bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of functionally active, low frequency copy number variants at 15q21.3 and 12q21.31 associated with prostate cancer risk
Authors: Demichelis Francesca , Setlur Sunita R. , Banerjee Samprit , Chakravarty Dimple , Chen Jin Yun Helen , Chen Chen X. , Huang Julie , Beltran Himisha , Oldridge Derek A. , Kitabayashi Naoki , Stenzel Birgit , Schaefer Georg , Horninger Wolfgang , Bektic Jasmin , Chinnaiyan Arul M. , Goldenberg Sagit , Siddiqui Javed , Regan Meredith M. , Kearney Michale , Soong T. David , Rickman David S. , Elemento Olivier , Wei John T. , Scherr Douglas S. , Sanda Martin A. , Bartsch Georg , Lee Charles , Klocker Helmut , Rubin Mark A.
Published: April 2012

Copy number variants (CNVs) are a recently recognized class of human germ line polymorphisms and are associated with a variety of human diseases, including cancer. Because of the strong genetic influence on prostate cancer, we sought to identify functionally active CNVs associated with susceptibility of this cancer type. We queried low-frequency biallelic CNVs from 1,903 men of Caucasian origin enrolled in the Tyrol Prostate Specific Antigen Screening Cohort and discovered two CNVs strongly associated with prostate cancer risk. The first risk locus (
P
= 7.7 × 10
−4
, odds ratio = 2.78) maps to 15q21.3 and overlaps a noncoding enhancer element that contains multiple activator protein 1 (AP-1) transcription factor binding sites. Chromosome conformation capture (Hi-C) data suggested direct
cis
-interactions with distant genes. The second risk locus (
P
= 2.6 × 10
−3
, odds ratio = 4.8) maps to the
α-1,3-mannosyl-glycoprotein 4-β-N-acetylglucosaminyltransferase C
(
MGAT4C
) gene on 12q21.31. In vitro cell-line assays found this gene to significantly modulate cell proliferation and migration in both benign and cancer prostate cells. Furthermore,
MGAT4C
was significantly overexpressed in metastatic versus localized prostate cancer. These two risk associations were replicated in an independent PSA-screened cohort of 800 men (15q21.3, combined
P
= 0.006; 12q21.31, combined
P
= 0.026). These findings establish noncoding and coding germ line CNVs as significant risk factors for prostate cancer susceptibility and implicate their role in disease development and progression.
Differential effects of poly(ADP-ribose) polymerase inhibition on DNA break repair in human cells are revealed with Epstein–Barr virus
Authors: Ma Wenjian , Halweg Christopher J. , Menendez Daniel , Resnick Michael A.
Published: April 2012

Poly(ADP-ribose) polymerase (PARP) inhibitors can generate synthetic lethality in cancer cells defective in homologous recombination. However, the mechanism(s) by which they affect DNA repair has not been established. Here we directly determined the effects of PARP inhibition and PARP1 depletion on the repair of ionizing radiation-induced single- and double-strand breaks (SSBs and DSBs) in human lymphoid cell lines. To do this, we developed an in vivo repair assay based on large endogenous Epstein–Barr virus (EBV) circular episomes. The EBV break assay provides the opportunity to assess quantitatively and simultaneously the induction and repair of SSBs and DSBs in human cells. Repair was efficient in G1 and G2 cells and was not dependent on functional p53. shRNA-mediated knockdown of PARP1 demonstrated that the PARP1 protein was not essential for SSB repair. Among 10 widely used PARP inhibitors, none affected DSB repair, although an inhibitor of DNA-dependent protein kinase was highly effective at reducing DSB repair. Only Olaparib and Iniparib, which are in clinical cancer therapy trials, as well as 4-AN inhibited SSB repair. However, a decrease in PARP1 expression reversed the ability of Iniparib to reduce SSB repair. Because Iniparib disrupts PARP1–DNA binding, the mechanism of inhibition does not appear to involve trapping PARP at SSBs.
Structural insights into biased G protein-coupled receptor signaling revealed by fluorescence spectroscopy
Authors: Rahmeh Rita , Damian Marjorie , Cottet Martin , Orcel Hélène , Mendre Christiane , Durroux Thierry , Sharma K. Shivaji , Durand Grégory , Pucci Bernard , Trinquet Eric , Zwier Jurriaan M. , Deupi Xavier , Bron Patrick , Banères Jean-Louis , Mouillac Bernard , Granier Sébastien
Published: April 2012

G protein-coupled receptors (GPCRs) are seven-transmembrane proteins that mediate most cellular responses to hormones and neurotransmitters, representing the largest group of therapeutic targets. Recent studies show that some GPCRs signal through both G protein and arrestin pathways in a ligand-specific manner. Ligands that direct signaling through a specific pathway are known as biased ligands. The arginine-vasopressin type 2 receptor (V2R), a prototypical peptide-activated GPCR, is an ideal model system to investigate the structural basis of biased signaling. Although the native hormone arginine-vasopressin leads to activation of both the stimulatory G protein (Gs) for the adenylyl cyclase and arrestin pathways, synthetic ligands exhibit highly biased signaling through either Gs alone or arrestin alone. We used purified V2R stabilized in neutral amphipols and developed fluorescence-based assays to investigate the structural basis of biased signaling for the V2R. Our studies demonstrate that the Gs-biased agonist stabilizes a conformation that is distinct from that stabilized by the arrestin-biased agonists. This study provides unique insights into the structural mechanisms of GPCR activation by biased ligands that may be relevant to the design of pathway-biased drugs.
Structure of thePlasmodium6-cysteine s48/45 domain
Authors: Arredondo Silvia A. , Cai Mengli , Takayama Yuki , MacDonald Nicholas J. , Anderson D. Eric , Aravind L. , Clore G. Marius , Miller Louis H.
Published: April 2012

