bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of prenatal stress on memory, nicotine withdrawal and 5HT1A expression in raphe nuclei of adult rats
Authors: Said N. , Lakehayli S. , Khachibi M. El , Ouahli M. El , Nadifi S. , Hakkou F. , Tazi A.
Published: April 2015

Maternal distress has often been associated with cognitive deficiencies and drug abuse in rats. This study examined these behavioral effects in offspring of mothers stressed during gestation. To this end, pregnant dams were subjected to daily electric foot shocks during the last 10 days of pregnancy. We measured litter parameters and body weights of the descendants after weaning (21 days) and at adulthood (80 days). Afterwards, prenatally stressed and control rats' performances in the novel object recognition test were compared in order to evaluate their memory while others underwent the Water consumption test to assess the nicotine withdrawal intensity after perinatal manipulations. Meanwhile, another set of rats were sacrificed and 5HT1A receptors' mRNA expression was measured in the raphe nuclei by quantitative Real Time PCR. We noticed no significant influence of maternal stress on litter size and body weight right after weaning. However, control rats were heavier than the stressed rats in adulthood. The results also showed a significant decrease in the recognition score in rats stressed in utero compared to the controls. Moreover, a heightened anxiety symptom was observed in the prenatally stressed offspring following nicotine withdrawal. Additionally, the Real Time PCR method revealed that prenatal stress induced a significant decrease in 5HT1A receptors’ levels in the raphe nuclei. Nicotine had a similar effect on these receptors’ expression in both nicotine‐treated control and prenatally stressed groups. Taken together, these findings suggest that the cognitive functions and drug dependence can be triggered by early adverse events in rats.
Mobile Advertising: An Empirical Study of Temporal and Spatial Differences in Search Behavior and Advertising Response
Authors: Goh Khim-Yong , Chu Junhong , Wu Jing
Published: April 2015

Using clickstream panel data from an automobile ad campaign conducted on a mobile platform, we investigate the relevance of mobile advertising, the interrelationships between ad content, information search behavior, and advertising response. Temporally, we compare mobile users’ search behavior and advertising response before and during a focal campaign event of an automobile show. Spatially, we examine their search behavior and advertising response in relation to their proximity to the show's location. Estimation results from individual-user random effects binary Logit and Poisson count models show that users’ responses to mobile advertising are related to the depth and breadth of search and the ad content. While informative and persuasive ad content exhibits differential non-linear effects on the depth and breadth of search, they have similar effects on advertising response. Interestingly, spatial and temporal proximity of mobile ad campaigns may not lead to increased relevance of mobile campaigns; it depends on the type of ad content and the type of measure used to assess relevance.
Diabetic Ketoacidosis and Acute Mountain Sickness: Case Report and Review of Treatment Options in Type 1 Diabetes Mellitus
Authors: Miller Steven C.M.
Published: April 2015

A 30-year-old man with a 20-year history of well-controlled type 1 diabetes mellitus and no microvascular complications traveled from near sea level to an altitude of 3000 m within 6 hours. At altitude, his blood glucose levels began to rise, necessitating increased insulin delivery. Typical symptoms of acute mountain sickness (AMS) developed, and he became increasingly hyperglycemic and unwell. Upon presentation to an emergency clinic, diabetic ketoacidosis (DKA) was diagnosed and was managed with insulin, intravenous fluids with potassium, and acetazolamide orally. No other potential causes for diabetic ketoacidosis were identified. Hyperglycemia, ketosis, and acidosis resolved with treatment as expected, but an increased insulin requirement was noted for the next 48 hours, until returning to expected levels when acetazolamide was discontinued. This case describes an episode of mild diabetic ketoacidosis potentially precipitated by moderate to severe acute mountain sickness, and an apparent hyperglycemic effect of acetazolamide. Individuals with type 1 diabetes traveling to altitude and their physicians should be vigilant for this complication and should be aware of the effects of conventional first-line therapies for acute mountain sickness on insulin requirement, glycemic control, and preexisting microvascular diabetes complications.
Late Quaternary sea-level history and the antiquity of mammoths (Mammuthus exilisandMammuthus columbi), Channel Islands National Park, California, USA
Authors: Muhs Daniel R. , Simmons Kathleen R. , Groves Lindsey T. , McGeehin John P. , Randall Schumann R. , Agenbroad Larry D.
Published: April 2015

Fossils of Columbian mammoths (Mammuthus columbi) and pygmy mammoths (Mammuthus exilis) have been reported from Channel Islands National Park, California. Most date to the last glacial period (Marine Isotope Stage [MIS] 2), but a tusk ofM. exilis(or immatureM. columbi) was found in the lowest marine terrace of Santa Rosa Island. Uranium-series dating of corals yielded ages from 83.8 ± 0.6 ka to 78.6 ± 0.5 ka, correlating the terrace with MIS 5.1, a time of relatively high sea level. Mammoths likely immigrated to the islands by swimming during the glacial periods MIS 6 (~ 150 ka) or MIS 8 (~ 250 ka), when sea level was low and the island–mainland distance was minimal, as during MIS 2. Earliest mammoth immigration to the islands likely occurred late enough in the Quaternary that uplift of the islands and the mainland decreased the swimming distance to a range that could be accomplished by mammoths. Results challenge the hypothesis that climate change, vegetation change, and decreased land area from sea-level rise were the causes of mammoth extinction at the Pleistocene/Holocene boundary on the Channel Islands. Pre-MIS 2 mammoth populations would have experienced similar or even more dramatic changes at the MIS 6/5.5 transition.
Fulton Receives 2014 Jason Morgan Early Career Award
Authors:   AGU
Published: April 2015

