bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of cloud and water vapor simulations in CMIP5 climate models using NASA “A‐Train” satellite observations
Authors: Jiang Jonathan H. , Su Hui , Zhai Chengxing , Perun Vincent S. , Del Genio Anthony , Nazarenko Larissa S. , Donner Leo J. , Horowitz Larry , Seman Charles , Cole Jason , Gettelman Andrew , Ringer Mark A. , Rotstayn Leon , Jeffrey Stephen , Wu Tongwen , Brient Florent , Dufresne Jean‐Louis , Kawai Hideaki , Koshiro Tsuyoshi , Watanabe Masahiro , LÉcuyer Tristan S. , Volodin Evgeny M. , Iversen Trond , Drange Helge , Mesquita Michel D. S. , Read William G. , Waters Joe W. , Tian Baijun , Teixeira Joao , Stephens Graeme L. 
Published: June 2012

Using NASA's A‐Train satellite measurements, we evaluate the accuracy of cloud water content (CWC) and water vapor mixing ratio (H2O) outputs from 19 climate models submitted to the Phase 5 of Coupled Model Intercomparison Project (CMIP5), and assess improvements relative to their counterparts for the earlier CMIP3. We find more than half of the models show improvements from CMIP3 to CMIP5 in simulating column‐integrated cloud amount, while changes in water vapor simulation are insignificant. For the 19 CMIP5 models, the model spreads and their differences from the observations are larger in the upper troposphere (UT) than in the lower or middle troposphere (L/MT). The modeled mean CWCs over tropical oceans range from ∼3% to ∼15× of the observations in the UT and 40% to 2× of the observations in the L/MT. For modeled H2Os, the mean values over tropical oceans range from ∼1% to 2× of the observations in the UT and within 10% of the observations in the L/MT. The spatial distributions of clouds at 215 hPa are relatively well‐correlated with observations, noticeably better than those for the L/MT clouds. Although both water vapor and clouds are better simulated in the L/MT than in the UT, there is no apparent correlation between the model biases in clouds and water vapor. Numerical scores are used to compare different model performances in regards to spatial mean, variance and distribution of CWC and H2O over tropical oceans. Model performances at each pressure level are ranked according to the average of all the relevant scores for that level.
Acidic stress induces the formation of P-bodies, but not stress granules, with mild attenuation of bulk translation inSaccharomyces cerevisiae
Authors: Iwaki Aya , Izawa Shingo 
Published: June 2012

The stress response of eukaryotic cells often causes an attenuation of bulk translation activity and the accumulation of non-translating mRNAs into cytoplasmic mRNP (messenger ribonucleoprotein) granules termed cytoplasmic P-bodies (processing bodies) and SGs (stress granules). We examined effects of acidic stress on the formation of mRNP granules compared with other forms of stress such as glucose deprivation and a high Ca2+ level in Saccharomyces cerevisiae. Treatment with lactic acid clearly caused the formation of P-bodies, but not SGs, and also caused an attenuation of translation initiation, albeit to a lesser extent than glucose depletion. P-body formation was also induced by hydrochloric acid and sulfuric acid. However, lactic acid in SD (synthetic dextrose) medium with a pH greater than 3.0, propionic acid and acetic acid did not induce P-body formation. The results of the present study suggest that the assembly of yeast P-bodies can be induced by external conditions with a low pH and the threshold was around pH 2.5. The P-body formation upon acidic stress required Scd6 (suppressor of clathrin deficiency 6), a component of P-bodies, indicating that P-bodies induced by acidic stress have rules of assembly different from those induced by glucose deprivation or high Ca2+ levels.
Existence of memory in membrane channels: analysis of ion current through a voltage‐dependent potassium single channel
Authors: Peng Zhang‐Yan , Lan Tong‐Han , Yang Lei , Mei Hu Chao , Ping Jia Hua , Jie Xu Yong , Lin Che Xiang 
Published: June 2012

AbstractIon current fluctuation of voltage‐dependent potassium channel in LβT2 cells has been investigated by autocorrelation function and DFA (detrended fluctuation analysis) methods. The calculation of the autocorrelation function exponent and DFA exponent of the sample was based on the digital signals or the 0–1 series corresponding to closing and opening of channels after routine evolution, rather than the sequence of sojourn times. The persistent character of the correlation of the time series was evident from the slow decay of the autocorrelation function. DFA exponent α was significantly greater than 0.5. The main outcome has been the demonstration of the existence of memory in this ion channel. Thus, the ion channel current fluctuation provided information about the kinetics of the channel protein. The result suggests the correlation character of the ion channel protein non‐linear kinetics indicates whether the channel is open or not.
Genomics-aided structure prediction
Authors: Sułkowska Joanna I. , Morcos Faruck , Weigt Martin , Hwa Terence , Onuchic José N. 
Published: June 2012

