bluuebunny/crossref_metadata_2025_split huggingface dataset:
BOLDMirror: a global mirror system of DNA barcode data
Authors: Liu D. , Liu L. , Guo G. , Wang W. , Sun Q. , Parani M. , Ma J. 
Published: December 2012

AbstractDNA barcoding is a novel concept for taxonomic identification using short, specific genetic markers and has been applied to study a large number of eukaryotes. The huge amount of data output generated by DNA barcoding requires well‐organized information systems. Besides the Barcode of Life Data system (BOLD) established in Canada, the mirror system is also important for the international barcode of life project (iBOL). For this purpose, we developed the BOLDMirror, a global mirror system of DNA barcode data. It is open‐sourced and can run on the LAMP (Linux + Apache + MySQL + PHP) environment. BOLDMirror has data synchronization, data representation and statistics modules, and also provides spaces to store user operation history. BOLDMirror can be accessed at http://www.boldmirror.net and several countries have used it to setup their site of DNA barcoding.
DNA barcoding applied to ex situ tropical amphibian conservation programme reveals cryptic diversity in captive populations
Authors: Crawford Andrew J. , Cruz Catalina , Griffith Edgardo , Ross Heidi , Ibáñez Roberto , Lips Karen R. , Driskell Amy C. , Bermingham Eldredge , Crump Paul 
Published: December 2012

AbstractAmphibians constitute a diverse yet still incompletely characterized clade of vertebrates, in which new species are still being discovered and described at a high rate. Amphibians are also increasingly endangered, due in part to disease‐driven threats of extinctions. As an emergency response, conservationists have begun ex situ assurance colonies for priority species. The abundance of cryptic amphibian diversity, however, may cause problems for ex situ conservation. In this study we used a DNA barcoding approach to survey mitochondrial DNA (mtDNA) variation in captive populations of 10 species of Neotropical amphibians maintained in an ex situ assurance programme at El Valle Amphibian Conservation Center (EVACC) in the Republic of Panama. We combined these mtDNA sequences with genetic data from presumably conspecific wild populations sampled from across Panama, and applied genetic distance‐based and character‐based analyses to identify cryptic lineages. We found that three of ten species harboured substantial cryptic genetic diversity within EVACC, and an additional three species harboured cryptic diversity among wild populations, but not in captivity. Ex situ conservation efforts focused on amphibians are therefore vulnerable to an incomplete taxonomy leading to misidentification among cryptic species. DNA barcoding may therefore provide a simple, standardized protocol to identify cryptic diversity readily applicable to any amphibian community.
Gene expression profile of mouse white adipose tissue during inflammatory stress: age‐dependent upregulation of major procoagulant factors
Authors: Starr Marlene E. , Hu Yanling , Stromberg Arnold J. , Carmical Joseph R. , Wood Thomas G. , Evers B. Mark , Saito Hiroshi 
Published: December 2012

SummaryTolerance to physiological stress resulting from inflammatory disease decreases significantly with age. High mortality rates, increased cytokine production, and pronounced thrombosis are characteristic complications of aged mice with acute systemic inflammation induced by injection with lipopolysaccharide (LPS). As adipose tissue is now recognized as an important source of cytokines, we determined the effects of aging on visceral white adipose tissue gene expression during LPS‐induced inflammation in male C57BL/6 mice. Microarray analysis revealed that the expression of 6025 genes was significantly changed by LPS; of those, the expression of 667 showed an age‐associated difference. Age‐associated differences were found in many genes belonging to the inflammatory response and blood clotting pathways. Genes for several procoagulant factors were upregulated by LPS; among these, tissue factor, thrombospondin‐1, and plasminogen activator inhibitors‐1 and ‐2, exhibited age‐associated increases in expression which could potentially contribute to augmented thrombosis. Further analysis by qRT–PCR, histological examination, and cell fraction separation revealed that most inflammatory and coagulant‐related gene expression changes occur in resident stromal cells rather than adipocytes or infiltrating cells. In addition, basal expression levels of 303 genes were altered by aging, including increased expression of component of Sp100‐rs (Csprs). This study indicates that adipose tissue is a major organ expressing genes for multiple inflammatory and coagulant factors and that the expression of many of these is significantly altered by aging during acute inflammation. Data presented here provide a framework for future studies aimed at elucidating the impact of adipose tissue on age‐associated complications during sepsis and systemic inflammation.
Quantification of in vivo oxidative damage in Caenorhabditis elegans during aging by endogenous F3‐isoprostane measurement
Authors: Labuschagne Christiaan F. , Stigter Edwin C. A. , Hendriks Margriet M. W. B. , Berger Ruud , Rokach Joshua , Korswagen Hendrik C. , Brenkman Arjan B. 
Published: December 2012