Patrick Fulton received the 2014 Jason Morgan Early Career Award at the 2014 American Geophysical Union Fall Meeting, held 15–19 December in San Francisco, Calif. The award is for significant early career contributions in tectonophysics.
Conquering Uncertainties in Tropical Climate Forecasts
Authors: Betz Eric
Published: April 2015

The key to better predictions of atmospheric temperature trends in the tropics may lie in more accurate measurements of sea surface temperatures.
GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach
Authors: Schmidt Ellen M. , Zhang Ji , Zhou Wei , Chen Jin , Mohlke Karen L. , Chen Y. Eugene , Willer Cristen J.
Published: April 2015

Motivation: The majority of variation identified by genome wide association studies falls in non-coding genomic regions and is hypothesized to impact regulatory elements that modulate gene expression. Here we present a statistically rigorous software tool GREGOR (Genomic Regulatory Elements and Gwas Overlap algoRithm) for evaluating enrichment of any set of genetic variants with any set of regulatory features. Using variants from five phenotypes, we describe a data-driven approach to determine the tissue and cell types most relevant to a trait of interest and to identify the subset of regulatory features likely impacted by these variants. Last, we experimentally evaluate six predicted functional variants at six lipid-associated loci and demonstrate significant evidence for allele-specific impact on expression levels. GREGOR systematically evaluates enrichment of genetic variation with the vast collection of regulatory data available to explore novel biological mechanisms of disease and guide us toward the functional variant at trait-associated loci.

Availability and implementation: GREGOR, including source code, documentation, examples, and executables, is available at http://genome.sph.umich.edu/wiki/GREGOR.

Contact: cristen@umich.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
PDIviz: analysis and visualization of protein–DNA binding interfaces
Authors: Ribeiro Judemir , Melo Francisco , Schüller Andreas
Published: April 2015

Summary: Specific recognition of DNA by proteins is a crucial step of many biological processes. PDIviz is a plugin for the PyMOL molecular visualization system that analyzes protein–DNA binding interfaces by comparing the solvent accessible surface area of the complex against the free protein and free DNA. The plugin provides three distinct three-dimensional visualization modes to highlight interactions with DNA bases and backbone, major and minor groove, and with atoms of different pharmacophoric type (hydrogen bond donors/acceptors, hydrophobic and thymine methyl). Each mode comes in three styles to focus the visual analysis on the protein or DNA side of the interface, or on the nucleotide sequence. PDIviz allows for the generation of publication quality images, all calculated data can be written to disk, and a command line interface is provided for automating tasks. The plugin may be helpful for the detailed identification of regions involved in DNA base and shape readout, and can be particularly useful in rapidly pinpointing the overall mode of interaction.

Availability and implementation: Freely available at http://melolab.org/pdiviz/ as a PyMOL plugin. Tested with incentive, educational, and open source versions of PyMOL on Windows, Mac and Linux systems.

Contact:  aschueller@bio.puc.cl

Supplementary Information:  Supplementary data are available at Bioinformatics online.
FastMotif: spectral sequence motif discovery
Authors: Colombo Nicoló , Vlassis Nikos
Published: April 2015

Motivation: Sequence discovery tools play a central role in several fields of computational biology. In the framework of Transcription Factor binding studies, most of the existing motif finding algorithms are computationally demanding, and they may not be able to support the increasingly large datasets produced by modern high-throughput sequencing technologies.

Results: We present FastMotif, a new motif discovery algorithm that is built on a recent machine learning technique referred to as Method of Moments. Based on spectral decompositions, our method is robust to model misspecifications and is not prone to locally optimal solutions. We obtain an algorithm that is extremely fast and designed for the analysis of big sequencing data. On HT-Selex data, FastMotif extracts motif profiles that match those computed by various state-of-the-art algorithms, but one order of magnitude faster. We provide a theoretical and numerical analysis of the algorithm’s robustness and discuss its sensitivity with respect to the free parameters.

Availability and implementation: The Matlab code of FastMotif is available from http://lcsb-portal.uni.lu/bioinformatics.

Contact:  vlassis@adobe.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Accurate prediction of RNA nucleotide interactions with backbone k-tree model
Authors: Ding Liang , Xue Xingran , LaMarca Sal , Mohebbi Mohammad , Samad Abdul , Malmberg Russell L. , Cai Liming
Published: April 2015

Motivation: Given the importance of non-coding RNAs to cellular regulatory functions, it would be highly desirable to have accurate computational prediction of RNA 3D structure, a task which remains challenging. Even for a short RNA sequence, the space of tertiary conformations is immense; existing methods to identify native-like conformations mostly resort to random sampling of conformations to achieve computational feasibility. However, native conformations may not be examined and prediction accuracy may be compromised due to sampling. State-of-the-art methods have yet to deliver satisfactory predictions for RNAs of length beyond 50 nucleotides.

