bluuebunny/crossref_metadata_2025 huggingface dataset:
Mycobacterium marinum infection complicated by anti-tumour necrosis factor therapy
Authors: Ramos José M. , García-Sepulcre Mariana F. , Rodríguez Juan C. , Padilla Sergio , Gutiérrez Félix
Published: February 2010

Mycobacteria other than tuberculosis infections in patients taking various tumour necrosis factor (TNF)-αinhibitors have been reported in the literature. We describe sporotrichoid spread ofMycobacterium marinumin a man with Crohn's disease treated with infliximab. After starting ethambutol and rifampicin and discontinuing infliximab, a worsening appeared.M. marinuminfection may have a potential local spread and systemic dissemination in patients treated with TNF-αinhibitors.
Endocarditis caused by Lactobacillus jensenii in an immunocompetent patient
Authors: Fradiani Piera Assunta , Petrucca Andrea , Ascenzioni Fiorentina , Di Nucci Giandomenico , Teggi Antonella , Bilancini Silvia , Cipriani Paola
Published: February 2010

Lactobacilli are Gram-positive rod-shaped bacteria that inhabit the oral cavity, gastrointestinal tract, vagina and nasal cavity. In this report, a rare case of Lactobacillus jensenii endocarditis in a 47-year-old immunocompetent patient is described. Blood cultures and a replaced mitral valve were positive for L. jensenii as assessed by 16S rRNA gene sequencing. Based on susceptibility tests the patient was successfully treated with a mixture of teicoplanin and meropenem antimicrobial therapy.
Diversity of CRISPR loci in Escherichia coli
Authors: Díez-Villaseñor C. , Almendros C. , García-Martínez J. , Mojica F. J. M.
Published: February 2010

CRISPR (clustered regularly interspaced short palindromic repeats) and CAS (CRISPR-associated sequence) proteins are constituents of a novel genetic barrier that limits horizontal gene transfer in prokaryotes by means of an uncharacterized mechanism. The fundamental discovery of small RNAs as the guides of the defence apparatus arose as a result of Escherichia coli studies. However, a survey of the system diversity in this species in order to further contribute to the understanding of the CRISPR mode of action has not yet been performed. Here we describe two CRISPR/CAS systems found in E. coli, following the analysis of 100 strains representative of the species' diversity. Our results substantiate different levels of activity between loci of both CRISPR types, as well as different target preferences and CRISPR relevances for particular groups of strains. Interestingly, the data suggest that the degeneration of one CRISPR/CAS system in E. coli ancestors could have been brought about by self-interference.
Isethionate formation from taurine in Chromohalobacter salexigens: purification of sulfoacetaldehyde reductase
Authors: Krejčík Zdeněk , Hollemeyer Klaus , Smits Theo H. M. , Cook Alasdair M.
Published: February 2010

Bacterial generation of isethionate (2-hydroxyethanesulfonate) from taurine (2-aminoethanesulfonate) by anaerobic gut bacteria was established in 1980. That phenomenon in pure culture was recognized as a pathway of assimilation of taurine-nitrogen. Based on the latter work, we predicted from genome-sequence data that the marine gammaproteobacterium Chromohalobacter salexigens DSM 3043 would exhibit this trait. Quantitative conversion of taurine to isethionate, identified by mass spectrometry, was confirmed, and the taurine-nitrogen was recovered as cell material. An eight-gene cluster was predicted to encode the inducible vectorial, scalar and regulatory enzymes involved, some of which were known from other taurine pathways. The genes (Csal_0153–Csal_0156) encoding a putative ATP-binding-cassette (ABC) transporter for taurine (TauAB1B2C) were shown to be inducibly transcribed by reverse transcription (RT-) PCR. An inducible taurine : 2-oxoglutarate aminotransferase [EC 2.6.1.55] was found (Csal_0158); the reaction yielded glutamate and sulfoacetaldehyde. The sulfoacetaldehyde was reduced to isethionate by NADPH-dependent sulfoacetaldehyde reductase (IsfD), a member of the short-chain alcohol dehydrogenase superfamily. The 27 kDa protein (SDS-PAGE) was identified by peptide-mass fingerprinting as the gene product of Csal_0161. The putative exporter of isethionate (IsfE) is encoded by Csal_0160; isfE was inducibly transcribed (RT-PCR). The presumed transcriptional regulator, TauR (Csal_0157), may autoregulate its own expression, typical of GntR-type regulators. Similar gene clusters were found in several marine and terrestrial gammaproteobacteria, which, in the gut canal, could be the source of not only mammalian, but also arachnid and cephalopod isethionate.
An archaeal order with multiple minichromosome maintenance genes
Authors: Walters Alison D. , Chong James P. J.
Published: February 2010