The s48/45 domain was first noted inPlasmodiumproteins more than 15 y ago. Previously believed to be unique toPlasmodium, the s48/45 domain is present in other aconoidasidans. InPlasmodium, members of the s48/45 family of proteins are localized on the surface of the parasite in different stages, mostly by glycosylphosphatydylinositol-anchoring. Members such as P52 and P36 seem to play a role in invasion of hepatocytes, and Pfs230 and Pfs48/45 are involved in fertilization in the sexual stages and have been consistently studied as targets of transmission-blocking vaccines for years. In this report, we present the molecular structure for the s48/45 domain corresponding to the C-terminal domain of the blood-stage protein Pf12 fromPlasmodium falciparum, obtained by NMR. Our results indicate that this domain is a β-sandwich formed by two sheets with a mixture of parallel and antiparallel strands. Of the six conserved cysteines, two pairs link the β-sheets by two disulfide bonds, and the third pair forms a bond outside the core. The structure of the s48/45 domain conforms well to the previously defined surface antigen 1 (SAG1)-related-sequence (SRS) fold observed in the SAG family of surface antigens found inToxoplasma gondii. Despite extreme sequence divergence, remarkable spatial conservation of one of the disulfide bonds is observed, supporting the hypothesis that the domains have evolved from a common ancestor. Furthermore, a homologous domain is present in ephrins, raising the possibility that the precursor of the s48/45 and SRS domains emerged from an ancient transfer to Apicomplexa from metazoan hosts.
Practices, Perceptions, and Concerns of Primary Care Physicians about Opioid Dependence Associated with the Treatment of Chronic Pain
Authors: Keller Craig E. , Ashrafioun Lisham , Neumann Anne M. , Van Klein Justin , Fox Chester H. , Blondell Richard D.
Published: April 2012

When prescribing opioids to treat chronic pain, physicians face the dilemma of balancing effective pain management while avoiding iatrogenic opioid addiction. Through mailed surveys, the current study assessed concerns, perceptions, and practices of primary care physicians related to this dilemma. Of the 35 (43%) physicians that replied, 32 (91.4%) reported to prescribe opioids for pain. Twenty-six (81.3%) physicians mentioned that “legitimate pain” was the main reason why most patients who are opioid dependent begin using opioids. Most physicians (71.5%) rated their knowledge/comfort of treatment/management of opioid dependence as being low. Although these physicians believed training is essential to learning about the risks involved with chronic pain and opioid dependence, many of these physicians evaluated their own medical training in these areas as unsatisfactory. Training programs may better equip primary care physicians when addressing the treatment of chronic pain and addiction to opioids.
Characteristics of Psychopathology and the Relationship between Routes of Drug Administration and Psychiatric Symptoms in Heroin Addicts
Authors: Wang Qing-Liang , Liu Zhi-Min
Published: April 2012

The objective of this study was to explore the characteristics of comorbid psychiatric symptoms and the relationship between different routes of drug administration and psychiatric symptoms. Five hundred and nine heroin addicts were studied in Drug Detoxification and Rehabilitation Centers in Yunnan and Heilongjiang provinces of China. The measure instrument, including demographic characteristics, history of drug abuse, and the Symptom Checklist-90 (SCL-90) scale (Chinese version), was administered to eligible heroin addicts. Among the subjects, comorbid psychopathology conditions were more severe on all dimensions of SCL-90 comparing with normal adults and the average score of Depression was highest among the 9 dimensions in heroin addicts; psychiatric symptoms were more severe in heroin injecting group than in “chasing the dragon” group and only the difference in Obsessive-Compulsive was significant, but more significant differences were found between snorting heroin addicts and chasing or injecting heroin addicts, and the average score of each dimension of SCL-90 was higher in the snorting group than in the other 2 groups. The reasons of the results and meaning for the present study are discussed. In summary, comorbid psychiatric symptoms in the heroin addicts were very common and severe and their severity varied with different routes of drug administration, suggesting that routes of drug administration should be considered as an important risk factor to mental health of heroin addicts.
Naphthalene Addiction
Authors: Praharaj Samir Kumar , Kongasseri Sreejayan
Published: April 2012

Inhalant abuse such as kerosene, petrol, gasoline, and typewriter correction fluid has been reported from India. Naphthalene or mothballs, a commonly used substance in households and freely available in the market is an uncommon form of inhalant abuse which may lead to severe medical complications. We report an adolescent with addiction to naphthalene balls who developed severe anemia.
Exploration of the Comorbidity of Alcohol Use Disorders and Mental Health Disorders among Inpatients Presenting to All Hospitals in New South Wales, Australia
Authors: Lai Harry Man Xiong , Sitharthan Thiagarajan , Huang Qi Rong
Published: April 2012

