bluuebunny/crossref_metadata_2025 huggingface dataset:
The Importance of Both Research and its Proper Review: A Historical Perspective
Authors: Davies Hugh
Published: January 2012

It is self-evident that medical treatments have improved in recent centuries. Through a historical analysis this article demonstrates that experimental research has underpinned the success of modern medical therapy, but it also shows that there have been examples of unethical research and that these can still be found, even today. Whilst it is crucial that research continues, it is equally important that there is appropriate review. Although the health of research itself is central to our well-being, the community needs to be able to exercise its right to scrutinize such projects, not only to understand what the scientific medical community is undertaking but also to identify research it regards as unfair. In the United Kingdom this is the work of Research Ethics Committees.
Guinea Pig Duties: 6. Non-Consensual Clinical Research
Authors: Steiner T.J.
Published: January 2012

In the first five of these articles I have questioned the justice, and effectiveness, of total dependence in clinical research on willing volunteers. I have explored ways that might better and more equitably spread the burden of participating in clinical research as subjects of it. Here I consider this question: if consent is the barrier, must we regard consent as indispensable?
A Plea for Consistency in Ethical Review
Authors: Pothier David D. , Bredenkamp Corné-Louise
Published: January 2012

When considering submissions ethics committees should be consistent in all aspects of their review. A wide variation in performance is likely to result in the unfair dismissal of good research on the one hand with inadequate ethical review on the other, neither of which is acceptable. The recent annual reports for UK MRECs suggest that the level of unfavourable opinion ranges from 6.9% to 24.2% Although a certain level of inconsistency is inherent in the system of ethical review there is little research to determine how much of that inconsistency in inevitable and how much of it is the result of poor process. The time has come for high quality research to be done to assess the consistency and hence the validity of ethical review.
REC Members' Perceptions of Their Training Needs: Report of an AREC Audit
Authors: McGee Paula , Taylor Gordon , Rawbone Roger ,   On Behalf of the AREC Training Needs Working Group, Dawson Carol , McGarva Kate , McGee Paula , Nicholson Richard , Taylor Gordon
Published: January 2012

The Association of Research Ethics Committees is one of the leading providers of training and education for members of Research Ethics Committees. The introduction of the research governance strategy and the increasing complexity of ethical review place great demands on research ethics committee members that in turn creates challenges for training providers. This paper presents the outcome of an audit of REC members' views about training. Findings demonstrate that REC members are not a homogenous group. Several distinct sub-groups, each with particular training needs emerged. All showed a preference for short, easily accessible events in which there were opportunities for discussion.
Ethical Issues in Researching Pregnant Women: A Commentary
Authors: Jones Shirley , McGee Paula
Published: January 2012

This study appeared in full in the last issue of Research Ethics Review (2007; 3(1): 18). Rowena Jones is an obstetrician working in a busy hospital for women. Her research focuses on changes in women's brains during pregnancy1. Rowena plans to use magnetic resonance imaging to record images of the brains of women in the second and third trimesters and after birth at 6 and 24 weeks. Her sample consists of two groups of healthy women with uncomplicated and singleton pregnancies, the first primigravid and the second multiparous. There will be a minimum of five and a maximum of ten women in each group.
Whistle Blowing — What is it?
Authors: Bone Nick
Published: January 2012

This paper describes the provisions of the Public Interest Disclosure Act 1998.
Ethical Issues in Obtaining Informed Consent for Research from Those Recovering from Acute Mental Health Problems: A Commentary
Authors: Cameron Josh , Hart Angie
Published: January 2012

This study appeared in full in the last issue of Research Ethics Review (2007; 3 (3): 91). It concerned the ethical review of a qualitative research study in which the participants are recovering from acute mental health problems. Debate focussed on the issue of how informed consent was to be obtained.
Who Cares? The Declaration of Helsinki and ‘The Conscience of Physicians’
Authors: Appleyard James
Published: January 2012

The World Medical Association's ‘Declaration of Helsinki’ on Medical Research on Human Subjects is undergoing its sixth revision in its 44 years. The aim of this paper is to put the Declaration into an historical context, define and identify the core ethical principles, and illustrate how these are applied within the Declaration.
Retaining Older People in Longitudinal Research Studies: Some Ethical Issues
Authors: Tinker Anthea , Mein Gill , Bhamra Suneeta , Ashcroft Richard , Seale Clive
Published: January 2012

The increase in drop-out rates, especially among older people, in longitudinal studies is a matter for concern if the results are to be valid. The research reported here contains a number of pieces of evidence that might help address the problem. These include a literature review, a survey of some longitudinal studies, secondary (quantitative and qualitative) analysis of the data from a longitudinal study of civil servants (the Whitehall II study), and new data from focus groups and telephone interviews with participants from this current study. The findings relate to reasons why older people continue to take part in such studies, why they drop out and what might encourage them to continue participating. The main reasons for drop out relate to being older, having cognitive impairment and poor functioning, living alone, being a woman and being less educated. There were also a range of practical reasons including the study being too time-consuming and problems with transport.
Principled Ethics Review: Governance Arrangements for University Research Ethics Committees
Authors: Stibbs Timothy
Published: January 2012

