bluuebunny/crossref_metadata_2025 huggingface dataset:
What People Desire, Feel Conflicted About, and Try to Resist in Everyday Life
Authors: Hofmann Wilhelm , Vohs Kathleen D. , Baumeister Roy F.
Published: May 2012

In the present study, we used experience sampling to measure desires and desire regulation in everyday life. Our analysis included data from 205 adults, who furnished a total of 7,827 reports of their desires over the course of a week. Across various desire domains, results revealed substantial differences in desire frequency and strength, the degree of conflict between desires and other goals, and the likelihood of resisting desire and the success of this resistance. Desires for sleep and sex were experienced most intensively, whereas desires for tobacco and alcohol had the lowest average strength, despite the fact that these substances are thought of as addictive. Desires for leisure and sleep conflicted the most with other goals, and desires for media use and work brought about the most self-control failure. In addition, we observed support for a limited-resource model of self-control employing a novel operationalization of cumulative resource depletion: The frequency and recency of engaging in prior self-control negatively predicted people’s success at resisting subsequent desires on the same day.
Model order reduction methods applied to a welding model
Authors: Sikström Fredrik , Christiansson Anna-Karin , Lennartson Bengt
Published: May 2012

A finite element representation modelling transient heat conduction of gas tungsten arc welding of stainless steel is used to evaluate different methods for model order reduction. The focus is on establishing a linear low-order model of the dynamic relation between the welding current and the temperature measured by a radiation pyrometer. The objective of this low-order model is to design a model-based feedback controller and to investigate the consequences of applying feedback control of the process. Three different approaches for model reduction have been evaluated, namely the Krylov subspace method for moment matching, balanced truncation and parametric system identification. The study provides a knowledge base for the selection of model order reduction methods when dealing with large-scale systems like finite element models of transient heat conduction, and it recommends parametric system identification. It renders sufficient approximations for controller design, no linearization of the finite element model is required, and there is no limit on degrees of freedom of the finite element model.
The value ground of nursing
Authors: Snellman Ingrid , Gedda Kersti M
Published: May 2012

The aim of this literature study was to suggest a value ground for nursing anchored in two ethical principles: the principle of human value and the right to experience a meaningful life. Previous nursing research between the years 2000 and 2009 was analysed. Presented values suggested in this value ground are thus in line with the nursing context and science of today. Statements within ethical literature have been used in order to formulate arguments aimed at supporting the values that were found in the study. In the literature study six values were found: trust, nearness, sympathy, support, knowledge and responsibility. These values hold equal status and are not presented in hierarchical order. They vary due to the persons involved, nursing situations and cultural surroundings, but have the common requirement of being non-excluding. In order to implement the values within the value ground, two prerequisites are discussed and claimed as essential: ethical dialogue and a caring encounter between care provider and patients.
Patients’ silence following healthcare staff’s ethical transgressions
Authors: Brüggemann A Jelmer , Wijma Barbro , Swahnberg Katarina
Published: May 2012

The aim of this study was to examine to what extent patients remained silent to the health care system after they experienced abusive or wrongful incidents in health care. Female patients visiting a women’s clinic in Sweden ( n = 530) answered the Transgressions of Ethical Principles in Health Care Questionnaire (TEP), which was constructed to measure patients’ abusive experiences in the form of staff’s transgressions of ethical principles in health care. Of all the patients, 63.6% had, at some point, experienced staff’s transgressions of ethical principles, and many perceived these events as abusive and wrongful. Of these patients, 70.3% had remained silent to the health care system about at least one transgression. This silence is a loss of essential feedback for the health care system and should not automatically be interpreted as though patients are satisfied.
Trade Policies for Biofuels
Authors: Eggert Håkan , Greaker Mads
Published: May 2012

The purpose of the present article is to consider optimal trade policies for biofuels, taking into account the potential for carbon leakage and the complex set of policies used or discussed for biofuels. First, the authors consider the case of optimal trade policies and find that the combination of an import standard and a border carbon adjustment welfare dominates using only a border carbon adjustment (BCA). The import standard should be set such that the emissions per unit of output is as if the foreign biofuels industry were subject to the globally optimal green house gas (GHG) emission tax. Second, the authors study the same trade policies in the context of a blending mandate, which significantly alters the way the market works. Given the suboptimal implementation of a blending mandate, the optimal BCA depends on the domestic subsidy to biofuels production. High levels of subsidies may in fact imply a negative BCA; that is, the optimal policy would be to subsidize imports.
The GABA Excitatory/Inhibitory Shift in Brain Maturation and Neurological Disorders
Authors: Ben-Ari Yehezkel , Khalilov Ilgam , Kahle Kristopher T. , Cherubini Enrico
Published: May 2012