SummaryOxidative damage is thought to be a major cause in development of pathologies and aging. However, quantification of oxidative damage is methodologically difficult. Here, we present a robust liquid chromatography–tandem mass spectrometry (LC‐MS/MS) approach for accurate, sensitive, and linear in vivo quantification of endogenous oxidative damage in the nematode Caenorhabditis elegans, based on F3‐isoprostanes. F3‐isoprostanes are prostaglandin‐like markers of oxidative damage derived from lipid peroxidation by Reactive Oxygen Species (ROS). Oxidative damage was quantified in whole animals and in multiple cellular compartments, including mitochondria and peroxisomes. Mutants of the mitochondrial electron transport proteins mev‐1 and clk‐1 showed increased oxidative damage levels. Furthermore, analysis of Superoxide Dismutase (sod) and Catalase (ctl) mutants uncovered that oxidative damage levels cannot be inferred from the phenotype of resistance to pro‐oxidants alone and revealed high oxidative damage in a small group of chemosensory neurons. Longitudinal analysis of aging nematodes revealed that oxidative damage increased specifically with postreproductive age. Remarkably, aging of the stress‐resistant and long‐lived daf‐2 insulin/IGF‐1 receptor mutant involved distinct daf‐16‐dependent phases of oxidative damage including a temporal increase at young adulthood. These observations are consistent with a hormetic response to ROS.
Shifts in Discriminative Control with Increasing Periods of Recovery in the Rat
Authors: Ginsburg Brett C. , Lamb Richard J. 
Published: December 2012

BackgroundDuring recovery from alcoholism, other behavior likely increases. The development of alternative behavior may reduce attention to alcohol‐associated stimuli. This could result in greater persistence of the alternative behavior when individuals again encounter alcohol‐associated stimuli that might precipitate relapse. Developing animal models of this process could facilitate a better understanding of the mechanisms involved in relapse and recovery. However, current preclinical models of recovery and relapse rarely measure alternative behavior. Thus, our objective was to establish a procedure in rats in which an increase in alternative behavior (responding for food) reduced responding for ethanol (EtOH). The amount of responding for food and EtOH was then assessed after re‐exposure to the alcohol‐associated stimulus after varying the number of preceding sessions of increased responding for food and reduced responding for EtOH. These results were compared with those from a parallel group responding for saccharin solution instead of EtOH.MethodsThe solution (EtOH or saccharin) was always available following 5 responses. Presentation of flashing stimulus lights indicated food delivery followed 150 responses and resulted in responding predominately for the solution (84 to 86% of total responses). Presentation of solid stimulus lights indicated food delivery followed 5 responses and resulted in responding predominately for food (1 to 3% of total responses were for the solution). Rats were exposed to solid light conditions for 0, 1, 2, 4, or 16 consecutive sessions before being re‐exposed to the flashing stimulus lights in extinction.ResultsResponding for either solution resumed when rats were re‐exposed to the flashing stimulus lights (associated with solution‐predominate responding). However, more responses occurred on the food lever with longer recent histories of responding for food instead of the solution.ConclusionsThese results suggest that the longer alternative behavior replaces drinking, the more that attention to stimuli associated with drinking decreases. These results are consistent with the notion that the risk of relapse declines with longer periods of recovery because alternative behavior comes to predominate even in the presence of stimuli associated with drinking.
Effects of Voluntary Access to Sweetened Ethanol During Adolescence on Intake in Adulthood
Authors: Broadwater Margaret , Varlinskaya Elena I. , Spear Linda P. 
Published: December 2012

