bluuebunny/crossref_metadata_2025_split huggingface dataset:
Report on the SIGIR workshop on "entertain me"
Authors: Belkin Nicholas J. , Clarke Charles L.A. , Gao Ning , Kamps Jaap , Karlgren Jussi 
Published: January 2012

Searchers with a complex information need typically slice-and-dice their problem into several queries and subqueries, and laboriously combine the answers post hoc to solve their tasks. Consider planning a social event at the last day of SIGIR, in the unknown city of Beijing, factoring in distances, timing, and preferences on budget, cuisine, and entertainment. A system supporting the entire search episode should "know" a lot, either from profiles or implicit information, or from explicit information in the query or from feedback. This may lead to the (interactive) construction of a complexly structured query, but sometimes the most obvious query for a complex need is dead simple: entertain me. Rather than returning ten-blue-lines in response to a 2.4-word query, the desired system should support searchers during their whole task or search episode, by iteratively constructing a complex query or search strategy, by exploring the result-space at every stage, and by combining the partial answers into a coherent whole.
The workshop brought together a varied group of researchers covering both user and system centered approaches, who worked together on the problem and potential solutions. There was a strong feeling that we made substantial progress. First, there was general optimism on the wealth of contextual information that can be derived from context or natural interactions without the need for obstrusive explicit feedback. Second, the task of "contextual suggestions"--matching specific types of results against rich profiles--was identified as a manageable first step, and concrete plans for such as track were discussed in the aftermath of the workshop. Third, the identified dimensions of variation--such as the level of engagement, or user versus system initiative--give clear suggestions of the types of input a searcher is willing or able to give and the type of response expected from a system.
The impact of gender on early ill-health retirement in people with heart disease and depression
Authors: Paradise Matt B , Naismith Sharon L , Davenport Tracey A , Hickie Ian B , Glozier Nick S 
Published: January 2012

Objective: Depression and heart disease are major causes of early ill-health retirement. The effect of comorbid depression on the award of ill-health retirement in those with heart disease is unclear, however, and may differ by gender. Given the deleterious effects of ill-health retirement, identifying at-risk groups is important for guiding targeted interventions. Method: We retrospectively analysed baseline data of 20,655 participants from the 45 and Up Study (New South Wales, Australia), who had fully retired between the ages of 45 and 64. We examined the associations of depression and heart disease with ill-health retirement and then adjusted for the presence of common confounders. We then restricted the sample to the 1165 individuals with heart disease prior to retirement, to determine the impact of comorbid depression on IHR and analysed whether there was a differential impact by gender. Results: In the complete sample, 3836 out of 20,655 (18.6%) of the participants retired early due to ill health. Prior heart disease and depression were both independently and strongly associated with ill-health retirement. Those who retired due to ill health were also more likely to be men, less educated, report greater physical disability and were younger at retirement. Among the 1165 for whom heart disease predated any form of retirement, 40% retired due to ill health. Comorbid depression prior to ill-health retirement was strongly associated with an increased risk of this IHR in women (odds ratio = 2.85; 95% confidence interval = 1.20–6.77, p = 0.01), but not in men (interaction term, p = 0.045). Conclusions: Ill-health retirement is common in those with heart disease. Women appear to be particularly susceptible to the effects of comorbid depression. Given the policy emphasis on reducing the number of people leaving the workforce early, women with early heart disease may represent a particular group in whom interventions designed to detect and treat comorbid depression should be targeted.
Changes in psychological distress in Australian adults between 1995 and 2011
Authors: Jorm Anthony F , Reavley Nicola J 
Published: January 2012

Objective: To monitor changes in psychological distress in Australia over a 16-year period during which the availability of mental health services was increasing. Method: Data on psychological distress using the 4-NS scale were analysed from national surveys of adults carried out in 1995, 2003–04 and 2011. Results: No change in psychological distress was found. Conclusions: The data show no improvement in adult mental health during a period when the availability of pharmacological, psychological and population interventions increased. Regular population monitoring of mental health is needed in the future in order to identify emerging needs and to evaluate the impact of service improvements and preventive programmes.
Risk assessment of self- and other-directed aggression in adolescent psychiatric inpatient units
Authors: Phillips Natalie L , Stargatt Robyn , Brown Annya 
Published: January 2012

