bluuebunny/crossref_metadata_2025 huggingface dataset:
Data-intensive science: The Terapixel and MODISAzure projects
Authors: Agarwal Deb , Cheah You-Wei , Fay Dan , Fay Jonathan , Guo Dean , Hey Tony , Humphrey Marty , Jackson Keith , Jie Li  , Poulain Christophe , Ryu Youngryel , van Ingen Catharine
Published: August 2011

We live in an era in which scientific discovery is increasingly driven by data exploration of massive datasets. Scientists today are envisioning diverse data analyses and computations that scale from the desktop to supercomputers, yet often have difficulty designing and constructing software architectures to accommodate the heterogeneous and often inconsistent data at scale. Moreover, scientific data and computational resource needs can vary widely over time. The needs grow as the science collaboration broadens or as additional data is accumulated; the computational demand can have large transients in response to seasonal field campaigns or new instrumentation breakthroughs. Cloud computing can offer a scalable, economic, on-demand model that is well matched to some of these evolving science needs. This paper presents two of our experiences over the last year — the Terapixel Project, using workflow, high-performance computing and non-structured query language data processing to render the largest astronomical image for the WorldWide Telescope, and MODISAzure, a science pipeline for image processing, deployed using the Azure Cloud infrastructure.
Psychological counselling in post-Soviet Russia: Gendered perceptions in a feminizing profession
Authors: Griffin Gabriele , Karepova Maria
Published: August 2011

In this article the authors discuss psychological counselling as it emerges as a gendered profession in the transitional economy of Russia. Based on qualitative, semi-structured interviews with 23 female and three male practising counsellors, the article analyses their perceptions of their profession, focusing in particular on two key issues: (1) their reasons for entry into the profession; and (2) their expectations of their work as a profession. The authors argue that both female and male counsellors’ perceptions of their entry into this profession revealed highly gendered stances, and furthermore, that these were strongly imbricated in the legacies of Soviet employment policies and gender ideology.
Shall I leave or shall we fight? Effects of threatened group-based self-esteem on identity management strategies
Authors: Martiny Sarah E. , Kessler Thomas , Vignoles Vivian L.
Published: August 2011

We examined the interplay of social identity threat and group-based self-esteem on the motivation to use two identity management strategies, namely social competition and individual mobility. Following social identity theory, we postulated that threatened high group-based self-esteem leads to an increased motivation to use competitive identity management strategies. Furthermore, following realistic conflict theory and the rejection–identification model, we hypothesized that threat might reduce the desire for individual mobility among group members low in group-based self-esteem. Results of Study 1 ( N = 67), Study 2 ( N = 109), and Study 3 ( N = 101) supported these hypotheses. The results showed that threat leads to the motivation to show social competition for group members high in group-based self-esteem and that for group members low in group-based self-esteem threat decreases the motivation to leave the group. The results are discussed in relation to recent theories of intergroup relations.
Against the wind: Male victimization and the ideal of manliness
Authors: Andersen Torbjørn Herlof
Published: August 2011

• Summary: Boys and men are subjected to sexual assault, with perpetrators drawn from both sexes. This article discusses the necessity of recognizing the victim position as a possibility within an understanding of manliness. As well as being a necessary part of work with boys and men who have been subjected to abuse, the inclusion of the victim dimension will expand and add nuance to the perception of manliness in general. An argument for the involvement of social work in the field is offered based on an understanding of its mandate and responsibility as a profession.

• Findings: A traditional view of manliness stands in the way of men being taken seriously as assault victims. Despite more recent academic and professional discourses on men as victims, a traditional ideal of manliness is still a reality with considerable influence on institutions and attitudes. Sexually abused men tend to judge themselves according to an ideal of manliness that does not allow a man to be a victim, and are thereby silenced.

• Applications: These findings have relevance for social work students, for social work practice and supervision and for directing professional attention towards the aspects of gender issues represented in sexual abuse of males.
A bivariate INAR(1) process with application
Authors: Pedeli Xanthi , Karlis Dimitris
Published: August 2011

The study of time series models for count data has become a topic of special interest during the last years. However, while research on univariate time series for counts now flourishes, the literature on multivariate time series models for count data is notably more limited. In the present paper, a bivariate integer-valued autoregressive process of order 1 (BINAR(1)) is introduced. Emphasis is placed on models with bivariate Poisson and bivariate negative binomial innovations. We discuss properties of the BINAR(1) model and propose the method of conditional maximum likelihood for the estimation of its unknown parameters. Issues of diagnostics and forecasting are considered and predictions are produced by means of the conditional forecast distribution. Estimation uncertainty is accommodated by taking advantage of the asymptotic normality of maximum likelihood estimators and constructing appropriate confidence intervals for the fe-step-ahead conditional probability mass function. The proposed model is applied to a bivariate data series concerning daytime and nighttime road accidents in the Netherlands.
Transformed symmetric models
Authors: Cordeiro Gauss M , Andrade Marinho G
Published: August 2011

