bluuebunny/crossref_metadata_2025 huggingface dataset:
THE INFLUENCE OF VARIABLE HABITAT SUITABILITY CRITERIA ON PHABSIM HABITAT INDEX RESULTS
Authors: Ayllón D. , Almodóvar A. , Nicola G.G. , Elvira B.
Published: March 2011

The Physical Habitat Simulation System (PHABSIM) still probably remains as the most widespread habitat method used to establish inflow standards or to link habitat temporal variations with fish population dynamics. However, statistical uncertainties around the PHABSIM main output, the weighted usable area (WUA) over discharge curves, are usually ignored. Here, we assess the uncertainty in WUA curves and derived habitat duration curves induced by the variability around the PHABSIM biological model, the habitat suitability criteria, using brown trout Salmo trutta as the model species. Bootstrap analyses showed that the uncertainty around the WUA curves was rather high when bootstrap sample (BS) size was low and differed among age classes, being generally lower for young‐of‐the‐year (YOY). Width of 95% confidence intervals for maximum WUA magnitude increased with decreasing BS size, ranging from 19.3% for YOY trout at the largest BS size (40 transects, 270 habitat use observations) to 146% for juveniles at the smallest BS size (nine transects, 60 habitat use observations). The uncertainty arose primarily from the construction of the channel index variable. Nevertheless, results showed that the uncertainty in WUA values could be reduced down to acceptable levels by using general functional channel index categories. Likewise, the shape of WUA curves was also highly variable when BS was small. These patterns resulted in habitat duration curves being highly uncertain, much more in their amplitude than in their shape. Uncertainty about the flows corresponding to different habitat exceedance values increased with decreasing probability of exceedance. Width of peak flow confidence intervals ranged from 3.3% for YOY trout at the largest BS size to 226% for adults at the smallest BS size. Yet such levels of uncertainty do not necessarily entail critical errors in the decision‐making process because large variability in flow peak does not necessarily lead to large variability in WUA magnitude.
Brief overview of symbolic data and analytic issues
Authors: Billard L.
Published: March 2011

With the advent of contemporary computers, datasets can be massively huge, too large for direct analysis. One of the many approaches to this problem of size is to aggregate the data according to some appropriate scientific question of interest, with the resulting dataset perforce being one with symbolic‐valued observations such as lists, intervals, histograms, and the like. Other datasets, small or large, are naturally symbolic in nature. One aim here is to provide a brief nontechnical overview of symbolic data and discuss how they arise. We also provide brief insights into some of the issues that arise in their analyses. These include the need to take into account the internal variations inherent in symbolic data but not present in classical data. Another issue is that, by the nature of the aggregation, resulting datasets can contain “holes” or regions that are not possible; thus, accommodation for these need to be taken into account, when, e.g. seemingly interval data are actually some other form of symbolic data (such as histogram data). Also, we show how other forms of complex data differ from symbolic data; so, e.g. fuzzy data are a different domain than that for symbolic data. Finally, we look at further research needs for the subject. A more technical introduction to symbolic data and available analytic methodology is given by Noirhomme and Brito. © 2011 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 4: 149–156, 2011
p,p'‐DDE induces apoptosis and mRNA expression of apoptosis‐associated genes in testes of pubertal rats
Authors: Shi Yu‐Qin , Li Hao‐Wen , Wang Yu‐Ping , Liu Chang‐Jiang , Yang Ke‐Di
Published: March 2011

One,1‐dichloro‐2,2 bis(p‐chlorophenyl) ethylene (p,p'‐DDE), the major metabolite of 2,2‐bis(4‐chlorophenyl)‐1,1,1‐trichloroethane (DDT), is a known persistent organic pollutant and male reproductive toxicant. It has antiandrogenic effect. However, the mechanism by which p,p'‐DDE exposure causes male reproductive toxicity remains unknown. To elucidate the mechanism underpinning the testicular effects of p,p'‐DDE, we sought to investigate apoptotic effects and mRNA expression of apoptosis‐associated genes in the testis of pubertal rats, including Fas, FasL, calpain‐1, cytochrome c, Bax, Bcl‐w, Bak, and caspase‐3, ‐8, ‐9, ‐12. Animals were administered with different doses of p,p'‐DDE (0, 20, 60, 100 mg/kg body weight) every other day by intraperitoneal injection for 10 days. The results indicated that p,p'‐DDE exposure at over 20 mg/kg body weight showed the induction of apoptotic cell death. p,p'‐DDE could induce decrease in SOD and GSH‐Px activity of serum in 60 mg/kg body weight group. Significant elevations in the mRNA levels of Fas, FasL, calpain‐1, cytochrome c, Bax, Bak, and caspase‐3, ‐8, ‐9, ‐12 were observed in testis of rat treated with p,p'‐DDE. Taken together, these results lead us to speculate that in vivo exposure to p,p'‐DDE might induce testicular apoptosis in pubertal rats through the involvement of Fas/FasL, mitochondria and endoplasmic reticulum‐mediated pathways. © 2011 Wiley Periodicals, Inc. Environ Toxicol 2013.
Chromium(III) oxide nanoparticles induced remarkable oxidative stress and apoptosis on culture cells
Authors: Horie Masanori , Nishio Keiko , Endoh Shigehisa , Kato Haruhisa , Fujita Katsuhide , Miyauchi Arisa , Nakamura Ayako , Kinugasa Shinichi , Yamamoto Kazuhiro , Niki Etsuo , Yoshida Yasukazu , Iwahashi Hitoshi
Published: March 2011