Ionic currents and the network-driven patterns they generate differ in immature and adult neurons: The developing brain is not a “small adult brain.” One of the most investigated examples is the developmentally regulated shift of actions of the transmitter GABA that inhibit adult neurons but excite immature ones because of an initially higher intracellular chloride concentration [Cl−]i, leading to depolarizing and often excitatory actions of GABA instead of hyperpolarizing and inhibitory actions. The levels of [Cl−]i are also highly labile, being readily altered transiently or persistently by enhanced episodes of activity in relation to synaptic plasticity or a variety of pathological conditions, including seizures and brain insults. Among the plethora of channels, transporters, and other devices involved in controlling [Cl−]i, two have emerged as playing a particularly important role: the chloride importer NKCC1 and the chloride exporter KCC2. Here, the authors stress the importance of determining how [Cl−]i is dynamically regulated and how this affects brain operation in health and disease. In a clinical perspective, agents that control [Cl−]i and reinstate inhibitory actions of GABA open novel therapeutic perspectives in many neurological disorders, including infantile epilepsies, autism spectrum disorders, and other developmental disorders.
Cognitive reserve and patient-reported outcomes in multiple sclerosis
Authors: Schwartz Carolyn E , Snook Erin , Quaranto Brian , Benedict Ralph HB , Vollmer Timothy
Published: May 2012

Background:

Adaptation and compensation in the face of changing pathology may be better understood by considering the concept of cognitive reserve, which may protect against disability in multiple sclerosis (MS).

Objectives:

The present work investigates the relationship between cognitive reserve and demographic characteristics, health behaviors, and patient-reported outcomes (PROs).

Methods:

Cross-sectional data ( n=1142) were drawn from the North American Research Committee on MS (NARCOMS) Registry, from whom additional survey data were collected. Cognitive reserve was measured using the Stern and Sole-Padulles measures, the O*NET occupational classification system, and the Godin Leisure-Time Exercise Questionnaire. PROs were assessed using generic (SF -12v2, Perceived Deficits Questionnaire, Ryff Psychological Well-Being, Diener Satisfaction with Life Scale) and disease-specific (Patient-Determined Disease Steps, Performance Scales) measures. Psychometric analysis created unidimensional cognitive reserve subscales. Regression models examined relationships between cognitive reserve, demographic characteristics, and PROs.

Results:

The cognitive reserve measures assessed distinct but related constructs. Individuals with high cognitive reserve were more likely to report lower levels of perceived disability and perceived cognitive deficits, and higher levels of physical health, mental health, and well-being. Both active and passive reserve are associated with better outcomes, independent of demographic factors, and these associations apply to both generic and disease-specific outcomes.

Conclusions:

This expanded measurement of cognitive reserve captures both the passive and active aspects of the construct, and there is a consistent and substantial relationship with PROs. Individuals with high passive and/or active reserve are healthier and experience higher levels of well-being.
The resilient subject: Exploring subjectivity, identity and the body in narratives of resilience
Authors: Aranda Kay , Zeeman Laetitia , Scholes Julie , Morales Arantxa Santa-María
Published: May 2012

International research and policy interest in resilience has increased enormously during the last decade. Resilience is now considered to be a valuable asset or resource with which to promote health and well-being and forms part of a broader trend towards strength based as opposed to deficit models of health. And while there is a developing critique of resilience’s conceptual limits and normative assumptions, to date there is less discussion of the subject underpinning these notions, nor related issues of subjectivity, identity or the body. Our aim in this article is to begin to address this gap. We do so by re-examining the subject within two established narratives of resilience, as ‘found’ and ‘made’. We then explore the potential of a third narrative, which we term resilience ‘unfinished’. This latter story is informed by feminist poststructural understandings of the subject, which in turn, resonate with recently articulated understandings of an emerging psychosocial subject and the contribution of psychoanalysis to these debates. We then consider the potential value of this poststructural, performative and embodied psychosocial subject and discuss the implications for resilience theory, practice and research.
Can holism be practiced in a biomedical setting? A qualitative study of the integration of complementary medicine to a surgical department
Authors: Keshet Yael , Ben-Arye Eran , Schiff Elad
Published: May 2012

In recent decades, complementary medicine (CM) has been increasingly integrated to conventional healthcare organizations, in which the biomedical profession clearly maintains dominance. Our objective was to investigate empirically what integration and ‘holism’ mean to the diverse professional groups involved and whether treatment becomes more holistic when CM is integrated. A qualitative study was conducted in a general surgery department at a public hospital in Israel. Data were collected by means of observations of medical encounters and daily work, and 30 in-depth interviews with medical directors, surgeons, senior nurses, CM practitioners and hospitalized patients. We found that most of the interviewed nurses, surgeons and directors and some patients believed that CM treatments were of value in addressing the psychological needs of patients within this predominantly somatic-oriented department. To CM practitioners and some of the patients, integration means introducing and practicing a holistic outlook in this biomedical context, which involves elements such as Qi, energy, soul and spirit. Such practices were directed to a suitable audience, namely, patients as well as conventional medical staff who were willing to explore a holistic approach. We concluded that patient care tends to become more comprehensive when CM is integrated. Despite the overall dominance of biomedicine, holistic CM practices were introduced to the biomedical setting of the hospital. Yet, the question whether holistic CM practices and perceptions will eventually lead nurses and physicians toward paradigmatic integration, has still to be examined.
Bending analysis of soft core sandwich plates with embedded shape memory alloy wires using three-dimensional finite element method
Authors: Kheirikhah Mohammad M , Khadem Mahdi , Farahpour Peyman
Published: May 2012