Results: This paper presents a method to tackle a key step in the RNA 3D structure prediction problem, the prediction of the nucleotide interactions that constitute the desired 3D structure. The research is based on a novel graph model, called a backbone k-tree, to tightly constrain the nucleotide interaction relationships considered for RNA 3D structures. It is shown that the new model makes it possible to efficiently predict the optimal set of nucleotide interactions (including the non-canonical interactions in all recently revealed families) from the query sequence along with known or predicted canonical basepairs. The preliminary results indicate that in most cases the new method can predict with a high accuracy the nucleotide interactions that constitute the 3D structure of the query sequence. It thus provides a useful tool for the accurate prediction of RNA 3D structure.

Availability and Implementation: The source package for BkTree is available at http://rna-informatics.uga.edu/index.php?f=software&p=BkTree.

Contact:  lding@uga.edu or cai@cs.uga.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo
Authors: Tang Yin , Bouvier Emil , Kwok Chun Kit , Ding Yiliang , Nekrutenko Anton , Bevilacqua Philip C. , Assmann Sarah M.
Published: April 2015

Motivation: RNAs fold into complex structures that are integral to the diverse mechanisms underlying RNA regulation of gene expression. Recent development of transcriptome-wide RNA structure profiling through the application of structure-probing enzymes or chemicals combined with high-throughput sequencing has opened a new field that greatly expands the amount of in vitro and in vivo RNA structural information available. The resultant datasets provide the opportunity to investigate RNA structural information on a global scale. However, the analysis of high-throughput RNA structure profiling data requires considerable computational effort and expertise.

Results: We present a new platform, StructureFold, that provides an integrated computational solution designed specifically for large-scale RNA structure mapping and reconstruction across any transcriptome. StructureFold automates the processing and analysis of raw high-throughput RNA structure profiling data, allowing the seamless incorporation of wet-bench structural information from chemical probes and/or ribonucleases to restrain RNA secondary structure prediction via the RNAstructure and ViennaRNA package algorithms. StructureFold performs reads mapping and alignment, normalization and reactivity derivation, and RNA structure prediction in a single user-friendly web interface or via local installation. The variation in transcript abundance and length that prevails in living cells and consequently causes variation in the counts of structure-probing events between transcripts is accounted for. Accordingly, StructureFold is applicable to RNA structural profiling data obtained in vivo as well as to in vitro or in silico datasets. StructureFold is deployed via the Galaxy platform.

Availability and Implementation: StructureFold is freely available as a component of Galaxy available at: https://usegalaxy.org/.

Contact:  yxt148@psu.edu or sma3@psu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Antiseptic Body Washes for Reducing the Transmission of Methicillin-Resistant Staphylococcus aureus: A Cluster Crossover Study
Authors: Harris Patrick N. A. , Le Bich Diep , Tambyah Paul , Hsu Li Yang , Pada Surinder , Archuleta Sophia , Salmon Sharon , Mukhopadhyay Amartya , Dillon Jasmine , Ware Robert , Fisher Dale A.
Published: April 2015

Background.  Limiting the spread of methicillin-resistant Staphylococcus aureus (MRSA) within healthcare facilities where the organism is highly endemic is a challenge. The use of topical antiseptic agents may help interrupt the transmission of MRSA and reduce the risk of clinical infection. Octenidine dihydrochloride is a topical antiseptic that exhibits in vitro efficacy against a wide variety of bacteria, including S aureus.

Methods.  We conducted a prospective cluster crossover study to compare the use of daily octenidine body washes with soap and water in patients identified by active surveillance cultures to be MRSA-colonized, to prevent the acquisition of MRSA in patients with negative screening swabs. Five adult medical and surgical wards and 2 intensive care units were selected. The study involved an initial 6-month phase using octenidine or soap washes followed by a crossover in each ward to the alternative product. The primary and secondary outcomes were the rates of new MRSA acquisitions and MRSA clinical infections, respectively.

Results.  A total of 10 936 patients admitted for ≥48 hours was included in the analysis. There was a small reduction in MRSA acquisition in the intervention group compared with controls (3.0% vs 3.3%), but this reduction was not significant (odds ratio, 0.89; 95% confidence interval, .72–1.11; P = .31). There were also no significant differences in clinical MRSA infection or incidence of MRSA bacteremia.

Conclusions.  This study suggests that the targeted use of routine antiseptic washes may not in itself be adequate to reduce the transmission of MRSA in an endemic hospital setting.
Longimonas halophila gen. nov., sp. nov., isolated from a marine solar saltern
Authors: Xia Jun , Zhou Yan-Xia , Zhao Li-Hua , Chen Guan-Jun , Du Zong-Jun
Published: April 2015