In eukaryotes, a complex of six highly related minichromosome maintenance (MCM) proteins is believed to function as the replicative helicase. Until recently, systems for exploring the molecular mechanisms underlying eukaryotic MCM function have been biochemically intractable. To overcome this, molecular studies of MCM function have been carried out using MCM homologues from the archaea. Archaeal MCM systems studied to date possess a single functional MCM, which forms a homohexameric complex that displays DNA binding, ATPase and helicase activities. We have identified an archaeal order that possesses multiple MCM homologues. blast searches of available Methanococcales genomes reveal that members of this order possess between two and eight MCM homologues. Phylogenetic analysis suggests that an ancient duplication in the Methanococcales gave rise to two major groups of MCMs. One group contains Methanococcus maripaludis S2 McmD and possesses a conserved C-terminal insert similar to one observed in eukaryotic MCM3, while the other group contains McmA, -B and -C. Analysis of the genome context of MCMs in the latter group indicates that these genes could have arisen from phage-mediated events. When co-expressed in Escherichia coli, the four MCMs from M. maripaludis co-purify, indicating the formation of heteromeric complexes in vitro. The presence of homologues from both groups in all Methanococcales indicates that there could be functionally important differences between these proteins and that Methanococcales MCMs may therefore provide an interesting additional model for eukaryotic MCM function.
Dynamic changes in the human methylome during differentiation
Authors: Laurent Louise , Wong Eleanor , Li Guoliang , Huynh Tien , Tsirigos Aristotelis , Ong Chin Thing , Low Hwee Meng , Kin Sung Ken Wing , Rigoutsos Isidore , Loring Jeanne , Wei Chia-Lin
Published: February 2010

DNA methylation is a critical epigenetic regulator in mammalian development. Here, we present a whole-genome comparative view of DNA methylation using bisulfite sequencing of three cultured cell types representing progressive stages of differentiation: human embryonic stem cells (hESCs), a fibroblastic differentiated derivative of the hESCs, and neonatal fibroblasts. As a reference, we compared our maps with a methylome map of a fully differentiated adult cell type, mature peripheral blood mononuclear cells (monocytes). We observed many notable common and cell-type-specific features among all cell types. Promoter hypomethylation (both CG and CA) and higher levels of gene body methylation were positively correlated with transcription in all cell types. Exons were more highly methylated than introns, and sharp transitions of methylation occurred at exon–intron boundaries, suggesting a role for differential methylation in transcript splicing. Developmental stage was reflected in both the level of global methylation and extent of non-CpG methylation, with hESC highest, fibroblasts intermediate, and monocytes lowest. Differentiation-associated differential methylation profiles were observed for developmentally regulated genes, including the HOX clusters, other homeobox transcription factors, and pluripotence-associated genes such as POU5F1, TCF3, and KLF4. Our results highlight the value of high-resolution methylation maps, in conjunction with other systems-level analyses, for investigation of previously undetectable developmental regulatory mechanisms.
Positioned and G/C-capped poly(dA:dT) tracts associate with the centers of nucleosome-free regions in yeast promoters
Authors: Wu Randy , Li Hao
Published: February 2010

Eukaryotic transcriptional regulation is mediated by the organization of nucleosomes in promoter regions. Most Saccharomyces cerevisiae promoters have a highly stereotyped chromatin organization, where nucleosome-free regions (NFR) are flanked by well-ordered nucleosomes. We have found that yeast promoters fall into two classes differing in NFR sharpness, and that this distinction follows a known transcriptional dichotomy in yeast genes. A class of yeast promoters having well-defined NFRs are characterized by positioned patterns of poly(dA:dT) tracts with several novel features. First, poly(dA:dT) tracts are localized in a strand-dependent manner, with poly(dA) tracts lying proximal to transcriptional start sites and poly(dT) tracts lying distal, and collectively define a symmetry axis that is coincident with NFR centers. Second, poly(dA:dT) tracts are preferentially “capped” by G:C residues on the terminus proximal to the symmetry axis. Both signature features co-vary with fine positional variations between NFRs, establishing a closely knit relationship between poly(dA:dT) tracts, their capping patterns, and the central coordinates of NFRs. We found that these features are unique to promoters with well-defined NFRs, and that these promoters display significant difference between in vitro and in vivo nucleosome occupancy patterns. These observations are consistent with a model in which localized and G:C-capped poly(dA:dT) tracts initiate or facilitate the formation of NFRs at their center, possibly with chromatin remodeling and transcriptional machines involved.
Testing the synergistic effects of GnRH and testosterone on the reproductive physiology of pre‐adult pink salmonOncorhynchus gorbuscha
Authors: Crossin G. T. , Hinch S. G. , Cooke S. J. , Patterson D. A. , Lotto A. G. , Van Der Kraak G. , Zohar Y. , Klenke U. , Farrell A. P.
Published: February 2010

To test the hypothesis that the hypothalmic gonadotropin‐releasing hormone (GnRH) and testosterone (T) co‐treatment stimulates both the hypothalmo–pituitary–gonadal (HPG) and hypothalmo–pituitary–interrenal axes, the reproductive and osmoregulatory responses of pre‐adult pink salmonOncorhynchus gorbuschawere compared after GnRH and T administration either alone or in combination. Relative to controls, neither GnRH nor T treatment resulted in significantly greater ovarian or testicular growth, but co‐treatment significantly increased ovarian growth after 5 months. Interestingly, the stimulation was undetectable after 3 months. However, once daily photoperiod began shortening after the summer solstice,c.2 months before the natural spawning date, GnRH+T‐treated females were stimulated to produce larger ovaries. Final fish body length and the size of individual eggs did not differ among treatment groups. GnRH+T eggs, however, showed signs of advanced vitellogenesis relative to GnRH‐treated and control eggs, whereas T‐treated eggs became atretic. Testis size increased significantly from initial values and most males were spermiating, but this growth and development were independent of hormone treatments. Final plasma ion, metabolite and cortisol concentrations did not differ among treatment groups. It is concluded that GnRH+T co‐treatment was effective in stimulating female but not male maturation. GnRH and T treatment, however, presumably had little effect on the hypothalmo–pituitary–interrenal axis as observed by ionoregulatory status.
Roles of hepatocyte nuclear factors (HNF) in the regulation of reproduction in teleosts
Authors: Huang W.‐T. , Weng C.‐F.
Published: February 2010