In this article, bending behavior of the sandwich plates with embedded shape memory alloy wires in their face sheets is studied. Three-dimensional finite element method is used for constructing and analyzing the sandwich plates with flexible core and two stiff face sheets. Some important points such as continuity conditions of the displacements, satisfaction of inter-laminar transverse shear stresses, conditions of zero transverse shear stresses on the upper and lower surfaces and in-plane and transverse flexibility of the soft core are considered for the accurate modeling of the sandwich plate. Solutions for bending analysis of shape memory alloy wire-reinforced sandwich plates under various transverse loads are presented and the effects of plate dimensions, shape memory alloy wires diameter, boundary conditions and shape memory alloy wires embedding positions are studied. Comparison of the present results in special case with those of the three-dimensional theory of elasticity and some plate theories confirms the accuracy of the proposed model. According to the obtained numerical results, the local behavior of the sandwich plate in bending against various loading conditions was significantly improved by employing the shape memory alloy wires in the face sheets.
Combining Transcranial Electrical Stimulation With Electroencephalography
Authors: Miniussi Carlo , Brignani Debora , Pellicciari Maria C.
Published: May 2012

Although numerous studies have been performed using transcranial electrical stimulation (tES), our understanding of tES-induced effects on neural activity remains limited, especially regarding the effects on neural networks. The use of an approach, such as electroencephalography (EEG) in combination with tES, could allow for a more detailed understanding of the neural mechanisms involved in these observed changes. Co-registration of tES and EEG might provide high temporal resolution information regarding tES-induced modifications/modulations to cortical activity that corresponds to different stages of processing. This article aims at presenting new knowledge about this recent and innovative approach that can possibly provide information about the dynamics of human brain functions beyond what is possible by the use of either method alone.
Dose-finding clinical trial design for ordinal toxicity grades using the continuation ratio model: an extension of the continual reassessment method
Authors: Van Meter Emily M , Garrett-Mayer Elizabeth , Bandyopadhyay Dipankar
Published: May 2012

Background Various dose-finding clinical trial designs, including the continual reassessment method (CRM), dichotomize toxicity outcomes based on prespecified dose-limiting toxicity (DLT) criteria. This loss of toxicity information is particularly inefficient due to the small sample sizes in phase I trials, especially when Common Terminology Criteria for Adverse Events (CTCAE v4.0) are an established ordinal toxicity grading classification already used in the clinical practice.

Purpose The purpose of this simulation study is to incorporate ordinal toxicity grades as specified by CTCAE v4.0 using a continuation ratio (CR) model in the likelihood-based CRM.

Methods This simulation study compares the CR model design to the dichotomous CRM as well as an ordinal CRM that implements the proportional odds (PO) model. We compare six scenarios for model performance based on various safety and efficiency criteria and consider a range of dose–toxicity relationship models, including CR models, PO models, and models that violate the PO assumption.

Results The ordinal CRM performs as well as the dichotomous CRM in all scenarios considered, especially in situations where the starting dose is overly toxic, the ordinal designs show slight improvement in the estimation of the maximum tolerated dose (MTD) and fewer median patients exposed to excessively toxic dose levels as compared to the binary CRM. We also find slight discrepancies in the performance between the PO model and CR model; however, the differences were not substantial enough to strongly recommend one model over the other.

Limitations The CR model design does require slightly more input from clinical investigators prior to the start of the trial as compared to the dichotomous CRM. Investigators must specify the distribution of toxicity grades at the expected dose levels for a 10% and 90% DLT rate in this CR design. However, an R package will help with the implementation of this ordinal design.

Conclusions While the ordinal designs did not perform significantly better than the binary counterpart, we were able to incorporate maximal toxicity information available into a feasible dose-finding design without compromising overall design performance.
The temperature inside football helmets during head impact: a five-year study of collegiate football games
Authors: Rowson Steven , Duma Stefan M
Published: May 2012

The objective of this study was to measure in-helmet temperature at the time of impact in a large cohort of football players, as such data can provide new insight to the temperatures helmets should be evaluated at during experimental testing that assess helmet safety. A large cohort of Virginia Tech football players were instrumented with the HIT System (Simbex, Lebanon, NH, USA), which recorded in-helmet temperature and head acceleration for head impacts experienced during 60 games between 2006 and 2010. The average in-helmet temperature at time of impact was 76.4 °F ± 10.1 °F (24.6 °C ± 5.6 °C). In-helmet temperature was strongly correlated to the ambient temperature of the game. Head acceleration resulting from impact varied less than 10% across temperatures, and temperature did not significantly influence head acceleration. These data have implications for the testing conditions used in the laboratory when evaluating the safety of helmets.
Overcoming the stromal barrier: technologies to optimize drug delivery in pancreatic cancer
Authors: Dimou Anastasios , Syrigos Konstantinos N. , Saif Muhammad Wasif
Published: May 2012

