bluuebunny/crossref_metadata_2025 huggingface dataset:
Modelling the hydrothermomechanical properties of polymers close to glass transition
Authors: Engelhard M. , Lion A.
Published: April 2012

In this work a model to describe the behaviour of polymers close to glass transition depending on environmental influences will be presented. The focus lies here – besides modelling influences of mechanical or thermal loads – on the moisture‐depended properties of polymers. To this end an ansatz based on thermodynamics with internal state variables will be used and enhanced. Adding a second phase – here water – to the balance equations allows under certain circumstances to achieve one single entropy inequality. Based on the Coleman & Noll type of evaluation of the Clausius‐Duhem inequality formulated for the Gibbs free energy, a thermomechanically consistent material model is derived, which is based on a series expansion of the Gibbs free energy around thermodynamic equilibrium. Now, besides constraints emanating from the second law of thermodynamics, it is possible to obtain three relations between the stress, the temperature, the internal variables and the water content on the one side and the strain, the entropy and the chemical potential of the water content on the other. Adjusting the free parameters in these relations – taking into account the remaining entropy inequality – enables inter alia sufficiently accurate reproduction of measuring data from dynamic tension tests with PA 6.
Global space-time symmetries of quantized Euclidean and Minkowski superspaces
Authors: Gonera C. , Wodzislawski M.
Published: April 2012

Abstract

Starting with assumptions both simple and natural from “physical” point of view we present a direct construction of the transformations preserving wide class of (anti)commutation relations which describe Euclidean/Minkowski superspace quantizations. These generalized transformations act on deformed superspaces as the ordinary ones do on undeformed spaces but they depend on non(anti)commuting parameters satisfying some consistent (anti)commutation relations. Once the coalgebraic structure compatible with the algebraic one is introduced in the set of transformations we deal with quantum symmetry supergroup. This is the case for intensively studied so called
$ N = \frac{1}{2} $
supersymmetry as well as its three parameter extension. The resulting symmetry transformations — supersymmetric extension of θ — Euclidean group can be regarded as global counterpart of appropriately twisted Euclidean superalgebra that has been shown to preserve
$ N = \frac{1}{2} $
supersymmetry.
Optimization of neutrino oscillation facilities for large θ
13
Authors: Coloma Pilar , Fernandez-Martinez Enrique
Published: April 2012

Abstract

Up to now, future neutrino beam experiments have been designed and optimized in order to look for CP violation, θ
13 and the mass hierarchy under the conservative assumption that θ
13 is very small. However, the recent results from T2K and MINOS favor a θ
13 which could be as large as 8°. In this work, we propose a re-optimization for neutrino beam experiments in case this hint is confirmed. By switching from the first to the second oscillation peak, we find that the CP discovery potential of future oscillation experiments would not only be enhanced, but it would also be less affected by systematic uncertainties. In order to illustrate the effect, we present our results for a Super-Beam experiment, comparing the results obtained at the first and the second oscillation peaks for several values of the systematic errors. We also study its combination with a β-beam facility and show that the synergy between both experiments would also be enhanced due to the larger L/E. Moreover, the increased matter effects at the longer baseline also significantly improve the sensitivity to the mass hierarchy.
Preoperative Cholangitis and Metastatic Lymph Node Have a Negative Impact on Survival After Resection of Extrahepatic Bile Duct Cancer
Authors: Cho Jai Young , Han Ho‐Seong , Yoon Yoo‐Seok , Hwang Dae Wook , Jung Kyuwhan , Kim Ji Hoon , Kwon Yujin , Kim Haeryoung
Published: April 2012

Background

The significance of the presence of preoperative inflammation for the prognosis of patients with extrahepatic bile duct cancer (BDCA) was evaluated.

Methods

The clinical data of 84 patients who underwent surgery for BDCA from August 2003 to May 2009 were reviewed, and survival analysis was performed. The patients were classified into two groups according to the presence of preoperative cholangitis: Group A had no cholangitis (n = 59), and group B had cholangitis (n = 25).

Results

There were no differences in sex, mean age, TNM stage, biliary drainage, type of resection, or radicality between the two groups (p > 0.05). The 3‐year disease‐specific survival (DSS) and disease‐free survival (DFS) rates for the group B patients (21.5 and 11.9 %, respectively) were significantly lower than those for the group A patients (66.1 and 57.3 %, respectively; p = 0.013 and 0.001, respectively). The multivariate analysis showed that preoperative inflammation and lymph node metastasis were the independent prognostic factors for both overall survival (OS) [p = 0.021, relative risk (RR) = 2.224 and p = 0.015, RR = 2.367, respectively] and DFS (p = 0.014; RR = 2.192 and p = 0.013; RR = 2.240, respectively). The rates of angiolymphatic and perineural invasion were higher for group B than those for group A (p = 0.016 and 0.030, respectively).

