bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing safety of biological control introductions.
Authors: Barratt B. I. P. 
Published: March 2012

Abstract
Biological control is an important component of pest management systems. It was generally considered safe and sustainable until the validity of this consensus was challenged by researchers who pointed out that there was a lack of study, and hence evidence, to support it and provided examples of non-target impacts. Biosafety of biological control subsequently received considerable attention from both biocontrol practitioners and regulators. Many countries now have legislation in place, which is focused on risk assessment for biological control and protecting native and valued biota and the environment from potential adverse impacts. This review summarizes the biosafety debate and characterizes the direct and indirect risks of biological control mainly for weeds and insect pests. During a biological control programme, there are several ways in which aspects of biosafety can be considered and addressed: exploration in the native range of the target species; from literature and knowledge of the biological control agent and host; experience from use of the biological control agent elsewhere; and host-range tests. The value of post-release monitoring and retrospective studies for validation of pre-release predictions is discussed. A poorly studied aspect is analysis of the population impacts of non-target attack by biological control agents. The literature from the last 20-30 years can help define some useful principles by which a risk assessment can be conducted to minimize adverse environmental effects. It has become clear over this period that comprehensive assembly of information and robust quarantine testing to provide a well-structured risk assessment can reduce uncertainty in decision-making in this area.
Atomically controlled CVD processing of group IV semiconductors for ultra-large-scale integrations
Authors: Murota Junichi , Sakuraba Masao , Tillack Bernd 
Published: March 2012

Abstract
One of the main requirements for ultra-large-scale integrations (ULSIs) is atomic-order control of process technology. Our concept of atomically controlled processing is based on atomic-order surface reaction control by CVD. By ultraclean low-pressure CVD using SiH
4 and GeH
4 gases, high-quality low-temperature epitaxial growth of Si
1−x

Ge

x
(100) (x=0–1) with atomically flat surfaces and interfaces on Si(100) is achieved. Self-limiting formation of 1–3 atomic layers of group IV or related atoms in the thermal adsorption and reaction of hydride gases on Si
1-x

Ge

x
(100) are generalized based on the Langmuir-type model. By the Si epitaxial growth on top of the material already-formed on Si(100), N, B and C atoms are confined within about a 1 nm thick layer. In Si cap layer growth on the P atomic layer formed on Si
1−x

Ge

x
(100), segregation of P atoms is suppressed by using Si
2
H
6 instead of SiH
4 at a low temperature of 450 °C. Heavy C atomic-layer doping suppresses strain relaxation as well as intermixing between Si and Ge at the Si
1−x

Ge

x
/Si heterointerface. It is confirmed that higher carrier concentration and higher carrier mobility are achieved by atomic-layer doping. These results open the way to atomically controlled technology for ULSIs.
A strategy for building neuroanatomy ontologies
Authors: Osumi-Sutherland David , Reeve Simon , Mungall Christopher J. , Neuhaus Fabian , Ruttenberg Alan , Jefferis Gregory S. X. E. , Armstrong J. Douglas 
Published: March 2012

Abstract
Motivation: Advancing our understanding of how nervous systems work will require the ability to store and annotate 3D anatomical datasets, recording morphology, partonomy and connectivity at multiple levels of granularity from subcellular to gross anatomy. It will also require the ability to integrate this data with other data-types including functional, genetic and electrophysiological data. The web ontology language OWL2 provides the means to solve many of these problems. Using it, one can rigorously define and relate classes of anatomical structure using multiple criteria. The resulting classes can be used to annotate datasets recording, for example, gene expression or electrophysiology. Reasoning software can be used to automate classification and error checking and to construct and answer sophisticated combinatorial queries. But for such queries to give consistent and biologically meaningful results, it is important that both classes and the terms (relations) used to relate them are carefully defined.
Results: We formally define a set of relations for recording the spatial and connectivity relationships of neuron classes and brain regions in a broad range of species, from vertebrates to arthropods. We illustrate the utility of our approach via its application in the ontology that drives the Virtual Fly Brain web resource.
Availability and implementation: The relations we define are available from http://purl.obolibrary.org/obo/ro.owl. They are used in the Drosophila anatomy ontology (http://purl.obolibrary.org/obo/fbbt/2011-09-06/), which drives the web resource http://www.virtualflybrain.org
Contact: djs93@gen.cam.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure
Authors: Gautier Mathieu , Vitalis Renaud 
Published: March 2012