Pancreatic cancer has historically proven resistant to anticancer agents. On the one hand, drugs might be more efficient if higher levels could be achieved at the tumor site rather than the normal tissues. On the other hand, the thick stroma and the relative absence of abundant vessels may account at least partially for the failure of successive clinical trials to demonstrate effective treatments in this type of malignancy. In this context, the development and testing in clinical trials of treatment strategies that aim to optimize drug delivery is an important target in improving the prognosis of patients with pancreatic cancer.
Oral renin inhibitors in clinical practice: a perspective review
Authors: Bonanni Luca , Dalla Vestra Michele
Published: May 2012

Hypertension is an important risk factor for cardiovascular morbidity and mortality. The importance of the renin–angiotensin–aldosterone system (RAAS) in cardiovascular and renal diseases has long been recognized: for this reason the conventional therapies, such as angiotensin-converting enzyme (ACE) inhibitors and angiotensin receptor blockers (ARBs), β-blockers, and aldosterone antagonists represent the backbone of current antihypertensive therapy. Aliskiren is the first direct renin inhibitor (DRI) suitable for oral administration. By achieving more complete renin–angiotensin system inhibition, direct renin inhibitors may afford greater protection from hypertensive complications. Present evidence indicates that aliskiren reduces baseline systolic and diastolic blood pressure greater than placebo and that it is as effective as other first-line antihypertensive agents. Extra advantages can be reached when it is used in combination therapy. Clinical trials and in vitro studies also suggest that aliskiren has several cardioprotective and renoprotective effects. Therapy with aliskiren is well tolerated, but recently some concerns have arisen because of the early termination of the ALTITUDE study due to an increased incidence of adverse effects.
Aberrant mural cell recruitment to lymphatic vessels and impaired lymphatic drainage in a murine model of pulmonary fibrosis
Authors: Meinecke Anna-Katharina , Nagy Nadine , Lago Gabriela D'Amico , Kirmse Santina , Klose Ralph , Schrödter Katrin , Zimmermann Annika , Helfrich Iris , Rundqvist Helene , Theegarten Dirk , Anhenn Olaf , Orian-Rousseau Véronique , Johnson Randall S. , Alitalo Kari , Fischer Jens W. , Fandrey Joachim , Stockmann Christian
Published: May 2012

Pulmonary fibrosis is a progressive disease with unknown etiology that is characterized by extensive remodeling of the lung parenchyma, ultimately resulting in respiratory failure. Lymphatic vessels have been implicated with the development of pulmonary fibrosis, but the role of the lymphatic vasculature in the pathogenesis of pulmonary fibrosis remains enigmatic. Here we show in a murine model of pulmonary fibrosis that lymphatic vessels exhibit ectopic mural coverage and that this occurs early during the disease. The abnormal lymphatic vascular patterning in fibrotic lungs was driven by expression of platelet-derived growth factor B (PDGF-B) in lymphatic endothelial cells and signaling through platelet-derived growth factor receptor (PDGFR)–β in associated mural cells. Because of impaired lymphatic drainage, aberrant mural cell coverage fostered the accumulation of fibrogenic molecules and the attraction of fibroblasts to the perilymphatic space. Pharmacologic inhibition of the PDGF-B/PDGFR-β signaling axis disrupted the association of mural cells and lymphatic vessels, improved lymphatic drainage of the lung, and prevented the attraction of fibroblasts to the perilymphatic space. Our results implicate aberrant mural cell recruitment to lymphatic vessels in the pathogenesis of pulmonary fibrosis and that the drainage capacity of pulmonary lymphatics is a critical mediator of fibroproliferative changes.
Unexpected frequency of Upshaw-Schulman syndrome in pregnancy-onset thrombotic thrombocytopenic purpura
Authors: Moatti-Cohen Marie , Garrec Céline , Wolf Martine , Boisseau Pierre , Galicier Lionel , Azoulay Elie , Stepanian Alain , Delmas Yahsou , Rondeau Eric , Bezieau Stéphane , Coppo Paul , Veyradier Agnès
Published: May 2012

Pregnancy may be complicated by a rare but life-threatening disease called thrombotic thrombocytopenic purpura (TTP). Most cases of TTP are due to an acquired autoimmune or hereditary (Upshaw-Schulman syndrome [USS]) severe deficiency of a disintegrin and metalloprotease with thrombospondin type 1 repeats, member 13 (ADAMTS13). In the present study, we performed a cross-sectional analysis of the national registry of the French Reference Center for Thrombotic Microangiopathies from 2000-2010 to identify all women who were pregnant at their initial TTP presentation. Among 592 adulthood-onset TTP patients with a severe ADAMTS13 deficiency, 42 patients with a pregnancy-onset TTP were included. Surprisingly, the proportion of USS patients (n = 10 of 42 patients [24%]; confidence interval, 13%-39%) with pregnancy-onset TTP was much higher than that in adulthood-onset TTP in general (less than 5%) and was mostly related to a cluster of ADAMTS13 variants. In the present study, subsequent pregnancies in USS patients not given prophylaxis were associated with very high TTP relapse and abortion rates, whereas prophylactic plasmatherapy was beneficial for both the mother and the baby. Pregnancy-onset TTP defines a specific subgroup of patients with a strong genetic background. This study was registered at www.clinicaltrials.gov as number NCT00426686 and at the Health Authority, French Ministry of Health, as number P051064.
Efficient use of unlabeled data for protein sequence classification: a comparative study
Authors: Kuksa Pavel , Huang Pai-Hsi , Pavlovic Vladimir
Published: May 2012

