: challenges and opportunities
Authors: Revuelta Jose L. , Buey Ruben M. , Ledesma‐Amaro Rodrigo , Vandamme Erick J.
Published: July 2016

Vitamins and related compounds, such as provitamins, biopigments and antioxidants, belong to those few chemicals that appeal in a positive way to most people. These terms sound synonymous to vitality, good health and mental strenght, even to the layman. Everyone of us needs his/her daily intake of (pro)vitamins and antioxidants, normally provided by a balanced and varied diet. However, current food habits or preferences, food availabilities, as well as food processing, preservation or cooking methodologies and technologies, do not always assure a sufficient balanced natural daily (pro)vitamin supply to a healthy individual, and even more so for a stressed or sick human being. Today, modern society is seldom confronted with the notorious avitaminoses of the past, well known to the Western World, but they do still occur frequently in overpopulated, war‐ridden, poverty‐ or famine‐struck regions on our globe, as well as for surprisingly large population groups in developed countries.
A cost‐effective high‐throughput metabarcoding approach powerful enough to genotype ~44 000 year‐old rodent remains from Northern Africa
Authors: Guimaraes S. , Pruvost M. , Daligault J. , Stoetzel E. , Bennett E. A. , Côté N. M.‐L. , Nicolas V. , Lalis A. , Denys C. , Geigl E.‐M. , Grange T.
Published: July 2016

We present a cost‐effective metabarcoding approach, aMPlex Torrent, which relies on an improved multiplex PCR adapted to highly degraded DNA, combining barcoding and next‐generation sequencing to simultaneously analyse many heterogeneous samples. We demonstrate the strength of these improvements by generating a phylochronology through the genotyping of ancient rodent remains from a Moroccan cave whose stratigraphy covers the last 120 000 years. Rodents are important for epidemiology, agronomy and ecological investigations and can act as bioindicators for human‐ and/or climate‐induced environmental changes. Efficient and reliable genotyping of ancient rodent remains has the potential to deliver valuable phylogenetic and paleoecological information. The analysis of multiple ancient skeletal remains of very small size with poor DNA preservation, however, requires a sensitive high‐throughput method to generate sufficient data. We show this approach to be particularly adapted at accessing this otherwise difficult taxonomic and genetic resource. As a highly scalable, lower cost and less labour‐intensive alternative to targeted sequence capture approaches, we propose the aMPlex Torrent strategy to be a useful tool for the genetic analysis of multiple degraded samples in studies involving ecology, archaeology, conservation and evolutionary biology.
Binge Drinking Decreases Corticotropin‐Releasing Factor‐Binding Protein Expression in the Medial Prefrontal Cortex of Mice
Authors: Ketchesin Kyle D. , Stinnett Gwen S. , Seasholtz Audrey F.
Published: July 2016

Background

Dysregulation of the corticotropin‐releasing factor (CRF) system has been observed in rodent models of binge drinking, with a large focus on CRF receptor 1 (CRF‐R1). The role of CRF‐binding protein (CRF‐BP), a key regulator of CRF activity, in binge drinking is less well understood. In humans, single‐nucleotide polymorphisms in CRHBP are associated with alcohol use disorder and stress‐induced alcohol craving, suggesting a role for CRF‐BP in vulnerability to alcohol addiction.

Methods

The role and regulation of CRF‐BP in binge drinking were examined in mice exposed to the drinking in the dark (DID) paradigm. Using in situ hybridization, the regulation of CRF‐BP, CRF‐R1, and CRF mRNA expression was determined in the stress and reward systems of C57BL/6J mice after repeated cycles of DID. To determine the functional role of CRF‐BP in binge drinking, CRF‐BP knockout (CRF‐BP KO) mice were exposed to 6 cycles of DID, during which alcohol consumption was measured and compared to wild‐type mice.

Results

CRF‐BP mRNA expression was significantly decreased in the prelimbic (PL) and infralimbic medial prefrontal cortex (mPFC) of C57BL/6J mice after 3 cycles and in the PL mPFC after 6 cycles of DID. No significant changes in CRF or CRF‐R1 mRNA levels were observed in mPFC, ventral tegmental area, bed nucleus of the stria terminalis, or amygdala after 3 cycles of DID. CRF‐BP KO mice do not show significant alterations in drinking compared to wild‐type mice across 6 cycles of DID.

Conclusions

These results reveal that repeated cycles of binge drinking alter CRF‐BP mRNA expression in the mPFC, a region responsible for executive function and regulation of emotion and behavior, including responses to stress. We observed a persistent decrease in CRF‐BP mRNA expression in the mPFC after 3 and 6 DID cycles, which may allow for increased CRF signaling at CRF‐R1 and contribute to excessive binge‐like ethanol consumption.
Alcohol Vapor Inhalation as a Model of Alcohol‐Induced Organ Disease
Authors: Mouton Alan J. , Maxi John K. , Souza‐Smith Flavia , Bagby Gregory J. , Gilpin Nicholas W. , Molina Patricia E. , Gardner Jason D.
Published: July 2016

Background

Chronic intermittent ethanol vapor (CIEV) exposure has been used extensively to produce rodent models of alcohol dependence, but unlike other models of alcohol abuse, CIEV has not been assessed as a model of end‐organ damage. The purpose of this study was to characterize the effects of CIEV on peripheral organ systems affected by alcohol abuse, including the liver, lungs, and cardiovascular system.