Conclusions

The presence of preoperative inflammation is an independent poor prognostic factor for OS and DFS for patients with BDCA.
Optically Stimulated Luminescence Chronology of Terrace Sediments of Siang River, Higher NE Himalaya: Comparison of Quartz and Feldspar Chronometers
Authors: Srivastava Pradeep , Misra D. K.
Published: April 2012

Four levels of terraces located along Siang River, north of Main Central Thrust at Tuting, NE Himalaya are dated using Optically Stimulated Luminescence (OSL). The dating technique is applied using (1) Blue LED stimulation on Quartz (2) Infrared Stimulated Luminescence (IRSL) stimulation on Feldspar at 50 °C and (3) Infrared Stimulated Luminescence stimulation on Feldspar at an elevated temperature of 225 °C. The results indicated that the later two protocols on feldspars yielded overestimated ages that suggested incomplete bleaching of luminescence signals in feldspar. The ages derived using quartz suggested a nearly continued valley aggradation from >21-8 ka with three phases of bedrock incision. The phase of aggradation coincides with a climatic transition from cold and dry Last Glacial phase to warm and wet Holocene Optimum. The bedrock incision phases centered at <21 ka, ∼11 ka and ∼8 ka indicate towards major episodes of tectonic uplift in the region around Tuting.
Arsenic Exposure through Groundwater in the Middle Ganga Plain in the Varanasi Environs, India: A Future Threat
Authors: Raju N. Janardhana
Published: April 2012

The study area covers an about 100 km2 of the middle Ganga plain in Uttar Pradesh, experiencing intensive groundwater extraction. In order to recognize the arsenic contamination zones of the Varanasi environs, sixty eight groundwater samples have been collected and analyzed for major ions, iron and arsenic. Twenty one sediment samples in the four boreholes were also collected to deduce the source of arsenic in the groundwater. The preliminary survey reports for the first time indicates that part of rural and urban population of Varanasi environs are drinking and using for irrigation arsenic contaminated water mostly from hand tube wells (<70 m). The study area is a part of middle Ganga plain which comprises of Quaternary alluvium consists of an alternating succession of clay, clayey silt and sand deposits. The high arsenic content in groundwater samples of the study area indicates that 14% of the samples are exceeding the 10 μg/l and 5% of the samples are exceeding 50 μg/l. The high arsenic concentration is found in the villages such as Bahadurpur, Madhiya, Bhojpur, Ratanpur, Semra, Jalilpur, Kateswar, Bhakhara and Kodupur (eastern side of Ganga River in Varanasi), situated within the newer alluvium deposited during middle Holocene to Recent. The older alluvial aquifers situated in the western side of the Ganga River are arsenic safe (maximum As concentration of 9 μg/l) though the borehole sediments shows high arsenic (mean 5.2 mg/kg) and iron content (529 mg/kg) in shallow and medium depths. This may be due to lack of reducing conditions (i.e organic content) for releasing arsenic into the groundwater. Rainfall infiltration, organic matter from recently accumulated biomass from flood prone belt in the newer alluvium plays a critical role in releasing arsenic and iron present in sediments. The main mechanism for the release of As into groundwater in the Holocene sandy aquifer sediments of Varanasi environs may be due to the reductive dissolution of Fe oxyhydroxide present as coatings on sand grains as well as altered mica content. The high societal problems of this study will help to mitigate the severity of arsenic contamination by providing alternate drinking water resources to the people in middle Ganga plain and to arrange permanent arsenic safe drinking water source by the authorities.
Heavy Minerals and the Characters of Ilmenite in the Beach Placer Sands of Chavakkad-Ponnani, Kerala Coast, India
Authors: Nayak B. , Mohanty Sunati , Bhattacharyya P.
Published: April 2012

Indian beach placer sand deposits are, in general, ilmenite-rich. However, some concentrations are dominated by pyriboles. The Chavakkad-Ponnani (CP) area along the northern Kerala coast is one such deposit. This paper deals with the general character of the heavy minerals of CP with special emphasis on the characters of ilmenite. Most Indian beach sand ilmenites are of good quality. However, our observations on the ilmenites of CP using Optical Microscope, SEM and EPMA reveals that these are mineralogically very complex. The CP ilmenite varies from pure ilmenite to highly impure variety having intergrowths and inclusions of other oxide and silicate minerals. Ilmenite occurs as mix-crystals and forms intergrowth structure with hematite and Ti-hematite/ulvöspinel; contains inclusions of hematite, quartz, and monazite. On the other hand ilmenite also occurs as inclusions within hematite and garnet. The pyriboles are dominantly amphiboles with hornblende-composition. Interestingly an inclusion of gold has been recorded within amphibole of hornblende composition. Garnets are mostly of almandine and pyrope type. Subordinate heavy minerals are sillimanite, zircon and rutile. Characteristic morphology, mineralogy and chemistry of amphibole, garnet and ilmenite together indicate that the placer sands of CP area are derived from the amphibolites, granite gneisses and basic igneous rocks lying in the hinterland towards the eastern border of Kerala. Though the overall quality of ilmenite is poor, high-grade ilmenite concentrate can be generated (of course with lower yield), by adopting precise mineral processing techniques. The CP deposit can be considered as a second-grade deposit but it has potential for future exploitation.
Seamount Subduction and Rupture Characteristics of the March 11, 2011, Tohoku Earthquake
Authors: Kundu Bhaskar , Gahalaut V. K. , Catherine J. K.
Published: April 2012