Hepatocyte nuclear factor (HNF) families are composed of liver‐enriched transcription factors and upstream regulators of many liver‐specific genes. HNF are involved in liver‐specific gene expression, metabolism, development, cell growth and many cellular functions in the body. HNF genes can be activated or influenced by several hormones and insulin‐like growth factors (IGF), and different combinations of the four HNF factors form a network in controlling the expression of liver‐specific or liver‐enriched genes. The functions of these factors and their interactions within the gonads of bony fishes, however, are not well understood, and the related literature is scant. Recently, several members of the HNF families have been detected in teleost gonads together with their downstream genes (IGF‐I and IGF‐II), suggesting that these HNF could be upregulated in vitro by steroid hormones. Thus, the hormone–HNF–IGF–gonad interaction may be an alternative axis in the reproductive mechanism that acts in concert with the conventional hypothalamus–pituitary–gonad pathway. This may help the early development and maturation of the gonad or gamete, sexual maturity or reversion and spawning‐regulating mechanisms among fishes to be understood.
External and internal controls of lunar‐related reproductive rhythms in fishes
Authors: Takemura A. , Rahman M. S. , Park Y. J.
Published: February 2010

Reproductive activities of many fish species are, to some extent, entrained to cues from the moon. During the spawning season, synchronous spawning is repeated at intervals of c. 1 month (lunar spawning cycle) and 2 weeks (semi‐lunar spawning cycle) or daily according to tidal changes (tidal spawning cycle). In species showing lunar‐related spawning cycles, oocytes in the ovary develop towards and mature around a specific moon phase for lunar spawners, around spring tides for semi‐lunar spawners and at daytime high tides for tidal spawners. The production of sex steroid hormones also changes in accordance with synchronous oocyte development. Since the production of the steroid hormones with lunar‐related reproductive periodicity is regulated by gonadotropins, it is considered that the higher parts of the hypothalamus–pituitary–gonad axis play important roles in the perception and regulation of lunar‐related periodicity. It is likely that fishes perceive cues from the moon by sensory organs; however, it is still unknown how lunar cues are transduced as an endogenous rhythm exerting lunar‐related spawning rhythmicity. Recent research has revealed that melatonin fluctuated according to the brightness at night, magnetic fields and the tidal cycle. In addition, cyclic changes in hydrostatic pressure had an effect on monoamine contents in the brain. These factors may be indirectly related to the exertion of lunar‐related periodicity. Molecular approaches have revealed that mRNA expressions of light‐sensitive clock genes change with moonlight, suggesting that brightness at night plays a role in phase‐shifting or resetting of biological clocks. Some species may have evolved biological clocks in relation to lunar cycles, although it is still not known how lunar periodicities are endogenously regulated in fishes. This review demonstrates that lunar‐related periodicity is utilized and incorporated by ecological and physiological mechanisms governing the reproductive success of fishes.
Comparative energetics and physiology of parental care in smallmouth bass Micropterus dolomieu across a latitudinal gradient
Authors: Gravel M.‐A. , Couture P. , Cooke S. J.
Published: February 2010

The energetic and physiological status of parental smallmouth bass Micropterus dolomieu was investigated across the majority of their latitudinal range at the onset and near the end of care. Variables such as tissue lipid stores, plasma indicators of nutritional status and chronic stress and white muscle were used to define energetic and physiological status. Results showed that northern males (48° N) were larger and heavier than mid‐northern (44° N) and southern (36° N) latitude males. For a given body size, northern males had greater whole‐body lipid across the parental care period and tended to feed more (based on gut contents) than mid‐northern and southern latitude conspecifics. Indicators of nutritional status were also highest in northern males. Conversely, the southern males exhibited the greatest capacity for biosynthesis across the entire parental care period as indicated by the highest level of nucleoside diphosphate kinase activities. Collectively, these finding suggest that the energetic costs and physiological consequences of care vary across latitudes, providing some of the first mechanistic evidence of how environmental conditions can influence both the ecological and physiological costs of reproduction for wild animals during parental care. The data also suggest that lake‐specific processes that can vary independently of latitude may be important, necessitating additional research on fish reproductive physiology across landscapes.
The role of the maturation‐inducing steroid, 17,20β‐dihydroxypregn‐4‐en‐3‐one, in male fishes: a review
Authors: Scott A. P. , Sumpter J. P. , Stacey N.
Published: February 2010