This, the third seminar organised by the AREC university sector committee, included short presentations followed by parallel workshops. These proposed and explored basic principles for ethical review in the context of current models within the university REC sector. In this report, following an introduction, each of the speakers/workshop leaders summarizes their own perspective on the issues raised and discussed.
The Business of Medicine: A Response to Nathan Emmerich
Authors: Parker Colin
Published: January 2012

Nathan Emmerich, in a recent issue of Research Ethics Review, has suggested that the ‘professional ethicist’ should be considered an ‘expert member’ in the research ethics committee. He raised a number of interesting questions and in seeking to answer them one may come to what may be regarded as an unexpected conclusion – that there is a prior need to clearly explain the concept of ‘ethical expertise’ and the ‘ethics professional’.
The Equality Act, 2010
Authors: Humphreys Stephen
Published: January 2012

The Equality Act 2010 brings the concept of indirect discrimination to discrimination on the grounds of religion or belief. This has real potential to require a change in practice in certain types of clinical trials of which relevant ethics committees should be aware.
The Wrong Paradigm? Social Research and the Predicates of Ethical Scrutiny
Authors: Burr Jennifer , Reynolds Paul
Published: January 2012

We aim, in this paper, to discuss how far the ethical framework for assessing medical research, generalized into other institutional settings, is also appropriate for social science research, particularly qualitative research. Recently, researchers have raised concerns about ‘ethics creep’, incompatibility with participatory methodologies and the exclusion of service users. Researchers are increasingly raising questions as to whether the processes of governance and the paradigmatic assumptions pervading research ethics committees are fit for purpose when they deliberate on non-clinical research that uses social science methods. We review whether ethical scrutiny by research ethics committees is asking the wrong questions and holding research to the wrong standards.
Rethinking the Ethical Boundaries of a Grounded Theory Approach
Authors: Potrata Barbara
Published: January 2012

Grounded theory has become an established approach in (applied) qualitative research. Researchers could have an on-going, relative freedom when using this research strategy but their creativity will have been limited by the number of participants and interviews, and by the methodology that they have declared in their research ethics committee application. Since no robust evidence exists about potential harm in qualitative research in general and grounded theory in particular, we should rethink whether a greater freedom might be allowed to researchers when using a grounded theory approach. It is concluded that a greater freedom should be allowed, but only to skilled researchers as those with less experience might use less rigid rules to cover their lack of skills and research experience, potentially burdening the study participants unnecessarily.
The Role, Remit and Function of the Research Ethics Committee — 5. Collective Decision-Making and Research Ethics Committees
Authors: Edwards Sarah JL
Published: January 2012

Part 5, the concluding essay in the series describing and discussing the role, remit and function of research ethics committees, bases an enquiry into the nature of decision-making by research ethics committees on the processes followed by the committees in their deliberations leading to the final outcome.
Regulation and Paediatric Drug Trials: Patents, Plans, and Perverse Incentives
Authors: Gaifulinay Riana
Published: January 2012

The facilitation of tight regulatory frameworks necessary to ensure that new drugs are safe and effective have yet to be effectively applied within the paediatric population. Utilization of unlicensed and off-label drugs in children results in a variety of problems ranging from inefficacy, adverse reactions and in some cases death. This ethically questionable behaviour has led the European government to legally force pharmaceutical companies to propose paediatric applications and carry out clinical studies at early stages of drug development. The new European Paediatric Regulation implemented in 2007 opens a new era of paediatric drug development and will offer the opportunity to vastly improve children's health. However, this brighter outlook for the paediatric community might encourage potentially unethical behaviour in a pharmaceutical industry that finds itself in economically unstable times.

The article records the gradual evolution of the US Paediatric Exclusivity Plan and the underlying principle of the newly introduced European Paediatric Regulation. It discusses some of the potential drawbacks and detrimental consequences of implementing the new European regulation, and the prospects of avoiding these by critically evaluating the difficulties experienced by the US.
Ethical Review of Action Research: The Challenges for Researchers and Research Ethics Committees
Authors: Gelling Leslie , Munn-Giddings Carol
Published: January 2012

Action research has repeatedly demonstrated how it can facilitate problem solving and change in many settings through a process of collaboration which is driven by the community at the heart of the research. The ethical review of action research can be challenging for action researchers and research ethics committees. This paper explores how seven ethical principles can be used by action researchers and research ethics committees as the basis for ethical review. This paper concludes by offering some suggestions for a way forward for both action researchers and research ethics committees.
Incidence of therapy-related acute leukaemia in mitoxantrone-treated multiple sclerosis patients in Germany
Authors: Stroet Anke , Hemmelmann Claudia , Starck Michaela , Zettl Uwe , Dörr Jan , Paul Friedemann , Flachenecker Peter , Fleischer Vinzenz , Zipp Frauke , Nückel Holger , Kieseier Bernd C , Ziegler Andreas , Gold Ralf , Chan Andrew
Published: January 2012

Background: The incidence of therapy-related acute leukaemia (TRAL) in mitoxantrone treatment in multiple sclerosis (MS) is controversially discussed.