Objective: To examine the predictive validity of unstructured clinical risk assessment and associated risk factors for aggression in predicting self- and other-directed aggression in the first 4 weeks of admission for patients admitted to an Australian adolescent psychiatric inpatient facility. Method: A retrospective review of patient records was conducted at the Marian Drummond Adolescent Unit during late 2009 for the period of September 2006 to July 2009. Information collected included admission risk assessment ratings, aggressive incident reports, patient diagnoses, sex and history of aggression and self-harming behaviour. Results: A total of 193 adolescents (aged 13–18 years old) were included in retrospective analyses. The hypothesis that unstructured clinical risk assessment would be predictive of self- and other-directed aggression was partially supported. High risk assessment scores were predictive of engagement in other-directed aggression. A history of physical aggression was also found to be predictive of engagement in other-directed aggression; however, it was not as predictive as the risk assessment rating. High risk assessment scores were not predictive of self-directed aggression. A history of engaging in one or more acts of self-harm or suicide was the most predictive of engagement in self-directed aggression during inpatient stay. Female sex also predicted engagement in self-directed aggression. Conclusions: Based on professional expertise, prior experience and intuition, clinicians are relatively good predictors of other-directed aggression in adolescent inpatient units; however, they are less successful at predicting self-directed aggression in this population. It is possible that, unlike other-directed aggression, self-harming behaviour is heavily dependent on environmental factors and that admission to the inpatient unit removes these triggers from the individual’s environment.
The contribution of BDNF and 5-HTT polymorphisms and early life stress to the heterogeneity of major depressive disorder: A preliminary study
Authors: Quinn Candice R , Dobson-Stone Carol , Outhred Tim , Harris Anthony , Kemp Andrew H 
Published: January 2012

Objective: Two reported genetic polymorphisms related to the production of brain-derived neurotrophic factor (BNDF) and reuptake by the serotonin transporter (5-HTT) appear to contribute to depression in combination with stressful life events. The aim of the current study was to investigate the contribution of early life stress (ELS), BDNF (Val versus Met alleles) and 5-HTT polymorphisms (L versus S alleles) to melancholic ( n = 65) and non-melancholic depression ( n = 59). Methods: A mediation approach ((G × G) × E mediation model) was employed to confirm the indirect effects of ELS on the relationship between 5-HTTPLR × BDNF polymorphism combinations and depression subtype. A series of binary logistic regressions were then conducted to determine whether genotype, ELS, and their interaction were able to predict depression subtype. Results: Key findings indicated that BDNF and 5-HTT polymorphisms in combination with ELS contributed to the development of non-melancholic depression. An interaction between BDNF and ELS increased the risk of non-melancholia by 3.327, whereas the interaction between 5-HTT and ELS increased risk by 2.406. Conclusion: The results support a role for genetic factors in the development of non-melancholia. The lack of findings in melancholia indicates that other mechanisms may underlie the subtype. Alternatively, null findings may reflect a Type II error associated with a small sample size. Future studies should consider further examination of differential gene–environment interactions for melancholia versus non-melancholia.
The role of alprazolam for the treatment of panic disorder in Australia
Authors: Moylan Steven , Giorlando Francesco , Nordfjærn Trond , Berk Michael 
Published: January 2012