The major progestin in teleosts is not progesterone, as in tetrapods, but 17,20β‐dihydroxypregn‐4‐en‐3‐one (17,20β‐P) or, in certain species, 17,20β,21‐trihydroxy‐pregn‐4‐en‐3‐one (17,20β,21‐P). Several functions for 17,20β‐P and 17,20β,21‐P have been proposed (and in some cases proved). These include induction of oocyte final maturation and spermiation (milt production), enhancement of sperm motility (by alteration of the pH and fluidity of the seminal fluid) and acting as a pheromone in male cyprinids. Another important function, initiation of meiosis (the first step in both spermatogenesis and oogenesis), has only very recently been proposed. This is a process that takes place at puberty in all fishes and once a year in repeat spawners. The present review critically examines the evidence to support the proposed functions of 17,20β‐P in males, including listing of the evidence for the presence of 17,20β‐P in the blood plasma of male fishes and discussion of why, in many species, it appears to be absent (or present at low and, in some cases, unvarying concentrations); consideration of the evidence, obtained mainly from in vitro studies, for this steroid being predominantly produced by the testis, for its production being under the control of luteinizing hormone (gonadotrophin II) and, at least in salmonids, for two cell types (Leydig cells and sperm cells) being involved in its synthesis; discussion of the factors involved in the regulation of the switch from androgen to 17,20β‐P production that seems to occur in many species just at the time of spermiation; discussion of the effects of in vivo injection and application of 17,20β‐P (and closely related compounds) in males; a listing of previously published evidence that supports the proposed new function of 17,20β‐P as an initiator of meiosis; finally, discussion of the evidence for environmental endocrine disruption by progestins in fishes.
Functional and evolutionary insights into vertebrate kisspeptin systems from studies of fish brain
Authors: Akazome Y. , Kanda S. , Okubo K. , Oka Y.
Published: February 2010

The kiss1 gene product kisspeptin is now considered to be an essential regulator of the hypothalamic–pituitary–gonadal (HPG) axis in most vertebrate species. Recent findings in fishes are beginning to set a new stage for the kisspeptin study; the existence of paralogous kisspeptin genes as well as kisspeptin receptor (formerly called GPR54) genes has quite recently been reported in several fish and amphibian species. The fishes may provide excellent animal models for the study of general principles underlying the kisspeptin and kisspeptin receptor systems of vertebrates from the evolutionary viewpoint. Unlike placental and marsupial mammalian species mainly studied so far, many teleost species have two paralogous genes of kisspeptin, kiss1 and kiss2. Medaka, Oryzias latipes, in which kiss1 and kiss2 are expressed in distinctive hypothalamic neuron populations, is a good model system for the study of central regulation of reproduction. Here, the kiss1 system but not the kiss2 system shows expression dynamics strongly indicative of its direct involvement in the HPG axis regulation via its actions on GnRH1 neurons. On the other hand, the kiss1 gene is missing, and only kiss2 is expressed in some fish species. Also, there are some recent reports that Kiss2 peptide may be a potent regulator of reproduction in some fish species. The ancestral vertebrate probably already had two paralogous kiss genes, and their main function was the HPG axis regulation. In the species that retained both paralogues during evolution, either Kiss1 or Kiss2 predominantly retains its ability for the HPG axis regulation, while the other may assume new non‐reproductive functions (neofunctionalization). Alternatively, both the paralogues may assume complementary functions in the HPG axis regulation (subfunctionalization). After the divergence of teleost and tetrapod lineages, either one of the two paralogues, or even both in birds, have been lost (degradation) or became a pseudogene (non‐functionalization), but the remaining paralogue retained its original function of HPG axis regulation. The identification of multiple forms of kisspeptin receptors and the rather promiscuous ligand–receptor relationships has led to the further proposal that such promiscuousness may be the basis for the functional robustness of kisspeptin and kisspeptin receptor systems in the HPG axis regulation, when one or both paralogous genes are lost or functionally partitioned during evolution.
Progression through early drinking milestones in an adolescent treatment sample
Authors: Jackson Kristina M.
Published: February 2010

Aims  Research using nationally representative and community samples demonstrates a robust association between early onset of drinking and increased likelihood of numerous adverse outcomes. However, little is known about the subsequent drinking that occurs early in the drinking career. The present study dissects the transition from any alcohol use to treatment entry by taking a fine‐grained approach to examining the attainment and progression of drinking events in a sample of adolescents in substance use treatment.

Design/Setting  Data were taken from the Drug Abuse Treatment Outcome Study for Adolescents (DATOS‐A), a multi‐site, community‐based study of adolescents entering treatment.

Participants  Respondents included 3331 youth aged 12–18 years (mean = 15.75) admitted to treatment in 1993–95 (74% male, 52% white, 24% African American, 20% Hispanic).

Measurements  Age of attainment was obtained for five drinking‐related milestones, including first drink of alcohol, first time drunk, first monthly drinking, first drank five or more drinks/day on a weekly basis and first drank five or more drinks/day on a daily basis.

Findings  Most milestones were attained at a very early age, and average progression through adjacent drinking events was relatively swift, Movement through early drinking milestones was accelerated in girls and white youth. Youth who reported their first drink at an early age (age 10 or younger) showed slower progression, suggesting the existence of distinct processes underlying early use and drinking transitions within an individual.