A bacterial strain, designated SYD6T, was isolated from a marine solar saltern on the coast of Weihai, Shandong Province, PR China. Cells of strain SYD6Twere rod-shaped, red, and approximately 5.0–9.0 μm in length and 0.4–0.6 μm in width. The strain was Gram-stain-negative, facultatively anaerobic, heterotrophic, catalase-positive and oxidase-negative. Growth occurred in 4–25 % (w/v) NaCl [with 2–15 % (w/v) MgCl2.6H2O also present], at 20–50 °C and pH 6.5–8.5. Optimal growth was observed at 37–42 °C, pH 7.5–8.0, with 6–8 % (w/v) NaCl [with 2–4 % (w/v) MgCl2.6H2O]. Nitrate was not reduced. Glucose, sucrose, maltose, fructose and ribose stimulated growth, but not glycerol, xylose or mannitol. The G+C content of the genomic DNA was 61.5 mol% (HPLC). The sole methyl naphthoquinone was MK-7 and the predominant cellular fatty acids (>10 %) were iso-C15 : 02-OH/C16 : 1ω7c, iso-C16 : 0, C18 : 1ω7c/C18 : 1ω6cand C18 : 1ω7c. The predominant polar lipids were phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and an unknown lipid. Phylogenetic analysis, based on 16S rRNA gene sequences, demonstrated that strain SYD6Twas affiliated with the phylumBacteroidetes. The most closely related neighbours were species of the genusSalisaetaand strain SYD6Thad a 16S rRNA gene sequence similarity of 91.97 % withSalisaeta longaDSM 21114T. On the basis of these phenotypic and phylogenetic data, strain SYD6Trepresents a novel species of a new genus of the familyRhodothermaceae, for which the nameLongimonas halophilagen. nov., sp. nov. is proposed. The type strain of the type species is SYD6T( = CICC 10838T = KCTC 42399T).
The placenta shed from goats with classical scrapie is infectious to goat kids and lambs
Authors: Schneider David A. , Madsen-Bouterse Sally A. , Zhuang Dongyue , Truscott Thomas C. , Dassanayake Rohana P. , O'Rourke Katherine I.
Published: April 2015

The placenta of domestic sheep plays a key role in horizontal transmission of classical scrapie. Domestic goats are frequently raised with sheep and are susceptible to classical scrapie, yet potential routes of transmission from goats to sheep are not fully defined. Sparse accumulation of disease-associated prion protein in cotyledons casts doubt about the role of the goat's placenta. Thus, relevant to mixed-herd management and scrapie-eradication efforts worldwide, we determined if the goat's placenta contains prions orally infectious to goat kids and lambs. A pooled cotyledon homogenate, prepared from the shed placenta of a goat with naturally acquired classical scrapie disease, was used to orally inoculate scrapie-naı¨ve prion genotype-matched goat kids and scrapie-susceptible lambs raised separately in a scrapie-free environment. Transmission was detected in all four goats and in two of four sheep, which importantly identifies the goat's placenta as a risk for horizontal transmission to sheep and other goats.
benchmarkR: an R package for benchmarking genome-scale methods
Authors: Zhou Xiaobei , Law Charity W. , Robinson Mark D.
Published: April 2015

1

benchmarkRis an R package designed to assess and visualize the performance of statistical methods for datasets that have an independent truth (e.g., simulations or datasets with large-scale validation), in particular for methods that claim to control false discovery rates (FDR). We augment some of the standard performance plots (e.g., receiver operating characteristic, or ROC, curves) with information about how well the methods are calibrated (i.e., whether they achieve their expected FDR control). For example, performance plots are extended with a point to highlight the power or FDR at a user-set threshold (e.g., at a method’sestimated5% FDR). The package contains general containers to store simulation results (SimResults) and methods to create graphical summaries, such as receiver operating characteristic curves (rocX), false discovery plots (fdX) and power-to-achieved FDR plots (powerFDR); each plot is augmented with some form of calibration information. We find these plots to be an improved way to interpret relative performance of statistical methods for genomic datasets where many hypothesis tests are performed. The strategies, however, are general and will find applications in other domains.

2

Availability:

ThebenchmarkRpackage is available from:https://github.com/markrobinsonuzh/benchmarkR

3

Contact:

mark.robinson@imls.uzh.ch
The impact of odor–reward memory on chemotaxis in larval Drosophila
Authors: Schleyer Michael , Reid Samuel F. , Pamir Evren , Saumweber Timo , Paisios Emmanouil , Davies Alexander , Gerber Bertram , Louis Matthieu
Published: April 2015

How do animals adaptively integrate innate with learned behavioral tendencies? We tackle this question using chemotaxis as a paradigm. Chemotaxis in the Drosophila larva largely results from a sequence of runs and oriented turns. Thus, the larvae minimally need to determine (i) how fast to run, (ii) when to initiate a turn, and (iii) where to direct a turn. We first report how odor-source intensities modulate these decisions to bring about higher levels of chemotactic performance for higher odor-source intensities during innate chemotaxis. We then examine whether the same modulations are responsible for alterations of chemotactic performance by learned odor “valence” (understood throughout as level of attractiveness). We find that run speed (i) is neither modulated by the innate nor by the learned valence of an odor. Turn rate (ii), however, is modulated by both: the higher the innate or learned valence of the odor, the less often larvae turn whenever heading toward the odor source, and the more often they turn when heading away. Likewise, turning direction (iii) is modulated concordantly by innate and learned valence: turning is biased more strongly toward the odor source when either innate or learned valence is high. Using numerical simulations, we show that a modulation of both turn rate and of turning direction is sufficient to account for the empirically found differences in preference scores across experimental conditions. Our results suggest that innate and learned valence organize adaptive olfactory search behavior by their summed effects on turn rate and turning direction, but not on run speed. This work should aid studies into the neural mechanisms by which memory impacts specific aspects of behavior.
Anti‐inflammatory effects of activated protein C on human dendritic cells
Authors: Ohkuma Koichi , Matsuda Kouki , Kariya Ryusho , Goto Hiroki , Kamei Shintaro , Hamamoto Takayoshi , Okada Seiji
Published: April 2015