Chromium(III) oxide (Cr2O3) is used for industrial applications such as catalysts and pigments. In the classical form, namely the fine particle, Cr2O3 is insoluble and chemically stable. It is classified as a low‐toxicity chromium compound. Recently, industrial application of nanoparticles (a new form composed of small particles with a diameter of ≤100 nm, in at least one dimension) has been increasing. Cellular effects induced by Cr2O3 nanoparticles are not known. To shed light upon this, the release of soluble chromium from Cr2O3 nano‐ and fine‐particles in culture medium was compared. Fine Cr2O3 particles were insoluble in the culture medium; on the contrary, Cr2O3 nanoparticles released soluble hexavalent chromium into the culture medium. Cr2O3 nanoparticles showed severe cytotoxicity. The effect of Cr2O3 nanoparticles on cell viability was higher than that of fine particles. Cr2O3 nanoparticles showed cytotoxicity equal to that of hexavalent chromium (K2Cr2O7). Human lung carcinoma A549 cells and human keratinocyte HaCaT cells showed an increase in intracellular reactive oxygen species (ROS) level and activation of antioxidant defense systems on exposure to Cr2O3 nanoparticles. Exposure of Cr2O3 nanoparticles led to caspase‐3 activation, showing that the decrease in cell viability by exposure to Cr2O3 nanoparticles was caused by apoptosis. Cellular responses were stronger in the Cr2O3 nanoparticles‐exposed cells than in fine Cr2O3‐ and CrCl3‐exposed cells. Cellular uptake of Cr2O3 particles were observed in nano‐ and fine‐particles. The cellular influence of the extracellular soluble trivalent chromium was lower than that of Cr2O3 nanoparticles. Cr2O3 nanoparticles showed cytotoxicity by hexavalent chromium released at outside and inside of cells. The cellular influences of Cr2O3 nanoparticles matched those of hexavalent chromium. In conclusion, Cr2O3 nanoparticles have a high cytotoxic potential. © 2011 Wiley Periodicals, Inc. Environ Toxicol 2013.
Clinical Outcome and Management of Ureteral Obstruction Secondary to Gastric Cancer
Authors: Migita Kazuhiro , Watanabe Akihiko , Samma Shoji , Ohyama Takao , Ishikawa Hirofumi , Kagebayashi Yoriaki
Published: March 2011

Background

The clinical outcome of ureteral obstruction secondary to gastric cancer remains unclear. The present study was designed to evaluate the clinical outcome and predictive factors of survival in patients with ureteral obstruction secondary to gastric cancer.

Methods

Twenty‐five consecutive patients with ureteral obstruction secondary to gastric cancer between January 1998 and December 2007 were retrospectively analyzed. All patients had hydronephrosis; 13 patients had bilateral hydronephrosis, and 12 patients had unilateral hydronephrosis.

Results

Ten patients presented with pain, 3 patients with urinary tract infection, and 2 patients with acute renal failure. Seven (58%) of 12 patients with unilateral ureteral obstruction experienced progression to bilateral ureteral obstruction during the follow‐up period. Eighteen patients (61%) were eventually managed with urinary diversion. In total, 5 patients were managed with percutaneous nephrostomy, and 15 patients with retrograde ureteral stenting. All symptomatic patients responded to urinary diversion. The overall median survival was 5.8 months, and the 6‐month and 1‐year survival rates were 48 and 32%, respectively. Chemotherapy was found to be the only independent predictor of survival (p = 0.0498). Median survival in patients who received chemotherapy was 11.2 months, in comparison to 3.1 months in patients who did not receive chemotherapy (p = 0.0002).

Conclusions

The prognosis of ureteral obstruction secondary to gastric cancer was extremely poor, particularly when chemotherapy was not administered. The indications for palliative urinary diversion should be determined after considering the patient’s symptoms, the expected survival time, the possibility of further chemotherapeutic options, and the current quality of life.
Transthoracic Versus Transhiatal Esophagectomy for Esophageal Carcinoma: Experience from a Single Tertiary Care Institution
Authors: Kawoosa Nadeem UlNazeer , Dar Abdul Majeed , Sharma Mukand Lal , Ahangar Abdul Gani , Lone Ghulam Nabi , Bhat Mohammad Akbar , Singh Shyam
Published: March 2011

Background

There is a lot of controversy about the best surgical treatment for esophageal carcinoma.

Methods

In this retrospective study, 382 patients with carcinoma of the mid‐to‐distal esophagus underwent transthoracic or transhiatal esophagectomy. Early morbidity and mortality were compared. Principal endpoints were disease‐free survival (DFS) and overall survival (OS).

Results

A total of 177 patients underwent transthoracic esophagectomy, and 205 patients underwent transhiatal esophagectomy. Demographic characteristics and characteristics of the tumor were similar in the two groups. Perioperative and postoperative morbidity was higher after transhiatal esophagectomy. In‐hospital mortality was also higher after transhiatal esophagectomy. The median follow‐up was 4.3 years. Estimated 3‐year DFS rates were 44.63 and 31.21%, whereas the 3‐year OS rates were 57.06 and 41.46% for the transthoracic and transhiatal groups, respectively (statistically significant). Also, the estimated 5‐year DFS rates were 26.55 and 21.46%, whereas the 5‐year OS rates were 32.76 and 30.24% for the transthoracic and transhiatal groups, respectively (statistically not significant).