Abstract
Summary: With the development of next-generation sequencing and genotyping approaches, large single nucleotide polymorphism haplotype datasets are becoming available in a growing number of both model and non-model species. Identifying genomic regions with unexpectedly high local haplotype homozygosity relatively to neutral expectation represents a powerful strategy to ascertain candidate genes responding to natural or artificial selection. To facilitate genome-wide scans of selection based on the analysis of long-range haplotypes, we developed the R package rehh. It provides a versatile tool to detect the footprints of recent or ongoing selection with several graphical functions that help visual interpretation of the results.
Availability and implementation: Stable version is available from CRAN: http://cran.r-project.org/. Development version is available from the R-forge repository: http://r-forge.r-project.org/projects/rehh. Both versions can be installed directly from R. Function documentation and example data files are provided within the package and a tutorial is available as Supplementary Material. rehh is distributed under the GNU General Public Licence (GPL ≥ 2).
Contact: mathieu.gautier@supagro.inra.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Gender and survival in patients with heart failure: interactions with diabetes and aetiology. Results from the MAGGIC individual patient meta‐analysis†
Authors: Martínez‐Sellés Manuel , Doughty Robert N. , Poppe Katrina , Whalley Gillian A. , Earle Nikki , Tribouilloy Christophe , McMurray John J.V. , Swedberg Karl , Køber Lars , Berry Colin , Squire Iain ,   on behalf of the Meta‐Analysis Global Group In Chronic Heart Failure (MAGGIC)
Published: March 2012

AimThe aim of this study was to investigate the relationship between gender and survival of patients with heart failure, using data from both randomized trials and observational studies, and the relative contribution of age, left ventricular systolic function, aetiology, and diabetes to differences in prognosis between men and women.Methods and resultsData from 31 studies (41 949 patients; 28 052 men, 13 897 women) from the Meta‐Analysis Global Group In Chronic Heart Failure (MAGGIC) individual patient meta‐analysis were used. We performed survival analysis to assess the association of gender with mortality, adjusting for predictors of mortality, including age, reduced or preserved ejection fraction (EF), and ischaemic or non‐ischaemic aetiology. Women were older [70.5 (standard deviation 12.1) vs. 65.6 (standard deviation 11.6) years], more likely to have a history of hypertension (49.9% vs. 40.0%), and less likely to have a history of ischaemic heart disease (46.3% vs. 58.7%) and reduced EF (62.6% vs. 81.6%) compared with men. During 3 years follow‐up, 3521 (25%) women and 7232 (26%) men died. After adjustment, male gender was an independent predictor of mortality, and the better prognosis associated with female gender was more marked in patients with heart failure of non‐ischaemic, compared with ischaemic, aetiology (P‐value for interaction = 0.03) and in patients without, compared with those with, diabetes (P‐value for interaction <0.0001).ConclusionThis large, individual patient data meta‐analysis has demonstrated that survival is better for women with heart failure compared with men, irrespective of EF. This survival benefit is slightly more marked in non‐ischaemic heart failure but is attenuated by concomitant diabetes.
Comparison of Equipressor Doses of Norepinephrine, Epinephrine, and Phenylephrine on Septic Myocardial Dysfunction
Authors: Ducrocq Nicolas , Kimmoun Antoine , Furmaniuk Anna , Hekalo Zerin , Maskali Fatiha , Poussier Sylvain , Marie Pierre-Yves , Levy Bruno 
Published: March 2012

Background
Myocardial depression is a frequent event during septic shock and may mimic a cardiogenic shock state with decreased cardiac output. Nevertheless, data are scarce regarding the myocardial effects of vasopressors used to treat hypotension. In this study, the authors compared the effects of three commonly used vasopressors acting on different adrenergic receptors on myocardial function in a rodent model of septic shock, as explored with conductance catheter and positron emission tomography.