Alcohol is one of the most commonly used legal psychoactive substances, and its use often coexists with mental health disorders. This study explores the relationships between alcohol use and some common mental health disorders. Admissions to all New South Wales (NSW) hospitals were analyzed. The data were extracted from the NSW Department of Health Inpatient Statistics Data Collection for the period 1 July 2006 to 30 June 2007. Readmissions within 28 days were excluded. Data extraction and analyses were performed by using the SAS program. Chi-square tests and odds ratio were used to measure the association. Of the 1.8 million admissions, associations between alcohol use disorders and mental health disorders were strong (odds ratio 7.8 to 10.7, P < .001). A 33.8% of patients who used alcohol had at least 1 identifiable mental disorder. Higher comorbidity rates were observed for females (39.6%) and for those aged between 30 and 49 years. The most common mental disorders were anxiety disorders, bipolar affective disorders, major depressive disorders, personality disorders, schizophrenia, and severe stress disorders. Comorbidity with one of these mental disorders ranged from 1% to 17.6%, with significant associations (odds ratio 5.6 to 14.1). The average length of stay (ALOS) for alcohol use disorders were 6.4 days and the ALOS for the most common mental health admissions was 11.2 days. This study provides detailed information about the association between alcohol use and mental health disorders and extends our understanding of comorbidity presentations in inpatient admissions.
Comorbid Trajectories of Tobacco and Marijuana Use as Related to Psychological Outcomes
Authors: Brook Judith S. , Lee Jung Yeon , Brown Elaine N. , Finch Stephen J.
Published: April 2012

Heterogeneous classes of comorbid trajectories of tobacco and marijuana use were examined in order to determine how they are related to subsequent antisocial behavior, poor self-control, and internalizing behavior. Data are from a 4-wave longitudinal study of African American ( n = 243) and Puerto Rican ( n = 232) adolescents and adults in the community. Logistic regression analyses were employed to measure the association between the comorbid trajectories of tobacco and marijuana use and the psychological difficulty variables. The authors found 6 joint trajectory groups. The authors compared the non-or-experimental tobacco/marijuana use group with the other user groups in each of the psychological difficulty domains. The infrequent tobacco/late-onset marijuana use and chronic tobacco/marijuana use groups differed most strongly from the non-or-experimental tobacco/marijuana use group across the antisocial behavior, poor self-control, and internalizing problems domains. The chronic tobacco/maturing out marijuana use group also had significant associations in each of these domains. The infrequent tobacco/marijuana use and late-onset tobacco/infrequent marijuana use groups had no or weak associations with the psychological outcomes. Tobacco and marijuana cessation programs should identify and address comorbid use of tobacco and marijuana, and antisocial behavior, poor self-control, and internalizing problems, which are associated with histories of comorbid use of the 2 substances.
Non-Suicidal Self-Injury Within Offender Populations: A Systematic Review
Authors: Dixon-Gordon Katherine , Harrison Natalie , Roesch Ronald
Published: April 2012

Non-suicidal self-injury (NSSI), defined as deliberate self-directed tissue damage, presents a serious health concern for offender populations. Approximately one-third of offenders report a history of NSSI, and it is the most common reason for mental health treatment within correctional settings. To date, no review exists with a specific focus on NSSI in criminal justice contexts. Therefore, the primary aim of this article is to review research on NSSI within correctional settings. Specifically, we explore the role of risk factors for NSSI. We also examine the functions of NSSI within correctional contexts. In addition, we evaluate the evidence for potential assessment tools and treatments for NSSI. Taken together, our review suggests that risk factors for NSSI must be considered differently in correctional settings, due to the high base rates of these vulnerabilities. Further, although environmental control is a more salient function of NSSI within correctional settings, the primary motive for engaging in this behavior remains emotion regulation. Finally, despite the emergence of several promising treatments for NSSI within correctional settings, larger scale studies are necessary to determine the efficacy of these interventions.
Induction, Recovery, and Hematological Responses of Largemouth Bass to Chemo- and Electrosedation
Authors: Trushenski Jesse T , Bowker James D , Mulligan Bonnie L , Gause Brian R
Published: April 2012

Sedating fish before handling minimizes the risk of injury to both fish and handler and may also minimize the fish's stress response. We conducted two experiments to quantitatively compare induction and recovery times of largemouth bass Micropterus salmoides sedated with tricaine methanesulfonate (MS-222), eugenol, benzocaine, carbon dioxide (CO2), or electrosedation (pulsed DC). We also assessed the fish's hematological profile following sedation with MS-222, eugenol, and electrosedation. Induction times varied significantly among the sedatives evaluated; electrosedation yielded the fastest inductions (0.2 ± 0.1 min; mean ± SE) and CO2 yielded the slowest (3.6 ± 0.1 min). Times to recovery of equilibrium and responsiveness to tactile and visual–auditory stimuli also varied, ranging from 1.8 ± 0.3 to 3.7 ± 0.3 min and from 2.3 ± 0.3 to 4.0 ± 0.3 min, respectively, depending on the sedative used. Plasma cortisol concentrations were elevated at 0.5 h postsedation among fish sedated with eugenol and MS-222, whereas cortisol levels of electrosedated fish were comparatively low and stable throughout the experiment. Conversely, plasma glucose and lactate levels increased markedly from 0.5 to 2 h postsedation among electrosedated fish, whereas the responses among fish treated with eugenol or MS-222 were weak or negligible. Our results indicate that electrosedation, benzocaine, eugenol, and MS-222 are all effective in quickly sedating largemouth bass. Physiological and behavioral data suggest that largemouth bass generally recover within 6 h of sedation using MS-222, eugenol, or electrosedation.
Inhibitory Effects of Rosemary Oil on the In Vitro Growth of Six Common Finfish Pathogens
Authors: Ostrand Susan L , Glenn Richard A , Gannam Ann L , Hanson Kyle C
Published: April 2012