We introduce a theoretical framework that exploits the ever-increasing genomic sequence information for protein structure prediction. Structure-based models are modified to incorporate constraints by a large number of non-local contacts estimated from direct coupling analysis (DCA) of co-evolving genomic sequences. A simple hybrid method, called DCA-fold, integrating DCA contacts with an accurate knowledge of local information (e.g., the local secondary structure) is sufficient to fold proteins in the range of 1–3 Å resolution.
Coastal migrations, temporary use of neighbouring rivers, and growth of sea trout (Salmo trutta) from nine northern Baltic Sea rivers
Authors: Degerman Erik , Leonardsson Kjell , Lundqvist Hans 
Published: June 2012

Abstract
Degerman, E., Leonardsson, K., and Lundqvist, H. 2012. Coastal migrations, temporary use of neighbouring rivers, and growth of Sea trout (Salmo trutta) from nine northern Baltic Sea rivers – ICES Journal of Marine Science, 69: 971–980. The wild migratory trout (Salmo trutta) stocks in the northern Baltic Sea are threatened, and the fishery is thought to play a significant role in the population decline. Therefore, knowledge about the migration patterns of these stocks is needed to develop appropriate management plans. For this reason, we analysed the movement pattern from recaptures of mandatory releases of tagged hatchery-reared trout smolt from nine rivers in the region (1998–2007). The median time from release until recapture was 366 days, and the median migration distance at recapture was 27 km, with a dominating southward direction for northern stocks. Most of the recaptured fish were immature (65%), and recaptures in rivers (55%) dominated over recaptures along the coast (44%). Riverine recaptures were most frequent during autumn–spring. A total of 16% of all recaptures in rivers occurred in non-natal rivers. Straying was about twice as frequent among fish from small rivers as from large rivers. The results from the river Gideälven indicate that using broodstock from other rivers in stocking programmes may lead to a high proportion of strayers. In addition, temporary use of neighbouring rivers was more frequent in large rivers during winter. Growth, in terms of length increment, was high, especially in fish from southern parts of the Baltic, and higher than in neighbouring warmer and more saline sea areas.
Introduction to variability of the North Atlantic and its marine ecosystems, 2000–2009, the proceedings of an ICES/NAFO symposium held in Santander, Spain, 10–12 May 2011
Authors: Wiebe Peter H. , Rudels Bert , Cadrin Steven X. , Drinkwater Ken F. , Lavin Alicia 
Published: June 2012

Abstract
Wiebe, P. H., Rudels, B., Cadrin, S. X., Drinkwater, K. F., and Lavin, A. 2012. Introduction to Variability of the North Atlantic and its marine ecosystems, 2000–2009, the proceedings of an ICES/NAFO symposium held in Santander, Spain, 10–12 May 2011. – ICES Journal of Marine Science, 69: 697–702. An international symposium on decadal changes in the International Council for the Exploration of the Sea (ICES) and North Atlantic Fisheries Organization (NAFO) regions of the North Atlantic from 2001 to 2009, jointly sponsored by ICES and NAFO, took place in Santander, Spain, from 10 to 12 May 2011. During the period covered by the symposium, the upper ocean warmed, particularly in temperate and Arctic–boreal regions, and there were major biogeographic shifts and changes in the phenology of the biota that appear to be related to the physical changes.
Target strength and tilt-angle distribution of the lesser sandeel (Ammodytes marinus)
Authors: Kubilius Rokas , Ona Egil 
Published: June 2012