For the first time, we introduce a class of transformed symmetric models to extend the Box and Cox models to more general symmetric models. The new class of models includes all symmetric continuous distributions with a possible non-linear structure for the mean and enables the fitting of a wide range of models to several data types. The proposed methods offer more flexible alternatives to Box-Cox or other existing procedures. We derive a very simple iterative process for fitting these models by maximum likelihood, whereas a direct unconditional maximization would be more difficult. We give simple formulae to estimate the parameter that indexes the transformation of the response variable and the moments of the original dependent variable which generalize previous published results. We discuss inference on the model parameters. The usefulness of the new class of models is illustrated in one application to a real dataset.
Other(ing), self(portraying), negotiating: the spatial codification of values in Zagreb’s city-text
Authors: Šakaja Laura , Stanić Jelena
Published: August 2011

One of the essential characteristics of the post-socialist transition is rethinking history and negotiating its meanings. As the capital of the newly independent state of Croatia, Zagreb communicated and mediated a dynamic process of national identity building, closely linked to the politics of heritage. The article explores the role of statuary and street toponymy in post-socialist identity building in the Croatian capital. The removal/installation of public plaques and statuary as well as the renaming of streets and squares in postsocialist Zagreb was a revealing indicator and an instrument in the post-socialist (re)writing/(re)signifying of space. These political acts have disclosed the ‘Other’, in relation to whom the construction of post-socialist Croatian identity was developed. The article argues that symbolic rewriting of Zagreb’s city-text was organized and shaped primarily by discursive practices of Othering and Selfreferencing, as systematic acts of articulation in the frame of the politics of landscape. The transition process was accompanied by semantic displacements in the landscape which occured in three ways: by a) relocation of certain streets and monuments from central to more peripheral zones, or vice versa, b) resemiotization of memorials, and c) ‘secondary sacralization’, or resemiotization of places.
Effectiveness of Intensive Inpatient Rehabilitation Treatment on Disease Progression in Parkinsonian Patients
Authors: Frazzitta Giuseppe , Bertotti Gabriella , Riboldazzi Giulio , Turla Marinella , Uccellini Davide , Boveri Natalia , Guaglio Gabriele , Perini Michele , Comi Cristoforo , Balbi Pietro , Maestri Roberto
Published: August 2011

Background. Rehabilitation treatments have acute beneficial effects in Parkinson’s disease (PD) patients, but whether the effects persist over time is unclear. Objective. To assess whether an intensive rehabilitation treatment (IRT) is effective in improving motor performance compared with a control group in a 12-month follow-up, to investigate whether a second cycle administered after 1 year has the same efficacy as the first treatment, and to determine whether IRT reduces the need for increasing levodopa dosage. Methods. A total of 50 PD patients were randomly assigned to 2 groups; 25 participants had 4 weeks of inpatient physical therapy that included treadmill and stabilometric platform training. At discharge, these patients were invited to continue doing the learned exercises. After 12 months, the same treatment was repeated. The control group of 25 patients received only pharmacological treatment and was invited to practice generic physical exercise at home. The rating scales used for the clinical evaluation were the Unified Parkinson’s Disease Rating Scale Sections II and III (UPDRS II and III) and total (UPDRS tot). Results. The authors found that the beneficial effects of IRT persisted over time. A second rehabilitation cycle administered after 1 year was as effective as the first treatment. At the end of the study, daily medication dosage was reduced in treated patients, whereas it was significantly increased in control patients. Conclusion. These findings suggest that the natural worsening of symptoms associated with PD can be effectively counteracted by a properly designed IRT.
It’s Not Just About the French Fry
Authors: Morrison Zachary J. , Gregory David M. , Thibodeau Steven
Published: August 2011

The purpose of this article is to explore idiom of distress and its application to overweight and obese adolescent boys. This case study suggests that avoidance, as an idiom of distress, offers self-protection from suffering among this population. Fieldwork included 55 face-to-face contact hours, 25 virtual contact hours (i.e., text messaging, e-mails, phone calls), and 16 person-centered interviews. The daily suffering experienced by this group of boys, and their collective enactment of avoidance as a self-protective strategy, offer an understanding of their lives beyond their obese bodies. Avoidance behaviors, however, can result in negative social consequences such as isolation. Recognizing avoidance as an idiom of distress permits parents, teachers, health professionals, and researchers to interact with overweight and obese adolescent boys in a profoundly different way. Attending to the personhood of these vulnerable boys was an important finding of this qualitative study.
Acute Appendicitis Masquerading as Acute Scrotum
Authors: Dienye Paul O. , Jebbin Nze J.
Published: August 2011

Acute appendicitis presents typically with periumbilical pain that in a few hours settles at the right lower quadrant of the abdomen. Atypical presentations are common but association with acute scrotum is an extreme rarity. A 30-year-old fisherman presented at a rural medical facility with a 2-day complaint of severe pain at the right hemiscrotum followed about 24 hours later with mild diffuse abdominal pain. There was associated mild fever and nausea but no vomiting. There were no urinary symptoms and no recent sexual exposure. Initial physical examination revealed mild generalized tenderness worse at the right lower quadrant but the scrotum was not remarkable, and cremasteric sign was negative. He was admitted as a case of acute abdomen for close observation. Abdominal and scrotal ultrasound scan were normal. By the second day of admission, pain became marked at the right lower abdomen with associated vomiting. There was also marked tenderness at the right lower quadrant with rebound. A diagnosis of acute appendicitis was thus made and appendicectomy done after proper workup. The abdominal and scrotal pain stopped after surgery and the patient was discharged on the seventh postoperative day. Patients with unusual abdominal and scrotal pain should be admitted and closely observed and evaluated to prevent unnecessary scrotal exploration or negative appendicectomy.
Forging Violence Against Women: Documents, Regimes of Family and Intimate-Partner Abuse
Authors: Trinch Shonna
Published: August 2011