Methods
Septic shock was induced in rats by peritonitis. Eighteen hours after septic insult, vasopressors were titrated to increase mean arterial pressure by 20% compared with baseline values.

Results
We observed that peritonitis was associated with arterial hypotension and systolodiastolic dysfunction. Norepinephrine and epinephrine improved mean arterial pressure, cardiac output, and preload recruitable stroke work, a load-independent measure of systolic function, as well as diastolic function and ventriculoarterial coupling. Heart rate, myocardial oxygen consumption, and arrhythmia incidence were furthermore increased in the epinephrine group. Conversely, phenylephrine, a peripheral α-agonist, exhibited deleterious effects on systolodiastolic function and ventriculoarterial coupling. Conductance catheter and positron emission tomography yielded identical results with regard to myocardial function evolution under vasopressor treatment.

Conclusions
Phenylephrine, a drug without β-1 effects, was associated with decreased ventricular performance and ventriculoarterial uncoupling, whereas epinephrine and norepinephrine improved global hemodynamics and myocardial function in severely hypokinetic and hypotensive experimental septic shock. Nevertheless, epinephrine was associated with increased myocardial oxygen consumption. Thus, norepinephrine appears to be a more reliable and safer strategy as a first-line therapy in this particular setting.
Rapid Test for Fecal Calprotectin Levels in Children With Crohn Disease
Authors: Kolho KL , Turner D. , Veereman‐Wauters G. , Sladek M. , de Ridder L. , Shaoul R. , Paerregaard A. , Dias J. Amil , Koletzko S. , Nuti F. , Bujanover Y. , Staiano A. , Bochenek K. , Finnby L. , Levine A. , Veres G. 
Published: March 2012

ABSTRACTAssessment of fecal calprotectin, a surrogate marker of mucosal inflammation, is a promising means to monitor therapeutic response in pediatric inflammatory bowel disease, especially if the result is readily available. We tested the performance of a novel calprotectin rapid test, Quantum Blue, versus the conventional enzyme‐linked immunosorbent assay in 134 stool samples from 56 pediatric patients with Crohn disease. The intraclass correlation coefficient analysis reflected good agreement (intraclass correlation coefficient 0.97 [95% confidence interval 0.95–0.98]) but agreement was better in lower values, where dilutions were not required. Using a cutoff of 100 μg/g for normal values, the percentage agreement between the 2 tests was 87%. The optimal cutoff values to guide clinical decisions in the therapy of inflammatory bowel disease have yet to be determined.
High levels of DJ‐1 protein in nipple fluid of patients with breast cancer
Authors: Oda Miki , Makita Masujiro , Iwaya Keiichi , Akiyama Futoshi , Kohno Norio , Tsuchiya Benio , Iwase Takuji , Matsubara Osamu 
Published: March 2012

As we have previously demonstrated that some breast cancer cell lines secrete DJ‐1 protein, we examined here whether breast cancer cells secrete DJ‐1 protein in vivo. To this end, the levels of DJ‐1 protein present in 136 specimens of nipple fluid was examined by enzyme‐linked immunosorbent assay (ELISA). The average concentration of DJ‐1 protein detected in diluted samples from 47 patients with invasive ductal carcinoma (IDC) was 22.4 ng/mL, while it was 18.6 ng/mL in 26 patients with ductal carcinoma in situ (DCIS). In contrast, the average DJ‐1 concentration in samples from 63 women with benign lesions was 2.7 ng/mL, demonstrating that higher DJ‐1 protein levels were detected in nipple fluid in the presence of cancer cells than in the presence of benign lesions (P < 0.0001). When a cut‐off level of 3.0 ng/mL was applied, the higher level of DJ‐1 was shown to be of significant clinical value for predicting the presence of breast cancer (85.9% specificity, 75% sensitivity; P < 0.0001). Multivariate logistic analysis that included established factors such as nipple discharge cytology, ductoscopic cytology, and carcinoembryonic antigen level further showed that the level of DJ‐1 protein alone is of significant value for predicting the presence of breast cancer. Immunohistochemistry and in situ hybridization also showed that the low expression of DJ‐1 protein, despite high mRNA expression, was significantly correlated with high DJ‐1 protein levels in the nipple fluid. These data indicate that breast cancer cells secrete DJ‐1 protein in vivo, and that its level is a potential indicator of breast cancer in patients with nipple discharge. (Cancer Sci 2012; 103: 1172–1176)
Combining cognitive behavioral therapy and contingency management to enhance their effects in treating cannabis dependence: less can be more, more or less
Authors: Carroll Kathleen M. , Nich Charla , LaPaglia Donna M. , Peters Erica N. , Easton Caroline J. , Petry Nancy M. 
Published: March 2012