Additives are commonly used in feed to enhance fish performance, health, and well-being. In recent years, antibiotics have received increased scrutiny owing to concerns about overuse and their environmental impact. These concerns have generated a desire for naturally derived alternatives for the aquafeed industry. For screening purposes, we examined the in vitro effects of an essential oil on bacteria commonly associated with fish diseases. Six concentrations of rosemary Rosmarinus officinalis oil (0.1, 0.3, 0.5, 0.7, and 0.9 μL/μL of 1% Tween-20 and pure rosemary oil [1.0]) were used against Flavobacterium psychrophilum, Yersinia ruckeri, Aeromonas salmonicida, and three warmwater bacterial pathogens, A. hydrophila, Edwardsiella ictaluri, and E. tarda, along with a control treatment (1% Tween-20 only). After incubation, the mean zone of inhibition around the disks was measured. While most concentrations were found to inhibit pathogen growth, a concentration of 50% or more was found to have significantly higher effects on most of the pathogens tested. Rosemary oil was found to inhibit the growth of F. psychrophilum to the greatest extent and had a limited effect on the other fish pathogens. Although rosemary oil was shown to inhibit the growth of some bacterial fish pathogens in experimental trials, further laboratory and field studies are required to determine whether rosemary oil as a feed additive has any application as part of an integrated fish health management strategy.
Prospective memory reminders: A laboratory investigation of initiation source and age effects
Authors: Henry Julie D. , Rendell Peter G. , Phillips Louise H. , Dunlop Leigh , Kliegel Matthias
Published: April 2012

Prior research indicates that, in some circumstances, reminders may facilitate prospective remembering. However, it remains unclear whether this effect is dependent on the initiation source (self vs. external), whether it is moderated by task type (event vs. time based), or whether the provision of standardized reminders particularly benefits older adults. In the current study, young ( n = 48) and older adults ( n = 47) were tested on a laboratory-based prospective memory task in which they encountered three counterbalanced reminder conditions: no reminders, self-initiated reminders, and experimenter-initiated reminders. The results indicated that while the provision of reminders enhanced prospective memory performance, no difference was seen between self-initiated and experimenter-initiated reminder conditions, nor was there any interaction with age or prospective memory type (event vs. time based). These data support the role of both self- and externally generated external reminders as an aid to prospective remembering. However, the absence of any interaction with age is not consistent with theoretical models of ageing that consider the provision of such reminders to reduce strategic demands (or increase automatic processing).
Playing with Arp2/3 uncovers cellular rudder
Authors: Leslie Mitch
Published: April 2012

Study shows that lamellipodia allow cells to move in a specific direction.
Effects of Extruder Screw Speeds on Physical Properties and In Vitro Starch Hydrolysis of Precooked Pinto, Navy, Red, and Black Bean Extrudates
Authors: Simons Courtney W. , Hall Clifford , Tulbek Mehmet
Published: April 2012

Precooked pinto, navy, red, and black bean flours were extruded at different screw speeds (320, 380, and 440 rpm) with a twin‐screw extruder. Effect of speed on physical properties and in vitro starch hydrolysis was investigated. Increasing screw speeds reduced water activity, expansion index, and texture. Extrudates could not be obtained from pinto bean flour at 440 rpm because of the high shear effect. Water absorption index and water solubility index were not significantly affected by screw speed but were significantly higher than for unextruded precooked flour. A significant change in color was observed in navy beans, characterized by increasing b values on the Hunter color scale. Resistant starch ranged from 3.65 to 4.83% db and was not significantly affected by screw speed. Glycemic index of all extrudates was high, ranging from 81.3 to 86.9.
Tuber Rot of Potato Caused by Phytophthora nicotianae: Isolate Aggressiveness and Cultivar Susceptibility
Authors: Taylor Raymond J. , Pasche Julie S. , Shew H. David , Lannon K. R. , Gudmestad Neil C.
Published: April 2012

A study was undertaken in 2008 and 2009 to examine potato (Solanum tuberosum) cultivar susceptibility, the potential of other host species to act as sources of inoculum for potato infections, and other aspects of potato–Phytophthora nicotianae interactions. Twelve isolates of P. nicotianae collected from five leaf, one petiole, and six tuber infections of potato from five states, as well as isolates from a variety of other host species, were evaluated for ability to cause tuber rot of potato via inoculation studies. Additionally, the susceptibility of 27 potato cultivars commonly grown in the United States to tuber infection by P. nicotianae was determined. Eighty-three percent of the isolates recovered from potato were highly aggressive, infecting tubers at nearly four times greater incidences than isolates originating from nonpotato hosts. With the exception of two tobacco isolates, zoospores of all isolates recovered from nonpotato hosts were able to infect potato tubers. Russet cultivars were significantly less susceptible to P. nicotianae than red and white cultivars in 2008, and red cultivars in 2009. Umatilla Russet was the most resistant cultivar in both years, whereas Red Norland and Dakota Rose were the most susceptible in both years. Results of a survey for P. nicotianae conducted in four states from 2008 through 2010 confirmed previous observations of naturally occurring infections of potato in Missouri, Nebraska, and Texas, as well as infections of potato in Michigan (documented for the first time). All isolates recovered in the survey were sensitive to mefenoxam (EC50 < 1.0 μg/ml).
Soil Solarization and Biological Control for Managing Mesocriconema xenoplax and Short Life in a Newly Established Peach Orchard
Authors: Nyczepir A. P. , Kluepfel D. A. , Waldrop V. , Wechter W. P.
Published: April 2012

