bluuebunny/crossref_metadata_2025_split huggingface dataset:
The easy road to genome‐wide medium density SNP screening in a non‐model species: development and application of a 10 K SNP‐chip for the house sparrow (Passer domesticus)
Authors: Hagen Ingerid J. , Billing Anna M. , Rønning Bernt , Pedersen Sindre A. , Pärn Henrik , Slate Jon , Jensen Henrik 
Published: March 2013

AbstractWith the advent of next generation sequencing, new avenues have opened to study genomics in wild populations of non‐model species. Here, we describe a successful approach to a genome‐wide medium density Single Nucleotide Polymorphism (SNP) panel in a non‐model species, the house sparrow (Passer domesticus), through the development of a 10 K Illumina iSelect HD BeadChip. Genomic DNA and cDNA derived from six individuals were sequenced on a 454 GS FLX system and generated a total of 1.2 million sequences, in which SNPs were detected. As no reference genome exists for the house sparrow, we used the zebra finch (Taeniopygia guttata) reference genome to determine the most likely position of each SNP. The 10 000 SNPs on the SNP‐chip were selected to be distributed evenly across 31 chromosomes, giving on average one SNP per 100 000 bp. The SNP‐chip was screened across 1968 individual house sparrows from four island populations. Of the original 10 000 SNPs, 7413 were found to be variable, and 99% of these SNPs were successfully called in at least 93% of all individuals. We used the SNP‐chip to demonstrate the ability of such genome‐wide marker data to detect population sub‐division, and compared these results to similar analyses using microsatellites. The SNP‐chip will be used to map Quantitative Trait Loci (QTL) for fitness‐related phenotypic traits in natural populations.
Chronic antioxidant therapy lowers blood pressure in adult but not in young Dahl salt hypertensive rats: the role of sympathetic nervous system
Authors: Vaněčková I. , Vokurková M. , Rauchová H. , Dobešová Z. , Pecháňová O. , Kuneš J. , Vorlíček J. , Zicha J. 
Published: March 2013

AbstractAimIt is well‐known that salt hypertension is associated with increased oxidative stress. Since the development of salt hypertension is age‐dependent, we were interested whether young and adult salt hypertensive Dahl rats differ in oxidative stress level and/or in the effects of chronic antioxidant therapy on blood pressure (BP) level and on the participation of particular vasoconstrictor/vasodilator systems in BP maintenance.MethodsYoung (5‐week‐old) and adult (12‐week‐old) salt‐sensitive (Dahl‐S) male rats were fed high‐salt diet (5% NaCl) and drank tempol solution (2 mm) for 5 weeks. BP was monitored with radiotelemetry and vasoconstrictor/vasodilator balance was evaluated at the end of experiment. Moreover, NO synthase activity, superoxide production and lipoperoxidation were determined in heart, kidney and aorta in separate subgroups of Dahl rats.ResultsTempol treatment had quite opposite BP effects in young and adult Dahl‐S rats. While it tended to increase BP in young salt hypertensive Dahl‐S rats, it significantly lowered BP in the adult ones due to reduced sympathetic vasoconstriction. Importantly, high salt intake substantially reduced NO synthase activity in heart and kidney, and markedly increased superoxide production in kidneys and aorta of adult Dahl‐S rats in which BP correlated positively with superoxide production in thoracic aorta and lipoperoxidation in kidneys.ConclusionChronic antioxidant therapy lowered BP only in adult salt hypertensive Dahl‐S rats in which superoxide levels were increased in both kidneys and aorta. Blood pressure reduction induced by chronic tempol treatment is related to attenuated sympathetic vasoconstriction rather than to augmented NO‐dependent vasodilatation.
Early effects of an x‐ray contrast medium on renal T2*/T2MRI as compared to short‐term hyperoxia, hypoxia and aortic occlusion in rats
Authors: Arakelyan K. , Cantow K. , Hentschel J. , Flemming B. , Pohlmann A. , Ladwig M. , Niendorf T. , Seeliger E. 
Published: March 2013