ABSTRACTAims  To evaluate reciprocal enhancement (combining treatments to offset their relative weaknesses) as a strategy to improve cannabis treatment outcomes. Contingency management (CM) with reinforcement for homework completion and session attendance was used as a strategy to enhance cognitive–behavioral therapy (CBT) via greater exposure to skills training; CBT was used as a strategy to enhance durability of CM with rewards for abstinence.Setting  Community‐based out‐patient treatment program in New Haven, Connecticut, USA.Design  Twelve‐week randomized clinical trial of four treatment conditions: CM for abstinence alone or combined with CBT, CBT alone or combined with CM with rewards for CBT session attendance and homework completion.Participants  A total of 127 treatment‐seeking young adults (84.3% male, 81.1% minority, 93.7% referred by criminal justice system, average age 25.7 years).Measurements  Weekly urine specimens testing positive for cannabis, days of cannabis use via the time‐line follow‐back method.Findings  Within treatment, reinforcing homework and attendance did not significantly improve CBT outcomes, and the addition of CBT worsened outcomes when added to CM for abstinence (75.5 versus 57.1% cannabis‐free urine specimens, F = 2.25, P = 0.02). The CM for abstinence condition had the lowest percentage of cannabis‐negative urine specimens and the highest mean number of consecutive cannabis‐free urine specimens (3.3, F = 2.33, P = 0.02). Attrition was higher in the CBT alone condition, but random effect regression analyses indicated this condition was associated with the greatest rate of change overall. Cannabis use during the 1‐year follow‐up increased most rapidly for the two enhanced groups.Conclusions  Combining contingency management and cognitive–behavioural therapy does not appear to improve success rates of treatment for cannabis dependence in clients involved with the criminal justice system.
Drug treatment and the conditionality of HIV treatment access: a qualitative study in a Russian city
Authors: Rhodes Tim , Sarang Anya 
Published: March 2012

ABSTRACTAims  We explored social factors affecting access to antiretroviral HIV treatment (ART) among people who inject drugs (PWID) in a Russian city with a large HIV burden.Design  Qualitative interview study.Setting  Community settings in Ekaterinburg, Russian Federation.Participants  42 PWID living with HIV and 11 health practitioners.Measurements  Thematic analyses of in‐depth qualitative interviews.Findings  Access to ART was felt by participants to be contingent upon their capacity to demonstrate a commitment to becoming ‘drug free’. We identify, across interview accounts, a treatment access narrative of ‘treat drugs before HIV’. This narrative is upheld by ART providers' concerns to maximize clinical outcome in the face of adherence doubts, as well as by would‐be patients' perceptions of expectations placed upon them by the treatment system and their own doubts regarding treatment engagement. This has the effect of reproducing a habit of ART delay and disengaging people from the treatment system. Difficulties accessing ART, and the perceived rationing of treatment on account of untreated drug use, were experienced as ‘moral discipline’ for falling short of treatment ‘deservedness’. Participants describe a ‘Catch 22’ system, where they are invited to treat their drug use in a setting where effective drug treatment was perceived as unavailable.Conclusions  Inadequate drug treatment practices act as structural obstacles to realizing HIV treatment. Evidence internationally suggests that effective drug treatment, including opioid substitution therapy, improves access and adherence to antiretroviral treatment among people who inject drugs. Policy shifts are urgently needed in this setting to enable systemic improvements to drug treatment, especially given large HIV treatment demand.
Anopheles gambiae corazonin: gene structure, expression and effect on mosquito heart physiology
Authors: Hillyer J. F. , Estévez‐Lao T. Y. , Funkhouser L. J. , Aluoch V. A. 
Published: March 2012