We suggest that the spatial location of the 2011 Tohoku earthquake rupture and slip distribution on it was strongly influenced by the subduction of seamount chains. Subduction of seamounts across the Japan trench caused weak coupling on the plate interface which acted as barriers to the 2011 Tohoku earthquake rupture and thus delimited it.
Hypogonadism in male cancer patients
Authors: Burney Basil O. , Garcia Jose M.
Published: April 2012

Prevalence of hypogonadism in men with cancer has been reported between 40% and 90%, which is significantly higher than in the general population. Hypogonadism is likely to affect the quality of life in these patients by contributing to non‐specific symptoms, including decreased energy, anorexia, sarcopenia, weight loss, depression, insomnia, fatigue, weakness, and sexual dysfunction. Pathogenesis of hypogonadism in cancer patients is thought to be multi‐factorial. Inflammation may play an important role, but leptin, opioids, ghrelin, and high‐dose chemotherapy through different mechanisms have all been implicated as the cause. Hypogonadism is also associated with poor survival in cancer patients. Data looking into the treatment of hypogonadal male cancer patients with testosterone are limited. However, improvements in body weight, muscle strength, lean body mass, and quality of life have been shown in hypogonadal men with other chronic diseases on testosterone replacement therapy. Prospective and interventional trials are needed to test the efficacy and safety of testosterone treatment in improving quality of life of these patients.
Identity and Representation in Russia's Regions: Adopting a Critical Theory Perspective
Authors: Makarychev Andrey
Published: April 2012

In this paper, the author seeks to find pathways of extrapolating the critical potential of post-structuralist reasoning to the study of Russia's domestic regions' policies. He argues that ideas, norms and rhetorical frames are important ideational arguments to explain policy outcomes in specific Russia's region and in the whole system of Russian federalism. Analysis of Russian regionalism, therefore, can be enriched by engaging with and adopting the new concepts and tools bringing attention to the power of regional identities as exemplified by different types of discourses.
Oncosuppressive role of p53‐induced miR‐205 in triple negative breast cancer
Authors: Piovan Claudia , Palmieri Dario , Di Leva Gianpiero , Braccioli Luca , Casalini Patrizia , Nuovo Gerard , Tortoreto Monica , Sasso Marianna , Plantamura Ilaria , Triulzi Tiziana , Taccioli Cristian , Tagliabue Elda , Iorio Marilena V. , Croce Carlo M.
Published: April 2012

An increasing body of evidence highlights an intriguing interaction between microRNAs and transcriptional factors involved in determining cell fate, including the well known “genome guardian” p53. Here we show that miR‐205, oncosuppressive microRNA lost in breast cancer, is directly transactivated by oncosuppressor p53.

Moreover, evaluating miR‐205 expression in a panel of cell lines belonging to the highly aggressive triple negative breast cancer (TNBC) subtype, which still lacks an effective targeted therapy and characterized by an extremely undifferentiated and mesenchymal phenotype, we demonstrated that this microRNA is critically down‐expressed compared to a normal‐like cell line. Re‐expression of miR‐205 where absent strongly reduces cell proliferation, cell cycle progression and clonogenic potential in vitro, and inhibits tumor growth in vivo, and this tumor suppressor activity is at least partially exerted through targeting of E2F1, master regulator of cell cycle progression, and LAMC1, component of extracellular matrix involved in cell adhesion, proliferation and migration.
Fear Avoidance Beliefs Predict Disability in Older Adults With Chronic Low Back Pain
Authors: Camacho‐Soto Alejandra , Sowa Gwendolyn A. , Perera Subashan , Weiner Debra K.
Published: April 2012

Objectives

To determine whether fear avoidance beliefs (FABs) in older adults with chronic low back pain (CLBP) are significantly associated with gait speed decline and/or self‐report of greater disability.

Design

Cross‐sectional analysis.

Setting

An academic medical center (single site).

Participants

Two hundred English‐speaking participants aged 65 years and older with CLBP every day or almost every day of moderate or greater intensity for ≥3 months.

Main Outcome Measurements

The physical activity portion of the FAB questionnaire assessed FABs. Disability was measured with gait speed and the Roland Morris Questionnaire. Covariates measured included age, gender, body mass index, chronic disease (Cumulative Illness Rating Scale), depression (Geriatric Depression Scale), and pain (McGill Pain Questionnaire Short Form).

Results

FABs were significantly associated with the Roland Morris Questionnaire (P < .0001) and gait speed (P = .002) after controlling for all covariates.

Conclusion

FABs related to physical activity in older adults with CLBP were significantly associated with both self‐reported and performance‐based disability after controlling for known confounders. Previous studies have reported similar associations between self‐reported measures of disabling back pain and FABs. Ours is the first study to examine the relationship between FAB and gait speed, a powerful predictor of morbidity and mortality. Future work should examine whether targeting fear avoidance in addition to other psychosocial measures in older adults with CLBP improves gait speed and functional independence.
Calorimetric and Spectroscopic investigations οf β-lactoglobulin upon interaction with copper ion
Authors: Divsalar Adeleh , Damavandi Sajedeh Ebrahim , Saboury Ali Akbar , Seyedarabi Arefeh , Moosavi-Movahedi Ali Akbar
Published: April 2012