Conclusions

Transhiatal esophagectomy was associated with higher perioperative and postoperative morbidity and in‐hospital mortality than transthoracic esophagectomy. The DFS and OS were higher in the transthoracic group and were statistically significant at 3 years but statistically insignificant at 5 years.
Laparoscopic Treatment of Crohn’s Disease
Authors: Fichera Alessandro
Published: March 2011

The surgical and medical management of inflammatory bowel disease (IBD) has significantly evolved over the course of the last two decades. On the medical side, the introduction of biologic therapy has significantly changed the characteristics of the patients undergoing surgery for Crohn’s disease (CD), while its impact on the need for surgical intervention and the surgical outcomes of these patients is still debated. On the surgical side, the introduction of and the growing experience with minimally invasive approaches to IBD have had a significant impact on outcomes and quality of life in this patient population. During the past three decades the evidence has been accumulating in favor of a minimally invasive approach to CD. Clearly, this is probably one of the most challenging diseases to treat laparoscopically for the colorectal surgeon, especially when the disease is located in the colon and involves multiple segments.
From glycosylation disorders to dolichol biosynthesis defects: a new class of metabolic diseases
Authors: Cantagrel Vincent , Lefeber Dirk J.
Published: March 2011

Polyisoprenoid alcohols are membrane lipids that are present in every cell, conserved from archaea to higher eukaryotes. The most common form, alpha‐saturated polyprenol or dolichol is present in all tissues and most organelle membranes of eukaryotic cells. Dolichol has a well defined role as a lipid carrier for the glycan precursor in the early stages of N‐linked protein glycosylation, which is assembled in the endoplasmic reticulum of all eukaryotic cells. Other glycosylation processes including C‐ and O‐mannosylation, GPI‐anchor biosynthesis and O‐glucosylation also depend on dolichol biosynthesis via the availability of dolichol‐P‐mannose and dolichol‐P‐glucose in the ER. The ubiquity of dolichol in cellular compartments that are not involved in glycosylation raises the possibility of additional functions independent of these protein post‐translational modifications. The molecular basis of several steps involved in the synthesis and the recycling of dolichol and its derivatives is still unknown, which hampers further research into this direction. In this review, we summarize the current knowledge on structural and functional aspects of dolichol metabolites. We will describe the metabolic disorders with a defect in known steps of dolichol biosynthesis and recycling in human and discuss their pathogenic mechanisms. Exploration of the developmental, cellular and biochemical defects associated with these disorders will provide a better understanding of the functions of this lipid class in human.
The impact of mass spectrometry in the diagnosis of congenital disorders of glycosylation
Authors: Sturiale Luisa , Barone Rita , Garozzo Domenico
Published: March 2011

Contribution of mass spectrometry (MS) in the diagnosis and characterization of congenital disorders of glycosylation (CDG) has long been known. CDG type I diseases are characterized by the under‐occupancy of protein N‐glycosylation sites. Electrospray (ESI) MS and matrix assisted laser desorption ionization (MALDI) MS are effective for underglycosylation analyses of intact serum Transferrin (Tf) in CDG‐I patients by mass determination of individual component glycoforms. Thus, high‐throughput methods developed to speed‐up analytical times found increasing application in clinical testing for CDG detection. ESI MS recognizable glycoform profiles of serum Tf have been reported in CDG‐I different from PMM2‐CDG and in individual CDG‐II defects. MALDI MS analysis of acidic and neutral N‐linked glycans released from total plasma or targeted glycoproteins, is the mainstream tool to explore abnormal oligosaccharide structure and changes in the relative amount of individual oligosaccharides in CDG‐II patients. Here we briefly review state‐of‐the‐art and updates of MS‐based applications for the diagnosis of CDG with special emphasis to detectable glycosylation profiles reported in different CDG types.
A Functional Outcomes Survey of Elderly Patients who Sustained Distal Radius Fractures
Authors: Amorosa Louis F. , Vitale Mark A. , Brown Shervondalonn , Kaufmann Robert A.
Published: March 2011

Purpose

This study aims to examine the subjective functional outcomes of patients 70 years or older who sustained distal radius fractures through the use of the Disability of the Arm, Shoulder, and Hand (DASH) and Short Form-8 Health (SF-8) surveys.

Methods

Patients at least 70 years old with a distal radius fracture between 2000 and 2004 were identified and their charts reviewed. They were contacted to answer the DASH and SF-8 surveys. The radiographic injury parameters examined were articular stepoff greater than 2 mm, dorsal tilt on the lateral radiograph, ulnar variance, and presence of an ulnar styloid fracture.

Results

Fifty-eight patients answered the DASH and SF-8 surveys. The mean age at the time of injury in the survey group was 78 years old (range 70-94 years). Mean follow-up period was 33 months (range 13-65 months). Average DASH and SF-8 scores were 22.3 (SD 22.4) and 31.5 (SD 6.9), respectively. DASH scores were inversely correlated with SF-8 scores ( R=-0.65, p<0.01). Patients who sustained an associated ulnar styloid fracture demonstrated worse DASH scores than those without an ulnar styloid fracture (presence of ulnar styloid fracture: mean DASH 26.2, no ulnar styloid fracture: mean DASH 12.9, p=0.04). There were no significant differences in functional outcome for any other radiographic parameters assessed. Males had statistically better DASH scores than the females (males: mean DASH 6.9, females: mean DASH 24.4, p= 0.003). No difference was found in functional outcome scores among different treatment groups.