Abstract
Kubilius, R., and Ona, E. 2012. Target strength and tilt-angle distribution of lesser sandeel (Ammodytes marinus) – ICES Journal of Marine Science, 69: 1099–1107. North Sea stocks of lesser sandeel have recently become depleted, and improved methods for abundance estimation are sought. This paper focuses on the acoustic target strength (TS) and orientation of sandeel, measured simultaneously in several field experiments. A specially designed cubic cage, fitted with an echosounder and a video camera, was lowered onto the sea bottom, trapping wild sandeel inside. Methods for manually selecting valid echotraces from individual sandeel are described. Scattered mean TS values from several experiments are reported. These are, in spite of the observed variability, summarized in a TS–fish length (cm) relationship as TS = 20logL – 93.1 (dB) at 200 kHz. We believe that the accuracy of the relationship may still be debated; incorporating larger uncertainty in the overall mean TS will increase the total uncertainty of the stock biomass estimate from sandeel acoustic surveys. This uncertainty is now, using standard narrow-beam echosounders, dominated by the fish patchiness relative to the survey coverage. Results from pilot investigations of the sandeel swimming orientation using video cameras are also presented, showing that sandeel usually has an anguilliform swimming pattern with substantial positive (head-up) tilt. The spread of the tilt-angle distribution is also larger than for more neutrally buoyant fishes.
Exemplifying a Dispositional Approach to Cross-Cultural Spiral of Silence Research: Fear of Social Isolation and the Inclination to Self-Censor
Authors: Matthes Jörg , Hayes Andrew F. , Rojas Hernando , Shen Fei , Min Seong-Jae , Dylko Ivan B. 
Published: June 2012

Abstract
This article tests the cross-cultural generality of one tenet of spiral of silence theory using an individual difference approach. We argue that the spiral of silence phenomenon is, in part, a manifestation of individual differences in stable personality traits that can be measured universally regardless of country or context—specifically, fear of social isolation (FSI) and willingness to self-censor. In accordance with the theory’s predictions, we examine whether people relatively high in trait FSI are more likely to self-censor their opinions in hostile opinion environments than low FSI individuals. We tested this hypothesis using data from an international online sample of over 2,200 participants spread across four continents and nine countries. Results of partially measurement-invariant multigroup confirmatory factor analyses confirmed the prediction in all countries except for China.
Estimation of the Contribution of Norketamine to Ketamine-induced Acute Pain Relief and Neurocognitive Impairment in Healthy Volunteers
Authors: Olofsen Erik , Noppers Ingeborg , Niesters Marieke , Kharasch Evan , Aarts Leon , Sarton Elise , Dahan Albert 
Published: June 2012

Background
The N-methyl-D-aspartate receptor antagonist ketamine is metabolized in the liver into its active metabolite norketamine. No human data are available on the relative contribution of norketamine to ketamine-induced analgesia and side effects. One approach to assess the ketamine and norketamine contributions is by measuring the ketamine effect at varying ketamine and norketamine plasma concentrations using the CYP450 inducer rifampicin.

Methods
In 12 healthy male volunteers the effect of rifampicin versus placebo pretreatment on S-ketamine-induced analgesia and cognition was quantified; the S-ketamine dosage was 20 mg/h for 2 h. The relative ketamine and norketamine contribution to effect was estimated using a linear additive population pharmacokinetic-pharmacodynamic model.

Results
S-ketamine produced significant analgesia, psychotropic effects (drug high), and cognitive impairment (including memory impairment and reduced psychomotor speed, reaction time, and cognitive flexibility). Modeling revealed a negative contribution of S-norketamine to S-ketamine- induced analgesia and absence of contribution to cognitive impairment. At ketamine and norketamine effect concentrations of 100 ng/ml and 50 ng/ml, respectively, the ketamine contribution to analgesia is -3.8 cm (visual analog pain score) versus a contribution of norketamine of +1.5 cm, causing an overall effect of -2.3 cm. The blood-effect site equilibration half-life ranged from 0 (cognitive flexibility) to 11.8 (pain intensity) min and was 6.1 min averaged across all endpoints.

Conclusions
This first observation that norketamine produces effects in the opposite direction of ketamine requires additional proof. It can explain the observation of ketamine-related excitatory phenomena (such as hyperalgesia and allodynia) upon the termination of ketamine infusions.
The impact of seed head age and orientation on seed release thresholds
Authors: Borger Catherine P. D. , Renton Michael , Riethmuller Glen , Hashem Abul 
Published: June 2012