BackgroundThe prevalence of alcohol use during adolescence is concerning given that early age of alcohol initiation is correlated with the development of alcohol‐related problems later in life. The purpose of this series of studies was to assess whether voluntary ethanol (EtOH) exposure during adolescence would influence EtOH drinking behavior in adulthood using an animal model.MethodsPair‐housed Sprague‐Dawley adolescent (postnatal day [P] 28 to 42) rats of both sexes were given single bottle access to 1 of 3 solutions in their home cages—10% EtOH in “supersac” (0.125% saccharin and 3% sucrose) (EtOH/SS), supersac without EtOH (SS), or water—for 30 minutes every other day for a total of 8 drinking days or were left nonmanipulated (NM). Animals were NM thereafter until adulthood (P70) at which time they were given 1‐bottle, 30 minute limited access tests with 20% EtOH every other day (Exp 1), 10% EtOH in SS (Exp 2), or SS without EtOH (Exp 3).ResultsAdolescent EtOH/SS exposure increased adulthood consumption of EtOH/SS (Exp 2), but not 20% unsweetened EtOH (Exp 1) or SS (Exp 3), with this increase most pronounced at the beginning of the 8 intake day procedure. Access to SS (without EtOH) during adolescence produced an analogous effect, with increased adult SS consumption during the first 2 intake days, but no increases in either of the EtOH test solutions.ConclusionsSolution‐specific increases in adulthood intake after adolescent exposure are most likely associated with solution acceptance due to familiarity. This is an important consideration for future intake studies assessing the influence of EtOH exposure during adolescence on intake of EtOH in adulthood.
Effects of Sibship Size and Composition on Younger Brothers’ and Sisters’ Alcohol Use Initiation: Findings from an Australian Twin Sample
Authors: Richmond‐Rakerd Leah S. , Slutske Wendy S. , Heath Andrew C. , Martin Nicholas G. 
Published: December 2012

BackgroundThe effects of sibship size and structure on delinquency are well established. Specifically, having a large family and many brothers has been shown to predict offending. However, despite strong links between delinquency and alcohol use, the contribution of sibship factors to drinking behaviors remains largely unexplored. The current study investigated the impact of sibship size and composition on younger brothers’ and sisters’ ages of drinking and intoxication onset.MethodsWe employed a sample of 4,281 same‐sex twins from the Australian Twin Register to examine whether (i) large sibship size facilitates earlier age at first drink (AFD) and age at first intoxication (AFI) in males and females, (ii) having many older brothers predicts earlier ages of AFD and AFI in males, and (iii) having many older brothers results in later AFD and AFI in females. We tested whether effects were moderated by parental divorce and alcohol misuse and mediated by familial religion.ResultsSibling effects were minimal before accounting for family context. However, when parental divorce and excessive parental drinking were included as moderators, sibling effects were significantly amplified among individuals from homes of divorce, and effects were strongest when siblings were close in age.ConclusionsStrong close in age older sibling effects indicate that proximal sibling attitudes and behaviors about alcohol likely interact with structural factors to influence younger siblings’ drinking. Sibship factors were much more influential in one population (individuals from homes of divorce) than another (respondents with a parental history of excessive drinking), suggesting that sibling effects vary depending on the type of co‐occurring familial risk. Prevention efforts performed at the family level, and introduced before first use of alcohol, are likely to delay drinking initiation and help prevent future alcohol problems.
Childhood Trauma Exposure and Alcohol Dependence Severity in Adulthood: Mediation by Emotional Abuse Severity and Neuroticism
Authors: Schwandt Melanie L. , Heilig Markus , Hommer Daniel W. , George David T. , Ramchandani Vijay A. 
Published: December 2012