Methods and results: In a retrospective meta-analysis from six centres, we observed six cases of acute myeloid leukaemia (AML) (incidence 0.41% for patients with mean follow up after end of treatment of 3.6 years, n = 1.156; incidence 0.25% for all patients, n = 2.261). Potential influencing factors such as myelotoxic or glucocorticosteroid pretreatment/cotreatment were present in all but one case of TRAL. Between 1990 and 2010, 11 cases of TRAL were reported to the Drug Commission of the German Medical Association (estimated risk of 0.09–0.13%).

Conclusions: Regional differences in reported TRAL incidence may point to confounding cofactors such as administration protocols and cotreatments.
Health literacy and the Clozapine patient
Authors: Brosnan Susan , Barron Elizabeth , Sahm LJ
Published: January 2012

Aims: To estimate the prevalence of limited health literacy in patients receiving clozapine for schizophrenia. To develop and produce a pharmacist-designed clozapine patient information leaflet (PIL) which has a higher readability score than the company–produced PIL.

Study design: This was a cross sectional prevalence study.

Methods: Ethical approval for the study was granted by the local ethics committee. Patients, over 18 years, attending the Clozapine Clinic of a Cork urban teaching hospital, were asked to participate in the study. Demographics such as gender, age, employment and smoking status, were gathered from all participants. The total daily clozapine dose, duration of clozapine treatment, and information regarding the clozapine DVD was also noted. The Rapid Estimate of Adult Literacy in Medicine (REALM) health literacy (HL) screening tool was then administered to each patient. A user-friendly PIL on clozapine was designed by the pharmacist, which was assessed for readability and compared to the company-produced PIL using the FRES and FKGL. Data were analysed using SPSS Version 15.

Results: Forty patients (65% male, 95% unemployed and 70% smokers) of average age 38.0 years (±11.2) completed the REALM. The average score was 60.6 (±8.7). Twenty-nine patients (72.5%) were found to have “adequate” health literacy. The remaining eleven patients were found to have either “marginal” or “low” health literacy. The pharmacist-designed PIL would have been readable by 95% of the study population, in contrast to 72.5% with the company-designed PIL.

Conclusions: More than a quarter of the population were found to have marginal or low health literacy. Patient information should be matched to the health literacy level of the target population.
Student Outcomes in Inquiry Instruction
Authors: Saunders-Stewart Katie S. , Gyles Petra D. T. , Shore Bruce M.
Published: January 2012

Curricular reform efforts are underway in many countries, focused on adopting inquiry-based approaches to teaching and learning. Therefore, it is increasingly important to understand what outcomes students attain in inquiry environments. Derived from a literature review, a 23-item, criterion-referenced inventory is presented for theoretically implied and empirically based outcomes or benefits for students engaging in inquiry, and includes research on overlapping pedagogical topics such as discovery learning and problem-based learning. Student outcomes include knowledge and skills, intrinsic motivation, and development of expertise, among others. Supporting research is primarily available in the areas of cognitive and affective outcomes (e.g., knowledge, skills, motivation, attitudes, and creativity). This list can be used as a starting point for research or converted into professional development tools.
Differentiating Low Performance of the Gifted Learner
Authors: Figg Stephanie D. , Rogers Karen B. , McCormick John , Low Renae
Published: January 2012

The study aimed to empirically verify findings from qualitative studies that showed selective consumers could be distinguished from underachievers with regard to academic self-perception and thinking style preference. Participants, gifted males from an independent secondary boys’ school in Sydney, Australia, were categorized as achieving, underachieving, or selective consuming and administered the School Attitude Assessment Survey–Revised and the Thinking Style Inventory to assess academic self-perception and thinking style preference. A multivariate analysis (MANOVA) with a Bonferroni-adjusted alpha level to control for Type I errors showed a statistically significant difference in academic self-perception between achievers and underachievers only. Selective consumers could not statistically be distinguished from achievers or underachievers. Results, although not statistically significant, supported the trend currently reported in the literature that selective consumers differ qualitatively from underachievers.
Stepping Back While Staying Engaged
Authors: Marguc Janina , Kleef Gerben A. Van , Förster Jens
Published: January 2012

When do people respond to obstacles by mentally “stepping back” and taking a more distanced perspective? Manipulating obstacles to social goals, to personal goals, and in a computer game, three studies tested the hypothesis that people should increase psychological distance upon facing an obstacle primarily when distancing is relevant, that is, when the obstacle appears on their own path to a goal or when they are engaged and motivated to follow through with activities. As expected, participants who imagined a goal-relevant versus a goal-irrelevant obstacle indicated greater estimates for an unrelated spatial distance (Study 1). Moreover, chronically engaged participants provided smaller font size estimates after thinking about how to reach a personal goal with versus without an obstacle (Study 2), and participants primed with engagement indicated greater estimates for an unrelated spatial distance after navigating a maze with versus without an obstacle (Study 3). Implications for related research are discussed.
Glucose-6-phosphatase-β, implicated in a congenital neutropenia syndrome, is essential for macrophage energy homeostasis and functionality
Authors: Jun Hyun Sik , Cheung Yuk Yin , Lee Young Mok , Mansfield Brian C. , Chou Janice Y.
Published: January 2012