Conclusion

In elderly patients with distal radius fractures, the only radiographic parameter we found that affects functional outcome is an associated ulnar styloid fracture. Additionally, females had worse functional outcomes than males.
Spatial and temporal patterns of oxidative stress in the brain of gerbils submitted to different duration of global cerebral ischemia
Authors: Selakovic Vesna , Korenic Andrej , Radenovic Lidija
Published: March 2011

The present study was undertaken to examine spatial and temporal patterns of oxidative stress rate in the brain of Mongolian gerbils submitted to different duration of global ischemia/reperfusion. The common carotid arteries of gerbils were occluded for 5, 10, or 15 min. We followed the temporal ischemia‐induced oxidative stress rate, the most important factor that exacerbates brain damage by reperfusion, starting from 24 h up to 28 days after reperfusion. The spatial ischemia‐induced oxidative stress distribution was measured parallely in different brain regions: forebrain cortex, striatum, hippocampus and cerebellum. Post‐ischemic effects were followed in vivo by monitoring the neurological status of whole animals and at the intracellular level by standard biochemical assays in different brain regions. We measured superoxide production, superoxide dismutase activity, nitric oxide production, index of lipid peroxidation, and reduced glutathione. Our results revealed a pattern of dynamic changes in each oxidative stress parameter that corresponded with ischemia duration in all tested brain structures. The highest levels were obtained in the first 24 h after the insult. After that, they slowly returned to nearly control values 28 days after reperfusion (with the exception of SOD activity that returned to control values at fourth day after reperfusion). The most sensitive oxidative stress parameter was index of lipid peroxidation. Our study confirmed spatial distribution of ischemia‐induced oxidative stress. Tested brain structures showed different sensitivity to each oxidative stress parameter, although their basal levels were similar. These new findings could be valuable for creation and strategy of post‐ischemic therapy.
Synaptic changes in the brain of subjects with schizophrenia
Authors: Faludi Gábor , Mirnics Károly
Published: March 2011

Clinical, epidemiological, neuroimaging and postmortem data all suggest schizophrenia is a neurodevelopmental disorder, and that synaptic disturbances might play a critical role in developing the disease. In 1982, Feinberg proposed that the schizophrenia might arise as a result of abnormal synaptic pruning. His hypothesis has survived 40 years of accumulated data, and we review the critical findings related to synaptic dysfunction of schizophrenia. While it is clear that synaptic disturbances are integral and important for understanding the pathophysiology of schizophrenia, it has also become obvious that synaptic disturbances cannot be studied and understood as an independent disease hallmark, but only as a part of a complex network of homeostatic events. Development, glial–neural interaction, changes in energy homeostasis, diverse genetic predisposition, neuroimmune processes and environmental influences all can tip the delicate homeostatic balance of the synaptic morphology and connectivity in a uniquely individual fashion, thus contributing to the emergence of the various symptoms of this devastating disorder. Finally, we argue that based on a predominant change in gene expression pattern we can broadly sub‐stratify schizophrenia into “synaptic” “oligodendroglial”, “metabolic” and “inflammatory” subclasses.
Assessing civil society in Putin’s Russia: The plight of women’s crisis centers
Authors: Johnson Janet Elise , Saarinen Aino
Published: March 2011

The article assesses civil society in Putin’s Russia through the lens of the small social movement working against gender violence. Based on questionnaires distributed to movement organizations in 2008–2009, we find significant retrenchment among the NGO segment of the movement, adding evidence to the claim of Russia’s turn toward authoritarianism. However, this innovative, midlevel analysis–not the typical society-wide surveys nor the small number participant observation–also shows that the women’s crisis center movement has made some in-roads in transforming the state, revealing that some democratic opportunities remain at the local level.
A game-theoretic model for protest in the context of post-communism
Authors: Ash Konstantin
Published: March 2011

In recent years, large-scale protests have forced several incumbent governments in former Soviet countries from power. Scholarly examinations of these events have lacked a cohesive explanation of the reasons for the success of certain movements and the failure of others. This study uses prior research on the dynamics of protest to formulate a game-theoretic model for why protest takes place and how its eventual outcome comes about. The model is tested through logistic regression analyses of monthly protest data. The statistical analysis shows that elections, prior protests and government transgressions increase the likelihood of anti-government protests.
Vegetation history along the eastern, desert escarpment of the Sierra San Pedro Mártir, Baja California, Mexico
Authors: Holmgren Camille A. , Betancourt Julio L. , Rylander Kate A.
Published: March 2011

Plant macrofossils from 38 packrat middens spanning the last ~ 33,000 cal yr BP record vegetation between ~ 650 and 900 m elevation along the eastern escarpment of the Sierra San Pedro Mártir, northern Baja California. The middens span most of the Holocene, with a gap between ~ 4600 and 1800 cal yr BP, but coverage in the Pleistocene is uneven with a larger hiatus between 23,100 and 14,400 cal yr BP. The midden flora is relatively stable from the Pleistocene to Holocene. Exceptions includePinus californiarum,Juniperus californicaand other chaparral elements that were most abundant > 23,100 cal yr BP and declined after 14,400 cal yr BP. Despite being near the chaparral/woodland-desertscrub ecotone during glacial times, the midden assemblages reflect none of the climatic reversals evident in the glacial or marine record, and this is corroborated by a nearby semi-continuous pollen stratigraphy from lake sediments. Regular appearance of C4grasses and summer-flowering annuals since 13,600 cal yr BP indicates occurrence of summer rainfall equivalent to modern (JAS average of ~ 80–90 mm). This casts doubt on the claim, based on temperature proxies from marine sediments in the Guaymas Basin, that monsoonal development in the northern Gulf and Arizona was delayed until after 6200 cal yr BP.
Mississippi Valley regional source of loess on the southern Green Bay Lobe land surface, Wisconsin
Authors: Jacobs Peter M. , Mason Joseph A. , Hanson Paul R.
Published: March 2011