Activated protein C (APC) has an anticoagulant action and plays an important role in blood coagulation homeostasis. In addition to its anticoagulant action, APC is known to have cytoprotective effects, such as anti‐apoptotic action and endothelial barrier protection, on vascular endothelial cells and monocytes. However, the effects of APC on DCs have not been clarified. To investigate the effects of APC on human DCs, monocytes were isolated from peripheral blood and DC differentiation induced with LPS. APC significantly inhibited the production of inflammatory cytokines TNF‐α and IL‐6 during differentiation of immature DCs to mature DCs, but did not inhibit the production of IL‐12 and anti‐inflammatory cytokine IL‐10. Interestingly, treatment with 5 μg/mL, but not 25 μg/mL, of APC significantly enhanced production of IL‐10. In addition, protein C, which is the zymogen of APC, did not affect production of these cytokines. On the other hand, flow cytometric analysis of DC's surface molecules indicated that APC does not significantly affect expression of CD83, a marker of mDC differentiation, and the co‐stimulatory molecules CD40, CD80 and CD86. These results suggest that APC has anti‐inflammatory effects on human DCs and may be effective against some inflammatory diseases in which the pathogenesis involves TNF‐α and/or IL‐6 production.
Parental environmental effects due to contrasting watering adapt competitive ability, but not drought tolerance, in offspring of a semi‐arid annual Brassicaceae
Authors: Metz Johannes , von Oppen Jonathan , Tielbörger Katja
Published: April 2015

Parental effects (PE) can be adaptive and improve offspring performance when parents and offspring experience similar environmental conditions. However, it is unknown whether adaptive PE exist also in habitats where such similarity is unlikely due to strong temporal variation. In particular, we do not know whether PE can adapt offspring to fluctuating levels of neighbour competition in such habitats.

Here, we tested for adaptive PE in terms of two key environmental factors in a semi‐arid annual system, competition and drought. While rainfall was stochastic in the study site, the competitive environment was partly predictable: higher plant densities followed after favourable (rainy) years due to high seed production. We therefore expected PE to adapt the offspring's competitive ability to these (predictable) fluctuations in plant densities, rather than to adapt the offspring's drought tolerance to the (unpredictable) occurrence of intensified drought.

Parental plants of Biscutella didyma, an annual Brassicaceae, were raised under favourable watering and under drought conditions. Offspring performance was then tested under a full‐factorial combination of two neighbour regimes and six watering levels in the glasshouse.

Offspring of parents grown under favourable conditions were stronger competitors. This was associated with a small shift in phenology but not with higher parental seed provisioning. Offspring from parents grown under drought showed no improved drought tolerance. Moreover, no PE were detectable when offspring were grown without neighbours.

Our results suggest a novel path of adaptive PE: higher competitive ability was induced in offspring that were more likely to experience high neighbour densities. Together with the lack of adaptive PE towards drought tolerance, this emphasizes that a correlation between parental and offspring environment is crucial for adaptive PE to evolve. Our results also call for the inclusion of competitive effects in future PE studies.

Synthesis. This study demonstrates the important role of adaptive PE for plant fitness (regarding competition) but also their limits (regarding drought) in temporally variable environments, based on the predictability of the respective environmental factor.
Accuracy Assessment of NOAA Gridded Daily Reference Evapotranspiration for the Texas High Plains
Authors: Moorhead Jerry , Gowda Prasanna , Hobbins Mike , Senay Gabriel , Paul George , Marek Thomas , Porter Dana
Published: April 2015

The National Oceanic and Atmospheric Administration (NOAA) provides daily reference evapotranspiration (ETref) maps for the contiguous United States using climatic data from North American Land Data Assimilation System (NLDAS). This data provides large‐scale spatial representation of ETref, which is essential for regional scale water resources management. Data used in the development of NOAA daily ETref maps are derived from observations over surfaces that are different from short (grass — ETos) or tall (alfalfa — ETrs) reference crops, often in nonagricultural settings, which carries an unknown discrepancy between assumed and actual conditions. In this study, NOAA daily ETos and ETrs maps were evaluated for accuracy, using observed data from the Texas High Plains Evapotranspiration (TXHPET) network. Daily ETos, ETrs and the climatic data (air temperature, wind speed, and solar radiation) used for calculating ETref were extracted from the NOAA maps for TXHPET locations and compared against ground measurements on reference grass surfaces. NOAA ETref maps generally overestimated the TXHPET observations (1.4 and 2.2 mm/day ETos and ETrs, respectively), which may be attributed to errors in the NLDAS modeled air temperature and wind speed, to which reference ETref is most sensitive. Therefore, a bias correction to NLDAS modeled air temperature and wind speed data, or adjustment to the resulting NOAA ETref, may be needed to improve the accuracy of NOAA ETref maps.
Effects of Climate and Land Cover on Hydrology in the Southeastern U.S.: Potential Impacts on Watershed Planning
Authors: LaFontaine Jacob H. , Hay Lauren E. , Viger Roland J. , Regan R. Steve , Markstrom Steven L.
Published: April 2015