This article examines how legal texts can be read to broaden our understanding of intimate-partner violence in the United States. Documents, as repositories of the way institutions remember for the public, can provide insight into how people, and in this case, female victims and state actors, define this particular type of violence against women. These documents demonstrate how kin, household and family are both involved and implicated in this highly gendered and targeted aggression. The data presented should factor into new definitions of intimate-partner abuse, because they illustrate how the surrounding network of family members, along with providing help to women that are victimized, may also be at risk of being harmed by men that batter their wives and girlfriends.
Assassinating Justly: Reflections on Justice and Revenge in the Osama Bin Laden Killing
Authors: Berkowitz Roger
Published: August 2011

Assassination has always been part of war and in recent years it has played increasingly important roles in United States military policy. The assassination of Osama bin Laden offers itself as an example of an assassination that nevertheless claims to be just. Comparing the bin Laden assassination with the assassination of Simon Petlura by Sholom Schwartzbard in 1927 and the kidnapping and trial of Adolf Eichmann in 1961, this article argues that assassinations, which under certain conditions are justified under international law, can also be just, but only when they are accompanied by the risk of a jury trial.
Effects of Ascorbic Acid Intake on the Intima-Media Thickness and Blood Flow Velocities of the Carotid Artery in Patients With Sickle Cell Anemia
Authors: Olowoyeye Omodele A. , Jaja Smith I. , Kehinde Michael O. , Awosanya Gbolahan O. , Irurhe Nicholas K. , Adeyomoye Adekunle A. , Soyebi Kofoworola O. , Arogundade Rasheed A. , Adekunle Ololade M. , Soneye Busola K. , Tubi Omobolanle O.
Published: August 2011

This study aims to investigate and compare the effects of six-week oral vitamin C supplementation on blood velocities, intima-media thickness, and cross-sectional diameter (CSD) of the common carotid artery of sickle cell anemia (SCA) and non–sickle cell anemia (NSCA) subjects using sonography. Results showed that the CSD and end-diastolic velocity were significantly higher ( P < .002 and P < .001, respectively) in the SCA subjects than in the NSCA subjects in the presupplementation phase. Calculated resistivity index (RI) was significantly lower in the SCA subjects ( P < .003). Vitamin C supplementation had a slight effect on all the measured parameters in the NSCA subjects but caused a significant increase in peak systolic velocity (PSV) ( P < .02) and RI ( P < .01) in SCA. A comparison of change in each measured variable between the groups showed significant differences. Oral supplementation with vitamin C should be encouraged in patients with SCA as prophylaxis against endothelial damage, thereby preventing vaso-occlusive crises and their associated morbidity.
Carbon nanotube/ultrafine grade Ti(C,N) based cermets composite
Authors: Li Y , Liu N , Li Y
Published: August 2011

Effects of CNT addition on the microstructure and mechanical properties of Ti(C,N)–WC–Mo–Ni cermets were studied. Ti(C,N) based cermets present the typical dark core/grey rim and white core/grey rim grains. The amount of the typical dark core/grey rim grains decreases with the increase in CNT addition. For 1 wt- CNT addition, the value of TRS is 1174·5 MPa, which is about 1·45 times than that of cermet without CNT addition whose strength is 807·3 MPa. The cermet with 5·0 wt- CNTs increased the fracture toughness from 10·2 to 15·9 MPa m1/2. The hardness does not change initially, decreases with further increase in the addition of CNTs.
Protrusion and whisker growth on tin coated copper substrate under stresses
Authors: Xu C H , Qin X M , Guo W H , Li Y
Published: August 2011

Tin thin films were coated on copper substrates using chemical method. Tin coated copper specimens under continuously applied compressive and tensile stresses were oxidised at 100°C for 8 days. Protrusion and whisker growth behaviour of tin coated copper specimens was characterised by scanning electron microscope, X-ray diffractometer and transmission electron microscope. The results show that continuously applied compressive stress on tin coated copper specimens would enhance the growth of whisker while tensile stress would reduce whisker growth. A SnO2 layer was formed during oxidation and intermetallics of Cu3Sn and Cu6Sn5 were formed between SnO2 layer and copper substrate, which built up the residual compressive stresses in the coated tin layer. Continuously applied stress on the specimens can change the magnitude of residual compressive stress in coated tin layer, which affects the driving force for protrusion and whisker formation and growth.
Evolution of microstructures of galvanised and galvannealed coatings formed in 0·2 wt- aluminium–zinc bath
Authors: Mandal G K , Das S K , Balasubramaniam R , Mehrotra S P
Published: August 2011

The present investigation examines the evolution of the microstructures of galvanised steel during the galvannealing process with a special reference to the formation and breakdown behaviour of aluminium rich inhibition layer at the substrate/coating interface. The interstitial free steel was galvanised in a molten zinc bath with 0·2 wt- aluminium content. The bath temperature and strip entry temperatures were 460 and 480°C respectively. Aluminium of 0·2 wt- was chosen to retard the formation of iron–zinc intermetallic compounds in the coating. The as dipped galvanised interstitial free steel was annealed above the melting point of zinc in a salt bath at 480°C for a period ranging from 1 to 60 s. After annealing, the as galvanised coatings exhibited microstructural changes as a function of test time. The present work highlights the possible mechanisms of nucleation of iron–zinc intermetallic compounds during galvannealing treatment of steel galvanised in aluminium containing zinc bath.
Neo-Liberalism, Privatization and the Outsourcing of Migration Management: A Five-Country Comparison
Authors: Menz Georg
Published: August 2011