Objective: To investigate the potential impact of increasing prescription rates of alprazolam for the treatment of panic disorder (PD) in Australia through a review of efficacy, tolerability and adverse outcome literature. Methods: Data were sourced by a literature search using MEDLINE, Embase, PsycINFO and a manual search of scientific journals to identify relevant articles. Clinical practice guidelines from the American Psychiatric Association, National Institute of Clinical Excellence, Royal Australian and New Zealand College of Psychiatrists and World Federation of Societies of Biological Psychiatry were sourced. Prescription data were sourced from Australian governmental sources. Results: Alprazolam has shown efficacy for control of PD symptoms, particularly in short-term controlled clinical trials, but is no longer recommended as a first-line pharmacological treatment due to concerns about the risks of developing tolerance, dependence and abuse potential. Almost no evidence is available comparing alprazolam to current first-line pharmacological treatment. Despite this, prescription rates are increasing. A number of potential issues including use in overdose and impact on car accidents are noted. Conclusion: Although effective for PD symptoms in clinical trials, a number of potential issues may exist with use. Consideration of its future place in PD treatment in Australia may be warranted.
Changes in the prevalence of psychological distress and use of antidepressants or anti-anxiety medications associated with comorbid chronic diseases in the adult Australian population, 2001–2008
Authors: Atlantis Evan , Sullivan Thomas , Sartorius Norman , Almeida Osvaldo P 
Published: January 2012

Objective: To investigate changes in the prevalence of psychological distress and use of antidepressants or anti-anxiety medications associated with comorbid chronic diseases in the adult Australian population from 2001 to 2008. Methods: Participants were 48,359 adults aged ≥ 25 years from the 2001, 2004–05 or 2007–08 Australian National Health Surveys. Clinically significant psychological distress was determined with the 10-item Kessler Psychological Distress Scale (using scores ≥ 30). Contemporaneous use of antidepressants or anti-anxiety medications and the presence of chronic diseases including diabetes, cardiovascular disease, cancer, asthma and arthritis were by self-report. Results: Overall, the prevalence of psychological distress was relatively stable (3.9 vs. 3.7%) between 2001 and 2008, but increased from 5.9 to 7.0% and 4.6 to 5.0% for people with diabetes and cardiovascular disease. In contrast, the use of antidepressants or anti-anxiety medications decreased from 7.3 to 4.8% across all disease categories. On average, the odds of psychological distress and use of antidepressants or anti-anxiety medications was 1.15 to 1.59-fold and 1.10 to 1.64-fold higher, respectively, for all chronic diseases after adjustments for socio-demographic and lifestyle variables. After further adjustment for all chronic disease predictors fitted jointly, these associations decreased in strength (percentage change in the log odds ratio) by 14 to 98%. Each additional chronic disease increased the odds of both psychological distress (1.34-fold higher) and use of antidepressants or anti-anxiety medications (1.40-fold higher) in a dose–response manner. Conclusions: Although the prevalence of psychological distress changed little for adult Australians between 2001 and 2008, it increased for people with diabetes and cardiovascular disease. Conversely, the reported use of antidepressants or anti-anxiety medications progressively decreased for people with, and without, chronic diseases. Overall, there was a persistently higher psychopathology burden associated with each and increasing number of comorbid chronic diseases.
Survivors of self-inflicted stab wounds
Authors: Gerard Andrew , de Moore Gregory , Nielssen Olav , Large Matthew 
Published: January 2012

Objective: There are a number of studies describing the survivors of self-incised wounds, but few studies have described the psychiatric condition of survivors of self-inflicted stab wounds. We aimed to describe the characteristics of a complete series of patients treated for self-inflicted stab wounds in a major hospital, and to compare the characteristics of patients with psychotic illness to those with other conditions. Methods: A review of the files of all patients who had a psychiatric evaluation after presenting for treatment following deliberate self-harm. Stab wounds were defined as wounds made by a sharp instrument in which the width was less than the depth. Results: There were 41 survivors of self-inflicted stab wounds among 2119 patients assessed after deliberate self-harm. Of these, 15 were diagnosed with a psychotic illness and the remainder had other conditions, including depression, personality disorder and substance use disorder. There was little difference in the demographic features, clinical variables and in the proportion who were intoxicated between patients diagnosed with psychotic illness and those with other disorders. The patients with psychosis were more likely to have inflicted multiple stab wounds, to have stabbed their chest or abdomen and to have reported the intention of committing suicide. Conclusions: The results suggest that a significant proportion of patients who present for treatment after stabbing themselves suffer from a psychotic illness. However, there were few differences in the characteristics of the patients who had a diagnosis of psychosis and those with other disorders.
The Dynamic International Prognostic Scoring System for myelofibrosis predicts outcomes after hematopoietic cell transplantation
Authors: Scott Bart L. , Gooley Ted A. , Sorror Mohamed L. , Rezvani Andrew R. , Linenberger Michael L. , Grim Jonathan , Sandmaier Brenda M. , Myerson David , Chauncey Thomas R. , Storb Rainer , Buxhofer-Ausch Veronika , Radich Jerald P. , Appelbaum Frederick R. , Deeg H. Joachim 
Published: January 2012