Glucose-6-phosphatase-β (G6Pase-β or G6PC3) deficiency, also known as severe congenital neutropenia syndrome 4, is characterized not only by neutropenia but also by impaired neutrophil energy homeostasis and functionality. We now show the syndrome is also associated with macrophage dysfunction, with murine G6pc3−/− macrophages having impairments in their respiratory burst, chemotaxis, calcium flux, and phagocytic activities. Consistent with a glucose-6-phosphate (G6P) metabolism deficiency, G6pc3−/− macrophages also have a lower glucose uptake and lower levels of G6P, lactate, and ATP than wild-type macrophages. Furthermore, the expression of NADPH oxidase subunits and membrane translocation of p47phox are down-regulated, and G6pc3−/− macrophages exhibit repressed trafficking in vivo both during an inflammatory response and in pregnancy. During pregnancy, the absence of G6Pase-β activity also leads to impaired energy homeostasis in the uterus and reduced fertility of G6pc3−/− mothers. Together these results show that immune deficiencies in this congenital neutropenia syndrome extend beyond neutrophil dysfunction.
Aβ delays fibrin clot lysis by altering fibrin structure and attenuating plasminogen binding to fibrin
Authors: Zamolodchikov Daria , Strickland Sidney
Published: January 2012

Alzheimer disease is characterized by the presence of increased levels of the β-amyloid peptide (Aβ) in the brain parenchyma and cerebral blood vessels. This accumulated Aβ can bind to fibrin(ogen) and render fibrin clots more resistant to degradation. Here, we demonstrate that Aβ42 specifically binds to fibrin and induces a tighter fibrin network characterized by thinner fibers and increased resistance to lysis. However, Aβ42-induced structural changes cannot be the sole mechanism of delayed lysis because Aβ overlaid on normal preformed clots also binds to fibrin and delays lysis without altering clot structure. In this regard, we show that Aβ interferes with the binding of plasminogen to fibrin, which could impair plasmin generation and fibrin degradation. Indeed, plasmin generation by tissue plasminogen activator (tPA), but not streptokinase, is slowed in fibrin clots containing Aβ42, and clot lysis by plasmin, but not trypsin, is delayed. Notably, plasmin and tPA activities, as well as tPA-dependent generation of plasmin in solution, are not decreased in the presence of Aβ42. Our results indicate the existence of 2 mechanisms of Aβ42 involvement in delayed fibrinolysis: (1) through the induction of a tighter fibrin network composed of thinner fibers, and (2) through inhibition of plasmin(ogen)–fibrin binding.
Caveolin-1 regulation of store-operated Ca2+influx in human airway smooth muscle
Authors: Sathish Venkatachalem , Abcejo Amard J. , Thompson Michael A. , Sieck Gary C. , Prakash Y.S. , Pabelick Christina M.
Published: January 2012

Caveolae, plasma membrane invaginations with constitutive caveolin proteins, harbour proteins involved in intracellular calcium ([Ca2+]i) regulation. In human airway smooth muscle (ASM), store-operated Ca2+entry (SOCE) is a key component of [Ca2+]iregulation, and contributes to increased [Ca2+]iin inflammation. SOCE involves proteins Orai1 and stromal interaction molecule (STIM)1. We investigated the link between caveolae, SOCE and inflammation in ASM.

[Ca2+]iwas measured in human ASM cells using fura-2. Small interference RNA (siRNA) or overexpression vectors were used to alter expression of caveolin-1 (Cav-1), Orai1 or STIM1. Tumour necrosis factor (TNF)-α was used as a representative pro-inflammatory cytokine.

TNF-α increased SOCE following sarcoplasmic reticulum Ca2+depletion, and increased whole-cell and caveolar Orai1 (but only intracellular STIM1). Cav-1 siRNA decreased caveolar and whole-cell Orai1 (but not STIM1) expression, and blunted SOCE, even in the presence of TNF-α. STIM1 overexpression substantially enhanced SOCE: an effect only partially reversed by Cav-1 siRNA. In contrast, Orai1 siRNA substantially blunted SOCE even in the presence of TNF-α. Cav-1 overexpression significantly increased Orai1 expression and SOCE, especially in the presence of TNF-α.

These results demonstrate that caveolar expression and regulation of proteins such as Orai1 are important for [Ca2+]iregulation in human ASM cells and its modulation during inflammation.
The impact of ageing and sex on the association between sleepiness and sleep disordered breathing
Authors: Morrell Mary J. , Finn Laurel , McMillan Alison , Peppard Paul E.
Published: January 2012

The aim of our study was to investigate age-related changes in sleepiness symptoms associated with sleep disordered breathing (SDB).

Wisconsin Sleep Cohort participants were assessed using polysomnography, the Epworth Sleepiness Scale (ESS) and the multiple sleep latency test (MSLT). SDB was defined as an apnoea/hypopnoea index ≥15 events·h−1, and sleepiness as ESS ≥10 and MSLT ≤5 min. Odds ratios were calculated using generalised estimating equations associating sleepiness with SDB, and conditional logistic regression examining changes in longitudinal sleepiness status (ESS only). Models werea prioristratified by sex.

ESS was measured in 1,281 participants and MSLT in 998 at multiple time-points (ESS n=3,695; MSLT n=1,846). Significant interactions were found between SDB and age in males, but not females. The odds ratios modelled for sleepiness in a 40-yr-old male with SDB were significant compared to a male without SDB (ESS 2.1 and MSLT 2.9); however, these associations were not significant at 60 yrs of age. The within-subject odds ratio for sleepiness was also significant at 40 yrs of age (OR 3.4), but not at 60 yrs of age.