Current debates in migration studies underestimate or neglect altogether the implications of the privatization of migration management. Outsourcing control and detention functions to private companies is part of the paradigm of new public management. Such outsourcing has created self-reinforcing mechanisms and lock-in effects. However, the extent to which such privatization is embraced varies internationally depending on the degree of neo-liberalization of the state. Empirically, the article therefore analyses developments in countries with divergent levels of privatization of migration management, including the UK, Australia, the USA, Germany and the Netherlands.
FERM domain mutations induce gain of function in JAK3 in adult T-cell leukemia/lymphoma
Authors: Elliott Natalina E. , Cleveland Susan M. , Grann Victor , Janik John , Waldmann Thomas A. , Davé Utpal P.
Published: August 2011

Adult T-cell leukemia/lymphoma (ATLL) is an incurable disease where most patients succumb within the first year of diagnosis. Both standard chemotherapy regimens and mAbs directed against ATLL tumor markers do not alter this aggressive clinical course. Therapeutic development would be facilitated by the discovery of genes and pathways that drive or initiate ATLL, but so far amenable drug targets have not been forthcoming. Because the IL-2 signaling pathway plays a prominent role in ATLL pathogenesis, mutational analysis of pathway components should yield interesting results. In this study, we focused on JAK3, the nonreceptor tyrosine kinase that signals from the IL-2R, where activating mutations have been found in diverse neoplasms. We screened 36 ATLL patients and 24 ethnically matched controls and found 4 patients with mutations in JAK3. These somatic, missense mutations occurred in the N-terminal FERM (founding members: band 4.1, ezrin, radixin, and moesin) domain and induced gain of function in JAK3. Importantly, we show that these mutant JAK3s are inhibited with a specific kinase inhibitor already in human clinical testing. Our findings underscore the importance of this pathway in ATLL development and offer a therapeutic handle for this incurable cancer.
Dexamethasone in patients with acute lung injury from acute monocytic leukaemia
Authors: Azoulay É. , Canet E. , Raffoux E. , Lengliné E. , Lemiale V. , Vincent F. , de Labarthe A. , Seguin A. , Boissel N. , Dombret H. , Schlemmer B.
Published: August 2011

The use of steroids is not required in myeloid malignancies and remains controversial in patients with acute lung injury (ALI) or acute respiratory distress syndrome (ARDS). We sought to evaluate dexamethasone in patients with ALI/ARDS caused by acute monocytic leukaemia (AML FAB-M5)viaeither leukostasis or leukaemic infiltration.

Dexamethasone (10 mg every 6 h until neutropenia) was added to chemotherapy and intensive care unit (ICU) management in 20 consecutive patients between 2005 and 2008, whose data were compared with those from 20 historical controls (1994–2002). ICU mortality was the primary criterion. We also compared respiratory deterioration rates, need for ventilation and nosocomial infections.

17 (85%) patients had hyperleukocytosis, 19 (95%) had leukaemic masses, and all 20 had severe pancytopenia. All patients presented with respiratory symptoms and pulmonary infiltrates prior to AML FAB-M5 diagnosis. Compared with historical controls, dexamethasone-treated patients had a significantly lower ICU mortality rate (20%versus50%; p=0.04) and a trend for less respiratory deterioration (50%versus80%; p=0.07). There were no significant increases in the rates of infections with dexamethasone.

In conclusion, in patients with ALI/ARDS related to AML FAB-M5, adding dexamethasone to conventional chemotherapy seemed effective and safe. These results warrant a controlled trial of dexamethasoneversusplacebo in AML FAB-M5 patients with noninfectious pulmonary infiltrates.
Skin mucus of Cyprinus carpio inhibits cyprinid herpesvirus 3 binding to epidermal cells
Authors: Raj Victor Stalin , Fournier Guillaume , Rakus Krzysztof , Ronsmans Maygane , Ouyang Ping , Michel Benjamin , Delforges Cédric , Costes Bérénice , Farnir Frédéric , Leroy Baptiste , Wattiez Ruddy , Melard Charles , Mast Jan , Lieffrig François , Vanderplasschen Alain
Published: August 2011