Loess has been recognized on the glacial land surface of the Green Bay Lobe for over 100 yr, but no systematic explanation of the source of the loess has been advanced. Intriguingly, the loess on the Green Bay Lobe land surface is thicker than predicted by regional thinning trends from the Mississippi Valley and is geographically separated from much loess of southwest Wisconsin by a sandy region devoid of loess. Mapping based on soil survey interpretation indicates that the loess occurs above an escarpment marking the eastern end of the sandy loess-free region. Particle size fining trends demonstrate that the loess was transported by northwesterly winds. Clay mineralogy of the Green Bay Lobe loess is distinctly different than glaciogenic sediments and matches loess of the Mississippi Valley, indicating a regional source and long distance transport of the loess. We propose the loess was transported from the regional source along a surface of transport produced by migration of eolian sand through low-relief landscapes including the glacial Lake Wisconsin basin. Eolian sand migration caused repeated entrainment of dust leading to east-southeastward transport. The loess accumulated above an escarpment that limited sand mobility and re-entrainment of loess beyond this topographic barrier.
Discovery, Identification and Comparative Analysis of Non-Specific Lipid Transfer Protein (nsLtp) Family in Solanaceae
Authors: Liu Wanfei , Huang Dawei , Liu Kan , Hu Songnian , Yu Jun , Gao Gang , Song Shuhui
Published: March 2011

Plant non-specific lipid transfer proteins (nsLtps) have been reported to be involved in plant defense activity against bacterial and fungal pathogens. In this study, we identified 135 (122 putative and 13 previously identified) Solanaceae nsLtps, which are clustered into 8 different groups. By comparing with Boutrot’s nsLtp classification, we classified these eight groups into five types (I, II, IV, IX and X). We compared Solanaceae nsLtps with Arabidopsis and Gramineae nsLtps and found that (1) Types I, II and IV are shared by Solanaceae, Gramineae and Arabidopsis; (2) Types III, V, VI and VIII are shared by Gramineae and Arabidopsis but not detected in Solanaceae so far; (3) Type VII is only found in Gramineae whereas type IX is present only in Arabidopsis and Solanaceae; (4) Type X is a new type that accounts for 52.59% Solanaceae nsLtps in our data, and has not been reported in any other plant so far. We further built and compared the three-dimensional structures of the eight groups, and found that the major functional diversification within the nsLtp family could be predated to the monocot/dicot divergence, and many gene duplications and sequence variations had happened in the nsLtp family after the monocot/dicot divergence, especially in Solanaceae.
A Multifunctional Lentiviral-Based Gene Knockdown with Concurrent Rescue that Controls for Off-Target Effects of RNAi
Authors: Feng Yunfeng , Nie Linghu , Thakur Meghna Das , Su Qin , Chi Zhenfen , Zhao Yongliang , Longmore Gregory D.
Published: March 2011

The efficient, stable delivery of siRNA into cells, and the appropriate controls for non-specific off-target effects of siRNA are major limitations to functional studies using siRNA technology. To overcome these drawbacks, we have developed a single lentiviral vector that can concurrently deplete endogenous gene expression while expressing an epitope-tagged siRNA-resistant target gene in the same cell. To demonstrate the functional utility of this system, we performed RNAi-depleted α-actinin-1 (α-ACTN1) expression in human T cells. α-ACTN1 RNAi resulted in inhibited chemotaxis to SDF-1α, but it can be completely rescued by concurrent expression of RNAi-resistant α-ACTN1 (rr-α-ACTN1) in the same cell. The presence of a GFP tag on rr-α-ACTN1 allowed for detection of appropriate subcellular localization of rr-α-ACTN1. This system provides not only an internal control for RNAi off-target effects, but also the potential tool for rapid structure-function analyses and gene therapy.
Similarity scaling and vorticity structure in high-Reynolds-number stably stratified turbulent wakes
Authors: DIAMESSIS PETER J. , SPEDDING GEOFFREY R. , DOMARADZKI J. ANDRZEJ
Published: March 2011

The mean velocity profile scaling and the vorticity structure of a stably stratified, initially turbulent wake of a towed sphere are studied numerically using a high-accuracy spectral multi-domain penalty method model. A detailed initialization procedure allows a smooth, minimum-transient transition into the non-equilibrium (NEQ) regime of wake evolution. A broad range of Reynolds numbers,Re= UD/ν ∈ [5 × 103, 105] and internal Froude numbers,Fr= 2U/(ND) ∈ [4, 64] (U,Dare characteristic velocity and length scales, andNis the buoyancy frequency) is examined. The maximum value ofReand the range ofFrvalues considered allow extrapolation of the results to geophysical and naval applications.

At higherRe, the NEQ regime, where three-dimensional turbulence adjusts towards a quasi-two-dimensional, buoyancy-dominated flow, lasts significantly longer than at lowerRe. AtRe= 5 × 103, vertical fluid motions are rapidly suppressed, but atRe= 105, secondary Kelvin–Helmholtz instabilities and ensuing turbulence are clearly observed up toNt≈ 100. The secondary motions intensify with increasing stratification strength and have significant vertical kinetic energy.