The effects of soil solarization, with and without a Pseudomonas spp. cocktail or wheat rotation as alternatives to chemical control of Mesocriconema xenoplax, were investigated from 2004 to 2011. Preplant solarization and soil fumigation (67% methyl bromide + 33% chloropicrin mixture; henceforth, referred to as MBr) was initiated in 2004 in an orchard infested with M. xenoplax and a history of peach tree short life (PTSL). Plots consisted of nine treatments: (i) nonsolarized soil-alone, (ii) nonsolarized soil with bacteria cocktail (nonsolar-bacteria), (iii) nonsolarized soil with wheat (nonsolar-wheat), (iv) nonsolarized soil with bacteria cocktail and wheat (nonsolar-bacteria-wheat), (v) solarized soil-alone, (vi) solarized soil with bacteria cocktail solar-bacteria), (vii) solarized soil with wheat (solar-wheat), (viii) solarized soil with bacteria cocktail and wheat (solar-bacteria-wheat), and (ix) preplant MBr fumigation. Peach trees were planted into all plots in 2005. Nematode populations were suppressed 20 months longer after orchard establishment in solar-alone and solar-wheat plots than solar-bacteria and solar-bacteria-wheat plots. Pseudomonas spp. cocktails did not have a pronounced effect in suppressing M. xenoplax in this study. Fumigation effect on M. xenoplax population density dissipated 24 months after application. Solar-wheat-treated soil was as effective as preplant MBr fumigation in increasing tree survival from PTSL for at least 6 years after orchard establishment.
Distribution, Cultivar Susceptibility, and Epidemiology of Apium virus Y on Celery in Coastal California
Authors: Koike Steven T. , Liu Hsing-Yeh , Sears John , Tian Tongyan , Daugovish Oleg , Dara Surendra
Published: April 2012

Apium virus Y (ApVY) is a potyvirus that was recently found to cause crop loss to celery (Apium graveolens) in California. Symptoms on leaves exhibit varying forms of chlorosis and necrosis. Depending on the cultivar, celery petioles could also exhibit extensive necrotic, sunken, elongated lesions. Severely affected plants were unmarketable. Disease incidence surveys found that a susceptible celery (cv. 414) showed 55% (2007) and 71% (2008) disease. Because it was noted that the Apiaceae weed poison hemlock (Conium maculatum) was present in almost all areas where ApVY affected celery, a 4-year survey collected overwintered hemlock from six coastal county regions and tested composite samples for ApVY using reverse transcription–polymerase chain reaction (RT-PCR) and ApVY-specific primers. These plants were consistently positive for ApVY. Seeds collected from these plants were also positive when tested with the same RTPCR method. However, when ApVY-positive hemlock seeds were germinated and the resulting seedlings tested, all results were negative. The failure of ApVY to be transmitted from hemlock seeds to seedlings was further documented by collecting newly germinated hemlock seedlings from the field and testing them with RT-PCR. All such seedlings were negative for ApVY even though large, adjacent, overwintered hemlock plants tested positive. Two crops of celery seed were produced from ApVY-positive mother plants; celery seed from these infected plants likewise tested positive for ApVY, but seedlings grown from the seed lots were negative for ApVY. Twenty-one celery and celeriac cultivars were inoculated with ApVY using viruliferous aphids, planted in a replicated field trial, and then grown to maturity. Seven cultivars remained symptomless, tested negative for ApVY, and showed signs of possible resistance. The epidemiology of disease caused by ApVY in California evidently involves poison hemlock as a common overwintering host with subsequent vectoring of the virus from hemlock to celery via aphids. ApVY was not seedborne in this weed host or in celery in our experiments. Our data suggest that growers can manage this disease by controlling poison hemlock weed populations and by planting celery cultivars that are not susceptible to ApVY.
Races of Puccinia graminis f. sp. tritici with Combined Virulence to Sr13 and Sr9e in a Field Stem Rust Screening Nursery in Ethiopia
Authors: Olivera P. D. , Jin Y. , Rouse M. , Badebo A. , Fetch T. , Singh R. P. , Yahyaoui A.
Published: April 2012

North American durum lines, selected for resistance to TTKSK (Ug99) and related races of Puccinia graminis f. sp. tritici in Kenya, became susceptible in Debre Zeit, Ethiopia, suggesting the presence of stem rust races that were virulent to the TTKSK-effective genes in durum. The objective of this study was to characterize races of P. graminis f. sp. tritici present in the Debre Zeit, Ethiopia stem rust nursery. Three races of P. graminis f. sp. tritici were identified from 34 isolates: JRCQC, TRTTF, and TTKSK. Both races JRCQC and TRTTF possess virulence on stem rust resistance genes Sr13 and Sr9e, which may explain why many TTKSK-resistant durum lines tested in Kenya became susceptible in Debre Zeit. The Sr9e-Sr13 virulence combination is of particular concern because these two genes constitute major components of stem rust resistance in North American durum cultivars. In addition to Sr9e and Sr13 virulence, race TRTTF is virulent to at least three stem rust resistance genes that are effective to race TTKSK, including Sr36, SrTmp, and resistance conferred by the 1AL.1RS rye translocation. Race TRTTF is the first known race with virulence to the stem rust resistance carried by the 1AL.1RS translocation, which represents one of the few effective genes against TTKSK in winter wheat cultivars in the United States. Durum entries exhibiting resistant to moderately susceptible infection response at the Debre Zeit nursery in 2009 were evaluated for reaction to races JRCQC, TRTTF, and TTKSK at the seedling stage. In all, 47 entries were resistant to the three races evaluated at the seedling stage, whereas 26 entries exhibited a susceptible reaction. These results suggest the presence of both major and adult plant resistance genes, which would be useful in durum-wheat-breeding programs. A thorough survey of virulence in the population of P. graminis f. sp. tritici in Ethiopia will allow characterization of the geographic distribution of the races identified in the Debre Zeit field nursery.
Group size elicits specific physiological response in herbivores
Authors: Michelena Pablo , Pillot Marie-Hélène , Henrion Carole , Toulet Sylvain , Boissy Alain , Bon Richard
Published: April 2012