Conclusions  This study provides data relevant to understanding drinking progression/natural history in a large clinical sample, especially for differences by gender and ethnicity. The findings have implications for the identification of intermediate stages that might benefit from selected intervention programs.
Gender differences in genetic and environmental influences on gambling: results from a sample of twins from the National Longitudinal Study of Adolescent Health
Authors: Beaver Kevin M. , Hoffman Taylor , Shields Ryan T. , Vaughn Michael G. , DeLisi Matt , Wright John Paul
Published: February 2010

Aims  To examine the extent to which genetic factors and shared and non‐shared environmental factors are implicated in the development of gambling behaviors and to examine whether there are gender differences in the genetic and environmental contributors to gambling behaviors.

Design  A genetically informative analysis was performed by using DeFries–Fulker (DF) analysis.

Setting  Analysis of secondary data drawn from the National Longitudinal Study of Adolescent Health (Add Health).

Participants  A total of 324 monozygotic (MZ) twins and 278 same‐sex dizygotic (DZ) twins were included in the analysis. Of these twins, there were 150 male MZ twins, 144 male DZ twins, 174 female MZ twins and 134 female DZ twins.

Measurements  Gambling behavior was measured through eight self‐reported questions that tapped a range of items designed to measure problems related to gambling. Self‐reported measures of self‐control and delinquent involvement were also included to examine the degree to which these factors covaried with gambling behavior.

Findings  The results of the DF analysis indicated that when male and female twin pairs were analyzed simultaneously, genetic factors explained approximately 70% of the variance in gambling and non‐shared environmental factors explained the remaining variance. When gender‐specific models were calculated, substantial gender differences emerged. For males, genetic factors explained approximately 85% of the variance in gambling, with the non‐shared environment accounting for the remaining variance. For females, genetic factors explained none of the variance in gambling behaviors, while the shared environment explained 45% of the variance and the non‐shared environment explained 55% of the variance.

Conclusions  Analysis of twins from the Add Health data suggests that there are significant gender differences in the genetic and environmental underpinnings to gambling behaviors.
Trends in and predictors of second‐hand smoke exposure indexed by cotinine in children in England from 1996 to 2006
Authors: Sims Michelle , Tomkins Susannah , Judge Ken , Taylor Gordon , Jarvis Martin J , Gilmore Anna
Published: February 2010

Aims To explore trends in and predictors of second‐hand smoke (SHS) exposure in children. To identify whether inequalities in SHS exposure are changing over time.

Design Repeated cross‐sectional study with data from eight annual surveys conducted over an 11‐year period from 1996 to 2006.

Setting England.

Participants Nationally representative samples of children aged 4–15 years living in private households.

Measurements Saliva cotinine (4–15‐year‐olds), current smoking status (8–15‐year‐olds), smoking status of parents and carers, smoking in the home, socio‐demographic variables.

Findings The most important predictors of SHS exposure were modifiable factors—whether people smoke in the house on most days, whether the parents smoke and whether the children are looked after by carers who smoke. Children from more deprived households were more exposed and this remained the case even after parental smoking status has been controlled for. Exposure over time has fallen markedly among children (59% decline over 11 years in geometric mean cotinine), with the most marked decline observed in the period immediately preceding smoke‐free legislation. Declines in exposure have generally been greater in children most exposed at the outset. For example, in children whose parents both smoke, median cotinine declined annually by 0.115 ng/ml compared with 0.019 ng/ml where neither parent smokes (P < 0.05).

Conclusions In the 11 years leading up to smoke‐free legislation in England, the overall level of SHS exposure in children as well as absolute inequalities in exposure have been declining. Further efforts to encourage parents and carers to quit and to avoid smoking in the home would benefit child health.
Missing data assumptions and methods in a smoking cessation study
Authors: Barnes Sunni A. , Larsen Michael D. , Schroeder Darrell , Hanson Andrew , Decker Paul A.
Published: February 2010

Aim  A sizable percentage of subjects do not respond to follow‐up attempts in smoking cessation studies. The usual procedure in the smoking cessation literature is to assume that non‐respondents have resumed smoking. This study used data from a study with a high follow‐up rate to assess the degree of bias that may be caused by different methods of imputing missing data.

Design and methods  Based on a large data set with very little missing follow‐up information at 12 months, a simulation study was undertaken to compare and contrast missing data imputation methods (assuming smoking, propensity score matching and optimal matching) under various assumptions as to how the missing data arose (randomly generated missing values, increased non‐response from smokers and a hybrid of the two).

Findings  Missing data imputation methods all resulted in some degree of bias which increased with the amount of missing data.

Conclusion  None of the missing data imputation methods currently available can compensate for bias when there are substantial amounts of missing data.
Impact of injecting drug use on mortality in Danish HIV‐infected patients: a nation‐wide population‐based cohort study
Authors: Larsen Mette V. , Omland Lars H. , Gerstoft Jan , Larsen Carsten S. , Jensen Janne , Obel Niels , Kronborg Gitte
Published: February 2010

Objectives  To estimate the impact of injecting drug use (IDU) on mortality in HIV‐infected patients in the highly active antiretroviral therapy (HAART) era.