Summary1.It has been established that the timing of abscission has a major impact on the dispersal distances achieved by individual seeds, and yet there is little information available on seed release thresholds.2.The current research usedConyza bonariensisto examine seed release thresholds of seed heads at varying ages and at varying orientations (in relation to the direction of the air flow).3.Wind speeds of 0–70 m s−1were used to remove the seeds from seed heads harvested directly prior to exposure to wind. Seed head age at the time of harvest from the plant (0–10 days old, where day 0 is the day on which the seed head opens) and seed head orientation (in relation to the direction of air) were altered.4.While seed loss increased with increasing wind speed, average loss from seed heads increased from 49·4% on the day they opened to 92·8% from seed heads open for 10 days. Further, there was an average seed loss of 76·4%, 72·5%, 73·9%, 65·3% and 58·8% for wind orientations of 0, 45, 90, 135 and 180°, where 0° indicates wind directed up towards the base of the hemispherical seed head (simulating an updraft), 90° indicate wind directed towards the side of the seed head (horizontal wind) and 180° indicate wind directed down towards the top of the seed head (simulating a downdraft).5.Seeds were released in the strongest wind events and were more likely to be released in updrafts or horizontal winds rather than downdrafts. Both of these factors interact with seed aging in a way that will increase the potential dispersal distance. Given that minor changes to abscission can have major impacts on maximum dispersal distance; these factors need to be taken into account when formulating models on dispersal.6.This research supports the theory that where greater dispersal confers an evolutionary advantage, wind‐dispersed plants would be likely to evolve strategies to ensure maximum dispersal capability.
Expression and significance of stem cell markers in pulmonary sclerosing haemangioma
Authors: Lin Xu‐Yong , Fan Chui‐Feng , Dong Xin‐Jun , Yu Juan‐Han , Dai Shun‐Dong , Wang En‐Hua 
Published: June 2012

Lin X‐Y, Fan C‐F, Dong X‐J, Yu J‐H, Dai S‐D & Wang E‐H  (2012) Histopathology 61, 178–185  Expression and significance of stem cell markers in pulmonary sclerosing haemangiomaAims:  The two major types of cells of pulmonary sclerosing haemangioma (PSH) with the same origin show significant differences in morphological phenotype. Whether these differences are caused by their different differentiation status is still uncertain. The aim of this study was to analyse their differentiation status by detecting the expression of several stem cell markers in PSH.Methods and results:  The expression of stem cell markers was examined by using streptavidin peroxidase (SP) immunohistochemisty in 45 PSH specimens. Also, the two types of cells were, respectively, captured by laser capture microdissection (LCM) from 28 PSH specimens, and total RNA was then extracted followed by reverse transcription–polymerase chain reaction (RT–PCR). The results demonstrated that the expression rates of ABCG2, Notch1 and Notch3 in polygonal cells were significantly higher than those in cuboidal cells (P < 0.05), and the expression levels of ABCG2, Notch3 and Jagged1 in polygonal cells were clearly higher than those in cuboidal cells (P < 0.05).Conclusion:  The data obtained provided evidence that the two types of cells in PSH may be different in differentiation status. The differentiation difference between the two types of cells might lead to variation in their morphological phenotype.
Nodal cytotoxic molecule (CM)‐positive Epstein–Barr virus (EBV)‐associated peripheral T cell lymphoma (PTCL): a clinicopathological study of 26 cases
Authors: Kato Seiichi , Takahashi Emiko , Asano Naoko , Tanaka Tsutomu , Megahed Nirmeen , Kinoshita Tomohiro , Nakamura Shigeo 
Published: June 2012

Kato S, Takahashi E, Asano N, Tanaka T, Megahed N, Kinoshita T & Nakamura S  (2012) Histopathology 61, 186–199Nodal cytotoxic molecule (CM)‐positive Epstein–Barr virus (EBV)‐associated peripheral T cell lymphoma (PTCL): a clinicopathological study of 26 casesAims:  The clinicopathological distinctiveness of nodal cytotoxic molecule (CM)‐positive Epstein–Barr virus (EBV)‐associated peripheral T cell lymphoma (PTCL) remains to be clarified. We investigated 26 patients with this lymphoma compared to nodal CM+ EBV− PTCL (n = 39) and extranasal natural killer/T cell lymphoma of nasal type (ENKTL, n = 44).Methods and results:  Nodal CM+ EBV+ PTCL patients were more likely to have B symptoms (P = 0.019) and hepatic involvement (P = 0.026) than nodal CM+ EBV− PTCL patients. The former also had more Stage III/IV disease (P = 0.025) but much less cutaneous involvement (P < 0.001) than ENKTL patients at diagnosis. This nodal EBV+ lymphoma possessed a distinctive immunophenotype of high CD8+, CD56− pattern with an aggressive clinical course (median, 6.6 months). Thrombocytopenia was present in 11 (50%) patients and found to be the strongest prognostic indicator (P = 0.001) in this nodal EBV+ group. For all nodal CM+ PTCL cases CD5 negativity, but not EBV positivity, was the significant adverse prognostic factor (P < 0.002) in a multivariate analysis, independent of prognostic index for PTCL (PIT) or International Prognostic Index (IPI) scores.Conclusions:  Nodal CM+ EBV+ PTCL constitutes a unique group of lymphomas distinct from ENKTL. The data provide support for our assertion that nodal CM+ PTCL should be distinguished in the 2008 WHO category of PTCL, not otherwise specified.
Expression of vascular endothelial growth factor and vascular endothelial growth factor receptors 1 and 2 in invasive breast carcinoma: prognostic significance and relationship with markers for aggressiveness
Authors: Dhakal Hari Prasad , Naume Bjørn , Synnestvedt Marit , Borgen Elin , Kaaresen Rolf , Schlichting Ellen , Wiedswang Gro , Bassarova Assia , Holm Ruth , Giercksky Karl‐Erik , Nesland Jahn M 
Published: June 2012

