bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean
Authors: Gómez‐Pereira Paola R. , Schüler Margarete , Fuchs Bernhard M. , Bennke Christin , Teeling Hanno , Waldmann Jost , Richter Michael , Barbe Valérie , Bataille Elodie , Glöckner Frank Oliver , Amann Rudolf 
Published: September 2011

SummaryBacteroidetes are widespread in marine systems where they play a crucial role in organic matter degradation. Whole genome analysis of several strains has revealed a broad glycolytic and proteolytic potential. In this study, we used a targeted metagenomic approach to investigate the degradation capabilities of distinct Bacteroidetes clades from two contrasting regions of the North Atlantic Ocean, the Polar Biome (BPLR) and the North Atlantic Subtropical (NAST). We present here the analysis of 76 Bacteroidetes fosmids, of which 28 encode the 16S rRNA gene as phylogenetic marker, and their comparison to complete Bacteroidetes genomes. Almost all of the 16S rRNA harbouring fosmids belonged to clades that we previously identified in BPLR and NAST. The majority of sequenced fosmids could be assigned to Bacteroidetes affiliated with the class Flavobacteria. We also present novel genomic information on the classes Cytophagia and Sphingobacteria, suggesting a capability of the latter for attachment to algal surfaces. In our fosmid set we identified a larger potential for polysaccharide degradation and cell surface attachment in the phytoplankton‐rich BPLR. Particularly, two flavobacterial fosmids, one affiliated with the genus Polaribacter, showed a whole armoury of enzymes that likely function in degradation of sulfated polysaccharides known to be major constituents of phytoplankton cell walls. Genes involved in protein and peptidoglycan degradation, although present in both fosmid sets, seemed to have a slight preponderance in NAST. This study provides support for the hypothesis of a distinct specialization among marine Bacteroidetes for the degradation of certain types of polymers.
Rhodoferax‐related pufM gene cluster dominates the aerobic anoxygenic phototrophic communities in German freshwater lakes
Authors: Salka Ivette , Čuperová Zuzana , Mašín Michal , Koblížek Michal , Grossart Hans‐Peter 
Published: September 2011

SummaryThe presence of aerobic anoxygenic phototrophs (AAPs) has been repeatedly reported from various marine environments, but their distribution in freshwater lakes was neglected until recently. We investigated the phylogenetic composition of AAP communities in 10 lakes in Northeastern Germany with different trophic status including oligotrophic Lake Stechlin and humic matter rich Lake Grosse Fuchskuhle. The AAP community was composed by members of Alpha‐ and Betaproteobacteria, but their contribution varied largely among the studied lakes. Our results show that AAP community composition in the studied lakes was affected mostly by pH and humic matter content. While alkaline lakes were mostly composed of Betaproteobacteria, the acidic and humic matter rich south‐west (SW) basin of Lake Grosse Fuchskule was dominated (87%) by Alphaproteobacteria. The most frequent group within Betaproteobacteria was a cluster of pufM genes which was phylogenetically related to Rhodoferax representing 38.5% of all retrieved sequences. Alphaproteobacteria‐related sequences had a broader phylogenetic diversity including six different taxa dominated by Sphingomonas‐ and Rhodobacter‐like bacteria in lakes with alkaline to neutral pH. In the acidic and humic matter‐rich SW basin of Lake Grosse Fuchskuhle, however, Methylobacterium‐related sequences dominated the AAP community. We suggest that the variable AAP community structure might reflect the potential of these bacteria to cope with the contrasting conditions in freshwater environments.
Off‐label intravenous thrombolysis in acute stroke
Authors: Guillan M. , Alonso‐Canovas A. , Garcia‐Caldentey J. , Sanchez‐Gonzalez V. , Hernandez‐Medrano I. , DeFelipe‐Mimbrera A. , Matute M. C. , Alonso‐Arias M. A. , Alonso de Leciñana M. , Masjuan J. 
Published: September 2011