Design  Population‐based, nation‐wide prospective cohort study in Denmark (the Danish HIV Cohort Study).

Methods  A total of 4578 HIV‐infected patients were followed from 1 January 1997 or date of HIV diagnosis. We calculated mortality rates stratified on IDU. One‐, 5‐ and 10‐year survival probabilities were estimated by Kaplan–Meier methods, and Cox regression analyses were used to estimate mortality rate ratios (MRR).

Results  Of the patients, 484 (10.6%) were categorized as IDUs and 4094 (89.4%) as non‐IDUs. IDUs were more likely to be women, Caucasian, hepatitis C virus (HCV) co‐infected and younger at baseline; 753 patients died during observation (206 IDUs and 547 non‐IDUs). The estimated 10‐year survival probabilities were 53.2% [95% confidence interval (CI): 48.1–58.3] in the IDU group and 82.1% (95% CI: 80.7–83.6) in the non‐IDU group. IDU as route of HIV infection more than tripled the mortality in HIV‐infected patients (MRR: 3.2; 95% CI: 2.7–3.8). Adjusting for potential confounders did not change this estimate substantially. The risk of HIV‐related death was not increased in IDUs compared to non‐IDUs (MRR 1.1; 95% CI 0.7–1.7).

Conclusions  Although Denmark's health care system is tax paid and antiretroviral therapy is provided free of charge, HIV‐infected IDUs still suffer from substantially increased mortality in the HAART era. The increased risk of death seems to be non‐HIV‐related and is due probably to the well‐known risk factors associated with intravenous drug abuse.
Proposed diagnostic criteria for internet addiction
Authors: Tao Ran , Huang Xiuqin , Wang Jinan , Zhang Huimin , Zhang Ying , Li Mengchen
Published: February 2010

Objective  The objective of this study was to develop diagnostic criteria for internet addiction disorder (IAD) and to evaluate the validity of our proposed diagnostic criteria for discriminating non‐dependent from dependent internet use in the general population.

Methods  This study was conducted in three stages: the developmental stage (110 subjects in the survey group; 408 subjects in the training group), where items of the proposed diagnostic criteria were developed and tested; the validation stage (n = 405), where the proposed criteria were evaluated for criterion‐related validity; and the clinical stage (n = 150), where the criteria and the global clinical impression of IAD were evaluated by more than one psychiatrist to determine inter‐rater reliability.

Results  The proposed internet addiction diagnostic criteria consisted of symptom criterion (seven clinical symptoms of IAD), clinically significant impairment criterion (functional and psychosocial impairments), course criterion (duration of addiction lasting at least 3 months, with at least 6 hours of non‐essential internet usage per day) and exclusion criterion (exclusion of dependency attributed to psychotic disorders). A diagnostic score of 2 + 1, where the first two symptoms (preoccupation and withdrawal symptoms) and at least one of the five other symptoms (tolerance, lack of control, continued excessive use despite knowledge of negative effects/affects, loss of interests excluding internet, and use of the internet to escape or relieve a dysphoric mood) was established. Inter‐rater reliability was 98%.

Conclusion  Our findings suggest that the proposed diagnostic criteria may be useful for the standardization of diagnostic criteria for IAD.
Addiction research centres and the nurturing of creativity: Centre for Social Research on Alcohol and Drugs (SoRAD), Stockholm University, Sweden
Authors: Stenius Kerstin , Ramstedt Mats , Olsson Börje
Published: February 2010

The Centre for Social Research on Alcohol and Drugs (SoRAD) was established as a national research centre and department within the Faculty of Social Science at Stockholm University in 1997, following a Government Report and with the aim to strengthen social alcohol and drug research. Initially, core funding came from the Swedish Council for Working Life and Social Research and from the Ministry of Health and Social Affairs for several long‐term projects. Today, SoRAD, with 25 senior and junior researchers, has core funding from the university but most of its funding comes from external national and international grants. Research is organized under three themes: consumption, problems and norms, alcohol and drug policy and societal reactions, treatment and recovery processes. SoRADs scientific approach, multi‐disciplinarity, a mix of qualitative and quantitative methods and international comparisons was established by the centre's first leader, Robin Room. Regular internal seminars are held and young researchers are encouraged to attend scientific meetings and take part in collaborative projects. SoRAD researchers produce government‐funded monthly statistics on alcohol consumption and purchase, and take part in various national government committees, but SoRADs research has no clear political or bureaucratic constraints. One of the future challenges for SoRAD will be the proposed system for university grants allocation, where applied social science will have difficulties competing with basic biomedical research if decisions are based on publication and citation measures.
Predictors of the recurrence of hepatic encephalopathy in lactulose‐treated patients
Authors: BAJAJ J. S. , SANYAL A. J. , BELL D. , GILLES H. , HEUMAN D. M.
Published: February 2010

Aliment Pharmacol Ther 31, 1012–1017

Background  Lactulose is considered first‐line therapy for hepatic encephalopathy. However, the effect of adherence with lactulose on recurrence of hepatic encephalopathy outside clinical trials remains unclear.

Aim  To determine the association of lactulose use with recurrence of hepatic encephalopathy episodes.