The age-related reductions in the association between sleepiness and SDB may have clinical implications for the diagnosis and treatment of SDB in older people as sleepiness is often used as a therapeutic target.
Comorbidity and healthcare costs in patients with obstructive sleep apnoea
Authors: Ronksley P.E. , Hemmelgarn B.R. , Tsai W.H.
Published: January 2012

Educational aims

To provide physicians with knowledge of common comorbid conditions associated with obstructive sleep apnoea (OSA).

To emphasise the healthcare burden and costs associated with OSA.

Recognise the role of risk stratification in identifying patients who are likely to develop OSA-related complications.

OSA is common, with an estimated prevalence of up to 20%. Observational studies have found OSA to be associated with increased cardiovascular morbidity, mortality and healthcare costs. Continuous positive airway pressure (CPAP) has been shown to be an effective therapy for OSA. Unfortunately, clinical trials assessing the effectiveness of CPAP to mitigate associated morbidity are limited and those that have been conducted show variable findings, with not all patients benefiting from treatment. Given the prevalence of OSA in the general population, treatment of all individuals would be costly and unnecessary. Recent work suggests that the heterogeneity in clinical trial results may be driven by the inability to identify at-risk groups. Identifying patients with clinically relevant sequelae may be useful for targeting treatment to those at greatest risk. In this review, we discuss the potential association between OSA and comorbid conditions, as well as the economic and health impact of such associations. We also highlight the importance of risk stratification in identifying patients who are likely to develop OSA-related complications and adverse health outcomes.
Medical thoracoscopy/pleuroscopy: step by step
Authors: Loddenkemper R. , Lee P. , Noppen M. , Mathur P.N.
Published: January 2012

Medical thoracoscopy/pleuroscopy is considered to be one of the main areas of interventional pulmonology and should be included in the training programme of the chest physician. As with all technical procedures, there is a learning curve before full competence in medical thoracoscopy/pleuroscopy is achieved. Therefore, appropriate training is mandatory. This article describes the knowledge and skills required, the contraindications and potential complications and their prevention and the instruments used, as well as step-by-step information on how to perform medical thoracoscopy/pleuroscopy, which is even easier to learn than flexible bronchoscopy.
Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing
Authors: Koepke Tyson , Schaeffer Scott , Krishnan Vandhana , Jiwan Derick , Harper Artemus , Whiting Matthew , Oraguzie Nnadozie , Dhingra Amit
Published: January 2012

Background

Sweet cherry (Prunus avium L.), a non-model crop with narrow genetic diversity, is an important member of sub-family Amygdoloideae within Rosaceae. Compared to other important members like peach and apple, sweet cherry lacks in genetic and genomic information, impeding understanding of important biological processes and development of efficient breeding approaches. Availability of single nucleotide polymorphism (SNP)-based molecular markers can greatly benefit breeding efforts in such non-model species. RNA-seq approaches employing second generation sequencing platforms offer a unique avenue to rapidly identify gene-based SNPs. Additionally, haplotype markers can be rapidly generated from transcript-based SNPs since they have been found to be extremely utile in identification of genetic variants related to health, disease and response to environment as highlighted by the human HapMap project.

Results

RNA-seq was performed on two sweet cherry cultivars, Bing and Rainier using a 3' untranslated region (UTR) sequencing method yielding 43,396 assembled contigs. In order to test our approach of rapid identification of SNPs without any reference genome information, over 25% (10,100) of the contigs were screened for the SNPs. A total of 207 contigs from this set were identified to contain high quality SNPs. A set of 223 primer pairs were designed to amplify SNP containing regions from these contigs and high resolution melting (HRM) analysis was performed with eight important parental sweet cherry cultivars. Six of the parent cultivars were distantly related to Bing and Rainier, the cultivars used for initial SNP discovery. Further, HRM analysis was also performed on 13 seedlings derived from a cross between two of the parents. Our analysis resulted in the identification of 84 (38.7%) primer sets that demonstrated variation among the tested germplasm. Reassembly of the raw 3'UTR sequences using upgraded transcriptome assembly software yielded 34,620 contigs containing 2243 putative SNPs in 887 contigs after stringent filtering. Contigs with multiple SNPs were visually parsed to identify 685 putative haplotypes at 335 loci in 301 contigs.

Conclusions

This approach, which leverages the advantages of RNA-seq approaches, enabled rapid generation of gene-linked SNP and haplotype markers. The general approach presented in this study can be easily applied to other non-model eukaryotes irrespective of the ploidy level to identify gene-linked polymorphisms that are expected to facilitate efficient Gene Assisted Breeding (GAB), genotyping and population genetics studies. The identified SNP haplotypes reveal some of the allelic differences in the two sweet cherry cultivars analyzed. The identification of these SNP and haplotype markers is expected to significantly improve the genomic resources for sweet cherry and facilitate efficient GAB in this non-model crop.
Sequence based polymorphic (SBP) marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome
Authors: Sahu Binod B , Sumit Rishi , Srivastava Subodh K , Bhattacharyya Madan K
Published: January 2012

Background

Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have made possible the identification of single nucleotide polymorphisms (SNPs) for any genomic regions. Here a sequence based polymorphic (SBP) marker technology for generating molecular markers for targeted genomic regions in Arabidopsis is described.

