bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐precision measurements of ionospheric TEC gradients with the Very Large Array VHF system
Authors: Helmboldt J. F. , Lazio T. J. W. , Intema H. T. , Dymond K. F. 
Published: January 2012

We have used a relatively long, contiguous VHF observation of a bright cosmic radio source (Cygnus A) with the Very Large Array (VLA) to demonstrate the capability of this instrument to study the ionosphere. This interferometer, and others like it, can observe ionospheric total electron content (TEC) fluctuations on a much wider range of scales than is possible with many other instruments. We have shown that with a bright source, the VLA can measure differential TEC values between pairs of antennas (δTEC) with a precision of 3 × 10−4 TECU. Here, we detail the data reduction and processing techniques used to achieve this level of precision. In addition, we demonstrate techniques for exploiting these high‐precision δTEC measurements to compute the TEC gradient observed by the array as well as small‐scale fluctuations within the TEC gradient surface. A companion paper details specialized spectral analysis techniques used to characterize the properties of wave‐like fluctuations within this data.
Do Behavioral Syndromes Affect Foraging Strategy and Risk‐Taking in a Juvenile Fish Predator?
Authors: Nannini Michael A. , Parkos Joseph , Wahl David H. 
Published: January 2012

AbstractBehavioral syndromes often have individuals varying along a continuum of personality traits. Some individuals exhibit bold or aggressive behaviors and are willing to explore novel stimuli, whereas others are shy and tend to avoid novel stimuli. Species that undergo an ontogenetic diet shift may experience a particularly important benefit if the shift to more‐profitable prey is linked to this willingness to explore novel stimuli. However, actively selecting more‐evasive prey can make these predators more vulnerable to predation themselves. We used largemouth bass Micropterus salmoides as a model to examine the role of behavioral syndromes in structuring predator strategies for dealing with these conflicting environmental pressures. Exploration behavior was first determined by testing willingness to explore a novel environment. Behaviors were then measured in two other contexts where exploration and boldness could potentially have fitness consequences: (1) the likelihood of consuming a novel prey item and (2) movement in the presence of a predator. Fish that tended to be exploratory consumed more total prey biomass than did fish that avoided a novel environment; however, the nonexploratory fish were more discriminating and targeted novel fish prey to a greater extent than did bold fish. Activity in the presence of a predator was not related to any other factor measured. Although our results provide no evidence that behavioral syndromes influence the predator avoidance behavior of largemouth bass, these syndromes do appear to play an important role in prey selection. Our study indicates that although behavioral syndromes do not necessarily affect behavior across all environmental contexts, they may influence feeding strategies and thus could potentially affect the timing of dietary shifts.
Patterns of Hybridization of Nonnative Cutthroat Trout and Hatchery Rainbow Trout with Native Redband Trout in the Boise River, Idaho
Authors: Neville Helen M. , Dunham Jason B. 
Published: January 2012

Abstract
Hybridization is one of the greatest threats to native fishes. Threats from hybridization are particularly important for native trout species as stocking of nonnative trout has been widespread within the ranges of native species, thus increasing the potential for hybridization. While many studies have documented hybridization between native cutthroat trout Oncorhynchus clarkii and nonnative rainbow trout O. mykiss, fewer have focused on this issue in native rainbow trout despite widespread threats from introductions of both nonnative cutthroat trout and hatchery rainbow trout. Here, we describe the current genetic (i.e., hybridization) status of native redband trout O. mykiss gairdneri populations in the upper Boise River, Idaho. Interspecific hybridization was widespread (detected at 14 of the 41 sampled locations), but high levels of hybridization between nonnative cutthroat trout and redband trout were detected in only a few streams. Intraspecific hybridization was considerably more widespread (almost 40% of sampled locations), and several local populations of native redband trout have been almost completely replaced with hatchery coastal rainbow trout O. mykiss irideus; other populations exist as hybrid swarms, some are in the process of being actively invaded, and some are maintaining genetic characteristics of native populations. The persistence of some redband trout populations with high genetic integrity provides some opportunity to conserve native genomes, but our findings also highlight the complex decisions facing managers today. Effective management strategies in this system may include analysis of the specific attributes of each site and population to evaluate the relative risks posed by isolation versus maintaining connectivity, identifying potential sites for control or eradication of nonnative trout, and long-term monitoring of the genetic integrity of remaining redband trout populations to track changes in their status.
Received February 24, 2011; accepted August 4, 2011
Na+–K+–2Cl− cotransporter type 2 trafficking and activity: The role of interacting proteins
Authors: Carmosino Monica , Procino Giuseppe , Svelto Maria 
Published: January 2012