Methods  Patients with cirrhosis who were initiated on lactulose after an index hepatic encephalopathy episode in a liver‐transplant centre were retrospectively reviewed. Recurrence of hepatic encephalopathy, precipitating factors and adherence on lactulose were investigated using chart review and electronic pharmacy records. Patients with/without hepatic encephalopathy recurrence were compared, and predictors of recurrence were analysed.

Results  A total of 137 patients with cirrhosis (age 55 ± 6years, MELD 17 ± 7) who were initiated on lactulose after the index hepatic encephalopathy episode were included. Of these, 103 patients developed recurrent hepatic encephalopathy 9 ± 1 months after their index episode; 39 (38%) of these were not adherent on lactulose, 56 (54%) were adherent and 8 (8%) had lactulose‐associated dehydration leading to recurrence. Recurrent hepatic encephalopathy precipitants in lactulose‐adherent patients were sepsis (19%), GI bleeding (15%), hyponatremia (4%) and TIPS (7%). Overall, all patients who did not suffer recurrence were adherent on lactulose. In contrast, the adherence rate for those who recurred was only 64% (P = 0.00001). On multivariate regression, lactulose non‐adherence (OR 3.26) and MELD score (OR 1.14) were the factors that predicted recurrence.

Conclusion  Lactulose non‐adherence and lactulose‐associated dehydration were associated with nearly half of recurrent hepatic encephalopathy episodes.
Haematopoeitic cell transplantation for Fanconi anaemia – when and how?
Authors: MacMillan Margaret L. , Wagner John E.
Published: February 2010

Allogeneic haematopoietic cell transplantation (HCT) remains the only treatment that can correct the haematological manifestations in patients with Fanconi anaemia. Over the last two decades, sequential changes to the approach to HCT have resulted in reduced regimen‐related toxicity, superior engraftment and less graft‐versus‐host disease (GVHD), resulting in improved survival. The two pivotal changes that most influenced these improvements were the addition of fludarabine to the preparative regimen to augment engraftment, and the use of T cell depletion to reduce GVHD. With these improved HCT outcomes, indications for HCT are quite consistent regardless of donor source. Emphasis is now being placed on developing HCT regimens that will improve quality of life by reducing late effects, particularly the risk of malignancy, sterility and endocrinopathies. This paper will review the unique challenges of HCT in FA patients, with particular emphasis on the timing and approach to HCT.
Prolonged survival with improved tolerability in higher‐risk myelodysplastic syndromes: azacitidine compared with low dose ara‐C
Authors: Fenaux Pierre , Gattermann Norbert , Seymour John F. , Hellström‐Lindberg Eva , Mufti Ghulam J. , Duehrsen Ulrich , Gore Steven D. , Ramos Fernando , Beyne‐Rauzy Odile , List Alan , McKenzie David , Backstrom Jay , Beach Charles L.
Published: February 2010

In the phase III AZA‐001 trial, low‐dose cytarabine (LDara‐C), the most widely used low‐dose chemotherapy in patients with higher‐risk myelodysplastic syndrome (MDS) who are ineligible for intensive treatment, was found to be associated with poorer survival compared with azacitidine. This analysis further compared the efficacy and the toxicity of these two drug regimens. Before randomization, investigators preselected patients to receive a conventional care regimen, one of which was LDara‐C. Of 94 patients preselected to LDara‐C, 45 were randomized to azacitidine and 49 to LDara‐C. Azacitidine patients had significantly more and longer haematologicalal responses and increased red blood cell transfusion independence. Azacitidine prolonged overall survival versus LDara‐C in patients with poor cytogenetic risk, presence of −7/del(7q), and French‐American‐British subtypes refractory anaemia with excess blasts (RAEB) and RAEB in transformation. When analyzed per patient year of drug exposure, azacitidine treatment was associated with fewer grade 3–4 cytopenias and shorter hospitalisation time than LDara‐C in these higher‐risk MDS patients.
Ranking and classification of fishing areas using fuzzy models and techniques
Authors: SYLAIOS G. K. , KOUTROUMANIDIS T. , TSIKLIRAS A. C.
Published: February 2010

Abstract Fuzzy‐logic‐based methods and fuzzy logic formalism have been demonstrated as appropriate to address the uncertainty and subjectivity in complex environmental problems. This study investigates the use of three fuzzy logic methods in fisheries analysis, aiming towards the grouping and ranking of fishing subareas, according to their fisheries yield. Initially, a simple fuzzyc‐means clustering model was applied to the fishing subareas examined. A rule‐based Mamdani‐type fuzzy inference system was then developed to allow the direct fishing subarea classification. Finally, a species‐economic value weighted global fuzzy membership model was introduced, serving as an indirect classification and ranking scheme. Global memberships were plotted on simple ternary diagrams, producing representations that serve as tools in fisheries management. All methods examined the performance of the Greek fishing subareas, based on the annual landings series of the 10 most abundant fish species in terms of landed biomass, during the period 1985–1999.
A mail survey to estimate the fishery dynamics of southern Florida's bonefish charter fleet
Authors: LARKIN M. F. , AULT J. S. , HUMSTON R. , LUO J.
Published: February 2010