Background

Recent studies in computational primary protein sequence analysis have leveraged the power of unlabeled data. For example, predictive models based on string kernels trained on sequences known to belong to particular folds or superfamilies, the so-called labeled data set, can attain significantly improved accuracy if this data is supplemented with protein sequences that lack any class tags–the unlabeled data. In this study, we present a principled and biologically motivated computational framework that more effectively exploits the unlabeled data by only using the sequence regions that are more likely to be biologically relevant for better prediction accuracy. As overly-represented sequences in large uncurated databases may bias the estimation of computational models that rely on unlabeled data, we also propose a method to remove this bias and improve performance of the resulting classifiers.

Results

Combined with state-of-the-art string kernels, our proposed computational framework achieves very accurate semi-supervised protein remote fold and homology detection on three large unlabeled databases. It outperforms current state-of-the-art methods and exhibits significant reduction in running time.

Conclusion

The unlabeled sequences used under the semi-supervised setting resemble the unpolished gemstones; when used as-is, they may carry unnecessary features and hence compromise the classification accuracy but once cut and polished, they improve the accuracy of the classifiers considerably.
Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms
Authors: Lin Xiaotong , Liu Mei , Chen Xue-wen
Published: May 2012

Background

Protein-protein interactions play vital roles in nearly all cellular processes and are involved in the construction of biological pathways such as metabolic and signal transduction pathways. Although large-scale experiments have enabled the discovery of thousands of previously unknown linkages among proteins in many organisms, the high-throughput interaction data is often associated with high error rates. Since protein interaction networks have been utilized in numerous biological inferences, the inclusive experimental errors inevitably affect the quality of such prediction. Thus, it is essential to assess the quality of the protein interaction data.

Results

In this paper, a novel Bayesian network-based integrative framework is proposed to assess the reliability of protein-protein interactions. We develop a cross-species in silico model that assigns likelihood scores to individual protein pairs based on the information entirely extracted from model organisms. Our proposed approach integrates multiple microarray datasets and novel features derived from gene ontology. Furthermore, the confidence scores for cross-species protein mappings are explicitly incorporated into our model. Applying our model to predict protein interactions in the human genome, we are able to achieve 80% in sensitivity and 70% in specificity. Finally, we assess the overall quality of the experimentally determined yeast protein-protein interaction dataset. We observe that the more high-throughput experiments confirming an interaction, the higher the likelihood score, which confirms the effectiveness of our approach.

Conclusion

This study demonstrates that model organisms certainly provide important information for protein-protein interaction inference and assessment. The proposed method is able to assess not only the overall quality of an interaction dataset, but also the quality of individual protein-protein interactions. We expect the method to continually improve as more high quality interaction data from more model organisms becomes available and is readily scalable to a genome-wide application.
A unified computational model for revealing and predicting subtle subtypes of cancers
Authors: Ren Xianwen , Wang Yong , Wang Jiguang , Zhang Xiang-Sun
Published: May 2012

Background

Gene expression profiling technologies have gradually become a community standard tool for clinical applications. For example, gene expression data has been analyzed to reveal novel disease subtypes (class discovery) and assign particular samples to well-defined classes (class prediction). In the past decade, many effective methods have been proposed for individual applications. However, there is still a pressing need for a unified framework that can reveal the complicated relationships between samples.

Results

We propose a novel convex optimization model to perform class discovery and class prediction in a unified framework. An efficient algorithm is designed and software named OTCC (Optimization Tool for Clustering and Classification) is developed. Comparison in a simulated dataset shows that our method outperforms the existing methods. We then applied OTCC to acute leukemia and breast cancer datasets. The results demonstrate that our method not only can reveal the subtle structures underlying those cancer gene expression data but also can accurately predict the class labels of unknown cancer samples. Therefore, our method holds the promise to identify novel cancer subtypes and improve diagnosis.

Conclusions

We propose a unified computational framework for class discovery and class prediction to facilitate the discovery and prediction of subtle subtypes of cancers. Our method can be generally applied to multiple types of measurements, e.g., gene expression profiling, proteomic measuring, and recent next-generation sequencing, since it only requires the similarities among samples as input.
LKB1 tumor suppressor protein regulates actin filament assembly through Rho and its exchange factor Dbl independently of kinase activity
Authors: Xu Xiaojian , Omelchenko Tatiana , Hall Alan
Published: May 2012

Background

Germline mutations in LKB1 result in Peutz-Jeghers Syndrome characterized by intestinal hamartomas and increased incidence of epithelial cancers. LKB1 encodes a serine/threonine kinase that plays an important role in regulating energy metabolism through the AMPK/mTOR signaling pathway. In addition, LKB1 is homologous to PAR-4, a polarity protein first described in C. elegans, while activation of LKB1 in mammalian epithelial cells induces the polarized assembly of actin filaments.