These results agree with existing scaling of buoyancy-driven shear onRe/Fr2and suggest that, in the field, the NEQ regime may last up toNt≈ 1000. At a given highRevalue, during the NEQ regime, the scale separation between Ozmidov and Kolmogorov scale is independent ofFr. This first systematic numerical investigation of stratified turbulence (as defined by Lilly,J. Atmos. Sci.vol. 40, 1983, p. 749), in a controlled localized flow with turbulent initial conditions suggests that a reconsideration of the commonly perceived life cycle of a stratified turbulent event may be in order for the correct turbulence parametrizations of such flows in both geophysical and operational contexts.
The action of waving cylindrical rings in a viscous fluid
Authors: NGUYEN HOA , ORTIZ RICARDO , CORTEZ RICARDO , FAUCI LISA
Published: March 2011

Dinoflagellates (Pfisteria piscicida) are unicellular micro-organisms that swim due to the action of two eucaryotic flagella: a trailing, longitudinal flagellum that propagates planar waves and a transverse flagellum that propagates helical waves. Motivated by the wish to understand the role of the transverse flagellum in dinoflagellate motility, we study the fundamental fluid dynamics of a waving cylindrical tube wrapped into a closed helix. Given an imposed travelling wave on the structure, we determine that the helical ring propels itself in the direction normal to the plane of the circular axis of the helix. The magnitude of this translational velocity is proportional to the square of the helix amplitude. Additionally, the helical ring exhibits rotational motion tangential to its axis. These calculated swimming velocities are consistent when using the method of regularized Stokeslets with prescribed wave kinematics, regularized Stokeslets with dynamic forcing and Lighthill's slender-body theory, except in cases where the slenderness parameter is not small. The translational velocity results are nearly indistinguishable using the three approaches, leading to the conjecture that the main contribution to this velocity at a cross-section is the far-field flow generated by the portion on the opposite side of the ring. The largest contribution to the rotational velocity at a cross-section comes from the cross-section itself and others nearby, thus the geometric details of the slender body have a larger effect on the results.
Drops climbing uphill on an oscillating substrate
Authors: BENILOV E. S. , BILLINGHAM J.
Published: March 2011

Recent experiments by Brunet, Eggers & Deegan (Phys. Rev. Lett., vol. 99, 2007, p. 144501 and Eur. Phys. J., vol. 166, 2009, p. 11) have demonstrated that drops of liquid placed on an inclined plane oscillating vertically are able to climb uphill. In the present paper, we show that a two-dimensional shallow-water model incorporating surface tension and inertia can reproduce qualitatively the main features of these experiments. We find that the motion of the drop is controlled by the interaction of a ‘swaying’ (odd) mode driven by the in-plane acceleration and a ‘spreading’ (even) mode driven by the cross-plane acceleration. Both modes need to be present to make the drop climb uphill, and the effect is strongest when they are in phase with each other.
Kinetic theory of the standard map in the localized weak-stochasticity regime
Authors: BALESCU R.
Published: March 2011

The well-known Chirikov–Taylor standard map is studied using the methods
of non-equilibrium statistical mechanics. It appears possible to simplify the
master equation whenever the stochasticity parameter is small and the initial density
profile is sharply localized in phase space: this defines the ‘localized weak-stochasticity’ (LWS) regime. The resulting equation of evolution of the density
profile involves a convolution in time. Its most conspicuous feature is the absence
of a ‘short’ intrinsic time scale: the memory time is infinite. The master equation
can therefore not be Markovianized as in usual kinetic theory (or as in the diffusive
regime of the standard map). Moreover, the initial value of the fluctuations influences
the rate of change of the density profile at all times. Quite unexpectedly, the
contributions of the two terms of the master equation to the density profile are of
the same order of magnitude. As a result, they practically cancel each other. It is
this curious feature that explains the suppression of the motion by the islands and
the KAM barriers that is well known from the study of individual standard map
orbits. The LWS approximation is valid for a limited time (which is very long when
the initial localization is very sharp).
John P. Dougherty: Some recollections
Authors: FARLEY DONALD T.
Published: March 2011

What follows are some personal recollections of John that I thought
might be of interest to some readers of this special issue of the Journal of Plasma
Physics.
Editorial
Authors: Cairns Alan , Infeld Eryk
Published: March 2011

This special issue marks the 65th birthday of John Dougherty, the founding
father of this Journal and its Editor for the first 27 years of its life. Since the
Journal is so much John's creation, we thought that it would not be appropriate
to let this occasion pass without recognition, and we are pleased that a number
of John's former students and a selection of people who have contributed
regularly to the Journal or have been Associate Editors have agreed to
contribute to this issue.

Most plasma physicists will probably associate John with at least three major
contributions to the subject. The first is his classic work with Don Farley on
scattering of electromagnetic waves from a plasma, and we are very pleased
that Don has written a short note about the genesis of this work and about his
collaboration with John. The second is his book on plasma physics written with
P. C. Clemmow, which, some 30 years after its publication, is still one of the best
available texts on some advanced aspects of the subject. It received the rare
accolade of being reprinted in the Addison-Wesley Advanced Book Classics
series 21 years after its first publication. Finally, there is his editorship of this
Journal, which he continued long after his own interests had shifted from
plasma physics to fundamental aspects of statistical mechanics. Under John's
stewardship, the Journal published papers on all aspects of plasma physics, but
perhaps became specially noted for thoughtful contributions to basic aspects of
the subject.