Results

A ~3X genome coverage sequence of the Arabidopsis thaliana ecotype, Niederzenz (Nd-0) was obtained by applying Illumina's sequencing by synthesis (Solexa) technology. Comparison of the Nd-0 genome sequence with the assembled Columbia-0 (Col-0) genome sequence identified putative single nucleotide polymorphisms (SNPs) throughout the entire genome. Multiple 75 base pair Nd-0 sequence reads containing SNPs and originating from individual genomic DNA molecules were the basis for developing co-dominant SBP markers. SNPs containing Col-0 sequences, supported by transcript sequences or sequences from multiple BAC clones, were compared to the respective Nd-0 sequences to identify possible restriction endonuclease enzyme site variations. Small amplicons, PCR amplified from both ecotypes, were digested with suitable restriction enzymes and resolved on a gel to reveal the sequence based polymorphisms. By applying this technology, 21 SBP markers for the marker poor regions of the Arabidopsis map representing polymorphisms between Col-0 and Nd-0 ecotypes were generated.

Conclusions

The SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for cloning genes based on their genetic map positions and identifying tightly linked molecular markers for selecting desirable genotypes in animal and plant breeding experiments.
Endophytic fungal association via gibberellins and indole acetic acid can improve plant growth under abiotic stress: an example of Paecilomyces formosus LHL10
Authors: Khan Abdul Latif , Hamayun Muhammad , Kang Sang-Mo , Kim Yoon-Ha , Jung Hee-Young , Lee Joong-Hwan , Lee In-Jung
Published: January 2012

Background

Endophytic fungi are little known for exogenous secretion of phytohormones and mitigation of salinity stress, which is a major limiting factor for agriculture production worldwide. Current study was designed to isolate phytohormone producing endophytic fungus from the roots of cucumber plant and identify its role in plant growth and stress tolerance under saline conditions.

Results

We isolated nine endophytic fungi from the roots of cucumber plant and screened their culture filtrates (CF) on gibberellins (GAs) deficient mutant rice cultivar Waito-C and normal GAs biosynthesis rice cultivar Dongjin-byeo. The CF of a fungal isolate CSH-6H significantly increased the growth of Waito-C and Dongjin-byeo seedlings as compared to control. Analysis of the CF showed presence of GAs (GA1, GA3, GA4, GA8, GA9, GA12, GA20 and GA24) and indole acetic acid. The endophyte CSH-6H was identified as a strain of Paecilomyces formosus LHL10 on the basis of phylogenetic analysis of ITS sequence similarity. Under salinity stress, P. formosus inoculation significantly enhanced cucumber shoot length and allied growth characteristics as compared to non-inoculated control plants. The hypha of P. formosus was also observed in the cortical and pericycle regions of the host-plant roots and was successfully re-isolated using PCR techniques. P. formosus association counteracted the adverse effects of salinity by accumulating proline and antioxidants and maintaining plant water potential. Thus the electrolytic leakage and membrane damage to the cucumber plants was reduced in the association of endophyte. Reduced content of stress responsive abscisic acid suggest lesser stress convened to endophyte-associated plants. On contrary, elevated endogenous GAs (GA3, GA4, GA12 and GA20) contents in endophyte-associated cucumber plants evidenced salinity stress modulation.

Conclusion

The results reveal that mutualistic interactions of phytohormones secreting endophytic fungi can ameliorate host plant growth and alleviate adverse effects of salt stress. Such fungal strain could be used for further field trials to improve agricultural productivity under saline conditions.
Thin-film fixed-bed reactor (TFFBR) for solar photocatalytic inactivation of aquaculture pathogen Aeromonas hydrophila
Authors: Khan Sadia J , Reed Robert H , Rasul Mohammad G
Published: January 2012

Background

Outbreaks of infectious diseases by microbial pathogens can cause substantial losses of stock in aquaculture systems. There are several ways to eliminate these pathogens including the use of antibiotics, biocides and conventional disinfectants, but these leave undesirable chemical residues. Conversely, using sunlight for disinfection has the advantage of leaving no chemical residue and is particularly suited to countries with sunny climates. Titanium dioxide (TiO2) is a photocatalyst that increases the effectiveness of solar disinfection. In recent years, several different types of solar photocatalytic reactors coated with TiO2 have been developed for waste water and drinking water treatment. In this study a thin-film fixed-bed reactor (TFFBR), designed as a sloping flat plate reactor coated with P25 DEGUSSA TiO2, was used.

Results

The level of inactivation of the aquaculture pathogen Aeromonas hydrophila ATCC 35654 was determined after travelling across the TFFBR under various natural sunlight conditions (300-1200 W m-2), at 3 different flow rates (4.8, 8.4 and 16.8 L h-1). Bacterial numbers were determined by conventional plate counting using selective agar media, cultured (i) under conventional aerobic conditions to detect healthy cells and (ii) under conditions designed to neutralise reactive oxygen species (agar medium supplemented with the peroxide scavenger sodium pyruvate at 0.05% w/v, incubated under anaerobic conditions), to detect both healthy and sub-lethally injured (oxygen-sensitive) cells. The results clearly demonstrate that high sunlight intensities (≥ 600 W m-2) and low flow rates (4.8 L h-1) provided optimum conditions for inactivation of A. hydrophila ATCC 3564, with greater overall inactivation and fewer sub-lethally injured cells than at low sunlight intensities or high flow rates. Low sunlight intensities resulted in reduced overall inactivation and greater sub-lethal injury at all flow rates.