The effect of copper(II) ions (Cu+2) on the structure of β-lactoglobulin (β-lg) was investigated spectroscopically using UV-visible, fluorescence and circular dichroism (CD) and calorimetrically using isothermal titration calorimetry (ITC), at different temperatures. Results of the UV-visible studies showed that adding Cu+2to β-lg solution caused increasing turbidity, indicative of protein aggregation. It was noticeable that the rate of increasing turbidity was directly proportional to increasing temperature. The far-UV CD studies displayed that the Cu+2cannot induce any significant changes in the secondary structures of β-lg at different temperatures. Also, the ITC data indicated that the binding process of Cu+2to β-lg is mainly entropically driven. The results highlight that copper ions cause the tertiary structure of β-lg to change and induce a slightly open structure leading to the formation of supramolecular aggregates in β-lg which may result in the reduced allergenicity of β-lg and its increased use in industrial applications.
Coexistence of rhinoscleroma with Rosai–Dorfman disease: is rhinoscleroma a cause of this disease?
Authors: Kumari J O
Published: April 2012

Introduction:

Rhinoscleroma and Rosai–Dorfman disease have been reported to coexist in the same patient at different sites. Rosai–Dorfman disease may have an aetiological relationship with rhinoscleroma, although this has not yet been proved.

Case report:

A case of a 42-year-old woman with recurrent nasal masses is presented, with histopathological proof of both conditions coexisting in the same nasal lesion.

Discussion:

The aetiopathology, clinical features and treatment of both diseases are discussed and a literature survey is reported. Histologically, the presence of Mikulicz cells with entrapped, rod-like, Gram-negative bacilli and Russell bodies suggests rhinoscleroma. Emperipolesis and S-100-positive histiocytes confirm the diagnosis of Rosai-Dorfman disease. The presence of both in the same slides from affected tissues has never been demonstrated before. In the light of this evidence, the author believes that rhinoscleroma must be considered in the aetiology of Rosai–Dorfman disease.
Patient Journey: Implications for Improving and Integrating Care for Older Adults with Chronic Obstructive Pulmonary Disease
Authors: Jackson Karen , Oelke Nelly D. , Besner Jeanne , Harrison Alexandra
Published: April 2012

Beacoup de patients, surtout les patients plus âgés, interagissent avec fournisseurs multiples, tout en avant accès aux services des soins de santé dans une variété de milieux divers pendants longues périodes. Comprendre les expériences des patients plus âgés pendant leurs voyages à travers le système de santé est essentielle pour améliorer l’intégration des services et la qualité des soins. Dans cette étude, nous avons résumé les expériences de quatre patients vivant avec la maladie pulmonaire obstructive chronique en interaction avec le système des soins de santé pendant une période de trois mois après la sortie de l’hôpital. Guidé par la méthodologie d’étude de cas, on a réunis les données par le biais des entretiens semi-structurés et des journaux de patients. Trois grands thèmes - le soutien social, la navigation à travers le système, et l’accès aux soins – ont émergé à partir des données. L’attention à la communication entre fournisseur-patient et prestataire-fournisseur, ainsi que le soutien social du patient, et les besoins des soins auto-administrés, pourraient améliorer l’intégration et les résultats des soins. Pour réaliser de ce que les patients perçoivent comme une système integrée et efficace, il faudra du temps et de l’engagement.
Social networks and HCV viraemia in anti-HCV-positive rural drug users
Authors: YOUNG A. M. , JONAS A. B. , HAVENS J. R.
Published: April 2012

Although social networks are known to play an important role in drug-using behaviours associated with hepatitis C virus (HCV) infection, literature on social networks and HCV is inconsistent. This exploratory study examined HCV RNA distribution within a social network of anti-HCV-positive non-medical prescription opioid users (NMPOUs) in rural Appalachia. Participants were tested serologically for HCV RNA, and behavioural, demographic, and network data were collected using interview-administered questionnaires. Multivariate analyses were performed using logistic regression. Behavioural and demographic characteristics did not differ by RNA status. In the multivariate model, recent injecting drug users (IDUs) were more likely to be RNA positive [odds ratio (OR) 4·06, 95% confidence interval (CI) 1·04–15·83], and turnover into an IDU's drug network was significantly protective (OR 0·15, 95% CI 0·03–0·75). This is the first study to date to examine HCV distribution in rural NMPOUs from a network perspective and demonstrates that network characteristics significantly contribute to the epidemiology of HCV in this understudied, high-risk population.
Secrets of image denoising cuisine
Authors: Lebrun M. , Colom M. , Buades A. , Morel J. M.
Published: April 2012

Digital images are matrices of equally spaced pixels, each containing a photon count. This photon count is a stochastic process due to the quantum nature of light. It follows that all images are noisy. Ever since digital images have existed, numerical methods have been proposed to improve the signal-to-noise ratio. Such ‘denoising’ methods require a noise model and an image model. It is relatively easy to obtain a noise model. As will be explained in the present paper, it is even possible to estimate it from a single noisy image.
Pricing futures by deterministic methods
Authors: Pironneau Olivier
Published: April 2012

In this article we will focus on only a small part of financial mathematics, namely the use of partial differential equations for pricing futures. Even within this narrow range it is hard to be systematic and complete, or even to do better than existing books such as Wilmott, Howison and Dewynne (1995), Achdou and Pironneau (2005), or software manuals such as Lapeyre, Martini and Sulem (2010). So this article may be valuable only to the extent that it reflects ten years of teaching, conferences and interaction with the protagonists of financial mathematics.