AbstractAimX‐ray contrast media (CM) can cause acute kidney injury (AKI). Medullary hypoxia is pivotal in CM‐induced AKI, as indicated by invasively and pin‐point measured tissue oxygenation. MRI provides spatially resolved blood oxygenation level–dependent data using T2* and T2 mapping. We studied CM effects on renal T2*/T2 and benchmarked them against short periods of hyperoxia, hypoxia and aortic occlusion (AO).MethodsRats were equipped with carotid artery catheters (tip towards aorta) and supra‐renal aortic occluders. T2*/T2 mapping was performed using a 9.4‐T animal scanner. CM (1.5 mL iodixanol) was injected into the thoracic aorta with the animal in the scanner followed by 2 h of T2*/T2 mapping. For T2*/T2 assessment, regions of interest in the cortex (C), outer medulla (OM), inner medulla (IM) and papilla (P) were determined according to morphological features.ResultsHyperoxia increased T2* in C (by 17%) and all medullary layers (25–35%). Hypoxia decreased T2* in C (40%) and all medullary layers (55–60%). AO decreased T2* in C (18%) and all medullary layers (30–40%). Upon injection of CM, T2* increased transiently, then decreased, reaching values 10–20% below baseline in C and OM and 30–40% below baseline in IM and P.ConclusionT2* mapping corroborates data previously obtained with invasive methods and demonstrates that CM injection affects renal medullary oxygenation. CM‐induced T2* decrease in OM was small vs. hypoxia and aortic occlusion. T2* decrease obtained for hypoxia was more pronounced than for AO. This indicates that T2* may not accurately reflect blood oxygenation under certain conditions.
Obesity and lifestyle advice in colorectal cancer survivors – how well are clinicians prepared?
Authors: Anderson A. S. , Caswell S. , Wells M. , Steele R. J. C. 
Published: March 2013

AbstractAimThis study aimed to assess colorectal clinicians' knowledge and understanding about the risks and benefits of weight management, to document current practice and to identify perceived barriers to providing lifestyle advice to colorectal cancer survivors.MethodQuestionnaires were sent to 768 clinicians (doctors and nurses) working in colorectal cancer, identified from professional databases. These data were complemented by in‐depth interviews exploring opportunities for and barriers to giving lifestyle advice.ResultsA total of 323 replies were received (42% response rate) and 20 respondents completed in‐depth interviews. Half (52%) reported that they were familiar with guidance for lifestyle advice for cancer survivors. Most (77%) thought reducing weight was important for improving the health of those who were overweight and 75% thought it appropriate to offer lifestyle advice to people with body mass index over 30 kg/m2. Half (50%) reported that weight reduction was an important service priority for normal clinical practice. Half (50%) of respondents said that they would value additional training in this area. Interview data revealed that current practice is influenced by the lack of evidence for the impact of weight management and a belief that ‘weight gain is good and weight loss bad’ in the cancer setting. Patient sensitivity, time available, role constraints and lack of skills in weight management were also factors.ConclusionThere is an awareness of the importance of weight management amongst colorectal cancer clinicians and some indication of advice being provided. However, current perceptions, knowledge and skills suggest scope for further training.
NMR mapping of RANTES surfaces interacting with CCR5 using linked extracellular domains
Authors: Schnur Einat , Kessler Naama , Zherdev Yuri , Noah Eran , Scherf Tali , Ding Fa‐Xiang , Rabinovich Svetlana , Arshava Boris , Kurbatska Victoria , Leonciks Ainars , Tsimanis Alexander , Rosen Osnat , Naider Fred , Anglister Jacob 
Published: March 2013