AbstractHaemolymph flow in mosquitoes is primarily driven by the contraction of a dorsal vessel that is subdivided into an abdominal heart and a thoracic aorta. The factors that regulate mosquito heart contractions are not understood, but in other insects heart physiology is partially controlled by several neurohormones. One of these is corazonin, a neuropeptide initially discovered because of its cardioacceleratory activity in the cockroach Periplaneta americana. In the present study, we describe the corazonin gene and transcript structure in the mosquito Anopheles gambiae, characterize its developmental expression, and test its role in modulating heart physiology. We show that the A. gambiae corazonin gene encodes the most common form of the corazonin peptide ([Arg7]‐corazonin) and that it is alternatively spliced, with the only difference between the transcripts occurring in the 5′ untranslated region. Analysis of the developmental expression of corazonin and the corazonin receptor revealed that transcription of both follows a bimodal distribution, with highest mRNA levels in 2nd instar larvae and during the pupa to adult transition. Finally, experiments where mosquitoes were injected with various doses of corazonin and experiments where the transcription of corazonin and the corazonin receptor were reduced by RNA interference failed to detect a significant role for this neuropeptide in modulating mosquito heart physiology.
Early breast development in girls after prenatal exposure to non‐persistent pesticides
Authors: Wohlfahrt‐Veje C. , Andersen H. R. , Schmidt I. M. , Aksglaede L. , Sørensen K. , Juul A. , Jensen T. K. , Grandjean P. , Skakkebæk N. E. , Main K. M. 
Published: March 2012

SummaryContemporary American and European girls experience breast development at earlier ages compared with 15–20 years ago. Alterations in BMI alone cannot account for these changes. Several currently used pesticides possess endocrine disrupting properties and may interfere with reproductive development, but human data are sparse. We examined girls whose mothers worked in greenhouses in the first trimester of pregnancy to assess the long‐term effects of prenatal pesticide exposure on puberty. Mothers were prenatally categorized as exposed or unexposed to pesticides. We studied the offspring of these greenhouse workers, and evaluated the anthropometry, pubertal staging in the girls, and blood samples were drawn at 3 months of age (n = 90) and again once at school age (6–11 years, n = 83). No clinical and biochemical differences were found between the exposed and unexposed girls at 3 months of age. Mean onset of B2+ was 8.9 years (95% CI: 8.2; 9.7) in prenatally exposed girls, compared with 10.4 years (9.2; 17.6) in the unexposed (p = 0.05), and 10.0 (9.7–10.3) years in a Danish reference population (p = 0.001). Exposed girls had higher serum androstenedione levels (geometric means: 0.58 vs. 0.79 nmol/L, p = 0.046) and lower Anti‐Müllerian Hormone (AMH) compared with the unexposed (geometric means: 16.4 vs. 21.3 pmol/L, p > 0.05) and the reference group (20.2 pmol/L, p = 0.012). Levels of testosterone, estradiol, prolactin, FSH, LH, SHBG, DHEAS, DHT, Inhibin A and Inhibin B did not differ between the groups. In conclusion, our findings suggest that prenatal exposure to currently approved pesticides may cause earlier breast development in girls. This association appeared not to be because of changes in gonadotropins, but rather to higher androgen levels, which indirectly may increase oestrogens through aromatization. In addition, lower serum AMH levels indicated a reduced pool of antral ovarian follicles. The long‐term consequences of our findings with regard to establishment of future reproductive function still remain unknown.