Abstract  Bonefish, Albula vulpes (L.), support an economically important recreational fishery in southern Florida, USA that has received little scientific study and has never been adequately assessed. A mail survey of 322 captains that comprise the southern Florida bonefish charter fleet was conducted to acquire a baseline understanding of the primary fishery statistics. The response rate was 59% and a follow‐up telephone survey of non‐respondents indicated no non‐response bias. Experience in the fishery ranged from 3 to 61 years. The annual fishing effort was 30 875 boat days. The majority of the fleet fishing effort occurred in the northern Florida Keys and is presumed to reflect bonefish abundance. The instantaneous mortality rate of released fish was 0.11 year−1. The majority of the respondents indicated that the bonefish stock had declined over the past decade.
Functional vs scenic restoration – challenges to improve fish and fisheries in urban waters
Authors: WOLTER C.
Published: February 2010

Abstract  Two rehabilitation projects were compared to determine their feasibility for successfully improving habitat for fish in urban waters. The first re‐meandering project involved channel reconstruction in the Müggelspree upstream of Berlin to create an aesthetically pleasing, stable, meandering channel. The second project addressed a typical habitat bottleneck for fish found in urban waterways; that of nursery habitats lost due to river engineering works. Rehabilitated and control sites were sampled before and after in the Müggelspree and once in the urban Spree River. A total of 30 303 fish belonging to 27 species were collected. The fish assemblage was dominated by generalist species with 81% roach, Rutilus rutilus (L.), and perch, Perca fluviatilis L. Species diversity did not improve in either the rural or urban stretch. In the Müggelspree, the loss of riverine habitats was mirrored by significant declines in the densities of chub, Leuciscus cephalus (L.), ide, Leuciscus idus (L.), gudgeon, Gobio gobio (L.), rheophilic and lithophilic species. By contrast, densities of rheophilic species around the artificial structures created in the urban Spree River, although the main effect was an overwhelming increase in roach and perch. The results suggest that if underlying bottlenecks can be identified, artificial structures can provide functional fish habitat that replaces the natural equivalent in urban river stretches. Consequently, even the most heavily degraded waters provide opportunities to improve fish diversity and fisheries using artificial habitat structures.
Patterns in taxonomic and functional diversity of lake phytoplankton
Authors: LONGHI MARIA L. , BEISNER BEATRIX E.
Published: February 2010

1. Patterns in phytoplankton diversity in lakes and their relationships with environmental gradients have been traditionally based on taxonomic analyses and indices, even though measures of functional diversity (FD) might be expected to be more responsive to such gradients.

2. We assessed the influence of water column physical structure, and other components of the overall environment, on lake phytoplankton diversity using two taxonomically based indices [species richness (S) and the Shannon index (H’)] and a FD index, to determine whether these different measures respond in similar ways to habitat structure. The study encompassed 45 lakes in Eastern Canada, within two lake districts [the Eastern Townships Region (ETR) and Laurentians Region (LR)] that vary in geology and landscape and in lake morphometry and chemistry.

3. Across all lakes, S and H’ were higher in lakes having greater vertical temperature heterogeneity and higher susceptibility to wind mixing. In addition, H’ declined with total phosphorus concentration. FD was only related to maximum lake depth, a variable that integrates many other habitat features.

4. Further insight into the factors affecting phytoplankton diversity was obtained by contrasting the two regions. The taxonomically based diversity measures differed little between the regions, while FD was higher in the ETR where more trait variants were present and more evenly distributed amongst species. Whereas factors driving S did not differ between the regions, we found region‐dependent patterns in the relationships of H’ and FD with maximum lake depth: both indices decreased with maximum depth in the region with lakes more exposed to wind (ETR) but increased in the more hilly landscape where lakes are more sheltered from wind mixing (LR).

5. Our study demonstrates that, for phytoplankton communities, a FD index can show simpler and stronger responses to environmental drivers than a taxonomically based index, while shedding further light onto the functional traits that are important in particular lake categories.
Long‐term variation in the littoral food web of an acidified mountain lake
Authors: LAYER KATRIN , HILDREW ALAN , MONTEITH DON , WOODWARD GUY
Published: February 2010

Evidence of chemical recovery from acidification in European freshwaters has emerged in recent years, with many previously damaged systems responding to decades of reduced acidifying emissions. Biological recovery, however, has often lagged behind, and this has been ascribed to several possible mechanisms, including inertia in the food web. We examined two decades of change in hindcasted food webs for Lochnagar, a Scottish mountain lake, to make inferences about the potential dynamical stability of the system and to assess the prospects for future biological recovery. Although community composition tracked temporal changes in acidity, this was neither sustained nor directional, and mainly manifested as shifts in relative abundances rather than the establishment of more acid‐sensitive species. The food web was highly interconnected and reticulate, especially in years when species richness was low, and subsidized by external inputs of detritus. Among the primary consumers, generalist herbivore–detritivores maintained feeding links with the scant algal resources, which appeared insufficient to support viable populations of specialist grazers. Together, these characteristics, which are shared with many other acidified freshwaters, are likely to make the community dynamically stable and resistant to invasions of potential new colonists, thereby slowing the pace of future biological recovery.