Conclusions

This is the first demonstration of the effectiveness of the TFFBR in the inactivation of Aeromonas hydrophila at high sunlight intensities, providing proof-of-concept for the application of solar photocatalysis in aquaculture systems.
Arabidopsisplants grown in the field and climate chambers significantly differ in leaf morphology and photosystem components
Authors: Mishra Yogesh , Johansson Jänkänpää Hanna , Kiss Anett Z , Funk Christiane , Schröder Wolfgang P , Jansson Stefan
Published: January 2012

Background

Plants exhibit phenotypic plasticity and respond to differences in environmental conditions by acclimation. We have systematically compared leaves of Arabidopsis thaliana plants grown in the field and under controlled low, normal and high light conditions in the laboratory to determine their most prominent phenotypic differences.

Results

Compared to plants grown under field conditions, the "indoor plants" had larger leaves, modified leaf shapes and longer petioles. Their pigment composition also significantly differed; indoor plants had reduced levels of xanthophyll pigments. In addition, Lhcb1 and Lhcb2 levels were up to three times higher in the indoor plants, but differences in the PSI antenna were much smaller, with only the low-abundance Lhca5 protein showing altered levels. Both isoforms of early-light-induced protein (ELIP) were absent in the indoor plants, and they had less non-photochemical quenching (NPQ). The field-grown plants had a high capacity to perform state transitions. Plants lacking ELIPs did not have reduced growth or seed set rates, but their mortality rates were sometimes higher. NPQ levels between natural accessions grown under different conditions were not correlated.

Conclusion

Our results indicate that comparative analysis of field-grown plants with those grown under artificial conditions is important for a full understanding of plant plasticity and adaptation.
Socioeconomic factors associated with drug consumption in prison population in Mexico
Authors: Nevárez-Sida Armando , Constantino-Casas Patricia , Castro-Ríos Angélica
Published: January 2012

Background

Consumption of illegal drugs is a public health problem in Mexico, and the prison population is a vulnerable group with higher rates of prevalence than in the general population. The objective of this study was to determine the main socioeconomic variables associated with drug consumption in the prison population.

Methods

Utilizing data from the Second Incarcerated Population Survey carried out by the Centre of Research and Teaching of Economics (CIDE) in Mexico, a logistic model in two stages was developed. The first stage analyzed the determinants of habitual drug consumption by prisoners (prior to admittance into prisons), while the second stage of the model addressed drug consumption within prisons.

Results

Prevalence of drug consumption previous to incarceration was 28.5%, although once people were imprisoned this figure dropped to 7.4%. The characteristics that most heavily influenced against the possibility of habitual drug consumption prior to admittance to prison were: preparatory school or higher, being employed and having children; while the variables associated negatively were: male gender, childhood home shared with adults who consumed illegal drugs; abandoning childhood home; and having previous prison sentences. Once in prison, the negative conditions in there are associated with drug consumption.

Conclusions

Work and study during incarceration, in addition to being instruments for rehabilitation, seem to exert an important positive association against drug consumption. However, this correlation seems to be minimized in the face of negative conditions of the penal institution; thus, public policies are necessary to improve the prisoner's environment.
Wild bitter gourd improves metabolic syndrome: A preliminary dietary supplementation trial
Authors: Tsai Chung-Huang , Chen Emily Chin-Fun , Tsay Hsin-Sheng , Huang Ching-jang
Published: January 2012

Background

Bitter gourd (Momordica charantia L.) is a common tropical vegetable that has been used in traditional or folk medicine to treat diabetes. Wild bitter gourd (WBG) ameliorated metabolic syndrome (MetS) in animal models. We aimed to preliminarily evaluate the effect of WBG supplementation on MetS in Taiwanese adults.

Methods

A preliminary open-label uncontrolled supplementation trial was conducted in eligible fulfilled the diagnosis of MetS from May 2008 to April 2009. A total of 42 eligible (21 men and 21 women) with a mean age of 45.7 ± 11.4 years (23 to 63 years) were supplemented with 4.8 gram lyophilized WBG powder in capsules daily for three months and were checked for MetS at enrollment and follow-up monthly. After supplementation was ceased, the participants were continually checked for MetS monthly over an additional three-month period. MetS incidence rate were analyzed using repeated-measures generalized linear mixed models according to the intention-to-treat principle.

Results

After adjusting for sex and age, the MetS incidence rate (standard error, p value) decreased by 7.1% (3.7%, 0.920), 9.5% (4.3%, 0.451), 19.0% (5.7%, 0.021), 16.7% (5.4%, 0.047), 11.9% (4.7%, 0.229) and 11.9% (4.7%, 0.229) at visit 2, 3, 4, 5, 6, and 7 compared to that at baseline (visit 1), respectively. The decrease in incidence rate was highest at the end of the three-month supplementation period and it was significantly different from that at baseline (p = 0.021). The difference remained significant at end of the 4th month (one month after the cessation of supplementation) (p = 0.047) but the effect diminished at the 5th and 6th months after baseline. The waist circumference also significantly decreased after the supplementation (p < 0.05). The WBG supplementation was generally well-tolerated.