With increasing group size, individuals commonly spend less time standing head-up (scanning) and more time feeding. In small groups, a higher predation risk is likely to increase stress, which will be reflected by behavioural and endocrine responses. However, without any predator cues, we ask how the predation risk is actually processed by animals as group size decreases. We hypothesize that group size on its own acts as a stressor. We studied undisturbed groups of sheep under controlled pasture conditions, and measuredin situthe cortisol and vigilance responses of identified individuals in groups ranging from 2 to 100 sheep. Both vigilance and average cortisol concentration decreased as group size increased. However, the cortisol response varied markedly among individuals in small groups, resulting in a lack of correlation between cortisol and vigilance responses. Further experiments are required to explore the mechanisms that underlie both the decay and the convergence of individual stress in larger groups, and whether these mechanisms promote adaptive anti-predator responses.
Algebraic structure of stochastic expansions and efficient simulation
Authors: Ebrahimi-Fard Kurusch , Lundervold Alexander , Malham Simon J. A. , Munthe-Kaas Hans , Wiese Anke
Published: April 2012

We investigate the algebraic structure underlying the stochastic Taylor solution expansion for stochastic differential systems. Our motivation is to constructefficientintegrators. These are approximations that generate strong numerical integration schemes that are more accurate than the corresponding stochastic Taylor approximation, independent of the governing vector fields and to all orders. The sinhlog integrator introduced byMalham & Wiese (2009)is one example. Herein, we show that the natural context to study stochastic integrators and their properties is the convolution shuffle algebra of endomorphisms; establish a new whole class of efficient integrators; and then prove that, within this class, the sinhlog integrator generates theoptimalefficient stochastic integrator at all orders.
Outcome of SurePath™ cervical samples reported as borderline nuclear change by cytological subtype and high‐risk HPV status
Authors: Gupta N. , Dudding N. , Crossley J. , Payyappilly S. J. , Smith J. H. F.
Published: April 2012

N. Gupta, N. Dudding, J. Crossley, S.J. Payyappilly and J.H.F. Smith  Outcome of SurePath™ cervical samples reported as borderline nuclear changes by cytological subtype and high‐risk HPV status

Background:  The average borderline rate in cervical cytology samples for English laboratories was 3.8% with the range being 2.0–6.8% at the time of the present study, which was undertaken in order to determine the association between different subtypes of borderline nuclear change (BNC), high‐grade cervical intraepithelial neoplasia (CIN) and high‐risk human papillomavirus (hrHPV) status.

Materials and methods:  Of 68 551 SurePathTM cervical samples reported in one laboratory over a period of 2 years, 2335 (3.4%) were reported as BNC. hrHPV status was known in 1112 cases (47.6%). The outcome was known only for women with hrHPV‐positive BNC, who were recommended for colposcopy under the National Health Service Cervical Screening Programme sentinel site protocol. Women with hrHPV‐negative BNC were returned to 3‐yearly recall. The cases were subdivided into BNC, high‐grade dyskaryosis cannot be excluded (B‐HG; 105 cases); BNC with koilocytosis (B‐K; 421 cases); BNC with other features of HPV (B‐HPV; 160 cases); and BNC, not otherwise specified (B‐NOS; 426 cases) and were correlated with the histological outcome where available.

Results:  The study population age ranged from 23 to 65 years. Cases that tested positive for hrHPV by Qiagen HCII assay comprised 78.1%, 81.0%, 73.1% and 67.8% of B‐HG, B‐K, B‐HPV and B‐NOS categories, respectively. CIN2 or worse (CIN2+) was found in 64.6%, 10.0%, 19.7% and 20.1% of hrHPV‐positive cases of B‐HG, B‐K, B‐HPV and B‐NOS, respectively, which was significantly higher in the B‐HG category (P < 0.001) and lower in the B‐K category compared with B‐NOS (p < 0.001) and B‐HPV (p = 0.006) respectively. CIN3+ comprised 55.6%, 6.3%, 26.3% and 19.1% of biopsies in the same categories, respectively.

Conclusions:  Subtyping BNC is useful, especially B‐K and B‐HG, which, respectively, had the lowest and highest rates of detection of both CIN2+ and CIN3+, confirming that koilocytosis is likely to be associated with transient HPV infection. Women with B‐HG should be referred to colposcopy in the absence of HPV triage.
Comparing midwife‐led and doctor‐led maternity care: a systematic review of reviews
Authors: Sutcliffe Katy , Caird Jenny , Kavanagh Josephine , Rees Rebecca , Oliver Kathryn , Dickson Kelly , Woodman Jenny , Barnett‐Paige Elaine , Thomas James
Published: April 2012

sutcliffe k., caird j., kavanagh j., rees r., oliver k., dickson k., woodman j., barnett‐paIge e. & thomas j. (2012) Comparing midwife‐led and doctor‐led maternity care: a systematic review of reviews. Journal of Advanced Nursing68(11), 2376–2386.

Aims.  A report of a systematic review of reviews which examines the impact of having midwives‐led maternity care for low‐risk women, rather than physicians.