Cyprinid herpesvirus 3 (CyHV-3) is the aetiological agent of a mortal and highly contagious disease in common and koi carp. The skin is the major portal of entry of CyHV-3 in carp after immersion in water containing the virus. In the present study, we used in vivo bioluminescence imaging to investigate the effect of skin mucus removal and skin epidermis lesion on CyHV-3 entry. Physical treatments inducing removal of the mucus up to complete erosion of the epidermis were applied on a defined area of carp skin just before inoculation by immersion in infectious water. CyHV-3 entry in carp was drastically enhanced on the area of the skin where the mucus was removed with or without associated epidermal lesion. To investigate whether skin mucus inhibits CyHV-3 binding to epidermal cells, tail fins with an intact mucus layer or without mucus were inoculated ex vivo. While electron microscopy examination revealed numerous viral particles bound on the fins inoculated after mucus removal, no particle could be detected after infection of mucus-covered fins. Finally, anti-CyHV-3 neutralising activity of mucus extract was tested in vitro. Incubation of CyHV-3 with mucus extract reduced its infectivity in a dose dependent manner. The present study demonstrates that skin mucus removal and epidermal lesions enhance CyHV-3 entry in carp. It highlights the role of fish skin mucus as an innate immune protection against viral epidermal entry.
Histological and transcriptome-wide level characteristics of fetal myofiber hyperplasia during the second half of gestation in Texel and Ujumqin sheep
Authors: Ren Hangxing , Li Li , Su Hongwei , Xu Lingyang , Wei Caihong , Zhang Li , Li Hongbin , Liu Wenzhong , Du Lixin
Published: August 2011

Background

Whether myofibers increase with a pulsed-wave mode at particular developmental stages or whether they augment evenly across developmental stages in large mammals is unclear. Additionally, the molecular mechanisms of myostatin in myofiber hyperplasia at the fetal stage in sheep remain unknown. Using the first specialized transcriptome-wide sheep oligo DNA microarray and histological methods, we investigated the gene expression profile and histological characteristics of developing fetal ovine longissimus muscle in Texel sheep (high muscle and low fat), as a myostatin model of natural mutation, and Ujumqin sheep (low muscle and high fat). Fetal skeletal muscles were sampled at 70, 85, 100, 120, and 135 d of gestation.

Results

Myofiber number increased sharply with a pulsed-wave mode at certain developmental stages but was not augmented evenly across developmental stages in fetal sheep. The surges in myofiber hyperplasia occurred at 85 and 120 d in Texel sheep, whereas a unique proliferative surge appeared at 100 d in Ujumqin sheep. Analysis of the microarray demonstrated that immune and hematological systems' development and function, lipid metabolism, and cell communication were the biological functions that were most differentially expressed between Texel and Ujumqin sheep during muscle development. Pathways associated with myogenesis and the proliferation of myoblasts, such as calcium signaling, chemokine (C-X-C motif) receptor 4 signaling, and vascular endothelial growth factor signaling, were affected significantly at specific fetal stages, which underpinned fetal myofiber hyperplasia and postnatal muscle hypertrophy. Moreover, we identified some differentially expressed genes between the two breeds that could be potential myostatin targets for further investigation.

Conclusions

Proliferation of myofibers proceeded in a pulsed-wave mode at particular fetal stages in the sheep. The myostatin mutation changed the gene expression pattern in skeletal muscle at a transcriptome-wide level, resulting in variation in myofiber phenotype between Texel and Ujumqin sheep during the second half of gestation. Our findings provide a novel and dynamic description of the effect of myostatin on skeletal muscle development, which contributes to understanding the biology of muscle development in large mammals.
A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6
Authors: Saski Christopher A , Feltus Frank A , Staton Margaret E , Blackmon Barbara P , Ficklin Stephen P , Kuhn David N , Schnell Raymond J , Shapiro Howard , Motamayor Juan Carlos
Published: August 2011

Background

The fermented dried seeds ofTheobroma cacao(cacao tree) are the main ingredient in chocolate. World cocoa production was estimated to be 3 million tons in 2010 with an annual estimated average growth rate of 2.2%. The cacao bean production industry is currently under threat from a rise in fungal diseases including black pod, frosty pod, and witches' broom. In order to address these issues, genome-sequencing efforts have been initiated recently to facilitate identification of genetic markers and genes that could be utilized to accelerate the release of robustT. cacaocultivars. However, problems inherent with assembly and resolution of distal regions of complex eukaryotic genomes, such as gaps, chimeric joins, and unresolvable repeat-induced compressions, have been unavoidably encountered with the sequencing strategies selected.

Results

Here, we describe the construction of a BAC-based integrated genetic-physical map of theT. cacaocultivar Matina 1-6 which is designed to augment and enhance these sequencing efforts. Three BAC libraries, each comprised of 10× coverage, were constructed and fingerprinted. 230 genetic markers from a high-resolution genetic recombination map and 96 Arabidopsis-derived conserved ortholog set (COS) II markers were anchored using pooled overgo hybridization. A dense tile path consisting of 29,383 BACs was selected and end-sequenced. The physical map consists of 154 contigs and 4,268 singletons. Forty-nine contigs are genetically anchored and ordered to chromosomes for a total span of 307.2 Mbp. The unanchored contigs (105) span 67.4 Mbp and therefore the estimated genome size ofT. cacaois 374.6 Mbp. A comparative analysis withA. thaliana, V. vinifera, andP. trichocarpasuggests that comparisons of the genome assemblies of these distantly related species could provide insights into genome structure, evolutionary history, conservation of functional sites, and improvements in physical map assembly. A comparison between the twoT. cacaocultivars Matina 1-6 and Criollo indicates a high degree of collinearity in their genomes, yet rearrangements were also observed.