All readers who know John, whether as authors, visitors to Cambridge or in
any other capacity, will be aware of his friendliness and willingness to help
others. On behalf of the plasma physics community, we would like to pass on
to him our appreciation of his contribution, our congratulations on the occasion
of his 65th birthday and our best wishes for the future.
Stability of solitary-wave solutions to a modified Zakharov–Kuznetsov equation
Authors: MUNRO S. , PARKES E. J.
Published: March 2011

In the context of ion-acoustic waves in a magnetized plasma comprising
cold ions and non-isothermal electrons, small-amplitude, weakly nonlinear waves
have been shown previously by Munro and Parkes to be governed by a modified
version of the Zakharov–Kuznetsov equation. In this paper, we consider solitary
travelling-wave solutions to this equation that propagate along the magnetic field.
We investigate the initial growth rate γ(k) of a small transverse sinusoidal
perturbation of wavenumber k. The instability range is shown to be 0 < k < 3. We
use the multiple-scale perturbation method developed by Allen and Rowlands to
determine a consistent expansion of γ about k = 0 and k = 3. By combining these
results in the form of a Padé approximant, an analytical expression for γ is found
that is valid for 0 < k < 3. γ is also determined by using the variational method
developed by Bettinson and Rowlands. The two results for γ are compared with a
numerical determination.
Cyclotron effects on wave dispersion in pulsar plasmas
Authors: KENNETT M. P. , MELROSE D. B. , LUO Q.
Published: March 2011

Dispersion in an intrinsically relativistic, one-dimensional, electron–positron
pair plasma (a pulsar plasma) is treated exactly, generalizing earlier results
that applied in the low-frequency limit and that neglected the cyclotron resonance.
The general theory involves two additional relativistic plasma dispersion functions,
evaluated at the normal and anomalous Doppler resonances. These two functions
are associated with the non-gyrotropic and gyrotropic parts of the response respectively.
The functions are evaluated for bell-type and Jüttner distributions. Wave
dispersion is discussed for a non-gyrotropic pulsar plasma with a highly relativistic
Alfvén speed. Emphasis is placed on crossings of the light line, defined in terms
of the parallel phase velocity. Subluminal waves exist only for sufficiently small
angles of propagation, and are confined to frequencies below about the mean gyrofrequency of the relativistic particles.
Effect of pump depletion and self-focusing (hot spot) on stimulated Raman scattering in laser–plasma interaction
Authors: MAHMOUD SALEH T. , SHARMA R. P.
Published: March 2011

A three-dimensional study of the pump depletion and self-focusing
(hot spot) effect on stimulated Raman scattering (SRS) reflectivity is presented
within the paraxial-ray approximation. The reflectivity of SRS is observed to
exhibit a maximum value in the case of optimum SRS gain with pump
depletion. The reflectivity with pump depletion is less than without pump
depletion and is the usual three-wave interaction case. The effect of plasma
temperature on SRS reflectivity is also discussed.
First-order effects in time-dependent Petschek-type reconnection
Authors: ALEXEEV ILYA V. , SEMENOV VLADIMIR S. , BIERNAT HELFRIED K.
Published: March 2011

The model of time-dependent Petschek-type reconnection is extended
to take into account first-order corrections with respect to the reconnection rate.
The plasma velocity inside the outflow region turns out to be smaller than the
zero-order Alfvén velocity, and therefore strong reconnection is less effective in
plasma acceleration. The model is also applied to study the effect of incoming
waves on reconnection. We show that incoming waves of Alfvén type, carrying an
electric current that is antiparallel to the initial current in the sheet, increase the
reconnection rate and cause additional acceleration of the plasma, so that this wave
can be considered as a potential trigger.
Do adult emotional and behavioural outcomes vary as a function of diverse childhood experiences of the public care system?
Authors: Dregan A. , Brown J. , Armstrong D.
Published: March 2011

Background

Longitudinal data from the 1970 British Cohort Study were used to examine the long-term adult outcomes of those who, as children, were placed in public care.

Method

Multivariate logistic estimation models were used to determine whether public care and placement patterns were associated with adult psychosocial outcomes. Seven emotional and behavioural outcomes measured at age 30 years were considered: depression, life dissatisfaction, self-efficacy, alcohol problems, smoking, drug abuse, and criminal convictions.

Results

The analyses revealed a significant association between public care status and adult maladjustment on depression [odds ratio (OR) 1.74], life dissatisfaction (OR 1.45), low self-efficacy (OR 1.95), smoking (OR 1.70) and criminal convictions (OR 2.13).

Conclusions

Overall, the present study findings suggest that there are enduring influences of a childhood admission to public care on emotional and behavioural adjustment from birth to adulthood. Some of the associations with childhood public care were relatively strong, particularly with respect to depression, self-efficacy and criminal convictions.
‘A blow to the men in Pink’: The Royal Society for the Prevention of Cruelty to Animals and Opposition to Hunting in the Twentieth Century
Authors: TICHELAR MICHAEL
Published: March 2011

In 1976 the RSPCA finally adopted a policy of opposition to fox hunting and the shooting of birds for sport after a long history of highly controversial internal debate and external lobbying by pressure groups. This article explores the possible long-term historical reasons behind the change of policy. It seeks to begin to fill a gap in the historical literature and explain the changes in public opinion towards hunting that occurred during the course of the twentieth century by looking at key episodes in the history of the RSPCA up to the 1970s. It shows there was a decline in aristocratic dominance on the ruling council of the RSPCA after the 1920s, but other reasons for the change in policy included the increasing influence of an urban/metropolitan view of the countryside after the 1950s; changing public attitudes towards farmers, who had been traditional supporters of hunting; and the increasing importance of environmentalism and ecology after 1960. By the end of the twentieth century it was no longer possible to argue that hunting was an essential feature of rural society and culture, despite the continuing popularity and survival of fox hunting with hounds.
Will, Obligatory Ends and the Completion of Practical Reason: Comments on Barbara Herman'sMoral Literacy
Authors: Reath Andrews
Published: March 2011

