bluuebunny/crossref_metadata_2025_split huggingface dataset:
benchmarkR: an R package for benchmarking genome-scale methods
Authors: Zhou Xiaobei , Law Charity W. , Robinson Mark D. 
Published: April 2015

Abstract1Summary: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.2Availability:ThebenchmarkRpackage is available from:https://github.com/markrobinsonuzh/benchmarkR3Contact:mark.robinson@imls.uzh.ch
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

AbstractActivated 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

Summary

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

AbstractThe 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

AbstractThe 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

Summary

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

AbstractIn 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.
Long‐term outcomes in a high‐risk bladder cancer screening cohort
Authors: Starke Nathan , Singla Nirmish , Haddad Ahmed , Lotan Yair 
Published: April 2015

ObjectiveTo evaluate the long‐term outcomes in patients at high risk of bladder cancer who participated in a bladder cancer screening trial.Materials and MethodsPatients 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.ResultsThe 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).ConclusionAt 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

ObjectiveTo 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 MethodsIn 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.ResultsA 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.ConclusionWith 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

BackgroundThere 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.MethodsForty 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.ResultsControlling 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.ConclusionsTo 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.
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

AbstractBackgroundThis 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 methodsMajor 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.ResultsA 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.ConclusionsSerum 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

AbstractThe 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.