AbstractThe central role of Na+–K+–2Cl− cotransporter type 2 (NKCC2) in vectorial transepithelial salt reabsorption in thick ascending limb cells from Henle's loop in the kidney is evidenced by the effects of loop diuretics, the pharmacological inhibitors of NKCC2, that are amongst the most powerful antihypertensive drugs available to date. Moreover, genetic mutations of the NKCC2 encoding gene resulting in impaired apical targeting and function of NKCC2 transporter give rise to a pathological phenotype known as type I Bartter syndrome, characterised by a severe volume depletion, hypokalaemia and metabolic alkalosis with high prenatal mortality. On the contrary, excessive NKCC2 activity has been linked with inherited hypertension in humans and in rodent models. Interestingly, in animal models of hypertension, NKCC2 upregulation is achieved by post‐translational mechanisms underlining the need to analyse the molecular mechanisms involved in the regulation of NKCC2 trafficking and activity to gain insights in the pathogenesis of hypertension.
A role for microtubules in endothelial cell protrusion in three‐dimensional matrices
Authors: Martins Gabriel G. , Kolega John 
Published: January 2012

AbstractBackground informationMost cells reside in vivo in a three‐dimensional (3D) environment surrounded by extracellular matrix and other neighbouring cells, conditions that are different from those found by cells cultured in vitro on two‐dimensional (2D) substrata. Cell morphology and behaviour are very different under these two different conditions, but the structural basis for these differences is still not understood, especially the role of microtubules (MTs). To address this issue, we studied the early spreading behaviour of bovine aortic endothelial cells (BAECs) cultured in 3D collagen matrices and on 2D substrata, in the presence of MT‐disrupting drugs.ResultsWe found that depolymerisation of MTs greatly reduces the ability of BAECs to form large and stable protrusions inside 3D collagen matrices, an effect that is less pronounced when the cells are cultured on 2D substrata. Colcemid‐treated BAECs inside 3D matrices begin assembling protrusions and pull on the matrix, but they fail to extend those protrusions deep into the matrix. It has been previously reported that MT disruption affects Rho signalling which may result in increased cell rigidity and adhesiveness to 2D matrices. Accordingly, we demonstrate that colcemid treatment indeed leads to activation of Rho‐kinase (ROCK) targets, which in turn results in activation of regulatory myosin light chains, and that blocking of ROCK mitigates some of the effects of MT disruption in cell spreading in 3D.ConclusionsOur results show that MT depolymerisation is particularly disruptive when cells interact with pliable 3D matrices, suggesting a role for MTs and the Rho pathway in the fine‐tuning of contractile and adhesive forces necessary to sustain cell motility in vivo.
Timing of gonadectomy in adult women with complete androgen insensitivity syndrome (CAIS): patient preferences and clinical evidence
Authors: Deans Rebecca , Creighton Sarah M. , Liao Lih‐Mei , Conway Gerard S. 
Published: January 2012

AbstractObjective  Adult women with complete androgen insensitivity syndrome (CAIS) are increasingly likely to defer or decline gonadectomy despite counselling about malignancy risk. The objectives of this study were to review the evidence on the risk of gonadal malignancy in adult women with CAIS and to explore women’s reasons for deferring gonadectomy.Study Design  A case series and literature review.Patients  Sixteen women with CAIS over the age of 18 years who have elected to defer gonadectomy.Results  Sixty‐two relevant papers were identified. Of these, 14 confirmed that tumours had been reported in 98 adults. Taking into account the limitations of combining historic case series, this review estimates a risk of gonadal malignancy of 14% (range 0% and 22%) in adults with CAIS. The most common reasons women offered for deferring gonadectomy included inconvenience of surgery, concern about surgical risk and reluctance to take hormone replacement therapy.Conclusions  Perceived benefits for retaining gonads in women with CAIS are prompting more women to keep their gonads in situ. An accurate estimate for adult malignancy risk is unavailable, and the risks currently quoted may be falsely reassuring.
Integrin signalling and function in immune cells
Authors: Zhang Yanbo , Wang Hongyan 
Published: January 2012