Chemokines constitute a large family of small proteins that regulate leukocyte trafficking to the site of inflammation by binding to specific cell‐surface receptors belonging to the G‐protein‐coupled receptor (GPCR) superfamily. The interactions between N–terminal (Nt‐) peptides of these GPCRs and chemokines have been studied extensively using NMR spectroscopy. However, because of the lower affinities of peptides representing the three extracellular loops (ECLs) of chemokine receptors to their respective chemokine ligands, information concerning these interactions is scarce. To overcome the low affinity of ECL peptides to chemokines, we linked two or three CC chemokine receptor 5 (CCR5) extracellular domains using either biosynthesis in Escherichia coli or chemical synthesis. Using such chimeras, CCR5 binding to RANTES was followed using 1H‐15N‐HSQC spectra to monitor titration of the chemokine with peptides corresponding to the extracellular surface of the receptor. Nt‐CCR5 and ECL2 were found to be the major contributors to CCR5 binding to RANTES, creating an almost closed ring around this protein by interacting with opposing faces of the chemokine. A RANTES positively charged surface involved in Nt‐CCR5 binding resembles the positively charged surface in HIV‐1 gp120 formed by the C4 and the base of the third variable loop of gp120 (V3). The opposing surface on RANTES, composed primarily of β2–β3 hairpin residues, binds ECL2 and was found to be analogous to a surface in the crown of the gp120 V3. The chemical and biosynthetic approaches for linking GPCR surface regions discussed herein should be widely applicable to the investigation of interactions of extracellular segments of chemokine receptors with their respective ligands.
Assessment of reproductive characteristics of Jatropha curcas L. in south Florida
Authors: Nietsche Silvia , Vendrame Wagner A. , Crane Jonathan H. , Pereira Marlon C. T. 
Published: March 2013

AbstractJatropha curcas L. (jatropha) is a species identified for biofuel production because of the high quality of the oil produced by its seeds. However, jatropha is undomesticated and little information is available about its reproductive characteristics. Breeding and genetic improvement programs are much needed for the jatropha development as a bioenergy crop. Information about floral display and mode of reproduction are considered essential for breeding programs. In this study, the total number of female flowers, male to female flower ratio, fruit set, in vitro pollen germination, and the formation of fruits by apomixis, self‐pollination, and natural pollination were evaluated in 17 jatropha accessions planted in South Florida. The total number of female flowers per inflorescence and male to female flower ration ranged from 2.8 to 9.1 and 9.9:1 to 55.4 : 1, respectively. During summer 2011, high fruit setting average was observed (75.5%). In vitro pollen germination varied from 64.6% during spring 2011 to 51.6% during fall 2011. The fruit set observed was from 10.1% to 64.0% through natural pollination and apomixes, respectively. Characteristics such as fruit fresh weight, number of seeds per fruit, seed dry weight, and oil content were influenced by mode of reproduction.
RADIOGRAPHIC LIVER SIZE IN PEKINGESE DOGS VERSUS OTHER DOG BREEDS
Authors: Choi Jihye , Keh Seoyeon , Kim Hyunwook , Kim Junyoung , Yoon Junghee 
Published: March 2013

Differential diagnoses for canine liver disease are commonly based on radiographic estimates of liver size, however little has been published on breed variations. Aims of this study were to describe normal radiographic liver size inPekingese dogs and to compare normal measurements for this breed with other dog breeds andPekingese dogs with liver disease. Liver measurements were compared for clinically normalPekingese (n = 61), normal non‐Pekingese brachycephalic (n = 45), normal nonbrachycephalic (n = 71), andPekingese breed dogs with liver disease (n = 22). For each dog, body weight, liver length,T11 vertebral length, thoracic depth, and thoracic width were measured on right lateral and ventrodorsal abdominal radiographs. Liver volume was calculated using a formula and ratios of liver length/T11 vertebral length and liver volume/body weight ratio were determined. NormalPekingese dogs had a significantly smaller liver volume/body weight ratio (16.73 ± 5.67,P< 0.05) than normal non‐Pekingese brachycephalic breed dogs (19.54 ± 5.03) and normal nonbrachycephalic breed dogs (18.72 ± 6.52). The liver length/T11 vertebral length ratio in normalPekingese (4.64 ± 0.65) was significantly smaller than normal non‐Pekingese brachycephalic breed dogs (5.16 ± 0.74) and normal nonbrachycephalic breed dogs (5.40 ± 0.74). Ratios of liver volume/body weight and liver length/T11 vertebral length in normalPekingese were significantly different fromPekingese with liver diseases (P< 0.05). Findings supported our hypothesis thatPekingese dogs have a smaller normal radiographic liver size than other breeds. We recommend using 4.64× the length of theT11 vertebra as a radiographic criterion for normal liver length inPekingese dogs.
Translating the complexities of flood risk science using KEEPER – a knowledge exchange exploratory tool for professionals in emergency response
Authors: Alexander M. , Viavattene C. , Faulkner H. , Priest S. 
Published: March 2013