Dhakal H P, Naume B, Synnestvedt M, Borgen E, Kaaresen R, Schlichting E, Wiedswang G, Bassarova A, Holm R, Giercksky K‐E & Nesland J M  (2012) Histopathology 61, 350–364Expression of vascular endothelial growth factor and vascular endothelial growth factor receptors 1 and 2 in invasive breast carcinoma: prognostic significance and relationship with markers for aggressivenessAims:  Vascular endothelial growth factor (VEGF), VEGF receptor 1 (VEGFR‐1) and VEGF receptor 2 (VEGFR‐2) play a role in breast cancer growth and angiogenesis. We examined the expression and relationship with clinical outcome and other prognostic factors.Methods and results:  Tumour sections from 468 breast cancer patients were immunostained for VEGF, VEGFR‐1, and VEGFR‐2, and their relationships with tumour vascularity, disseminated tumour cells (DTCs) in bone marrow and other clinicopathological parameters were evaluated. VEGF, VEGFR‐1 and VEGFR‐2 immunoreactivities were observed in invasive breast carcinoma cells. VEGF expression was significantly associated with VEGFR‐1 and VEGFR‐2 expression (P < 0.001). High‐level cytoplasmic expression of VEGFR‐1 was associated with significantly reduced distant disease‐free survival (DDFS) (P = 0.017, log‐rank) and breast cancer‐specific survival (BCSS) (P = 0.005, log‐rank) for all patients, and for node‐negative patients without systemic treatment (DDFS, P = 0.03, log‐rank; BCSS, P = 0.009, log‐rank). VEGFR‐1 expression was significantly associated with histopathological markers of aggressiveness (P < 0.05). Significantly reduced survival was observed in DTC‐positive patients as compared with DTC‐negative patients in the combined moderate/high VEGFR‐1 group (P < 0.001 for DDFS and BCSS), and the same was true for DDFS in the moderate VEGFR‐2 group (P = 0.006).Conclusions:  High‐level expression of VEGFR‐1 indicates reduced survival. Higher‐level expression of VEGFR‐1 or VEGFR‐2 in primary breast carcinomas combined with the presence of DTC selects a prognostically unfavourable patient group.
Boldness in two perch populations – long‐term differences and the effect of predation pressure
Authors: Magnhagen Carin , Hellström Gustav , Borcherding Jost , Heynen Martina 
Published: June 2012

Summary1. Populations of the same species often display different behaviours, for example, in their response to predators. The question is whether this difference is developed as part of a divergent selection caused by differences in predation pressure, or as a result of phenotypic responses to current environmental conditions.2. Two populations of Eurasian perch were investigated over a time span of 6 years to see whether risk‐taking behaviour in young‐of‐the‐year perch were consistent across cohorts, or if behaviour varied over time with changes in predation regime.3. Boldness was estimated in aquarium studies by looking at how the fish made trade‐offs between foraging in a risky area and staying in shelter. Predation risk of each year and lake was estimated from fishing surveys, using an individual‐based model calculating attack rates for cannibalistic perch.4. The average boldness scores were consistently lower in perch from Fisksjön compared with those in Ängersjön, although the magnitude of the difference varied among years. Variance component analyses showed that differences between lakes in boldness scores only explained 12 per cent of the total variation. Differences between years were contributing at least similarly or more to the total variance, and the variation was higher in Fisksjön than in Ängersjön.5. The observed risk‐taking behaviour of young‐of‐the‐year perch, compared across cohorts, was significantly correlated with the year‐specific estimates of cannibalistic attack rates, with lower boldness scores in years with higher predation pressure. In Fisksjön, with significant changes over the years in population structure, the range of both predation risk and boldness scores was wider than in Ängersjön.6. By following the two perch populations over several years, we have been able to show that the differences in risk‐taking behaviour mainly are due to direct phenotypic responses to recent experience of predation risk. Long‐term differences in behaviour among perch populations thus reflect consistent differences in predation regime rather than diverging inherent traits.