Conclusion

This is the first report to show that WBG improved MetS in human which provides a firm base for further randomized controlled trials to evaluate the efficacy of WBG supplementation.
RNAa-mediated overexpression of WT1 induces apoptosis in HepG2 cells
Authors: Qin Qi , Lin Yi-Wei , Zheng Xiang-Yi , Chen Hong , Mao Qi-Qi , Yang Kai , Huang Shou-Jiang , Zhao Zheng-Yan
Published: January 2012

Aim

Recent studies have reported that double-stranded RNA (dsRNA) can activate gene expression by targeting promoter sequence in a process termed RNA activation. The present study was conducted to evaluate the potential of WT1 induction by small activating RNA targeting the WT1 promoter (dsWT1) in the treatment of hepatocellular carcinoma.

Methods

The human hepatocellular carcinoma cell line HepG2 was transfected with dsRNA by liposomes. The expression of mRNA and protein in cells were investigated using real-time reverse real-time quantitative PCR and Western blot, respectively. Cell viability and clonogenicity were determined by MTT assay and clonogenicity assay, respectively. Cell apoptosis was evaluated by flow-cytometric analysis.

Results

Expressions of WT1 mRNA and protein in dsWT1 treated HepG2 cells were significantly elevated. Inhibition of cell viability by dsWT1 was dose-dependent and time-dependent. Reduction of the number and size of colonies formed were found in dsWT1 treated cells. dsWT1 induced significant apoptosis in HepG2 cells. The decreased anti-apoptotic protein Bcl-2 and elevated pro-apoptotic protein Bak expression were detected in dsWT1 treated cells. The level of pro-caspase-3 remarkably decreased and cleaved caspase-3 and PARP fragment were also detected in dsWT1 treated cells.

Conclusion

These data show that RNAa-mediated overexpression of WT1 may have therapeutic potential in the treatment of hepatocellular carcinoma.
Acute cholecystitis in high risk surgical patients: percutaneous cholecystostomy versus laparoscopic cholecystectomy (CHOCOLATE trial): Study protocol for a randomized controlled trial
Authors: Kortram Kirsten , van Ramshorst Bert , Bollen Thomas L , Besselink Marc G H , Gouma Dirk J , Karsten Tom , Kruyt Philip M , Nieuwenhuijzen Grard A P , Kelder Johannes C , Tromp Ellen , Boerma Djamila
Published: January 2012

Background

Laparoscopic cholecystectomy in acute calculous cholecystitis in high risk patients can lead to significant morbidity and mortality. Percutaneous cholecystostomy may be an alternative treatment option but the current literature does not provide the surgical community with evidence based advice.

Methods/Design

The CHOCOLATE trial is a randomised controlled, parallel-group, superiority multicenter trial. High risk patients, defined as APACHE-II score 7-14, with acute calculous cholecystitis will be randomised to laparoscopic cholecystectomy or percutaneous cholecystostomy. During a two year period 284 patients will be enrolled from 30 high volume teaching hospitals. The primary endpoint is a composite endpoint of major complications within three months following randomization and need for re-intervention and mortality during the follow-up period of one year. Secondary endpoints include all other complications, duration of hospital admission, difficulty of procedures and total costs.

Discussion

The CHOCOLATE trial is designed to provide the surgical community with an evidence based guideline in the treatment of acute calculous cholecystitis in high risk patients.

Trial Registration

Netherlands Trial Register (NTR): NTR2666
Equine poisoning by coffee husk (Coffea arabicaL.)
Authors: Delfiol Diego Jose Z , Oliveira-Filho Jose P , Casalecchi Fernanda L , Kievitsbosch Thatiane , Hussni Carlos A , Riet-Correa Franklin , Araujo-Jr João P , Borges Alexandre S
Published: January 2012

Background

In Brazil, coffee (Coffea arabica) husks are reused in several ways due to their abundance, including as stall bedding. However, field veterinarians have reported that horses become intoxicated after ingesting the coffee husks that are used as bedding. The objective of this study was to evaluate whether coffee husk consumption causes intoxication in horses.

Results

Six horses fed coast cross hayad libitumwere given access to coffee husks and excitability, restlessness, involuntary muscle tremors, chewing movements and constant tremors of the lips and tongue, excessive sweating and increased respiration and heart rates were the most evident clinical signs. Caffeine levels were measured in the plasma and urine of these horses on two occasions: immediately before the coffee husks were made available to the animals (T0) and at the time of the clinical presentation of intoxication, 56 h after the animals started to consume the husks (T56). The concentrations of caffeine in the plasma (p < 0.001) and urine (p < 0.001) of these animals were significantly greater at T56 than at T0.

Conclusions

It was concluded that consumption of coffee husks was toxic to horses due to the high levels of caffeine present in their composition. Therefore, coffee husks pose a risk when used as bedding or as feed for horses.