Background and purpose: Therapy for stroke with intravenous tissue plasminogen activator (IV‐tPA) is hampered by tight licensing restrictions; some of them have been discussed in recent literature. We assessed the safety and effectiveness of off‐label IV‐tPA in the clinical settings.Methods: Retrospective analysis of all the patients treated with IV‐tPA at our Stroke Unit. Patients were divided into two groups by licence criteria [on‐label group (OnLG), off‐label group (OffLG)]. Primary outcome measures were symptomatic intracranial haemorrhages (sICH), major systemic haemorrhages, modified Rankin scale (mRS) and mortality rate at 3 months.Results: Five hundred and five patients were registered, 269 (53.2%) were assigned to OnLG and 236 (46.9%) to OffLG. Inclusion criteria for the OffLG were aged >80 years (129 patients), time from onset of symptoms to treatment over 3 h (111), prior oral anticoagulant treatment with International Normalised Ratio ≤ 1.7 (41), combination of previous stroke and diabetes mellitus (14), surgery or severe trauma within 3 months of stroke (13), National Institutes of Health Stroke Scale score over 25 (11), intracranial tumours (5), systemic diseases with risk of bleeding (7) and seizure at the onset of stroke (2). No significant differences were identified between both groups regarding the proportion of sICH (OnLG 2.2% vs. OffLG 1.6%, P = 0.78) or the 3‐month mortality rate (11.1% vs. 19%: odds ratio (OR), 1.49; 95% CI, 0.86–2.55; P = 0.14). Multivariate analysis showed no significant differences in functional independence at 3 months between both groups (mRS <3 64.3% vs. 50.4%: OR mRS >2 1.7; 95% CI, 0.96–2.5; P = 0.07).Conclusion: Intravenous thrombolysis may be safe and efficacious beyond its current label restrictions.
Mass univariate analysis of event‐related brain potentials/fields I: A critical tutorial review
Authors: Groppe David M. , Urbach Thomas P. , Kutas Marta 
Published: September 2011

AbstractEvent‐related potentials (ERPs) and magnetic fields (ERFs) are typically analyzed via ANOVAs on mean activity in a priori windows. Advances in computing power and statistics have produced an alternative, mass univariate analyses consisting of thousands of statistical tests and powerful corrections for multiple comparisons. Such analyses are most useful when one has little a priori knowledge of effect locations or latencies, and for delineating effect boundaries. Mass univariate analyses complement and, at times, obviate traditional analyses. Here we review this approach as applied to ERP/ERF data and four methods for multiple comparison correction: strong control of the familywise error rate (FWER) via permutation tests, weak control of FWER via cluster‐based permutation tests, false discovery rate control, and control of the generalized FWER. We end with recommendations for their use and introduce free MATLAB software for their implementation.
Parsing relationships between dimensions of anxiety and action monitoring brain potentials in female undergraduates
Authors: Moser Jason S. , Moran Tim P. , Jendrusina Alexander A. 
Published: September 2011

AbstractAnxiety is associated with enhanced action monitoring. Research to date, however, has employed extreme group designs that fail to address the full spectrum of anxiety, and in which overlapping and co‐occurring symptoms obscure the exact nature of the relationships between anxiety and action monitoring. To address these limitations, relationships between distinct dimensions of anxiety and neural indicators of action monitoring were examined in a sample of female undergraduates. Results revealed that higher anxious apprehension (i.e., worry) was associated with enhanced early action monitoring activity, as indexed by the error‐related negativity/correct‐response negativity. Anxious arousal (i.e., somatic tension) on the other hand, was unrelated to measures of action monitoring. These findings suggest that the anxiety‐action monitoring link holds along the continuum of severity and is specific to the worry component of anxiety.
Monitoring force errors: Medial‐frontal negativity in a unimanual force‐production task
Authors: Armbrecht Anne‐Simone , Gibbons Henning , Stahl Jutta 
Published: September 2011