Conclusions

The results presented in this study are a stand-alone resource for functional exploitation and enhancement ofTheobroma cacaobut are also expected to complement and augment ongoing genome-sequencing efforts. This resource will serve as a template for refinement of theT. cacaogenome through gap-filling, targeted re-sequencing, and resolution of repetitive DNA arrays.
A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog
Authors: Nicholas Thomas J , Baker Carl , Eichler Evan E , Akey Joshua M
Published: August 2011

Background

Structural variation contributes to the rich genetic and phenotypic diversity of the modern domestic dog,Canis lupus familiaris, although compared to other organisms, catalogs of canine copy number variants (CNVs) are poorly defined. To this end, we developed a customized high-density tiling array across the canine genome and used it to discover CNVs in nine genetically diverse dogs and a gray wolf.

Results

In total, we identified 403 CNVs that overlap 401 genes, which are enriched for defense/immunity, oxidoreductase, protease, receptor, signaling molecule and transporter genes. Furthermore, we performed detailed comparisons between CNVs located within versus outside of segmental duplications (SDs) and find that CNVs in SDs are enriched for gene content and complexity. Finally, we compiled all known dog CNV regions and genotyped them with a custom aCGH chip in 61 dogs from 12 diverse breeds. These data allowed us to perform the first population genetics analysis of canine structural variation and identify CNVs that potentially contribute to breed specific traits.

Conclusions

Our comprehensive analysis of canine CNVs will be an important resource in genetically dissecting canine phenotypic and behavioral variation.
An evaluation of ciprofloxacin pharmacokinetics in critically ill patients undergoing continuous veno-venous haemodiafiltration
Authors: Spooner Almath M , Deegan Catherine , D'Arcy Deirdre M , Gowing Caitriona M , Donnelly Maria B , Corrigan Owen I
Published: August 2011

Background

The study aimed to investigate the pharmacokinetics of intravenous ciprofloxacin and the adequacy of 400 mg every 12 hours in critically ill Intensive Care Unit (ICU) patients on continuous veno-venous haemodiafiltration (CVVHDF) with particular reference to the effect of achieved flow rates on drug clearance.

Methods

This was an open prospective study conducted in the intensive care unit and research unit of a university teaching hospital. The study population was seven critically ill patients with sepsis requiring CVVHDF.

Blood and ultrafiltrate samples were collected and assayed for ciprofloxacin by High Performance Liquid Chromatography (HPLC) to calculate the model independent pharmacokinetic parameters; total body clearance (TBC), half-life (t1/2) and volume of distribution (Vd). CVVHDF was performed at prescribed dialysate rates of 1 or 2 L/hr and ultrafiltration rate of 2 L/hr. The blood flow rate was 200 ml/min, achieved using a Gambro blood pump and Hospal AN69HF haemofilter.

Results

Seventeen profiles were obtained. CVVHDF resulted in a median ciprofloxacin t1/2of 13.8 (range 5.15-39.4) hr, median TBC of 9.90 (range 3.10-13.2) L/hr, a median Vdssof 125 (range 79.5-554) L, a CVVHDF clearance of 2.47+/-0.29 L/hr and a clearance of creatinine (Clcr) of 2.66+/-0.25 L/hr. Thus CVVHDF, at an average flow rate of ~3.5 L/hr, was responsible for removing 26% of ciprofloxacin cleared. At the dose rate of 400 mg every 12 hr, the median estimated Cpmax/MIC and AUC0-24/MIC ratios were 10.3 and 161 respectively (for a MIC of 0.5 mg/L) and exceed the proposed criteria of >10 for Cpmax/MIC and > 100 for AUC0-24/MIC. There was a suggestion towards increased ciprofloxacin clearance by CVVHDF with increasing effluent flow rate.

Conclusions

Given the growing microbial resistance to ciprofloxacin our results suggest that a dose rate of 400 mg every 12 hr, may be necessary to achieve the desired pharmacokinetic - pharmacodynamic (PK-PD) goals in patients on CVVHDF, however an extended interval may be required if there is concomitant hepatic impairment. A correlation between ciprofloxacin clearance due to CVVHDF and creatinine clearance by the filter was observed (r2= 0.76), providing a useful clinical surrogate marker for ciprofloxacin clearance within the range studied.

Trial Registration

Current Controlled TrialsISRCTN52722850
Incorporation of n-3 PUFA and γ-linolenic acid in blood lipids and red blood cell lipids together with their influence on disease activity in patients with chronic inflammatory arthritis - a randomized controlled human intervention trial
Authors: Dawczynski Christine , Hackermeier Ursula , Viehweger Martin , Stange Rainer , Springer Monika , Jahreis Gerhard
Published: August 2011

Background and aim

Marine n-3 fatty acids and γ-linolenic acid both have anti-inflammatory effects and may be useful to help treat inflammatory diseases. The effects of these alone or combined were examined in patients with arthritis in a randomized controlled trial.

Design

Patients with rheumatoid arthritis or psoriatic arthritis were randomized into four groups in a double-blind, placebo-controlled parallel designed study. Patients received the respective capsules (1: 3.0 g n-3 LC-PUFA/d; 2: 3.2 g γ-linolenic acid/d; 3: 1.6 g n-3 LC-PUFA + 1.8 g γ-linolenic acid/d; 4: 3.0 g olive oil) for a twelve week period. Clinical status was evaluated and blood samples were taken at the beginning and at the end of the period. Differences before and after intervention were tested with paired t-test or with Wilcoxon test for non-normal data distribution.