SummaryIntegrins not only mediate cell–cell and cell–extracellular matrix adhesion, but also affect the multitude of signal transduction cascades in control of cell survival, proliferation, differentiation and organ development. Mutations in integrins or the major effectors of integrin signalling pathways cause defective organ development, immunodeficiency, cancer or autoimmune disease. Understanding of the signalling events that drive integrin activation and signalling is therefore crucial to uncover the molecular mechanisms of these diseases. This review discusses the key signalling complexes regulating integrin activation and function in both ‘inside‐out’ and ‘outside‐in’ pathways in T lymphocytes, including kinases, SLP‐76, VAV1, ADAP, SKAP‐55, RapL, RIAM, Rap1, Talin and Kindlin.
Estimation of tissue osteopontin levels before and after different traditional therapeutic modalities in psoriatic patients
Authors: El‐Eishi N.H. , Kadry D. , Hegazy R.A. , Rashed L. 
Published: January 2012

AbstractBackground  Several lines of evidences support a major role for Th1 cells in psoriasis. Treatment of psoriasis with cyclosporine, methotrexate and psoralen plus ultraviolet A (PUVA) is associated with clinical improvement and decrease in epidermal hyperplasia. Osteopontin (OPN) exerts a T‐helper type 1 (Th1) cytokine function, regulating inflammatory cell accumulation and function.Objective  To detect the effects of methotrexate, cyclosporine and PUVA on OPN expression in psoriatic plaques, and whether these changes correlate with clinical response.Methods  For three groups of psoriatic patients (each including 12 patients), the Psoriasis Area Severity Index (PASI) and levels of lesional skin OPN were determined using enzyme‐linked immunosorbent assays before and after treatment with methotrexate, cyclosporine or PUVA. Skin biopsies from 20 healthy volunteers served as control for OPN levels in normal skin.Results  Baseline lesional skin of psoriatic patients showed a statistically significant elevation of OPN levels in comparison to controls. Three months after therapy, the three therapeutic modalities were associated with a significant decrease in the mean levels of PASI and tissue OPN, with the PUVA group showing the highest level of reduction in OPN levels and cyclosporine group showing the highest level of reduction in PASI.Conclusion  Our study points to the possible role played by OPN in the pathogenesis of psoriasis and in reflecting disease severity. These standard therapeutic modalities used in the current study were associated with a significant decrease in PASI and OPN levels. They constitute highly effective therapeutic modalities for psoriasis, which might exert their anti‐psoriatic activity partially through altering the expression of OPN.
Status of oxidative stress on lesional skin surface of plantar warts
Authors: Arican O. , Ozturk P. , Kurutas E.B. , Unsal V. 
Published: January 2012

AbstractBackground  Warts are abnormal skin growths caused by human papilloma virus (HPV) infections within the skin of the patients. Sometimes the disease is difficult to treatment, and also, the relationship between HPV and some forms of skin cancers is important. The cutaneous oxidative stress status of warts is absent in the literature.Objectives  To evaluate the role of oxidative stress in affected skin areas in a group of patients with plantar warts.Methods  Thirty‐six consecutive patients with a diagnosis of plantar warts were enrolled. The samples were obtained by scraping the skin surface. Superoxide dismutase (SOD) and catalase (CAT) activities and malondialdehyde (MDA) levels were measured spectrophotometrically at samples.Results  The SOD activity was significantly lower, and the MDA level was significantly higher on the lesional area than on the non‐lesional area (P < 0.001 for each), and there was no significant difference in the CAT activity between both areas (P = 0.11).Conclusion  Cutaneous oxidative stress in patients with plantar warts may play a role in pathogenesis of the disease. The addition of topical drugs with antioxidative effects may be valuable in the treatment of warts.
Ca2+ signals of astrocytes are modulated by the NAD+/NADH redox state
Authors: Requardt Robert P. , Hirrlinger Petra G. , Wilhelm Franziska , Winkler Ulrike , Besser Stefanie , Hirrlinger Johannes 
Published: January 2012