AbstractThe effects of force production on medial‐frontal negativity (MFN), reflecting the activity of an internal action‐monitoring system, were investigated in a force‐production task. A precue indicated a low or high force before a stimulus signaled the execution of the same or opposite force. An incorrectly exerted force was assumed to involve an error of force selection if the opposite force was required (invalid precue), and an error of force execution if the same force was required (valid precue). The task was repeated to examine any improvements in monitoring sensitivity. No force‐related effects were observed on MFN amplitude. Although performance improved, there was no evidence of a force‐error sensitive monitoring system. As the MFN and motor activity were affected by the precue invalidity regardless of the response outcome, the MFN might reflect the activity of a general action‐evaluation system that is indirectly related to motor activation.
Intra‐operative frozen section analysis for suspected early‐stage ovarian cancer: 11 years of Gateshead Cancer Centre experience
Authors: Cross PA , Naik R , Patel A , Nayar AGN , Hemming JD , Williamson SLH , Henry JA , Edmondson RJ , Godfrey KA , Galaal K , Kucukmetin A , Lopes AD 
Published: September 2011

Please cite this paper as: Cross P, Naik R, Patel A, Nayar A, Hemming J, Williamson S, Henry J, Edmondson R, Godfrey K, Galaal K, Kucukmetin A, Lopes A. Intra‐operative frozen section analysis for suspected early‐stage ovarian cancer: 11 years of Gateshead Cancer Centre experience. BJOG 2012;119:194–201.Objective  In centres in which intra‐operative frozen section (FS) analysis is not performed, ‘apparent’ early‐stage ovarian cancer diagnosed after surgery on paraffin section may require further restaging laparotomy or adjuvant chemotherapy. Previous studies on FS analysis have reported high sensitivity, specificity and overall accuracy. The objective of this article is to present the largest published dataset on the accuracy of FS analysis over an 11‐year period from a single institution.Design  Diagnostic test accuracy.Setting  Northern Gynaecological Oncology Centre and Department of Cellular Pathology, Gateshead, UK.Population  1439 intra‐operative FS analyses performed between January 2000 and December 2010 for suspected ovarian cancer.Methods  Prospectively collected data on FS analysis were compared with gold standard paraffin section.Main outcome measures  Sensitivity, specificity, likelihood ratios and post‐test probability.Results  The overall sensitivity and specificity of FS analysis were 91.2% and 98.6%, respectively. Positive and negative likelihood ratios were 64.7% and 0.09%, respectively. The pre‐test probability of an ovarian tumour being borderline or malignant was 45.8%. When FS analysis was reported to be positive, the post‐test probability increased to 98% (confidence interval, 97–99%). Conversely, when FS analysis was reported to be negative, the post‐test probability decreased to 7% (confidence interval, 6–9%). The majority of false test results were either borderline tumours or of mucinous differentiation.Conclusions  Intra‐operative FS analysis has excellent diagnostic test accuracy and assists gynaecological oncologists to perform the appropriate surgery in 95% of cases, thereby preventing the morbidity of surgical staging in benign cases and the morbidity of restaging procedures or chemotherapy in early‐stage malignant tumours.
Preclinical development of CAT‐354, an IL‐13 neutralizing antibody, for the treatment of severe uncontrolled asthma
Authors: May RD , Monk PD , Cohen ES , Manuel D , Dempsey F , Davis NHE , Dodd AJ , Corkill DJ , Woods J , Joberty‐Candotti C , Conroy LA , Koentgen F , Martin EC , Wilson R , Brennan N , Powell J , Anderson IK 
Published: September 2011