Results

60 patients (54 rheumatoid arthritis, 6 psoriatic arthritis) were randomised, 47 finished per protocol. In group 1, the ratio of arachidonic acid (AA)/eicosapentaenoic acid (EPA) decreased from 6.5 ± 3.7 to 2.7 ± 2.1 in plasma lipids and from 25.1 ± 10.1 to 7.2 ± 4.7 in erythrocyte membranes (p ≤ 0.001). There was no significant influence on AA/EPA ratio due to interventions in group 2-4. In group 2, the intake of γ-linolenic acid resulted in a strong rise of γ-linolenic acid and dihomo-γ-linolenic acid concentrations in plasma lipids, cholesteryl esters, and erythrocyte membranes. The combination of n-3 LC-PUFA and γ-linolenic acid (group 3) led to an increase of γ-linolenic acid and dihomo-γ-linolenic acid concentrations in plasma lipids, cholesteryl esters, and erythrocyte mem-branes. This increase was only half of that in group 2.

Conclusions

Incorporation of eicosanoid precursor FAs was influenced by an intake of n-3 LC-PUFA and γ-linolenic acid suggesting a possible benefit for therapy of chronic inflammatory diseases.

Trial Registration

ClinicalTrials NCT01179971
Accumulation and aberrant composition of cholesteryl esters in Scrapie-infected N2a cells and C57BL/6 mouse brains
Authors: Vascellari Sarah , Banni Sebastiano , Vacca Claudia , Vetrugno Vito , Cardone Franco , Di Bari Michele A , La Colla Paolo , Pani Alessandra
Published: August 2011

Objective

Cholesterol changes have been described in prion-cell models and in experimental rodent scrapie; yet, the pattern of this association is still controversial.

Methods

To shed light on the matter, we analysed and compared cholesterol variations in ScN2a cells and in brains of Scrapie-infected C57Bl/6 mice, using two different methods: a fluorimetric-enzymatic cholesterol assay, and high performance liquid chromatography-mass spectroscopy (HPLC-MS).

Results

Compared to uninfected controls, similar cholesterol metabolism anomalies were observed in infected cells and brains by both methods; however, only HPLC-MS revealed statistically significant cholesterol variations, particularly in the cholesteryl esters (CE) fraction. HPLC-MS analyses also revealed different fatty acid composition of the CE fraction in cells and brains. In N2a cells, their profile reflected that of serum, while in normal brains cholesteryl-linoleate only was found at detectable levels. Following prion infection, most CE species were increased in the CE pool of ScN2a cells, whereas a conspicuous amount of cholesteryl-arachidonate only was found to contribute to the cerebral increase of CE. Of interest, oral pravastatin administration to Scrapie-infected mice, was associated with a significant reduction of cerebral free cholesterol (FC) along with a concomitant further increase of the CE pool, which included increased amounts of both cholesteryl-linoleate and cholesteryl-arachidonate.

Conclusion

Although mechanistic studies are needed to establish the pathophysiological relevance of changes in cerebral CE concentrations, to the best of our knowledge this is the first report to provide evidence of increased cholesterol esterification in brains of prion-infected mice, untreated and treated with pravastatin.
The laval questionnaire: a new instrument to measure quality of life in morbid obesity
Authors: Therrien Fanny , Marceau Picard , Turgeon Nathalie , Biron Simon , Richard Denis , Lacasse Yves
Published: August 2011

Background

Our recent review of the literature uncovered eleven obesity-specific quality of life questionnaires, all with incomplete demonstration of their measurement properties. Our objective was to validate a new self-administered questionnaire specific to morbid obesity to be used in clinical trials. The study was carried out at the bariatric surgery clinic of Laval Hospital, Quebec City, Canada.

Methods

This study followed our description of health-related quality of life in morbid obesity from which we constructed the Laval Questionnaire. Its construct validity and responsiveness were tested by comparing the baseline and changes at 1-year follow-up in 6 domain scores (symptoms, activity/mobility, personal hygiene/clothing, emotions, social interactions, sexual life) with those of questionnaires measuring related constructs (SF-36, Impact of Weight on Quality of Life-Lite, Rosenberg Self-Esteem Scale and Beck Depression Inventory-II).

Results

112 patients (67 who got bariatric surgery, 45 who remained on the waiting list during the study period) participated in this study. The analysis of the discriminative function of the questionnaire showed moderate-to-high correlations between the scores in each domain of our instrument and the corresponding questionnaires. The analysis of its evaluative function showed (1) significant differences in score changes between patients with bariatric surgery and those without, and (2) moderate-to-high correlations between the changes in scores in the new instrument and the changes in the corresponding questionnaires. Most of these correlations met the a priori predictions we had made regarding their direction and magnitude.