AbstractWithin flood risk management (FRM) decision making, there is a growing interest in participatory approaches to engage and integrate stakeholder expertise. Decision support tools are becoming common features in the FRM ‘toolkit’, yet there is a limited application of participatory methodologies in the construction of such tools. This paper reports on completed FRMRC research (Flood Risk Management Research Consortium, UK http://www.floodrisk.org.uk/) and the construction of a geographic information system‐based flood risk assessment tool, KEEPER – a Knowledge Exchange Exploratory tool for Professionals in Emergency Response. An iterative methodology was used to engage emergency professionals throughout the research process, allowing a mixing of scientific and professional expertise in the co‐production of KEEPER. KEEPER was both instrumental in facilitating participation and knowledge exchange, and informing recommendations for future tools in practice. This paper argues that participation is both essential for supporting pragmatic flood research and as a means of enhancing communication across traditionally divided communities.
Estimating monetary damages from flooding in the United States under a changing climate
Authors: Wobus C. , Lawson M. , Jones R. , Smith J. , Martinich J. 
Published: March 2013

AbstractExtreme precipitation events are likely to become more frequent and more extreme under a changing climate. It follows that monetary damages from flooding would also increase relative to baseline, yet this relationship has not been quantified at the scale of the entire United States. In this paper, we quantify how climate change could affect monetary damages from flooding in the coterminous United States. With publicly available historical flooding and precipitation data, we estimate region‐specific logistic regression models of the probability that severely damaging floods will occur under baseline conditions. We then use future precipitation projections driven by climate model outputs to estimate the probability that damaging floods could occur under a ‘business as usual’ climate change scenario. Our results project an increase in monetary damages from flooding in nearly all regions of the United States and a total increase in damages by the end of century of approximately 30% (assuming no change in built infrastructure or values). However, these changes vary between regions due to differences in the mechanisms driving flooding and general circulation model precipitation projections.
Rationality in flood risk management: the limitations of probabilistic risk assessment in the design and selection of flood protection strategies
Authors: Doorn N. 
Published: March 2013

AbstractThe introduction of new flood protection strategies prompts the need for a general framework for evaluating these strategies. The focus of this paper is on the rationality in selecting between flood protection strategies, more particularly on the question to what extent risk‐based design and probabilistic risk assessment (PRA) can provide a general framework for rational evaluation of different strategies. On the basis of Arrow's impossibility theorem and the standard literature on cost–benefit analysis, the limitations of risk‐based design and PRA are discussed. Applied to the context of flood risk management, it is shown that the problem of selecting between different flood protection strategies is susceptible to Arrow's impossibility theorem, which makes risk‐based design seem less suitable as a generally applicable procedure. The incommensurability of criteria in the selection of flood protection strategies is related to the uncertainties pertaining to the different flood protection strategies. When selecting between strategies, risk‐based design should therefore be complemented with other decision tools.
An algorithm for rapid flood inundation mapping from optical data using a reflectance differencing technique
Authors: Amarnath G. 
Published: March 2013

AbstractThis paper presents an algorithm for flood inundation mapping in the context of emergency response. Rapid satellite‐based flood inundation mapping and delivery of flood inundation maps during a flood event can provide crucial information for decision‐makers to put relief measures in place. With the development of remote sensing techniques, flood mapping for large areas can be done easily. The algorithm discussed here involves the use of shortwave infrared, near‐infrared and green spectral bands to develop a suitable band rationing technique for detecting surface water changes. This technique is referred to as Normalized Difference Surface Water Index (NDSWI). The NDSWI‐based approach produces the best results for mapping of flood‐inundated areas when verified with actual satellite data. Analysis of results reveals that NDSWI has the potential to detect floodwater turbidity, which was verified using principal component analysis. The application of the technique is informative about flood damages, which are illustrated using the floods in Pakistan in 2010 as an example.
Phasic‐like stimulation of the medial forebrain bundle augments striatal gene expression despite methamphetamine‐induced partial dopamine denervation
Authors: Howard Christopher D. , Pastuzyn Elissa D. , Barker‐Haliski Melissa L. , Garris Paul A. , Keefe Kristen A. 
Published: March 2013