Background.  A rising birth rate, increasing complexity of births, and economic constraints pose difficulties for maternity services in the UK. Evidence about the most effective, cost‐effective, and efficient ways to give maternity services is needed.

Data sources.  Searches were carried out in August–September 2009 of ten electronic databases, 16 key nursing and research websites, and reference lists of 56 relevant reviews. We also contacted 38 experts for information. No date restrictions were employed.

Review methods.  A narrative review of systematic reviews or ‘meta review’ was conducted using transparent and systematic procedures to limit bias at all stages. Systematic reviews that compared midwife‐led care during pregnancy and birth with physician‐led care were eligible for inclusion.

Results.  Three meta‐analytic reviews were included. Midwife‐led care for low‐risk women was found to be better for a range of maternal outcomes, reduced the number of procedures in labour, and increased satisfaction with care. For some maternal, foetal, and neonatal outcomes reviews found no evidence that care led by midwives is different to that led by physicians. No adverse outcomes associated with midwife‐led care were identified.

Conclusions.  For low‐risk women, health and other benefits can result from having their maternity care led by midwives rather than physicians. Moreover, there appear to be no negative impacts on mothers and infants receiving midwife‐led care.
Anthropogenic landscape change promotes asymmetric dispersal and limits regional patch occupancy in a spatially structured bird population
Authors: Pavlacky David C. , Possingham Hugh P. , Lowe Andrew J. , Prentis Peter J. , Green David J. , Goldizen Anne W.
Published: April 2012

1. Local extinctions in habitat patches and asymmetric dispersal between patches are key processes structuring animal populations in heterogeneous environments. Effective landscape conservation requires an understanding of how habitat loss and fragmentation influence demographic processes within populations and movement between populations.

2. We used patch occupancy surveys and molecular data for a rainforest bird, the logrunner (Orthonyx temminckii), to determine (i) the effects of landscape change and patch structure on local extinction; (ii) the asymmetry of emigration and immigration rates; (iii) the relative influence of local and between‐population landscapes on asymmetric emigration and immigration; and (iv) the relative contributions of habitat loss and habitat fragmentation to asymmetric emigration and immigration.

3. Whether or not a patch was occupied by logrunners was primarily determined by the isolation of that patch. After controlling for patch isolation, patch occupancy declined in landscapes experiencing high levels of rainforest loss over the last 100 years. Habitat loss and fragmentation over the last century was more important than the current pattern of patch isolation alone, which suggested that immigration from neighbouring patches was unable to prevent local extinction in highly modified landscapes.

4. We discovered that dispersal between logrunner populations is highly asymmetric. Emigration rates were 39% lower when local landscapes were fragmented, but emigration was not limited by the structure of the between‐population landscapes. In contrast, immigration was 37% greater when local landscapes were fragmented and was lower when the between‐population landscapes were fragmented. Rainforest fragmentation influenced asymmetric dispersal to a greater extent than did rainforest loss, and a 60% reduction in mean patch area was capable of switching a population from being a net exporter to a net importer of dispersing logrunners.

5. The synergistic effects of landscape change on species occurrence and asymmetric dispersal have important implications for conservation. Conservation measures that maintain large patch sizes in the landscape may promote asymmetric dispersal from intact to fragmented landscapes and allow rainforest bird populations to persist in fragmented and degraded landscapes. These sink populations could form the kernel of source populations given sufficient habitat restoration. However, the success of this rescue effect will depend on the quality of the between‐population landscapes.
British Dietetic Association evidence‐based guidelines for the dietary management of irritable bowel syndrome in adults
Authors: McKenzie Y. A. , Alder A. , Anderson W. , Wills A. , Goddard L. , Gulia P. , Jankovich E. , Mutch P. , Reeves L. B. , Singer A. , Lomer M. C. E. ,   on behalf of Gastroenterology Specialist Group of the British Dietetic Association
Published: April 2012

How to cite this article: McKenzie Y.A., Alder A., Anderson W., Wills A., Goddard L., Gulia P., Jankovich E., Mutch P., Reeves L.B., Singer A. & Lomer M.C.E. on behalf of Gastroenterology Specialist Group of the British Dietetic Association. (2012) British Dietetic Association evidence‐based practice guidelines for the dietary management of irritable bowel syndrome in adults. J Hum Nutr Diet . 25, 260–274

Background:  Irritable bowel syndrome (IBS) is a chronic debilitating functional gastrointestinal disorder. Diet and lifestyle changes are important management strategies. The aim of these guidelines is to systematically review key aspects of the dietary management of IBS, with the aim of providing evidence‐based guidelines for use by registered dietitians.

Methods:  Questions relating to diet and IBS symptom management were developed by a guideline development group. These included the role of milk and lactose, nonstarch polysaccharides (NSP), fermentable carbohydrates in abdominal bloating, probiotics and empirical or elimination diets. A comprehensive literature search was conducted and relevant studies from January 1985 to November 2009 were identified using the electronic database search engines: Cinahl, Cochrane Library, Embase, Medline, Scopus and Web of Science. Evidence statements, recommendations, good practice points and research recommendations were developed.

Results:  Thirty studies were critically appraised. A dietetic care pathway was produced following a logical sequence of treatment and formed the basis of these guidelines. Three lines of dietary management were identified. First line: Clinical and dietary assessment, healthy eating and lifestyle management with some general advice on lactose and NSP. Second line: Advanced dietary interventions to improve symptoms based on NSP, fermentable carbohydrates and probiotics. Third line: Elimination and empirical diets. Research recommendations were also identified relating to the need for adequately powered and well designed randomised controlled trials.