BackgroundChildhood trauma has been linked with a number of negative outcomes later in life, including alcohol dependence (AD). Previous studies have suggested a mediating role for neuroticism in the relationship between childhood trauma and psychopathology. In this study, we investigate the prevalence of multiple types of childhood trauma in treatment‐seeking alcohol‐dependent patients, and the associations between childhood trauma and AD severity using multiple mediation analysis.MethodsThe prevalence of 5 types of childhood trauma—emotional abuse, sexual abuse, physical abuse, emotional neglect, and physical neglect—was assessed in treatment‐seeking alcohol‐dependent patients (n = 280) and healthy controls (n = 137) using the Childhood Trauma Questionnaire. Multiple mediation analyses were used to model associations between childhood trauma measures and alcohol‐related outcomes, primarily the severity of AD in the alcohol‐dependent sample.ResultsChildhood trauma was significantly more prevalent and more severe in the alcohol‐dependent subjects. In addition, childhood trauma was found to influence AD severity, an effect that was mediated by neuroticism. When individual trauma types were examined, emotional abuse was found to be the primary predictor of AD severity, both directly and through the mediating effects of the impulsivity subfacet of neuroticism. Physical abuse also had a moderate direct effect on AD severity. Mediation analysis did not reveal any association between childhood trauma and Alcohol Use Disorders Identification Test score in the nondependent control sample.ConclusionsChildhood trauma is highly prevalent in treatment‐seeking alcoholics and may play a significant role in the development and severity of AD through an internalizing pathway involving negative affect. Our findings suggest that alcoholics with a history of childhood emotional abuse may be particularly vulnerable to severe dependence.
Genetic Markers of Comorbid Depression and Alcoholism in Women
Authors: Procopio Daniela O. , Saba Laura M. , Walter Henriette , Lesch Otto , Skala Katrin , Schlaff Golda , Vanderlinden Lauren , Clapp Peter , Hoffman Paula L. , Tabakoff Boris 
Published: December 2012

BackgroundAlcohol dependence (AD) is often accompanied by comorbid depression. Recent clinical evidence supports the benefit of subtype‐specific pharmacotherapy in treating the population of alcohol‐dependent subjects with comorbid major depressive disorder (MDD). However, in many alcohol‐dependent subjects, depression is a reactive response to chronic alcohol use and withdrawal and abates with a period of abstinence. Genetic markers may distinguish alcohol‐dependent subjects with MDD not tied chronologically and etiologically to their alcohol consumption. In this work, we investigated the association of adenylyl cyclase genes (ADCY1–9), which are implicated in both AD and mood disorders, with alcoholism and comorbid depression.MethodsSubjects from Vienna, Austria (n = 323) were genotyped, and single nucleotide polymorphisms (1,152) encompassing the genetic locations of the 9 ADCY genes were examined. The Vienna cohort contained alcohol‐dependent subjects differentiated using the Lesch Alcoholism Typology. In this typology, subjects are segregated into 4 types. Type III alcoholism is distinguished by co‐occurrence of symptoms of depression and by affecting predominantly females.ResultsWe identified 4 haplotypes associated with the phenotype of Type III alcoholism in females. One haplotype was in a genomic area in proximity to ADCY2, but actually within a lincRNA gene, 2 haplotypes were within ADCY5, and 1 haplotype was within the coding region of ADCY8. Three of the 4 haplotypes contributed independently to Type III alcoholism and together generated a positive predictive value of 72% and a negative predictive value of 78% for distinguishing women with a Lesch Type III diagnosis versus women designated as Type I or II alcoholics.ConclusionsPolymorphisms in ADCY8 and ADCY5 and within a lincRNA are associated with an alcohol‐dependent phenotype in females, which is distinguished by comorbid signs of depression. Each of these genetic locations can rationally contribute to the polygenic etiology of the alcoholism/depression phenotype, and the use of these genetic markers may aid in choosing appropriate and beneficial treatment strategies.
Quantifying Neodiprion sertifer nucleopolyhedrovirus DNA from insects, foliage and forest litter using the quantitative real‐time polymerase chain reaction
Authors: Krokene Paal , Heldal Inger , Fossdal Carl G. 
Published: December 2012

Neodiprion sertifer nucleopolyhedrovirus (NeseNPV) is widely used as a viral bio‐insecticide against larvae of the European pine sawfly N. sertifer (Geoff.) (Hymenoptera: Diprionidae), which is one of the most harmful defoliators of pines in Northern Europe. A major obstacle to studying this pathogenic virus in nature is the difficulty of confirming and quantifying the presence of NeseNPV.
In the present study, we developed real‐time polymerase chain reaction (PCR) primers, based on the caspid gene 39 sequence, for the specific and quantitative detection of NeseNPV. The quantitative real‐time PCR (qPCR) assay can detect virus from any substrate tested, including different insect life stages (egg, larval, adult), pine foliage, and litter or ground vegetation. The reproducible detection limit for the real‐time assay is 0.013 pg of viral DNA (0.013×10−12 g), corresponding to 136 viral genomes or approximately one to seven virus occlusion bodies per sample.
qPCR is a specific, quantitative, sensitive, reliable and flexible procedure, and is a good supplement to conventional microscopy‐ or bioassay‐based methods for detection of the virus. We have used qPCR to quantify the level of NeseNPV in samples collected in the field after aerial application of the virus, and demonstrated significantly higher virus levels in sawfly larvae from sprayed areas compared with unsprayed control areas 4 weeks after spraying.
This qPCR assay can be used to determine important aspects of the biology of NeseNPV (e.g. virus levels in different insect life stages and in their microhabitats on pine foliage and in forest litter).
Australian general practitioners' preferences for managing the care of people diagnosed with cancer
Authors: Johnson Claire E , Lizama Natalia , Garg Neeraj , Ghosh Manonita , Emery Jonathan , Saunders Christobel 
Published: December 2012