Results

To explore the mechanism by which LKB1 interacts with the actin cytoskeleton, we introduced LKB1 into HeLa cells that lack endogenous LKB1. This results in activation of the small GTPase Rho and the assembly of linear actin filaments associated with focal adhesions. These effects on the actin cytoskeleton are attenuated by siRNA-mediated depletion of the guanine nucleotide exchange factor Dbl. Co-expression of the LKB1 with the adaptor protein STRAD induces actin filament puncta associated with phospho-ezrin.

Conclusions

This study reveals that LKB1 regulates the actin cytoskeleton through a Dbl/Rho pathway.
Development of genomic resources for the prairie vole (Microtus ochrogaster): construction of a BAC library and vole-mouse comparative cytogenetic map
Authors: McGraw Lisa A , Davis Jamie K , Lowman Josh J , ten Hallers Boudewijn FH , Koriabine Maxim , Young Larry J , de Jong Pieter J , Rudd M Katharine , Thomas James W
Published: May 2012

Background

The prairie vole (Microtus ochrogaster) is a premier animal model for understanding the genetic and neurological basis of social behaviors. Unlike other biomedical models, prairie voles display a rich repertoire of social behaviors including the formation of long-term pair bonds and biparental care. However, due to a lack of genomic resources for this species, studies have been limited to a handful of candidate genes. To provide a substrate for future development of genomic resources for this unique model organism, we report the construction and characterization of a bacterial artificial chromosome (BAC) library from a single male prairie vole and a prairie vole-mouse (Mus musculus) comparative cytogenetic map.

Results

We constructed a prairie vole BAC library (CHORI-232) consisting of 194,267 recombinant clones with an average insert size of 139 kb. Hybridization-based screening of the gridded library at 19 loci established that the library has an average depth of coverage of ~10×. To obtain a small-scale sampling of the prairie vole genome, we generated 3884 BAC end-sequences totaling ~2.8 Mb. One-third of these BAC-end sequences could be mapped to unique locations in the mouse genome, thereby anchoring 1003 prairie vole BAC clones to an orthologous position in the mouse genome. Fluorescence in situ hybridization (FISH) mapping of 62 prairie vole clones with BAC-end sequences mapping to orthologous positions in the mouse genome was used to develop a first-generation genome-wide prairie vole-mouse comparative cytogenetic map. While conserved synteny was observed between this pair of rodent genomes, rearrangements between the prairie vole and mouse genomes were detected, including a minimum of five inversions and 16 inter-chromosomal rearrangements.

Conclusions

The construction of the prairie vole BAC library and the vole-mouse comparative cytogenetic map represent the first genome-wide modern genomic resources developed for this species. The BAC library will support future genomic, genetic and molecular characterization of this genome and species, and the isolation of clones of high interest to the vole research community will allow for immediate characterization of the regulatory and coding sequences of genes known to play important roles in social behaviors. In addition, these resources provide an excellent platform for future higher resolution cytogenetic mapping and full genome sequencing.
Phylogenetic analysis and molecular characteristics of seven variant Chinese field isolates of PRRSV
Authors: Wang Chengmin , Wu Bin , Amer Said , Luo Jing , Zhang Hongmei , Guo Yunhai , Dong Guoying , Zhao Baohua , He Hongxuan
Published: May 2012

Background

Porcine reproductive and respiratory syndrome (PRRS) has now been widely recognized as an economically important disease. The objective of this study was to compare the molecular and biological characteristics of porcine reproductive and respiratory syndrome virus (PRRSV) field isolates in China to those of the modified live virus (MLV) PRRS vaccine and its parent strain (ATCC VR2332).

Results

Five genes (GP2, GP3, GP4, GP5 and NSP2) of seven isolates of PRRSV from China, designated LS-4, HM-1, HQ-5, HQ-6, GC-2, GCH-3 and ST-7/2008, were sequenced and analyzed. Phylogenetic analyses based on the nucleotide sequence of the ORF2-5 and NSP2 showed that the seven Chinese isolates belonged to the same genetic subgroup and were related to the North American PRRSV genotype. Comparative analysis with the relevant sequences of another Chinese isolate (BJ-4) and North American (VR2332 and MLV) viruses revealed that these isolates have 80.8-92.9% homology with VR-2332, and 81.3-98.8% identity with MLV and 80.7-92.9% with BJ-4. All Nsp2 nonstructural protein of these seven isolates exhibited variations (a 29 amino acids deletion) in comparison with other North American PRRSV isolates. Therefore, these isolates were novel strain with unique amino acid composition. However, they all share more than 97% identity with other highly pathogenic Chinese PRRSV strains. Additionally, there are extensive amino acid (aa) mutations in the GP5 protein and the Nsp2 protein when compared with the previous isolates.