J. Neurochem. (2012) 120, 1014–1025.AbstractAstrocytes are important glial cells in the brain providing metabolic support to neurons as well as contributing to brain signaling. These different functional levels have to be highly coordinated to allow for proper cell and brain function. In this study, we show that in astrocytes the NAD+/NADH redox state modulates dopamine‐induced Ca2+ signals thereby connecting metabolism and Ca2+ signaling. Application of dopamine induced a dose‐dependent increase in Ca2+ signal frequency in these cells, which was dependent on D1‐receptor signaling, glycolytic activity, an increase in cytosolic NADH and inositol 1,4,5‐triphosphate receptor operated intracellular Ca2+ stores. Application of dopamine at a low concentration (1 μM) did not induce an increase in Ca2+ signal frequency by itself. However, simultaneously increasing cytosolic NADH content either by direct application of NADH or by application of lactate resulted in a pronounced increase in Ca2+ signal frequency. This increase could be blocked by co‐application of pyruvate, suggesting that indeed the NAD+/NADH redox state is regulating Ca2+ signals. We conclude that at the NAD+/NADH redox state metabolic and signaling information is integrated in astrocytes, thereby most likely contributing to precisely coordinate these different tasks of astrocytes.
Identification of F‐box only protein 7 as a negative regulator of NF‐kappaB signalling
Authors: Kuiken Hendrik J. , Egan David A. , Laman Heike , Bernards Rene , Beijersbergen Roderick L. , Dirac Annette M. 
Published: January 2012

AbstractThe nuclear factor κB (NF‐κB) signalling pathway controls important cellular events such as cell proliferation, differentiation, apoptosis and immune responses. Pathway activation occurs rapidly upon TNFα stimulation and is highly dependent on ubiquitination events. Using cytoplasmic to nuclear translocation of the NF‐κB transcription factor family member p65 as a read‐out, we screened a synthetic siRNA library targeting enzymes involved in ubiquitin conjugation and de‐conjugation for modifiers of regulatory ubiquitination events in NF‐κB signalling. We identified F‐box protein only 7 (FBXO7), a component of Skp, Cullin, F‐box (SCF)‐ubiquitin ligase complexes, as a negative regulator of NF‐κB signalling. F‐box protein only 7 binds to, and mediates ubiquitin conjugation to cIAP1 and TRAF2, resulting in decreased RIP1 ubiquitination and lowered NF‐κB signalling activity.
Using ESTs database to predict and validate single polymorphisms at the HLA system
Authors: Figueiredo T. C. , de Oliveira J. R. M. 
Published: January 2012

SummaryWe propose a bioinformatics pipeline in which we use an ESTs database to predict and validate single‐nucleotide polymorphisms (SNPs) directly linked to gene‐coding regions at the HLA class I genes (HLA‐A, HLA‐B and HLA‐C). Annotation originated from our analysis revealed various classes of possible new variations that may indicate possible new alleles. Thus, bioinformatics pipelines seem to be useful approaches to help screening for novel genetic variations at the HLA panel, and further analysis will foster this aim to provide celerity at the massive analysis of data currently generated in large‐scale high‐throughput experiments.
Polymorphisms of NOD2 and the risk of tuberculosis: a validation study in the Chinese population
Authors: Pan H. , Dai Y. , Tang S. , Wang J. 
Published: January 2012

SummaryA genome‐wide association study (GWAS) of leprosy reported four specific genetic polymorphisms of NOD2 that were associated with susceptibility to Mycobacterium leprae in China. Considering the role of NOD2 in innate immune defence, we performed a study in a Chinese population to determine whether the same SNPs of NOD2 that were associated with disease caused by M. leprae were also associated with disease caused by Mycobacterium tuberculosis. We performed a frequency‐matched case–control study in 1043 patients with pulmonary tuberculosis and 808 unaffected controls. All subjects were >15 years old and were Han Chinese from Jiangsu Province. We extracted DNA from a blood sample from each study participant. SNPs of rs3135499, rs7194886, rs8057341 and rs9302752 in the NOD2 gene were genotyped using a TaqMan‐based allelic discrimination system. Using all possible patients with tuberculosis as cases, no significant association was found between the four specific SNPs and the risk of tuberculosis. In a subgroup analysis restricted to cases with bacteriologically confirmed tuberculosis (sputum culture positive), the variant genotype of rs7194886 was significantly associated with an altered risk of tuberculosis. Compared with the CC genotype, individuals carrying the CT/TT genotype of rs7194886 had an increased risk [odds ratio (OR) 1.35, 95% confidence interval (CI) (1.05–1.72)]. The association was stronger among tobacco smokers and males. By haplotype analysis, rs9302752C–rs7194886T was associated with an increased risk of bacteriologically confirmed tuberculosis (sputum culture positive) (P = 0.039), but it was not significant after correcting for multiple comparisons. In summary, genetic polymorphisms of the SNP rs7194886 in the NOD2 gene, which were discovered in the GWAS of leprosy, might also be associated with the pulmonary tuberculosis in the Chinese population.
The influence of age and aerobic fitness: effects on mitochondrial respiration in skeletal muscle
Authors: Larsen S. , Hey‐Mogensen M. , Rabøl R. , Stride N. , Helge J. W. , Dela F. 
Published: January 2012