AbstractAimTo investigate general practitioners' (GPs) preferences for involvement in the management of people diagnosed with the seven most frequent cancers and any barriers to or concerns about an expanded role for GPs.MethodsA self‐report survey was mailed to a random sample of 1969 Australian GPs.ResultsIn all, 33% (648) of GPs participated. Participants were a median of 50 years and worked 38 h per week; 53% were male and 68% practiced in metropolitan areas. Most participants preferred to be involved in cancer prevention (86%) and initial diagnosis (85%). Fewer were interested in monitoring for recurrence (70%), follow up after treatment (68%), coordinating psychological support (70%) and palliative care (68%). Only 52% of GPs had a preference for providing supportive care to manage the symptoms of cancer treatment, 45% for managing postoperative care and 40% for coordinating treatment. On multivariate analysis, preference for involvement in more aspects of cancer management increased with age (P = 0.030), if the GP practiced in rural compared to metropolitan areas (P = 0.005), was a partner in a practice compared to a sole practitioner (P = 0.003), had previously received cancer‐specific training (P < 0.001) or was interested in future training (P < 0.001). Open responses identified limited time, communication and information transfer between GP and specialists as important barriers to involvement in cancer management.ConclusionWhile many GPs are currently involved in some aspects of cancer management, with training, good communication and support from specialists this role may be successfully expanded.
Necrolytic migratory erythema associated with glucagonoma syndrome diagnosed by 68Ga‐DOTANOC PET‐CT
Authors: Sahoo Manas K , Gupta Somesh , Singh Ishita , Pahwa Shivani , Durgapal Prashant , Bal Chandra Sekhar 
Published: December 2012

AbstractNecrolytic migratory erythema (NME) is a rare dermatological condition which presents a diagnostic challenge. Repeated negative skin biopsies and non‐detection of any pancreatic tumor in conventional imaging modalities like a computed tomography (CT) scan and ultrasonogram (USG) make the diagnosis more difficult. By the time the diagnosis is made, the patient usually presents with metastasis. We present a rare case of difficult to diagnose NME, as repeated skin biopsies and conventional imaging modalities like CT and USG could not detect the underlying glucagonoma. A 68Ga‐DOTANOC positron emission tomography PET‐CT was able to detect the underlying cause of NME as glucagonoma of the pancreas and the same investigation confirmed the absence of any metastasis elsewhere in the body. The tumor was excised and patient dramatically improved, and all skin lesions disappeared.
Observational, medical or surgical management of vesicoureteric reflux
Authors: Caillaud Caroline , Lacreuse Isabelle , Fothergill Helen , Becmeur François , Fischbach Michel 
Published: December 2012

AbstractThe clinical management of vesicoureteric reflux includes observational, medical and surgical procedures. The choice of management is often a joint decision made between the paediatric nephrologist and urologist. The use of prophylactic antibiotics has become increasingly debated. In recent years, the surgical treatment of reflux (including endoscopic intervention or ureteral reimplantation) has mainly been limited to cases of high‐grade reflux. There are several important risk factors that influence the final outcome which need to be identified and treated. The aim of reflux management is no longer to treat imperatively, but rather to avoid renal damage. It is perhaps time to revise the classic saying ‘diagnosed reflux – treated reflux’ with a new objective ‘diagnosed reflux – evaluated reflux’.ConclusionThe management and follow‐up of childhood reflux is a joint decision between the paediatric urologist and nephrologist and should be decided on a case‐by‐case basis.