Abstract
Studies by the International Working Group showed that the prognosis of myelofibrosis patients is predicted by the Dynamic International Prognostic Scoring System (DIPSS) risk categorization, which includes patient age, constitutional symptoms, hemoglobin, leukocyte count, and circulating blasts. We evaluated the prognostic usefulness of the DIPSS in 170 patients with myelofibrosis, 12 to 78 years of age (median, 51.5 years of age), who received hematopoietic cell transplantation (HCT) between 1990 and 2009 from related (n = 86) or unrelated donors (n = 84). By DIPSS, 21 patients had low-risk disease, 48 had intermediate-1, 50 had intermediate-2, and 51 had high-risk disease. Five-year incidence of relapse, relapse-free survival, overall survival, and nonrelapse mortality for all patients were 10%, 57%, 57%, and 34%, respectively. Among patients with DIPSS high-risk disease, the hazard ratio for post-HCT mortality was 4.11 (95% CI, 1.44-11.78; P = .008), and for nonrelapse mortality was 3.41 (95% CI, 1.15-10.09; P = .03) compared with low-risk patients. After a median follow-up of 5.9 years, the median survivals have not been reached for DIPSS risk groups low and intermediate-1, and were 7 and 2.5 years for intermediate-2 and high-risk patients, respectively. Thus, HCT was curative for a large proportion of patients with myelofibrosis, and post-HCT success was dependent on pre-HCT DIPSS classification.
A refinement of Sándor-Tóth's inequality
Authors: Minculete Nicuşor , Pozna Claudiu , Precup Radu-Emil 
Published: January 2012

Abstract
The objective of this article is to show a refinement of Sándor-Tóth's inequality related to the arithmetic functions which use unitary divisors. A new estimate of the average order of the arithmetic function given by Sándor-Tóth's inequality is suggested.
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases
Authors: Kumar Akhil , Suthers Patrick F , Maranas Costas D 
Published: January 2012

AbstractBackgroundIncreasingly, metabolite and reaction information is organized in the form of genome-scale metabolic reconstructions that describe the reaction stoichiometry, directionality, and gene to protein to reaction associations. A key bottleneck in the pace of reconstruction of new, high-quality metabolic models is the inability to directly make use of metabolite/reaction information from biological databases or other models due to incompatibilities in content representation (i.e., metabolites with multiple names across databases and models), stoichiometric errors such as elemental or charge imbalances, and incomplete atomistic detail (e.g., use of generic R-group or non-explicit specification of stereo-specificity).DescriptionMetRxn is a knowledgebase that includes standardized metabolite and reaction descriptions by integrating information from BRENDA, KEGG, MetaCyc, Reactome.org and 44 metabolic models into a single unified data set. All metabolite entries have matched synonyms, resolved protonation states, and are linked to unique structures. All reaction entries are elementally and charge balanced. This is accomplished through the use of a workflow of lexicographic, phonetic, and structural comparison algorithms. MetRxn allows for the download of standardized versions of existing genome-scale metabolic models and the use of metabolic information for the rapid reconstruction of new ones.ConclusionsThe standardization in description allows for the direct comparison of the metabolite and reaction content between metabolic models and databases and the exhaustive prospecting of pathways for biotechnological production. This ever-growing dataset currently consists of over 76,000 metabolites participating in more than 72,000 reactions (including unresolved entries). MetRxn is hosted on a web-based platform that uses relational database models (MySQL).
Transcriptome changes during fruit development and ripening of sweet orange (Citrus sinensis)
Authors: Yu Keqin , Xu Qiang , Da Xinlei , Guo Fei , Ding Yuduan , Deng Xiuxin 
Published: January 2012

Abstract

Background
The transcriptome of the fruit pulp of the sweet orange variety Anliu (WT) and that of its red fleshed mutant Hong Anliu (MT) were compared to understand the dynamics and differential expression of genes expressed during fruit development and ripening.