The hydrologic response to statistically downscaled general circulation model simulations of daily surface climate and land cover through 2099 was assessed for the Apalachicola‐Chattahoochee‐Flint River Basin located in the southeastern United States. Projections of climate, urbanization, vegetation, and surface‐depression storage capacity were used as inputs to the Precipitation‐Runoff Modeling System to simulate projected impacts on hydrologic response. Surface runoff substantially increased when land cover change was applied. However, once the surface depression storage was added to mitigate the land cover change and increases of surface runoff (due to urbanization), the groundwater flow component then increased. For hydrologic studies that include projections of land cover change (urbanization in particular), any analysis of runoff beyond the change in total runoff should include effects of stormwater management practices as these features affect flow timing and magnitude and may be useful in mitigating land cover change impacts on streamflow. Potential changes in water availability and how biota may respond to changes in flow regime in response to climate and land cover change may prove challenging for managers attempting to balance the needs of future development and the environment. However, these models are still useful for assessing the relative impacts of climate and land cover change and for evaluating tradeoffs when managing to mitigate different stressors.
A method for identifying Sound Scattering Layers and extracting key characteristics
Authors: Proud Roland , Cox Martin J. , Wotherspoon Simon , Brierley Andrew S.
Published: April 2015

Mid‐trophic level water‐column (pelagic) marine communities comprise millions of tonnes of zooplankton and micronekton that form dense and geographically extensive layers, known as sound scattering layers (SSLs) when observed acoustically. SSLs are ubiquitous in the global ocean, and individual layers can span entire ocean basins. Many SSLs exhibit clear diel vertical migration behaviour. Vertical migrations contribute substantially to the ‘biological pump’, such that SSLs have important global biogeochemical roles: SSLs are important conduits for vertical energy and nutrient flow. Ship‐based remote sensing of SSLs using acoustic instruments (echosounders) enables their shape and density to be quantified, but despite SSLs being discovered in the 1940s, there is no consistent method for identifying or characterising SSLs. This hampers ecological and biogeographical studies of SSLs.

We have developed an automated and reproducible method for SSL identification and characterisation, the sound scattering layer extraction method (SSLEM). It functions independently of echosounder frequency and the spatial scale (vertical and horizontal) of the data. Here we demonstrate the SSLEM through its application to identify SSLs in data gathered to a depth of 1000 m using 38 kHz hull‐mounted echosounders in the south‐west Indian Ocean and Tasman Sea.

SSLs were identified in the water column as horizontally extensive echoes that were above background noise. For each identified SSL, a set of 9 quantitative ‘SSL metrics’ (describing their shape, dynamics and acoustic backscattering distribution) were determined, enabling inferences to be made concerning the spatial arrangement, distribution and heterogeneity of the biological community. The method was validated by comparing its output to a set of visually derived SSL metrics that were evaluated independently by 8 students. The SSLEM outperformed the by‐eye analysis, identifying three times the number of SSLs and with greater validity; 95% of SSLs identified by the SSLEM were deemed valid, compared to 75% by the students.

In the same way that data obtained from satellites have enabled the study and characterisation of global phytoplankton distribution and production, we envisage that the SSLEM will facilitate robust, repeatable and quantitative analysis of the growing body of SSL observations arising from underway‐acoustic observations, enhancing our understanding of global ocean function.
“The first cut is the deepest”: a psychological, sexological and gynecological perspective on female genital cosmetic surgery
Authors: Barbara Giussy , Facchin Federica , Meschia Michele , Vercellini Paolo
Published: April 2015

In recent years increased numbers of healthy women and girls have been seeking female genital cosmetic surgery for esthetic reasons and/or to enhance sexual functioning. This phenomenon is associated with the development of a new vulvovaginal standard due to Internet pornography and the increased exposure of female genitalia. This strict standard may negatively affect women's psychological health and cause increased insecurity, which may drive even teenagers to seek female genital cosmetic surgery. Psychological counseling is recommended to inform women that surgery is not a definitive solution to treat psychologically based pain or dysfunction. Moreover, there is no robust evidence supporting the effectiveness of female genital cosmetic surgery, especially regarding sexual enhancement, as underlined by major scientific societies. The importance of a definite regulation of female genital cosmetic surgery should be emphasized and be based on an ethically oriented, multidisciplinary model aimed at providing exhaustive information on all gynecological, sexological, and psychological concerns raised by this type of surgery.
Bad guys suffer less (social pain): Moral status influences judgements of others’ social suffering
Authors: Riva Paolo , Brambilla Marco , Vaes Jeroen
Published: April 2015

Research on pain judgement has shown that several features of a target influence empathy for others’ pain. Considering the pivotal role of morality in social judgement, we investigated whether judgements of others’ social and physical suffering vary as a function of the target's moral status. Study 1 manipulated the moral characteristics of an unknown other and found that participants ascribed less social (but not physical) suffering to a target depicted as lacking moral status rather than to a target high in morality. Study 2 added a control condition in which no information about the target's moral qualities was provided, and showed that the effect of morality on social pain judgements was driven by the depiction of the target as lacking moral traits. Study 3 revealed the specific role of morality, as information on another evaluative dimension (i.e., competence) had no effects on pain judgements. Study 4 showed that social targets perceived as lacking moral qualities are thought to experience less social pain than highly moral targets because of their perceived lower level of humanity. Overall, our findings suggest that social (but not physical) pain might represent a capacity that is denied to social targets that are perceived low in morality.
Long‐term outcomes in a high‐risk bladder cancer screening cohort
Authors: Starke Nathan , Singla Nirmish , Haddad Ahmed , Lotan Yair
Published: April 2015

Objective

To evaluate the long‐term outcomes in patients at high risk of bladder cancer who participated in a bladder cancer screening trial.