Also, because the theory of partial differential equations is not always well known, we have chosen a pragmatic approach and left out the details of the theory or the proofs of some results, and refer the reader to other books. The numerical algorithms, on the other hand, are given in detail.
I Want to Be Like You
Authors: Matschke Christina , Sassenberg Kai
Published: April 2012

Entering a new group provides the potential of forming a new social identity. Starting from self-regulation models, we propose that goals (e.g., internal motivation to enter the group), strategies (e.g., approach and avoidance strategies), and events (e.g., the group’s response) affect the development of the social self. In two studies we manipulated the group’s response (acceptance vs. rejection) and assessed internal motivation as well as approach and avoidance strategies. It was expected, and we found, that when newcomers are accepted, their use of approach strategies (but not avoidance strategies) facilitates social identification. In line with self-completion theory, for highly internally motivated individuals approach strategies facilitated social identification even upon rejection. The results underline the active role of newcomers in their social identity development.
Mixed Discriminatory Judgments of Individuals’ Warmth and Competence-Related Abilities
Authors: Carlsson Rickard , Björklund Fredrik , Bäckström Martin
Published: April 2012

Although several studies have demonstrated that stereotypes can be mixed in terms of warmth and competence (e.g., cold but competent), the possibility of mixed discrimination has received very little attention so far. To this end, the present study investigated mixed discriminatory judgments of individuals. In two studies, the participants judged the empathic (warmth) and the cognitive (competence) ability of individuals who differed only in whether they belonged to a group typically stereotyped as warm but incompetent or cold but competent. Study 1 compared Greeks with Germans (nationality) and Study 2 preschool teachers with lawyers (occupation). In both studies, the judgments were discriminatory in a mixed pattern consistent with the groups’ stereotype content.
Antioxidant and bioenergetic coupling between neurons and astrocytes
Authors: Fernandez-Fernandez Seila , Almeida Angeles , Bolaños Juan P.
Published: April 2012

Oxidative and nitrosative stress underlie the pathogenesis of a broad range of human diseases, in particular neurodegenerative disorders. Within the brain, neurons are the cells most vulnerable to excess reactive oxygen and nitrogen species; their survival relies on the antioxidant protection promoted by neighbouring astrocytes. However, neurons are also intrinsically equipped with a biochemical mechanism that links glucose metabolism to antioxidant defence. Neurons actively metabolize glucose through the pentose phosphate pathway, which maintains the antioxidant glutathione in its reduced state, hence exerting neuroprotection. This process is tightly controlled by a key glycolysis-promoting enzyme and is dependent on an appropriate supply of energy substrates from astrocytes. Thus brain bioenergetic and antioxidant defence is coupled between neurons and astrocytes. A better understanding of the regulation of this intercellular coupling should be important for identifying novel targets for future therapeutic interventions.
Neisseria meningitidis and Neisseria gonorrhoeae are differently adapted in the regulation of denitrification: single nucleotide polymorphisms that enable species-specific tuning of the aerobic–anaerobic switch
Authors: Edwards James , Quinn Diana , Rowbottom Karyn-Anne , Whittingham Jean L. , Thomson Melanie J. , Moir James W. B.
Published: April 2012

The closely related pathogenic Neisseria species N. meningitidis and N. gonorrhoeae are able to respire in the absence of oxygen, using nitrite as an alternative electron acceptor. aniA (copper-containing nitrite reductase) is tightly regulated by four transcriptional regulators: FNR (fumarate and nitrate reductase), NarP, FUR (Ferric uptake regulator) and NsrR. The four regulators control expression of aniA in N. meningitidis by binding to specific and distinct regions of the promoter. We show in the present study that FUR and NarP are both required for the induction of expression of aniA in N. meningitidis, and that they bind adjacent to one another in a non-co-operative manner. Activation via FUR/NarP is dependent on their topological arrangement relative to the RNA polymerase-binding site. Analysis of the sequence of the aniA promoters from multiple N. meningitidis and N. gonorrhoeae strains indicates that there are species-specific single nucleotide polymorphisms, in regions predicted to be important for regulator binding. These sequence differences alter both the in vitro DNA binding and the promoter activation in intact cells by key activators FNR (oxygen sensor) and NarP (which is activated by nitrite in N. meningitidis). The weak relative binding of FNR to the N. gonorrhoeae aniA promoter (compared to N. meningitidis) is compensated for by a higher affinity of the gonococcal aniA promoter for NarP. Despite containing nearly identical genes for catalysing and regulating denitrification, variations in the promoter for the aniA gene appear to have been selected to enable the two pathogens to tune differentially their responses to environmental variables during the aerobic–anaerobic switch.
Dynamics in transient complexes of redox proteins
Authors: Ubbink Marcellus
Published: April 2012

Recent studies have provided experimental information about the initial stage of protein complex formation, the encounter complex. This stage is particularly important in the weak and transient complexes formed between electron transfer proteins and their partners. These studies are discussed and the role of the encounter complex is interpreted in terms of the specific requirements that the biological function puts on these complexes.
Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution
Authors: Korber Philipp
Published: April 2012