This paper discusses three inter-related themes in Barbara Herman'sMoral Literacy– the idea that, for Kant, the will is a ‘norm-constituted power’ whose activity is guided by its own internal norm, that the obligatory ends are reasonably viewed as the ends of all rational choice, and that morality ‘completes’ practical reason or rational agency.
A New Kantian Response to Maxim-Fiddling
Authors: Sneddon Andrew
Published: March 2011

There has long been a suspicion that Kant's test for the universalizability of maxims can be easily subverted: instead of risking failing the test, design your maxim for any action whatsoever in a manner guaranteed to pass. This is the problem of maxim-fiddling. The present discussion of this problem has two theses:

1]

That extant approaches to maxim-fiddling are not satisfactory;

2]

That a satisfactory response to maxim-fiddling can be articulated using Kantian resources, especially the first two formulations of the categorical imperative.

This approach to maxim-fiddling draws our attention to a Kantian notion of an offence against morality itself that has largely been overlooked.
Surface Ocean–Lower Atmosphere Processes
Authors: Schultz Colin
Published: March 2011

No system exists in isolation, and the ocean is no different. Understanding the mechanics directing a system as complicated as the ocean takes an interdisciplinary effort and well‐controlled studies. The Surface Ocean–Lower Atmosphere Study (SOLAS) program is an international effort to make sense of the physical and biogeochemical interactions that take place between the air and the sea. Having scientists ready to dissect these interactions will be increasingly important as the world begins to consider deliberately manipulating the system in an attempt to combat climate change. The AGU Monograph Surface Ocean–Lower Atmosphere Processes, edited by Corinne Le Quéré and Eric S. Saltzman, looks at the increasingly important interactions occurring at the boundary between these two systems. In this interview, Eos talks to Corinne Le Quéré.
Absence of scavenger receptor A promotes dendritic cell‐mediated cross‐presentation of cell‐associated antigen and antitumor immune response
Authors: Guo Chunqing , Yi Huanfa , Yu Xiaofei , Hu Fanlei , Zuo Daming , Subjeck John R , Wang Xiang‐Yang
Published: March 2011

Given the primary expression of scavenger receptor A (SRA) or CD204 on antigen‐presenting cells, we investigate the immunoregulatory activities of SRA/CD204 in the context of cross‐presentation of cell‐associated antigen and the immunogenicity of dying tumor cells. Immunization with dying prostate cancer cells results in profoundly increased control of subsequently inoculated tumors in SRA/CD204 knockout mice. Using OVA‐expressing RM1 prostate tumor line (RM1‐OVA), we show for the first time that SRA absence greatly enhances dendritic cells (DCs)‐mediated cross‐presentation of OVA antigen derived from dying RM1 cells. While the phagocytic ability of DCs is not significantly impacted by the lack of SRA/CD204, DCs deficient in SRA/CD204 display increased expression of inflammatory cytokines and chemokines, as well as co‐stimulatory molecules upon interaction with dying RM1 cells, implicating a suppressive regulation of the functional activation of DCs by SRA/CD204. Further, SRA/CD204‐deficient DCs pulsed with dying RM1‐OVA cells are more effective than wild‐type counterparts in priming antigen‐specific T‐cell responses, resulting in improved control of RM1 tumor growth in both prophylactic and therapeutic settings. Our findings suggest that the increased immunogenicity of dying tumor cells in SRA/CD204 knockout mice is attributed to the altered functions of DCs in the absence of SRA/CD204, which underscores the important role of SRA/CD204 in host immune homeostasis. Selective downregulation or blockade of this immunoregulatory molecule may lead to enhanced potency of DC‐based vaccines capable of breaking immune tolerance against cancer.
An indirect role for NK cells in a CD4+ T‐cell‐dependent mouse model of type I diabetes
Authors: Angstetra Eveline , Graham Kate L , Zhao Yuxing , Irvin Allison E , Elkerbout Lorraine , Santamaria Pere , Slattery Robyn M , Kay Thomas W , Thomas Helen E
Published: March 2011

CD8+ T cells kill pancreatic β‐cells in a cell–cell contact‐dependent mechanism in the non‐obese diabetic mouse. CD4+ T lymphocytes are also able to kill pancreatic β‐cells, but they do not directly contact β‐cells and may use another cell type as the actual cytotoxic cell. Natural killer (NK) cells could have this role but it is uncertain whether they are cytotoxic towards β‐cells. Therefore, the requirement for NK cells in β‐cell destruction in the CD4‐dependent T‐cell antigen receptor transgenic NOD4.1 mice was examined. NK cells failed to kill β‐cells in vitro, even in the absence of major histocompatibility complex class I. We observed only 9.7±1.1% of islet infiltrating NK cells from NOD4.1 mice expressing the degranulation marker CD107a. Diabetogenic CD4+ T cells transferred disease to NODscid.IL2Rγ−/− mice lacking NK cells, indicating that NK cells do not contribute to β‐cell death in vitro or in vivo. However, depletion of NK cells reduced diabetes incidence in NOD4.1 mice, suggesting that NK cells may help to maintain the right environment for cytotoxicity of effector cells.