Methods

Adult male Sprague‐Dawley rats were exposed to daily CIEV for a period of 8 weeks (14HR ON/10HR OFF), producing blood alcohol levels of ~200 mg/dl. Controls were exposed to room air. After 8 weeks, echocardiography was performed to assess cardiac function. Indices of liver injury (alanine and aspartate aminotransferases [ALT and AST]; cytochrome p450 2E1 [CYP2E1]; alcohol dehydrogenase [ADH]; Oil Red O and triglyceride content; lipid peroxidation; inflammatory cytokine expression; and macrophage infiltration), and lung inflammatory cell count, proinflammatory cytokine expression, and lipid peroxidation were measured.

Results

Left ventricular posterior wall thickness was significantly decreased, and systolic blood pressure was significantly elevated by CIEV compared with air controls. CIEV led to a significant increase in plasma ALT and triglycerides compared with room air controls. CIEV did not affect liver triglyceride content, lipid staining or peroxidation, but increased CYP2E1 and chemokine (C‐C motif) ligand 2 (CCL2) protein expression, while decreasing ADH expression. CIEV significantly increased numbers of both polymorphonuclear neutrophils and lymphocytes in the bronchoalveolar lavage fluid, indicative of pulmonary inflammation. However, CIEV did not produce significant changes in lung mass, pulmonary lipid peroxidation, inflammatory cytokine expression, or edema.

Conclusions

These results show that CIEV produces hepatic, pulmonary, and cardiovascular effects in rats similar to those found in other models of chronic alcohol administration. Alcohol vapor administration is a novel method of alcohol‐induced tissue injury with high potential for widespread use in alcohol toxicology research.
Improving Connectivity in Indonesia: The Challenges of Better Infrastructure, Better Regulations, and Better Coordination
Authors: Sandee Henry
Published: July 2016

This paper presents and discusses the main challenges that an archipelago like Indonesia is facing in improving its connectivity. Distinguishing between intra‐island, inter‐island, and international connectivity is essential in order to understand the nature of the challenges and causes behind the bottlenecks. High domestic shipping costs are identified as one key challenge. The Government of Indonesia has identified improved connectivity as a key issue in promoting economic growth, especially in the manufacturing sector, now that Indonesia can no longer rely on commodities as a driver of growth. Better infrastructure, regulations, and coordination among stakeholders are crucial components in promoting improved connectivity for manufacturing growth. Promoting investment in infrastructure is necessary, including both hard and soft infrastructure. However, Indonesian experience highlights that without regulatory reform and improved policy coordination, infrastructure investment will continue to lag behind. There is a need for an improved and empowered governance structure to turn investment plans into reality.
Economic Impacts of Improved Connectivity for ASEAN: An Application of the Geographical Simulation Model
Authors: Isono Ikumo , Kumagai Satoru
Published: July 2016

We compare the prioritized projects of the Master Plan on ASEAN Connectivity (MPAC) and the Comprehensive Asia Development Plan (CADP) by utilizing the Institute of Developing Economies/Economic Research Institute for ASEAN and East Asia Geographical Simulation Model. The prioritized projects of the MPAC mainly focus on specific hard or soft infrastructure projects connecting one remote area of an ASEAN member state to another and thus fail to capture the full potential of the infrastructure because of neglected important links within a state. On the other hand, the CADP emphasizes the importance of economic corridors or linkages between a large cluster and another cluster. Our simulation analysis shows that CADP projects will result in an addition to gross domestic product (GDP) of $US 1544bn over the period from 2021 to 2030 (in 2010 dollars) or an impact on ASEAN countries that is 12 times larger than MPAC projects. The results strongly suggest that the CADP projects should be adopted and implemented to fully realize the potential economic growth of the ASEAN countries. Moreover, the CADP will contribute more to narrowing the development gaps among the ASEAN countries than MPAC prioritized projects.
A Bootstrap Likelihood Approach to Bayesian Computation
Authors: Zhu Weixuan , Marin J. Miguel , Leisen Fabrizio
Published: July 2016

There is an increasing amount of literature focused on Bayesian computational methods to address problems with intractable likelihood. One approach is a set of algorithms known as Approximate Bayesian Computational (ABC) methods. One of the problems with these algorithms is that their performance depends on the appropriate choice of summary statistics, distance measure and tolerance level. To circumvent this problem, an alternative method based on the empirical likelihood has been introduced. This method can be easily implemented when a set of constraints, related to the moments of the distribution, is specified. However, the choice of the constraints is sometimes challenging. To overcome this difficulty, we propose an alternative method based on a bootstrap likelihood approach. The method is easy to implement and in some cases is actually faster than the other approaches considered. We illustrate the performance of our algorithm with examples from population genetics, time series and stochastic differential equations. We also test the method on a real dataset.