BACKGROUND AND PURPOSE IL‐13 is a pleiotropic Th2 cytokine considered likely to play a pivotal role in asthma. Here we describe the preclinical in vitro and in vivo characterization of CAT‐354, an IL‐13‐neutralizing IgG4 monoclonal antibody (mAb), currently in clinical development.EXPERIMENTAL APPROACH In vitro the potency, specificity and species selectivity of CAT‐354 was assayed in TF‐1 cells, human umbilical vein endothelial cells and HDLM‐2 cells. The ability of CAT‐354 to modulate disease‐relevant mechanisms was tested in human cells measuring bronchial smooth muscle calcium flux induced by histamine, eotaxin generation by normal lung fibroblasts, CD23 upregulation in peripheral blood mononuclear cells and IgE production by B cells. In vivo CAT‐354 was tested on human IL‐13‐induced air pouch inflammation in mice, ovalbumin‐sensitization and challenge in IL‐13 humanized mice and antigen challenge in cynomolgus monkeys.KEY RESULTS CAT‐354 has a 165 pM affinity for human IL‐13 and functionally neutralized human, human variant associated with asthma and atopy (R130Q) and cynomolgus monkey, but not mouse, IL‐13. CAT‐354 did not neutralize human IL‐4. In vitro CAT‐354 functionally inhibited IL‐13‐induced eotaxin production, an analogue of smooth muscle airways hyperresponsiveness, CD23 upregulation and IgE production. In vivo in humanized mouse and cynomolgus monkey antigen challenge models CAT‐354 inhibited airways hyperresponsiveness and bronchoalveolar lavage eosinophilia.CONCLUSIONS AND IMPLICATIONS CAT‐354 is a potent and selective IL‐13‐neutralizing IgG4 mAb. The preclinical data presented here support the trialling of this mAb in patients with moderate to severe uncontrolled asthma.
Alcohol Dependence is Related to Overall Internalizing Psychopathology Load Rather than to Particular Internalizing Disorders: Evidence from a National Sample
Authors: Kushner Matt G. , Wall Melanie M. , Krueger Robert F. , Sher Kenneth J. , Maurer Eric , Thuras Paul , Lee Susanne 
Published: September 2011

Background:  Alcohol dependence is more prevalent among those with any one of several anxiety or depressive (“internalizing”) disorders than among those in the general population. However, because internalizing disorders are highly intercorrelated, it is ambiguous whether alcohol dependence is related to internalizing psychopathology components that are: (i) unique to a particular internalizing disorder (“specific”); versus (ii) shared across a number of internalizing disorders (“general”). To clarify this ambiguity, we employed structural equation and logistic models to decompose the specific versus general components of internalizing psychopathology and then related these components separately to alcohol dependence.
Methods:  The data were based on face‐to‐face interviews of U.S. community residents collected in the 2001 to 2002 National Epidemiologic Survey on Alcohol and Related Conditions (NESARC; N = 43,093).
Results:  Both analytic approaches demonstrated that increases in the general internalizing psychopathology load are accompanied by increases in the prevalence of alcohol dependence. Once the general internalizing psychopathology load is accounted for, knowing whether a particular internalizing disorder is present or absent provides little additional information regarding the prevalence of alcohol dependence.
Conclusions:  The components of internalizing psychopathology that are associated with alcohol dependence are shared and cumulative among common anxiety and depressive disorders. These findings have the potential to influence clinical and scientific conceptualizations of the association between alcohol dependence and internalizing psychopathology.
Opioidergic Modulation of Ethanol Self‐Administration in the Ventral Pallidum
Authors: Kemppainen Heidi , Raivio Noora , Suo‐Yrjo Ville , Kiianmaa Kalervo 
Published: September 2011

Background:  Striatopallidal medium spiny neurons have been viewed as a final common path for drug reward and the ventral pallidum as an essential convergent point for hedonic and motivational signaling in the brain. The medium spiny neurons are GABAergic, but they colocalize enkephalin. Purpose of this study was to investigate the role of the opioidergic mechanisms of the ventral pallidum in ethanol self‐administration behavior.
Methods:  Effects of bilateral microinjections of μ‐, δ‐, and κ‐opioid receptor agonists and antagonists into the ventral pallidum on voluntary ethanol consumption were monitored in alcohol‐preferring Alko Alcohol (AA) rats using the 90‐minute limited access paradigm.
Results:  Stimulation of μ‐opioid receptors with DAMGO (0.01 to 0.1 μg) or morphine (1 to 10 μg) in the ventral pallidum decreased ethanol intake dose‐dependently. Conversely, blocking μ‐receptors with CTOP (0.3 to 3 μg) increased ethanol intake significantly. Unlike CTOP, DAMGO also increased locomotor activity. Consumption of ethanol was not modified significantly by a broad‐spectrum opioid receptor antagonist naltrexone, by δ‐opioid receptor agonist DPDPE or antagonist naltrindole, or by a κ‐opioid receptor agonist U50,488H or antagonist nor‐BNI.
Conclusions:  The study provides evidence for μ‐ but not δ‐ or κ‐opioid receptors in the ventral pallidum playing a role in the regulation of voluntary ethanol consumption. Furthermore, present findings give support to earlier work, suggesting an essential role of pallidal opioidergic transmission in drug reward.
To Approach or Avoid Alcohol? Automatic and Self‐Reported Motivational Tendencies in Alcohol Dependence
Authors: Barkby Helen , Dickson Joanne M. , Roper Louise , Field Matt 
Published: September 2011