Conclusions

These results might be useful to study the genetic diversity of PRRSV in China and to track the infection sources as well as for vaccines development.
Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa
Authors: Hu Ruibo , Qi Guang , Kong Yingzhen , Kong Dejing , Gao Qian , Zhou Gongke
Published: May 2012

Background

NAC (NAM, ATAF1/2 and CUC2) domain proteins are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. NAC transcription factors comprise of a large gene family represented by more than 100 members in Arabidopsis, rice and soybean etc. Recently, a preliminary phylogenetic analysis was reported for NAC gene family from 11 plant species. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, conserved motifs, and expression profiling analysis has been presented thus far for the model tree species Populus.

Results

In the present study, a comprehensive analysis of NAC gene family in Populus was performed. A total of 163 full-length NAC genes were identified in Populus, and they were phylogeneticly clustered into 18 distinct subfamilies. The gene structure and motif compositions were considerably conserved among the subfamilies. The distributions of 120 Populus NAC genes were non-random across the 19 linkage groups (LGs), and 87 genes (73%) were preferentially retained duplicates that located in both duplicated regions. The majority of NACs showed specific temporal and spatial expression patterns based on EST frequency and microarray data analyses. However, the expression patterns of a majority of duplicate genes were partially redundant, suggesting the occurrence of subfunctionalization during subsequent evolutionary process. Furthermore, quantitative real-time RT-PCR (RT-qPCR) was performed to confirm the tissue-specific expression patterns of 25 NAC genes.

Conclusion

Based on the genomic organizations, we can conclude that segmental duplications contribute significantly to the expansion of Populus NAC gene family. The comprehensive expression profiles analysis provides first insights into the functional divergence among members in NAC gene family. In addition, the high divergence rate of expression patterns after segmental duplications indicates that NAC genes in Populus are likewise to have been retained by substantial subfunctionalization. Taken together, our results presented here would be helpful in laying the foundation for functional characterization of NAC gene family and further gaining an understanding of the structure-function relationship between these family members.
RNAi-mediated silencing of the HD-Zip gene HD20 in Nicotiana attenuata affects benzyl acetone emission from corollas via ABA levels and the expression of metabolic genes
Authors: Ré Delfina A , Raud Brenda , Chan Raquel L , Baldwin Ian T , Bonaventure Gustavo
Published: May 2012

Background

The N. attenuata HD20 gene belongs to the homeodomain-leucine zipper (HD-Zip) type I family of transcription factors and it has been previously associated with the regulation of ABA accumulation in leaves and the emission of benzyl acetone (BA; 4-phenyl-2-butanone) from night flowers. In this study, N. attenuata plants stably reduced in the expression of HD20 (ir-hd20) were generated to investigate the mechanisms controlling the emission of BA from night flowers.

Results

The expression of HD20 in corollas of ir-hd20 plants was reduced by 85 to 90% compared to wild-type plants (WT) without affecting flower morphology and development. Total BA emitted from flowers of ir-hd20 plants was reduced on average by 60%. This reduction occurred mainly at the late phase of BA emission and it was correlated with 2-fold higher levels of ABA in the corollas of ir-hd20 plants. When a 2-fold decline in ABA corolla levels of these plants was induced by salt stress, BA emissions recovered to WT levels. Supplying ABA to WT flowers either through the cuticle or by pedicle feeding reduced the total BA emissions by 25 to 50%; this reduction occurred primarily at the late phase of emission (similar to the reduction observed in corollas of ir-hd20 plants). Gene expression profiling of corollas collected at 12 pm (six hours before the start of BA emission) revealed that 274 genes changed expression levels significantly in ir-hd20 plants compared to WT. Among these genes, more than 35% were associated with metabolism and the most prominent group was associated with the metabolism of aromatic compounds and phenylpropanoid derivatives.

Conclusions

The results indicated that regulation of ABA levels in corollas is associated with the late phase of BA emission in N. attenuata plants and that HD20 affects this latter process by mediating changes in both ABA levels and metabolic gene expression.
Genetic variants of NOXA and MCL1 modify the risk of HPV16-associated squamous cell carcinoma of the head and neck
Authors: Zhou Ziyuan , Sturgis Erich M , Liu Zhensheng , Wang Li-E , Wei Qingyi , Li Guojun
Published: May 2012

Abstracts

Background

The cooperation between phorbol 12-myristate 13-acetate induced protein 1 (NOXA) and myeloid cell leukemia 1 (MCL1) is critical in the intrinsic apoptotic pathway. Human papillomavirus 16 (HPV16), by inducing p53 and pRb-E2F degradation, may play an essential role in development of squamous cell carcinoma of the head and neck (SCCHN) through NOXA-MCL1 axis-mediated apoptosis. Therefore, genetic variants ofNOXAandMCL1may modify the SCCHN risk associated with HPV16 seropositivity.

Methods

HPV16 serology was obtained by immunoadsorption assay. Four functional SNPs in the promoter ofNOXA(rs9957673, rs4558496) andMCL1(rs9803935, rs3738485) were genotyped for 380 cases and 335 frequency-matched cancer-free controls of non-Hispanic whites.