Materials and Methods

Patients who were classified as high risk based on age ≥50 years, ≥10 pack‐years (combination of packs of tobacco per day and years of smoking) smoking and/or ≥15 years environmental exposure were enrolled in a one‐time screening trial using a nuclear matrix protein 22 (NMP22) assay, between March 2006 and November 2007, at Dallas Veterans Affairs Hospital. We assessed the subsequent detection of smoking‐related malignancies (bladder, lung and renal cell carcinoma [RCC]) in these patients up until 31 January 2014. Multivariable regression analysis was used to determine factors associated with bladder cancer diagnosis and survival.

Results

The study cohort included 925 patients, of whom 886 (95.8%) were smokers and 613 (66.3%) had received hazardous occupational exposure. At initial screening, 57 patients had a positive NMP22 test and two had bladder cancer. Another nine patients (1.0%) were diagnosed with bladder cancer during the median follow‐up of 78.4 months. The bladder cancers were non‐invasive (Ta) and seven were low grade and four high grade. RCC and lung cancer were diagnosed in 10 (1.1%) and 18 patients (1.9%), respectively. A total of 134 patients died, including three from RCC and 12 from lung cancer, but none from bladder cancer. Factors associated with worse overall survival on multivariable analysis were: lung cancer (hazard ratio [HR] 5.06; P < 0.001), microscopic or gross haematuria (HR 1.66; P = 0.006 and HR 2.11; P = 0.02, respectively), and >60 pack‐years smoking history (HR 4.51; P = 0.037).

Conclusion

At 6.5 years of follow‐up, no patients in this high‐risk cohort developed muscle‐invasive bladder cancer. Lung cancer, haematuria and >60 pack‐years smoking history are independent predictors of mortality. Other‐cause mortality is an important consideration in patients undergoing bladder cancer screening.
Percutaneous nephrolithotomy in super obese patients (body mass index ≥ 50 kg/m2): overcoming the challenges
Authors: Keheila Mohamed , Leavitt David , Galli Riccardo , Motamedinia Piruz , Theckumparampil Nithin , Siev Micheal , Hoenig David , Smith Arthur , Okeke Zeph
Published: April 2015

Objective

To analyse our experience with and the outcomes and lessons learned from percutaneous nephrolithotomy (PCNL) in the super obese (body mass index [BMI] ≥50 kg/m2).

Patients and Methods

In this institutional review board approved study we retrospectively reviewed our PCNL database between July 2011 and September 2014 and identified all patients with a BMI ≥ 50 kg/m2. Patient demographics, peri‐operative outcomes and complications were determined. Additionally, we identified a number of special PCNL considerations in the super obese that can maximize safe outcomes.

Results

A total of 21 PCNL procedures performed on 17 super obese patients were identified. The mean patient age was 54.8 years, the mean BMI was 57.2 kg/m2 and the mean stone area was 1 037 mm2. Full staghorn stones were observed in six patients and partial staghorns in four patients. The mean operating time was 106 min and the mean haemoglobin decrease was 1.2 g/dL. The overall stone‐free rate was 87%. There were four total complications: two Clavien grade II, one Clavien IIIb and one Clavien IVb. We identified several special considerations for safely preforming PCNL in the suber obese, including using extra‐long nephroscopes and graspers, using custom‐cut extra long access sheaths with suture ‘tails’ secured to easily retrieve the sheath, choosing the shortest possible access tract, readily employing flexible nephroscopes, placing nephroureteral tubes rather than nephrostomy tubes postoperatively, and meticulous patient positioning and padding.

Conclusion

With appropriate peri‐operative considerations and planning, PCNL is feasible and safe in the super obese. Stone clearance was similar to that reported in previous PCNL series in the morbidly obese, and is achievable with few complications.
Effectiveness of brief school‐based, group cognitive behavioural therapy for depressed adolescents in south west Nigeria
Authors: Bella‐Awusah Tolulope , Ani Cornelius , Ajuwon Ademola , Omigbodun Olayinka
Published: April 2015

Background

There is paucity of evidence‐based psychological interventions for depressive disorders in Africa, more so among depressed children and adolescents. This study aimed to determine the effects of a school‐based cognitive behavioural therapy programme (CBT) on depressed adolescents in South West Nigeria.

Methods

Forty students who scored 18 or above on the Beck Depression Inventory (BDI) were recruited from two schools (20 from each school). One school was designated intervention and the other a wait‐list control school. Five weekly sessions of group CBT programme were conducted in the intervention school. Primary outcome measure was the Beck Depression Inventory, and secondary outcome measures were the Short Mood and Feelings Questionnaire and the Impact Supplement of the Strengths and Difficulties Questionnaire.

Results

Controlling for baseline scores and other confounders, the intervention group had significantly lower depressive symptoms scores on the BDI and SMFQ 1 week post intervention with large effect sizes. The intervention group maintained the treatment effect with significantly lower depression scores 16 weeks post intervention compared with their baseline scores. The effect sizes remained large. The intervention and control groups did not differ in their SDQ impact supplement scores post intervention, but the intervention group improved significantly on this measure at 16 weeks.