Conclusion

The Laval Questionnaire is a valid measure of health-related quality of life in patients with morbid obesity and is responsive to treatment-induced changes.
Yolk sac tumor in a patient with transverse testicular ectopia
Authors: Zhu Yi-Ping , Zhang Shi-Lin , Ye Ding-Wei , Shi Guo-hai , Xiao Wen-jun
Published: August 2011

Transverse testicular ectopia (TTE) is a rare anomaly in which both testes descend through a single inguinal canal. We report a case of yolk sac tumor in the ectopic testis of a patient with TTE. A 24-year-old man presented to our hospital with a left inguinal-mass, right cryptorchidism and elevated alpha-fetoprotein (AFP). A left herniotomy 3 years earlier demonstrated both testes in the left scrotum, one above another positionally. Four months ago, a left scrotal mass appeared and radical orchiectomy of both testes revealed testicular yolk sac tumor of the ectopic testis. An enlarging left inguinal-mass appeared 2 months ago and he was referred to our hospital. Laboratory data showed an elevation of AFP (245.5 ng/ml) and a 46 XY karyotype. He underwent bilateral retroperitoneal lymph node dissection and simultaneous left inguinal mass dissection. Histopathologic examination revealed a diagnosis of recurrent yolk sac tumor in the left inguinal mass. The retroperitoneal lymph node was not enlarged and, on histopathology, was not involved. The patient has now been followed up for 8 months without evidence of biochemical or radiological recurrence.
Performance of the Tariff Method: validation of a simple additive algorithm for analysis of verbal autopsies
Authors: James Spencer L , Flaxman Abraham D , Murray Christopher JL
Published: August 2011

Background

Verbal autopsies provide valuable information for studying mortality patterns in populations that lack reliable vital registration data. Methods for transforming verbal autopsy results into meaningful information for health workers and policymakers, however, are often costly or complicated to use. We present a simple additive algorithm, the Tariff Method (termed Tariff), which can be used for assigning individual cause of death and for determining cause-specific mortality fractions (CSMFs) from verbal autopsy data.

Methods

Tariff calculates a score, or "tariff," for each cause, for each sign/symptom, across a pool of validated verbal autopsy data. The tariffs are summed for a given response pattern in a verbal autopsy, and this sum (score) provides the basis for predicting the cause of death in a dataset. We implemented this algorithm and evaluated the method's predictive ability, both in terms of chance-corrected concordance at the individual cause assignment level and in terms of CSMF accuracy at the population level. The analysis was conducted separately for adult, child, and neonatal verbal autopsies across 500 pairs of train-test validation verbal autopsy data.

Results

Tariff is capable of outperforming physician-certified verbal autopsy in most cases. In terms of chance-corrected concordance, the method achieves 44.5% in adults, 39% in children, and 23.9% in neonates. CSMF accuracy was 0.745 in adults, 0.709 in children, and 0.679 in neonates.

Conclusions

Verbal autopsies can be an efficient means of obtaining cause of death data, and Tariff provides an intuitive, reliable method for generating individual cause assignment and CSMFs. The method is transparent and flexible and can be readily implemented by users without training in statistics or computer science.
Phonologically-based biomarkers for major depressive disorder
Authors: Trevino Andrea Carolina , Quatieri Thomas Francis , Malyska Nicolas
Published: August 2011

Of increasing importance in the civilian and military population is the recognition of major depressive disorder at its earliest stages and intervention before the onset of severe symptoms. Toward the goal of more effective monitoring of depression severity, we introduce vocal biomarkers that are derived automatically from phonologically-based measures of speech rate. To assess our measures, we use a 35-speaker free-response speech database of subjects treated for depression over a 6-week duration. We find that dissecting average measures of speech rate into phone-specific characteristics and, in particular, combined phone-duration measures uncovers stronger relationships between speech rate and depression severity than global measures previously reported for a speech-rate biomarker. Results of this study are supported by correlation of our measures with depression severity and classification of depression state with these vocal measures. Our approach provides a general framework for analyzing individual symptom categories through phonological units, and supports the premise that speaking rate can be an indicator of psychomotor retardation severity.
Enhanced Inhibitory Synaptic Transmission in the Spinal Dorsal Horn Mediates Antinociceptive Effects of TC-2559
Authors: Cheng Long-Zhen , Han Lei , Fan Jing , Huang Lan-Ting , Peng Li-Chao , Wang Yun
Published: August 2011

Background:

TC-2559 is a selective α4β2 subtype of nicotinic acetylcholine receptor (nAChR) partial agonist and α4β2 nAChR activation has been related to antinociception. The aim of this study is to investigate the analgesic effect of TC-2559 and its underlying spinal mechanisms.

Results:

1) In vivo bioavailability study: TC-2559 (3 mg/kg) had high absorption rate in rats with maximal total brair concentration reached over 4.6 μM within first 15 min after administration and eliminated rapidly with brain half life of about 20 min after injection. 2) In vivo behavioral experiments: TC-2559 exerts dose dependent antinociceptive effects in both formalin test in mice and chronic constriction injury (CCI) model in rats by activation of α4β2 nAChRs; 3) Whole-cell patch-clamp studies in the superficial dorsal horn neurons of the spinal cord slices: perfusion of TC-2559 (2 μM) significantly increased the frequency, but not amplitude of spontaneous inhibitory postsynaptic currents (sIPSCs). The enhancement of sIPSCs was blocked by pre-application of DHpE (2 μM), a selective α4β2 nicotinic receptor antagonist. Neither the frequency nor the amplitude of spontaneous excitatory postsynaptic currents (sEPSCs) of spinal dorsal horn neurons were affected by TC-2559.

Conclusions:

Enhancement of inhibitory synaptic transmission in the spinal dorsal horn via activation of α4β2 nAChRs may be one of the mechanisms of the antinociceptive effects of TC-2559 on pathological pain models. It provides further evidence to support the notion that selective α4β2 subtype nAChR agonist may be developed as new analgesic drug for the treatment of neuropathic pain.