Genome-wide nucleosome maps revealed well-positioned nucleosomes as a major theme in eukaryotic genome organization. Promoter regions often show a conserved pattern with an NDR (nucleosome-depleted region) from which regular nucleosomal arrays emanate. Three mechanistic contributions to such NDR-array-organization and nucleosome positioning in general are discussed: DNA sequence, DNA binders and DNA-templated processes. Especially, intrinsic biophysics of DNA sequence preferences for nucleosome formation was prominently suggested to explain the majority of nucleosome positions (‘genomic code for nucleosome positioning’). Nonetheless, non-histone factors that bind DNA with high or low specificity, such as transcription factors or remodelling enzymes respectively and processes such as replication, transcription and the so-called ‘statistical positioning’ may be involved too. Recently, these models were tested for yeast by genome-wide reconstitution. DNA sequence preferences as probed by SGD (salt gradient dialysis) reconstitution generated many NDRs, but only few individual nucleosomes, at their proper positions, and no arrays. Addition of a yeast extract and ATP led to dramatically more in vivo-like nucleosome positioning, including regular arrays for the first time. This improvement depended essentially on the extract and ATP but not on transcription or replication. Nucleosome occupancy and close spacing were maintained around promoters, even at lower histone density, arguing for active packing of nucleosomes against the 5′ ends of genes rather than statistical positioning. A first extract fractionation identified a direct, specific, necessary, but not sufficient role for the RSC (remodels the structure of chromatin) remodelling enzyme. Collectively, nucleosome positioning in yeast is actively determined by factors beyond intrinsic biophysics, and in steady-state rather than at equilibrium.
Chloroplast lipid synthesis and lipid trafficking through ER–plastid membrane contact sites
Authors: Wang Zhen , Benning Christoph
Published: April 2012

Plant chloroplasts contain an intricate photosynthetic membrane system, the thylakoids, and are surrounded by two envelope membranes at which thylakoid lipids are assembled. The glycoglycerolipids mono- and digalactosyldiacylglycerol, and sulfoquinovosyldiacylglycerol as well as phosphatidylglycerol, are present in thylakoid membranes, giving them a unique composition. Fatty acids are synthesized in the chloroplast and are either directly assembled into thylakoid lipids at the envelope membranes or exported to the ER (endoplasmic reticulum) for extraplastidic lipid assembly. A fraction of lipid precursors is reimported into the chloroplast for the synthesis of thylakoid lipids. Thus polar lipid assembly in plants requires tight co-ordination between the chloroplast and the ER and necessitates inter-organelle lipid trafficking. In the present paper, we discuss the current knowledge of the export of fatty acids from the chloroplast and the import of chloroplast lipid precursors assembled at the ER. Direct membrane contact sites between the ER and the chloroplast outer envelopes are discussed as possible conduits for lipid transfer.
Cancer and the bromodomains of BAF180
Authors: Brownlee Peter M. , Chambers Anna L. , Oliver Antony W. , Downs Jessica A.
Published: April 2012

Chromatin remodelling complexes alter the structure of chromatin and have central roles in all DNA-templated activities, including regulation of gene expression and DNA repair. Mutations in subunits of the PBAF (polybromo/Brg1-associated factor) or SWI/SNF-B remodelling complex, including BAF180, are frequently associated with cancer. There are six potential acetyl-lysine-binding BDs (bromodomains) in BAF180, which may function to target the PBAF complex to promoters or sites of DNA repair. In the present review, we discuss what is currently known about the BDs of BAF180 and their potential significance in cancer.
Calcium signalling remodelling and disease
Authors: Berridge Michael J.
Published: April 2012

A wide range of Ca2+ signalling systems deliver the spatial and temporal Ca2+ signals necessary to control the specific functions of different cell types. Release of Ca2+ by InsP3 (inositol 1,4,5-trisphosphate) plays a central role in many of these signalling systems. Ongoing transcriptional processes maintain the integrity and stability of these cell-specific signalling systems. However, these homoeostatic systems are highly plastic and can undergo a process of phenotypic remodelling, resulting in the Ca2+ signals being set either too high or too low. Such subtle dysregulation of Ca2+ signals have been linked to some of the major diseases in humans such as cardiac disease, schizophrenia, bipolar disorder and Alzheimer's disease.
Metabolic sensors and their interplay with cell signalling and transcription
Authors: Krejčí Alena
Published: April 2012

There is an intimate, yet poorly understood, link between cellular metabolic status, cell signalling and transcription. Central metabolic pathways are under the control of signalling pathways and, vice versa, the cellular metabolic profile influences cell signalling through the incorporation of various metabolic sensors into the signalling networks. Thus information about nutrients availability directly and crucially influences crucial cell decisions. In the present review, I summarize our current knowledge of various metabolic sensors and give some examples of the integration of metabolically derived inputs into the signalling system and the regulation of transcription. I also discuss the Warburg effect where the cross-talk between metabolism and signalling is used to orchestrate rapid cell growth and division. It is becoming clear that future research will concentrate on the collection of small-molecule metabolites, whose concentration fluctuates in response to cellular energy levels, searching for their sensors that connect them to the signalling and transcriptional networks.
The relationship between ER–multivesicular body membrane contacts and the ESCRT machinery
Authors: Eden Emily R. , Burgoyne Thomas , Edgar James R. , Sorkin Alexander , Futter Clare E.
Published: April 2012