Results
The transcriptomes of WT and MT were sampled at four developmental stages using an Illumina sequencing platform. A total of 19,440 and 18,829 genes were detected in MT and WT, respectively. Hierarchical clustering analysis revealed 24 expression patterns for the set of all genes detected, of which 20 were in common between MT and WT. Over 89% of the genes showed differential expression during fruit development and ripening in the WT. Functional categorization of the differentially expressed genes revealed that cell wall biosynthesis, carbohydrate and citric acid metabolism, carotenoid metabolism, and the response to stress were the most differentially regulated processes occurring during fruit development and ripening.

Conclusion
A description of the transcriptomic changes occurring during fruit development and ripening was obtained in sweet orange, along with a dynamic view of the gene expression differences between the wild type and a red fleshed mutant.
Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development
Authors: Bizuayehu Teshome T , Lanes Carlos FC , Furmanek Tomasz , Karlsen Bård O , Fernandes Jorge MO , Johansen Steinar D , Babiak Igor 
Published: January 2012

Abstract

Background
MicroRNAs (miRNAs) play a major role in animal ontogenesis. Size variants of miRNAs, isomiRs, are observed along with the main miRNA types, but their origin and possible biological role are uncovered yet. Developmental profiles of miRNAs have been reported in few fish species only and, to our knowledge, differential expressions of isomiRs have not yet been shown during fish development. Atlantic halibut, Hippoglossus hippoglossus L., undergoes dramatic metamorphosis during early development from symmetrical pelagic larval stage to unsymmetrical flatfish. No data exist on role of miRNAs in halibut metamorphosis.

Results
miRNA profiling using SOLiD deep sequencing technology revealed a total of 199 conserved, one novel antisense, and one miRNA* mature form. Digital expression profiles of selected miRNAs were validated using reverse transcription quantitative PCR. We found developmental transition-specific miRNA expression. Expression of some miRNA* exceeded the guide strand miRNA. We revealed that nucleotide truncations and/or additions at the 3' end of mature miRNAs resulted in size variants showing differential expression patterns during the development in a number of miRNA families. We confirmed the presence of isomiRs by cloning and Sanger sequencing. Also, we found inverse relationship between expression levels of sense/antisense miRNAs during halibut development.

Conclusion
Developmental transitions during early development of Atlantic halibut are associated with expression of certain miRNA types. IsomiRs are abundant and often show differential expression during the development.
A novel expression system for production of soluble prion proteins in E. coli
Authors: Abskharon Romany NN , Ramboarina Stephanie , El Hassan Hassan , Gad Wael , Apostol Marcin I , Giachin Gabriele , Legname Giuseppe , Steyaert Jan , Messens Joris , Soror Sameh H , Wohlkonig Alexandre 
Published: January 2012

Abstract
Expression of eukaryotic proteins in Escherichia coli is challenging, especially when they contain disulfide bonds. Since the discovery of the prion protein (PrP) and its role in transmissible spongiform encephalopathies, the need to obtain large quantities of the recombinant protein for research purposes has been essential. Currently, production of recombinant PrP is achieved by refolding protocols. Here, we show that the co-expression of two different PrP with the human Quiescin Sulfhydryl OXidase (QSOX), a human chaperone with thiol/disulfide oxidase activity, in the cytoplasm of E. coli produces soluble recombinant PrP. The structural integrity of the soluble PrP has been confirmed by nuclear magnetic resonance spectroscopy, demonstrating that properly folded PrP can be easily expressed in bacteria. Furthermore, the soluble recombinant PrP produced with this method can be used for functional and structural studies.