Background:  Motivational conflict is central to alcohol dependence, with patients reporting motivation to limit their drinking at the same time as urges to drink alcohol. In addition, dual process models of addiction emphasise the power of automatic cognitive processes, particularly automatic approach responses elicited by alcohol‐related cues, as determinants of drinking behavior. We aimed to examine the strength of automatic and self‐reported alcohol approach and avoidance tendencies among alcohol‐dependent inpatients relative to matched controls.
Methods:enbsp; A total of 63 alcohol‐dependent patients undergoing detoxification and 64 light‐drinking controls completed a stimulus‐response compatibility (SRC) task, which assesses the speed of categorization of alcohol‐related pictures by making symbolic approach and avoidance movements. We also included modified versions of the SRC task to assess automatic motivational conflict, that is, strong approach and avoidance tendencies elicited simultaneously by alcohol‐related cues.
Results:  There were no differences between alcohol‐dependent patients and controls on the SRC task, although individual differences in the quantity of alcohol consumed before entering treatment were significantly positively correlated with the strength of approach (but not avoidance) tendencies elicited by alcohol‐related cues. Automatic approach tendencies were also positively correlated with self‐reported “approach” inclinations and negatively correlated with self‐reported “avoidance” inclinations.
Conclusions:  Although alcohol‐dependent patients and matched controls did not differ on automatic approach and avoidance tendencies elicited by alcohol‐related cues, individual differences in the quantity of alcohol consumed before entering treatment were associated with the strength of automatic approach tendencies elicited by alcohol cues.
TRAP Abortion Laws and Partisan Political Party Control of State Government
Authors: MEDOFF MARSHALL H. , DENNIS CHRISTOPHER 
Published: September 2011

AbstractTargeted Regulation of Abortion Providers (or TRAP) laws impose medically unnecessary and burdensome regulations solely on abortion providers in order to make abortion services more expensive and difficult to obtain. Using event history analysis, this article examines the determinants of the enactment of a TRAP law by states over the period 1974–2008. The empirical results find that Republican institutional control of a state's legislative/executive branches is positively associated with a state enacting a TRAP law, while Democratic institutional control is negatively associated with a state enacting a TRAP law. The percentage of a state's population that is Catholic, public anti‐abortion attitudes, state political ideology, and the abortion rate in a state are statistically insignificant predictors of a state enacting a TRAP law. The empirical results are consistent with the hypothesis that abortion is a redistributive issue and not a morality issue.
Land Rent and Housing Policy: A Case Study of the San Francisco Bay Area Rental Housing Market
Authors: BARTON STEPHEN E. 
Published: September 2011

AbstractIn the San Francisco Bay Area, where residential rent is among the highest in the United States, an analysis of data from several sources demonstrates that high rent cannot be accounted for by higher quality, higher operating costs, or higher construction costs. At least one‐third of the total rent paid is land rent. Despite increases in real incomes, very‐low‐income tenants in the Bay Area today have less income remaining after payment of rent than tenants did in 1960. High land rent is a long‐term feature of the Bay Area rental market that results mostly from its geography, the density of its urban centers, and a strong economy, rather than from regulatory barriers to new multifamily construction. Deregulation is not a sufficient response to the effects of land rent on low‐income tenants. Government should subsidize non‐profit housing organizations, particularly land trusts that remove residential land from the market. Taxes on land rent would be a particularly appropriate funding source.
Moral Capitalism: A Biblical Perspective
Authors: FRIEDMAN HERSHEY H. , ADLER WILLIAM D. 
Published: September 2011

AbstractWe argue that laissez‐faire capitalism in its current form is unsustainable, and that if it is to survive, we need to develop a new moral capitalism. An underexplored source on the subject that may provide insight into current difficulties is the Hebrew Bible. We explicate four basic principles of the Hebrew Bible and Talmud on economic affairs, and show how these ancient ideas can be used to create a more moral economic system.