Conclusions

To our knowledge, this is the first study of a school‐based group CBT programme for depressed adolescents in Africa. The programme showed good feasibility and promising effectiveness.
Repeat botulinum toxin A injections: a step forward in the challenge to evaluate current clinical practice
Authors: Russo Remo
Published: April 2015

This commentary is on the original article by Lidman et al. on pages 754–761 of this issue.
Serum cystatin C and microalbuminuria in burn patients with acute kidney injury
Authors: Yim Haejun , Kym Dohern , Seo Dong Kook , Yoon Jaechul , Yang Hyeong‐Tae , Lee Jeonghwan , Cho Yong‐Suk , Hur Jun , Chun Wook , Han Seong‐Woo
Published: April 2015

Background

This study was aimed at evaluating the effectiveness of serum cystatin C and microalbuminuria as diagnostic markers for acute kidney injury (AKI) in major burn patients.

Materials and methods

Major burn adult patients admitted to the burn intensive care unit within 24 h from the onset of injury were enrolled. Serum cystatin C and microalbuminuria (albumin–creatinine ratio, ACR) were obtained at postburn days 1, 3, 7, 14, 21 and 28. The patients were divided into two groups of the AKI group and the nonacute kidney injury group.

Results

A total of 97 patients were enrolled in this study. Acute kidney injury was diagnosed in 40 patients (41·2%) at postburn day 17·3 ± 7·9. The area under the curve of the receiver operating characteristic curve for serum cystatin C was 0·808 (95% CI, 0·711–0·905, P < 0·001) at postburn day 7 and 0·908 (95% CI, 0·843–0·973, P < 0·001) at postburn day 14. The results were 0·610 (95% CI, 0·497–0·724, P = 0·069) for ACR at postburn day 7 and 0·694 (95% CI, 0·589–0·798, P = 0·001) at postburn day 14. The optimal cut‐off value of serum cystatin C at postburn day 14 and ACR at postburn day 14 were 0·85 mg/L (sensitivity, 89·5%; specificity, 82·5%) and 41·51 mg/g cre (sensitivity, 60·5%; specificity, 61·4%), respectively. Serum cystatin C at postburn day 14 was the only significant factor in relation to AKI.

Conclusions

Serum cystatin C is a valuable diagnostic marker, whereas microalbuminuria is a relatively less significant marker for AKI in major burn patients.
Evolutionary perspective of cancer: myth, metaphors, and reality
Authors: Arnal Audrey , Ujvari Beata , Crespi Bernard , Gatenby Robert A. , Tissot Tazzio , Vittecoq Marion , Ewald Paul W. , Casali Andreu , Ducasse Hugo , Jacqueline Camille , Missé Dorothée , Renaud François , Roche Benjamin , Thomas Frédéric
Published: April 2015

The evolutionary perspective of cancer (which origins and dynamics result from evolutionary processes) has gained significant international recognition over the past decade and generated a wave of enthusiasm among researchers. In this context, several authors proposed that insights into evolutionary and adaptation dynamics of cancers can be gained by studying the evolutionary strategies of organisms. Although this reasoning is fundamentally correct, in our opinion, it contains a potential risk of excessive adaptationism, potentially leading to the suggestion of complex adaptations that are unlikely to evolve among cancerous cells. For example, the ability of recognizing related conspecifics and adjusting accordingly behaviors as in certain free‐living species appears unlikely in cancer. Indeed, despite their rapid evolutionary rate, malignant cells are under selective pressures for their altered lifestyle for only few decades. In addition, even though cancer cells can theoretically display highly sophisticated adaptive responses, it would be crucial to determine the frequency of their occurrence in patients with cancer, before therapeutic applications can be considered. Scientists who try to explain oncogenesis will need in the future to critically evaluate the metaphorical comparison of selective processes affecting cancerous cells with those affecting organisms. This approach seems essential for the applications of evolutionary biology to understand the origin of cancers, with prophylactic and therapeutic applications.
Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations
Authors: Paris Josephine R. , King R. Andrew , Stevens Jamie R.
Published: April 2015

Humans have exploited the earth's metal resources for thousands of years leaving behind a legacy of toxic metal contamination and poor water quality. The southwest of England provides a well‐defined example, with a rich history of metal mining dating to the Bronze Age. Mine water washout continues to negatively impact water quality across the region where brown trout (Salmo trutta L.) populations exist in both metal‐impacted and relatively clean rivers. We used microsatellites to assess the genetic impact of mining practices on trout populations in this region. Our analyses demonstrated that metal‐impacted trout populations have low genetic diversity and have experienced severe population declines. Metal‐river trout populations are genetically distinct from clean‐river populations, and also from one another, despite being geographically proximate. Using approximate Bayesian computation (ABC), we dated the origins of these genetic patterns to periods of intensive mining activity. The historical split of contemporary metal‐impacted populations from clean‐river fish dated to the Medieval period. Moreover, we observed two distinct genetic populations of trout within a single catchment and dated their divergence to the Industrial Revolution. Our investigation thus provides an evaluation of contemporary population genetics in showing how human‐altered landscapes can change the genetic makeup of a species.