AbstractAim:Mitochondrial function has previously been studied in ageing, but never in humans matched for maximal oxygen uptake (). Furthermore, the influence of ageing on mitochondrial substrate sensitivity is not known.Methods:Skeletal muscle mitochondrial respiratory capacity and mitochondrial substrate sensitivity were measured by respirometry in young (23 ± 3 years) and middle‐aged (53 ± 3 years) male subjects with similar . Protocols for respirometry included titration of substrates for complex I (glutamate), complex II (succinate) and both (octanoyl carnitine) for calculation of substrate sensitivity (C50). Myosin heavy chain (MHC) isoforms, citrate synthase (CS) and β‐hydroxy‐acyl‐CoA‐dehydrogenase (HAD) activity, mitochondrial DNA (mtDNA) content, protein levels of complexes I–V and antioxidant defence system [manganese superoxide dismutase (MnSOD)] were measured.Results:No differences were found in maximal mitochondrial respiration or C50 with glutamate (2.0 ± 0.3 and 1.8 ± 0.3 mm), succinate (3.7 ± 0.2 and 3.8 ± 0.4 mm) or octanoyl carnitine (47 ± 8 and 56 ± 7 μm) in young and middle‐aged subjects respectively. Normalizing mitochondrial respiration to mtDNA young subjects had a higher (P < 0.05) respiratory capacity per mitochondrion compared to middle‐aged subjects. HAD activity and mtDNA per mg tissue were higher in middle‐aged compared to young subjects. Middle‐aged had a higher MHC I isoform and a lower MHC IIX isoform content compared to young subjects.Conclusion:Mitochondrial substrate sensitivity is not affected by ageing. When young and middle‐aged men are carefully matched for , mitochondrial respiratory capacity is also similar. However, per mitochondrion respiratory capacity was lower in middle‐aged compared to young subjects. Thus, when matched for , middle‐aged seem to require a higher mitochondrial content than young subjects.
The impact of pandemic influenza A (H1N1) 2009 on the circulation of respiratory viruses 2009–2011
Authors: Mak Gannon C. , Wong Ann H. , Ho Winnie Y. Y. , Lim Wilina 
Published: January 2012

Please cite this paper as: Mak et al. (2012) The impact of pandemic influenza A (H1N1) 2009 on the circulation of respiratory viruses 2009–2011. Influenza and Other Respiratory Viruses 6(3), e6–e10.Surveillance of respiratory viruses has been conducted for many years at the public health laboratory in Hong Kong. With the occurrence of pandemic influenza A (H1N1) 2009, we observed a change in the seasonality of influenza activity with a seemingly corresponding change in the activity of respiratory syncytial virus, parainfluenza virus, and adenovirus during 2009–2011. This phenomenon could most likely be explained by virus interference.
MEASURING THE PERFORMANCE OF ORDINAL CLASSIFICATION
Authors: CARDOSO JAIME S. , SOUSA RICARDO 
Published: January 2012

Ordinal classification is a form of multiclass classification for which there is an inherent order between the classes, but not a meaningful numeric difference between them. The performance of such classifiers is usually assessed by measures appropriate for nominal classes or for regression. Unfortunately, these do not account for the true dimension of the error. The goal of this work is to show that existing measures for evaluating ordinal classification models suffer from a number of important shortcomings. For this reason, we propose an alternative measure defined directly in the confusion matrix. An error coefficient appropriate for ordinal data should capture how much the result diverges from the ideal prediction and how "inconsistent" the classifier is in regard to the relative order of the classes. The proposed coefficient results from the observation that the performance yielded by the Misclassification Error Rate coefficient is the benefit of the path along the diagonal of the confusion matrix. We carry out an experimental study which confirms the usefulness of the novel metric.