Activated EGFR (epidermal growth factor receptor) undergoes ESCRT (endosomal sorting complex required for transport)-mediated sorting on to ILVs (intraluminal vesicles) of endosomes before degradation in the lysosome. Sorting of endocytosed EGFR on to ILVs removes the catalytic domain of the EGFR from the cytoplasm, resulting in termination of receptor signalling. EGFR signalling is also subject to down-regulation through receptor dephosphorylation by the ER (endoplasmic reticulum)-localized PTP1B (protein tyrosine phosphatase 1B). PTP1B on the cytoplasmic face of the ER interacts with endocytosed EGFR via direct membrane contacts sites between the ER and endosomes. In the present paper, we review the relationship between ER–endosome membrane contact sites and ILV formation, and their potential role in the regulation of EGFR sorting on to ILVs, through PTP1B-mediated dephosphorylation of both EGFR and components of the ESCRT machinery.
From Beads on a String to the Pearls of Regulation: the Structure and Dynamics of Chromatin
Authors: Bowater Richard P. , Wood Ian C. , Luisi Ben F.
Published: April 2012

The assembly of eukaryotic chromatin, and the bearing of its structural organization on the regulation of gene expression, were the central topics of a recent conference organized jointly by the Biochemical Society and Wellcome Trust. A range of talks and poster presentations covered topical aspects of this research field and illuminated recent advances in our understanding of the structure and function of chromatin. The two-day meeting had stimulating presentations complemented with lively discourse and interactions of participants. In the present paper, we summarize the topics presented at the meeting, in particular highlighting subjects that are reviewed in more detail within this issue of Biochemical Society Transactions. The reports bring to life the truly fascinating molecular and structural biology of chromatin.
Vection during Conflicting Multisensory Information about the Axis, Magnitude, and Direction of Self-Motion
Authors: Ash April , Palmisano Stephen
Published: April 2012

We examined the vection induced by consistent and conflicting multisensory information about self-motion. Observers viewed displays simulating constant-velocity self-motion in depth while physically oscillating their heads left–right or back–forth in time with a metronome. Their tracked head movements were either ignored or incorporated directly into the self-motion display (as an added simulated self-acceleration). When this head oscillation was updated into displays, sensory conflict was generated by simulating oscillation along: (i) an orthogonal axis to the head movement; or (ii) the same axis, but in a non-ecological direction. Simulated head oscillation always produced stronger vection than ‘no display oscillation’—even when the axis/direction of this display motion was inconsistent with the physical head motion. When head-and-display oscillation occurred along the same axis: (i) consistent (in-phase) horizontal display oscillation produced stronger vection than conflicting (out-of-phase) horizontal display oscillation; however, (ii) consistent and conflicting depth oscillation conditions did not induce significantly different vection. Overall, orthogonal-axis oscillation was found to produce very similar vection to same-axis oscillation. Thus, we conclude that while vection appears to be very robust to sensory conflict, there are situations where sensory consistency improves vection.
Social support on international assignments: The relevance of socioemotional support from locals
Authors: Podsiadlowski Astrid , Vauclair Christin‐Melanie , Spiess Erika , Stroppa Christina
Published: April 2012

The first author received funding from the Commission of the European Communities as a Marie Curie International Reintegration Grant (FP/‐PEOPLE‐2007‐4‐3‐IRG) under grant agreement number PIRG02‐GA‐224818 for data analysis and write‐up. We want to thank our anonymous reviewers for their valuable comments and suggestions, and Ruth Lamont and Jaimee Stuart for their help with the preparation of the manuscript.

Social support takes on a special significance in the context of sojourners. Using the matching/specificity hypothesis we hypothesized that sojourners’ satisfaction is increased if there is an optimal match between type and source of social support. The Index of Sojourner Social Support (ISSS; Ong &Ward, 2005) Scale was used to examine this hypothesis in the context of instrumental and socioemotional support for sojourners on work assignments. The results showed that (a) both types of social support are positively related to satisfaction with the sojourn, (b) socioemotional support is more important in predicting satisfaction with a sojourn than instrumental support, and (c) support from locals is the most important source of social support. Furthermore, we found partial support for the matching/specificity hypothesis: Only the amount of support from locals was a significant moderator and only the relationship between socioemotional support and satisfaction with a sojourn was moderated. We discuss the relevance of source and type of support for cultural adjustment and the importance of contact with locals during international sojourns.
Two-Stage Estimation of Nonrecursive Choice Models
Authors: Alvarez R. Michael , Glasgow Garrett
Published: April 2012