AbstractMethamphetamine‐induced partial dopamine depletions are associated with impaired basal ganglia function, including decreased preprotachykinin mRNA expression and impaired transcriptional activation of activity‐regulated, cytoskeleton‐associated (Arc) gene in striatum. Recent work implicates deficits in phasic dopamine signaling as a potential mechanism linking methamphetamine‐induced dopamine loss to impaired basal ganglia function. This study thus sought to establish a causal link between phasic dopamine transmission and altered basal ganglia function by determining whether the deficits in striatal neuron gene expression could be restored by increasing phasic dopamine release. Three weeks after pretreatment with saline or a neurotoxic regimen of methamphetamine, rats underwent phasic‐ or tonic‐like stimulation of ascending dopamine neurons. Striatal gene expression was examined using in situ hybridization histochemistry. Phasic‐like, but not tonic‐like, stimulation induced immediate‐early genes Arc and zif268 in both groups, despite the partial striatal dopamine denervation in methamphetamine‐pretreated rats, with the Arc expression occurring in presumed striatonigral efferent neurons. Phasic‐like stimulation also restored preprotachykinin mRNA expression. These results suggest that disruption of phasic dopamine signaling likely underlies methamphetamine‐induced impairments in basal ganglia function, and that restoring phasic dopamine signaling may be a viable approach to manage long‐term consequences of methamphetamine‐induced dopamine loss on basal ganglia functions.
OVERBIDDING AND HETEROGENEOUS BEHAVIOR IN CONTEST EXPERIMENTS
Authors: Sheremeta Roman M. 
Published: March 2013

AbstractWe provide an overview of experimental literature on contests and point out the two main phenomena observed in most contest experiments: (i)overbiddingrelative to the standard Nash equilibrium prediction and (ii)heterogeneous behaviorofex antesymmetric contestants. Based on the sample of contest experiments that we review, the median overbidding rate is 72%. We provide different explanations for the overbidding phenomenon, including bounded rationality, utility of winning, other‐regarding preferences, probability distortion, and the shape of the payoff function. We also provide explanations for heterogeneous behavior of contestants based on differences in preferences toward winning, inequality, risk and losses, and demographic differences. Furthermore, we suggest mechanisms that can reduce overbidding and induce more homogeneous behavior. Finally, we discuss directions for future research.
Non‐invasive fibrosis biomarkers – APRI and Forns – are associated with liver stiffness in HIV‐monoinfected patients receiving antiretroviral drugs
Authors: Hasson Hamid , Merli Marco , Galli Laura , Gallotta Giulia , Carbone Alessia , Messina Emanuela , Bagaglio Sabrina , Morsica Giulia , Salpietro Stefania , Castagna Antonella , Lazzarin Adriano , Uberti‐Foppa Caterina 
Published: March 2013

AbstractBackground & AimsHIV‐monoinfected patients are susceptible to liver injury by different factors and may develop liver fibrosis, which requires adequate clinical management in terms of therapy and disease monitoring. We aimed to evaluate the presence of liver fibrosis identified by transient elastography (TE), its relationships with indirect biochemical markers [the aspartate aminotransferase/platelet ratio index (APRI), the Forns index and FIB‐4] and its predictive factors in HIV‐monoinfected patients receiving antiretroviral therapy (ART).MethodsSeventy‐two HIV‐monoinfected patients underwent TE and were evaluated using APRI, Forns and FIB‐4. The clinical, immunological, virological and other biochemical characteristics were evaluated at the time of TE, together with their history of ART.ResultsSeven patients (10%) had liver stiffness (LS) values predicting cirrhosis, and 12 (17%) had values predicting significant or advanced fibrosis. Higher indirect biochemical scores of liver fibrosis were significantly associated with higher LS values [APRI rs = 0.4296 (P < 0.001); Forns rs = 0.4754 (P < 0.001); FIB‐4 rs = 0.285 (P = 0.015)]. At multivariable analysis, APRI (β = 2.7405; P = 0.036), Forns (β = 1.4174; P = 0.029) and triglyceride levels (β = 1.3028; P = 0.007) were independently associated with LS.ConclusionsIndirect fibrosis biomarkers may increase the probability to detect liver injury enhancing a specific diagnostic workup and so contribute to improving the clinical management of HIV‐monoinfected patients with clinically suspected liver disease.