Results

Associations between the four polymorphisms and SCCHN risk were not significant, while we observed a significantly joint effect on SCCHN risk between the polymorphisms and HPV16 seropositivity. Notably, this effect modification was particularly pronounced for oropharyngeal cancer in subgroups including never smokers, never drinkers and younger subjects.

Conclusions

Our results suggested that polymorphisms ofNOXAandMCL1may modify the risk of HPV16-associated oropharyngeal cancer. The further identification of population subgroups at higher risk provides evidence that HPV-targeting treatment may help benefit SCCHN. However, larger studies are needed to validate our findings.
Association of ATP binding cassette transporter G8 rs4148217 SNP and serum lipid levels in Mulao and Han nationalities
Authors: Li Qing , Wei Xian-Liang , Yin Rui-Xing
Published: May 2012

Background

The association of ATP binding cassette transporter G8 gene (ABCG8) rs4148217 single nucleotide polymorphism (SNP) and serum lipid profiles is still controversial in diverse racial/ethnic groups. Mulao nationality is an isolated minority in China. The aim of this study was to evaluate the association ofABCG8rs4148217 SNP and several environmental factors with serum lipid levels in the Guangxi Mulao and Han populations.

Methods

A total of 634 subjects of Mulao nationality and 717 participants of Han nationality were randomly selected from our previous samples. Genotyping of theABCG8rs4148217 SNP was performed by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and then confirmed by direct sequencing.

Results

The genotypic and allelic frequencies ofABCG8rs4148217 SNP were different between the two nationalities (P < 0.01 for each), the frequency of A allele was higher in Mulao than in Han. The A allele carriers in Han had lower high-density lipoprotein cholesterol (HDL-C) and apolipoprotein (Apo) A1 levels than the A allele noncarriers (P < 0.05 for each), whereas the A allele carriers in Mulao had lower ApoA1 levels than the A allele noncarriers (P < 0.05). Subgroup analyses showed that the A allele carriers in Han had lower HDL-C and higher triglyceride (TG) levels in females but not in males than the A allele noncarriers (P < 0.05 for each), and the A allele carriers in Mulao had lower ApoA1 levels in females but not in males than the A allele noncarriers (P < 0.05). The levels of TG and HDL-C in Han, and ApoA1 in Mulao were associated with genotypes in females but not in males (P < 0.05-0.01). Serum lipid parameters were also correlated with several environmental factors (P < 0.05-0.001).

Conclusions

TheABCG8rs4148217 SNP is associated with serum TG, HDL-C and ApoA1 levels in our study populations, but this association is different between the Mulao and Han populations. There is a sex (female)-specific association in both ethnic groups.
Localized geometric topologies with bounded node degree for three-dimensional wireless sensor networks
Authors: Li Fan , Chen Zeming , Wang Yu
Published: May 2012

Three-dimensional (3D) wireless sensor networks have attracted a lot of attention due to their great potential usages in both commercial and civilian applications, such as environmental data collection, pollution monitoring, space exploration, disaster prevention, and tactical surveillance. Topology control in 3D sensor networks has been studied recently, and different 3D geometric topologies were proposed to be the underlying network topologies to achieve the sparseness of the communication networks. However, most of these proposed 3D topologies cannot bound the maximum node degree, i.e., some nodes may need to maintain a large number of neighbors in the constructed topologies, which is not energy efficient and may lead to large contention. In this article, we extend several existing 3D geometric topologies to a set of new 3D topologies with bounded node degree. We provide both theoretical analysis and simulation evaluation on their power efficiency and node degree distributions. Our simulation results over random 3D sensor networks confirm nice performances of these proposed 3D topologies.
On a hybrid algorithm for a family of total quasi-ϕ-asymptotically nonexpansive mappings in Banach spaces
Authors: Zuo Ping , Chang Shih-sen , Liu Min
Published: May 2012

The purpose of this article is to introduce the concept of total quasi- ϕ-asymptotically nonexpansive mapping which contains many kinds of mappings as its special cases and we prove a strong convergence theorem by using a hybrid method for finding a common element of the set of solutions for a generalized mixed equilibrium problems, the set of fixed points of a family of total quasi- ϕ-asymptotically nonexpansive mappings in uniformly smooth and strictly convex Banach space with the Kadec-Klee property. The results presented in the article improve and extend some recent results.

MR (2000) Subject Classification: 47H09; 47H05.
A never ending race for new and improved fluorescent proteins
Authors: Jones Alexander M , Ehrhardt David W , Frommer Wolf B
Published: May 2012

Bioluminescent and fluorescent proteins are now used as tools for research in all organisms. There has been massive progress over the past 15 years in creating a palette of fluorescent proteins with a wide spectrum of specific properties. One of the big challenges is to decide which variant may be best for a certain application. A recent article by Mann et al. in BMC Biotechnology describes a new orange fluorescent protein in plants.

See research article http://www.biomedcentral.com/1472-6750/12/17