Conclusions:  These guidelines provide evidence‐based details of how to achieve the successful dietary management of IBS.
Whole Transcriptome Analysis of the Coral Acropora millepora Reveals Complex Responses to CO2‐driven Acidification during the Initiation of Calcification
Authors: MOYA A. , HUISMAN L. , BALL E. E. , HAYWARD D. C. , GRASSO L. C. , CHUA C. M. , WOO H. N. , GATTUSO J.‐P. , FORÊT S. , MILLER D. J.
Published: April 2012

The impact of ocean acidification (OA) on coral calcification, a subject of intense current interest, is poorly understood in part because of the presence of symbionts in adult corals. Early life history stages of Acropora spp. provide an opportunity to study the effects of elevated CO2 on coral calcification without the complication of symbiont metabolism. Therefore, we used the Illumina RNAseq approach to study the effects of acute exposure to elevated CO2 on gene expression in primary polyps of Acropora millepora, using as reference a novel comprehensive transcriptome assembly developed for this study. Gene ontology analysis of this whole transcriptome data set indicated that CO2‐driven acidification strongly suppressed metabolism but enhanced extracellular organic matrix synthesis, whereas targeted analyses revealed complex effects on genes implicated in calcification. Unexpectedly, expression of most ion transport proteins was unaffected, while many membrane‐associated or secreted carbonic anhydrases were expressed at lower levels. The most dramatic effect of CO2‐driven acidification, however, was on genes encoding candidate and known components of the skeletal organic matrix that controls CaCO3 deposition. The skeletal organic matrix effects included elevated expression of adult‐type galaxins and some secreted acidic proteins, but down‐regulation of other galaxins, secreted acidic proteins, SCRiPs and other coral‐specific genes, suggesting specialized roles for the members of these protein families and complex impacts of OA on mineral deposition. This study is the first exhaustive exploration of the transcriptomic response of a scleractinian coral to acidification and provides an unbiased perspective on its effects during the early stages of calcification.
Large‐scale species delimitation method for hyperdiverse groups
Authors: PUILLANDRE N. , MODICA M. V. , ZHANG Y. , SIROVICH L. , BOISSELIER M.‐C. , CRUAUD C. , HOLFORD M. , SAMADI S.
Published: April 2012

Accelerating the description of biodiversity is a major challenge as extinction rates increase. Integrative taxonomy combining molecular, morphological, ecological and geographical data is seen as the best route to reliably identify species. Classic molluscan taxonomic methodology proposes primary species hypotheses (PSHs) based on shell morphology. However, in hyperdiverse groups, such as the molluscan family Turridae, where most of the species remain unknown and for which homoplasy and plasticity of morphological characters is common, shell‐based PSHs can be arduous. A four‐pronged approach was employed to generate robust species hypotheses of a 1000 specimen South‐West Pacific Turridae data set in which: (i) analysis of COI DNA Barcode gene is coupled with (ii) species delimitation tools GMYC (General Mixed Yule Coalescence Method) and ABGD (Automatic Barcode Gap Discovery) to propose PSHs that are then (iii) visualized using Klee diagrams and (iv) evaluated with additional evidence, such as nuclear gene rRNA 28S, morphological characters, geographical and bathymetrical distribution to determine conclusive secondary species hypotheses (SSHs). The integrative taxonomy approach applied identified 87 Turridae species, more than doubling the amount previously known in the Gemmula genus. In contrast to a predominantly shell‐based morphological approach, which over the last 30 years proposed only 13 new species names for the Turridae genus Gemmula, the integrative approach described here identified 27 novel species hypotheses not linked to available species names in the literature. The formalized strategy applied here outlines an effective and reproducible protocol for large‐scale species delimitation of hyperdiverse groups.
Mechano‐transcription of COX‐2 is a common response to lumen dilation of the rat gastrointestinal tract
Authors: Lin Y.‐M. , Li F. , Shi X.‐Z.
Published: April 2012

Background  In obstructive bowel disorders (OBDs) such as achalasia, pyloric stenosis, and bowel obstruction, the lumen of the affected segments is markedly dilated and the motility function is significantly impaired. We tested the hypothesis that mechanical stress in lumen dilation leads to induction of cyclooxygenase‐2 (COX‐2) in smooth muscle throughout the gastrointestinal (GI) tract, contributing to motility dysfunction.

Methods  Lumen dilation was induced in vivo with obstruction bands (12 × 3 mm) applied over the lower esophageal sphincter (LES), the pyloric sphincter, and the ileum in rats for 48 h. Mechanical stretch in vivo was also emulated by balloon distension of the distal colon. Direct stretch of muscle strips from the esophagus, gastric fundus, and ileum was mimicked in an in vitro tissue culture system.

Key Results  Partial obstruction in the LES, pylorus, and ileum significantly increased the expression of COX‐2 mRNA and protein in the muscularis externae of the dilated segment oral to the occlusions, but not in the aboral segment. Direct stretch of the lumen in vivo or of muscle strips in vitro markedly induced COX‐2 expression. The smooth muscle contractility was significantly suppressed in the balloon‐distended segments. However, treatment with COX‐2 inhibitor NS‐398 restored the contractility. Furthermore, in vivo administration of NS‐398 in gastric outlet obstruction significantly improved gastric emptying.

Conclusions & Inferences  Mechanical dilation of the gut lumen by occlusion or direct distension induces gene expression of COX‐2 throughout the GI tract. Mechanical stress‐induced COX‐2 contributes to motility dysfunction in conditions with lumen dilation.