Questions of causation are important issues in empirical research on political behavior. Most of the discussion of the econometric problems associated with multiequation models with reciprocal causation has focused on models with continuous dependent variables (e.g., Markus and Converse 1979; Page and Jones 1979). Yet, many models of political behavior involve discrete or dichotomous dependent variables; this paper describes two techniques which can consistently estimate reciprocal relationships between dichotomous and continuous dependent variables. The first, two-stage probit least squares (2SPLS), is very similar to two-stage instrumental variable techniques. The second, two-stage conditional maximum likelihood (2SCML), may overcome problems associated with 2SPLS, but has not been used in the political science literature. We demonstrate the potential pitfalls of ignoring the problems of reciprocal causation in nonrecursive choice models and examine the properties of both techniques using Monte Carlo simulations: we find that 2SPLS slightly outperforms 2SCML in terms of bias but that 2SCML produces more accurate standard errors. However, the 2SCML model offers an explicit statistical test for endogeneity. The results from our simulations, and the statistical test for exogeneity, lead us to advocate the use of 2SCML for estimation of this class of causal models. We then apply both of these techniques to an empirical example focusing on the relationship between voter preferences in a presidential election and the voter's uncertainty about the policy positions taken by the candidates. This example demonstrates the importance of these techniques for political science research.
Analyzing Censored and Sample-Selected Data with Tobit and Heckit Models
Authors: Sigelman Lee , Zeng Langche
Published: April 2012

Political scientists are making increasing use of the Tobit and Heckit models. This paper addresses some common problems in the application and interpretation of these models. Through numerical experiments and reanalysis of data from a study by Romer and Snyder (1994), we illustrate the consequences of using the standard Tobit model, which assumes a censoring point at zero, when the zeros are not due to censoring mechanisms or when actual censoring is not at zero. In the latter case, we also show that Greene's (1981) well-known results on the direction and size of the bias of the OLS estimator in the standard Tobit model do not necessarily hold. Because the Heckit model is often used as an alternative to Tobit, we examine its assumptions and discuss the proper interpretation of the Heckit/Tobit estimation results using Grier and co-workers' (1994) Heckit model of campaign contribution data. Sensitivity analyses of the Heckit estimation results suggest some conclusions rather different from those reached by Grier et al.
Publication Bias Reconsidered
Authors: Sigelman Lee
Published: April 2012

In political science and many other disciplines, statistically significant results—rejections of the null hypothesis—are achieved more frequently in published than in unpublished studies. Such “publication bias” is generally seen as the consequence of a widespread prejudice against statistically nonsignificant results. I argue that evidence of such a prejudice is in surprisingly short supply and that publication bias can occur even in the absence of such a prejudice and even if the review process is functioning perfectly. More importantly, publication bias may stem from dutiful application of standards of scientific inquiry rather than from irrational prejudice.
Item Similarity in Scale Analysis
Authors: Steenbergen Marco R.
Published: April 2012

A statistic—the similarity coefficient—is developed for assessing the property that a set of scale items measures one and only one construct. This statistic is rooted in an explicit measurement model and is flexible enough to be used in exploratory scale analyses, even in small samples. Methods for analyzing similarity coefficients are described and illustrated in analyses of Stimson's (1991) policy mood data and Markus' (1990) popular individualism items. The Appendix discusses the statistical properties of similarity coefficients.
Enzymatic identification of the load-bearing boundary lubricant in the joint.
Authors: Hills B A , Monds M K
Published: April 2012

Bovine articular cartilage and synovial fluid (SF) were co-incubated with one of three enzymes selected to destroy each of the three major contenders for the active ingredient imparting such remarkable load-bearing lubrication to the normal joint. Destroying hyaluronic acid (HA), alias hyaluronan, with hyaluronidase, both frictional and wear tests displayed no significant change in accordance with most previous studies of SF alone. Destroying surface-active phospholipid (SAPL) with phospholipase A2, there was a highly significant dose-dependent compromise of lubrication as recorded on both tests. Trypsin produced a somewhat surprising result in that lubrication of the cartilage actually improved. This result can be interpreted as indicating that lubricin is not the lubricant per se, but, as a water-soluble, macromolecular, proteinaceous carrier for phospholipid, its destruction caused more SAPL to be deposited as the true load-bearing lubricant. These results are discussed in the context that SAPL, lubricin and HA each have specific roles in a comprehensive lubrication system.
On Difference Equations, Probability Models and the “Generalized Event Count” Distribution
Authors: Amato Timothy W.
Published: April 2012

In this article, the mathematical and probabilistic foundations of Gary King's “generalized event count” (GEC) model for dealing with unequally dispersed event count data are explored. It is shown that the GEC model is a probability model that joins together the binomial, negative binomial, and Poisson distributions. Some aspects of the GEC's reparameterization are described and extended and it is shown how different reparameterizations lead to different interpretations of the dispersion parameter. The common mathematical and statistical structure of “unequally dispersed” event count models as models that require estimation of the “number of trials” parameter along with the “probability” component is derived. Some questions pertaining to estimation of this class of models are raised for future discussion.
The Generalization in the Generalized Event Count Model, with Comments on Achen, Amato, and Londregan
Authors: King Gary , Signorino Curtis S.
Published: April 2012

We use an analogy with the normal distribution and linear regression to demonstrate the need for the Generalized Event Count (GEC) model. We then show how the GEC provides a unified framework within which to understand a diversity of distributions used to model event counts, and how to express the model in one simple equation. Finally, we address the points made by Christopher Achen, Timothy Amato, and John Londregan. Amato's and Londregan's arguments are consistent with ours and provide additional interesting information and explanations. Unfortunately, the foundation on which Achen built his paper turns out to be incorrect, rendering all his novel claims about the GEC false (or in some cases irrelevant).