bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global tracking for robot manipulators using a simple causal PD controller plus feedforward
Authors: Nunes Eduardo V. L. , Hsu Liu 
Published: April 2009

SUMMARYThis paper shows that a well-known causal PD controller plus feedforward solves the global output feedback tracking control problem of robot manipulators, by requiring only the existence of the robot natural damping, no matter how small. To this end, we first demonstrate that a robot controlled by a causal PD is globally input-to-state stable (ISS) with respect to a bounded input disturbance. Then, we prove that the addition of a feedforward compensation renders the error system uniformly globally asymptotically stable. Furthermore, we present a possible extension to more general nonlinear systems and also to uncertain systems.
New Editors Appointed for Sections of Journal of Geophysical Research
Authors: Anonymous  
Published: April 2009

New editors have been appointed for the Atmospheres, Biogeosciences, and Oceans sections of the Journal of Geophysical Research (JGR).Joost de Gouw (NOAA, Boulder, Colo.) and Renyi Zhang (Texas A&M, College Station) are filling the vacancies of retiring Atmospheres section editors John Austin and Jose Fuentes. De Gouw and Zhang join the continuing editors Steven Ghan and Yinon Rudich. Sara Pryor (Indiana University, Bloomington) is joining the Atmospheres section editorial board as an associate editor now; she will transition to editor in January 2010.
A novel symbiosis between chemoautotrophic bacteria and a freshwater cave amphipod
Authors: Dattagupta Sharmishtha , Schaperdoth Irene , Montanari Alessandro , Mariani Sandro , Kita Noriko , Valley John W , Macalady Jennifer L 
Published: April 2009

Abstract
Symbioses involving animals and chemoautotrophic bacteria form the foundation of entire ecosystems at deep-sea hydrothermal vents and cold seeps, but have so far not been reported in terrestrial or freshwater environments. A rare example of a terrestrial ecosystem sustained by chemoautotrophy is found within the sulfide-rich Frasassi limestone cave complex of central Italy. In this study, we report the discovery of abundant filamentous bacteria on the exoskeleton of Niphargus ictus, a macroinvertebrate endemic to Frasassi. Using 16S rDNA sequencing and fluorescence in situ hybridization (FISH), we show that N. ictus throughout the large cave complex are colonized by a single phylotype of bacteria in the sulfur-oxidizing clade Thiothrix. The epibiont phylotype is distinct from Thiothrix phylotypes that form conspicuous biofilms in the cave streams and pools inhabited by N. ictus. Using a combination of 13C labeling, FISH, and secondary ion mass spectrometry (SIMS), we show that the epibiotic Thiothrix are autotrophic, establishing the first known example of a non-marine chemoautotroph-animal symbiosis. Conditions supporting chemoautotrophy, and the N. ictus-Thiothrix association, likely commenced in the Frasassi cave complex between 350 000 and 1 million years ago. Therefore, the N. ictus-Thiothrix symbiosis is probably significantly younger than marine chemoautotrophic symbioses, many of which have been evolving for tens to hundreds of million years.
Characterization of the complex bacterial communities colonizing biliary stents reveals a host-dependent diversity
Authors: Scheithauer Britta K , Wos-Oxley Melissa L , Ferslev Björn , Jablonowski Helmut , Pieper Dietmar H 
Published: April 2009

Abstract
This study provides a comprehensive survey of the spatial and temporal bacterial composition of biliary stent biofilms. The bacterial diversity, distribution and dynamics of 59 biliary and 4 pancreatic stent communities from 40 patients being treated at two different hospitals, which implant stents either simultaneously or consecutively, were characterized by single-strand conformation polymorphism (SSCP) analysis. Fifty-one phylotypes belonging to 5 bacterial phyla and 24 bacterial families were detected across 63 stents. This is a much broader diversity than previously detected through culture-dependent methods, particularly in regard to the diversity of obligate anaerobes. Stent bacterial diversity was patient-dependent and more similar when stents were implanted simultaneously rather than consecutively. Stent bacterial community composition differed between hospitals specifically because of the difference in abundance of Bifidobacteria. Co-colonization of Veillonella sp., Streptococcus anginosus and organisms closely related to Fusobacterium nucleatum revealed a potentially important attachment and survival strategy that has yet to be reported in biliary stents. This work reveals a more complete survey of the identities of bacterial species that form biofilms in biliary stents, their co-colonization patterns and the natural variation in species composition between different patients, hospitals and locations along the stent. Consideration of the community composition from individual patients will allow tailoring of prophylactic antibiotic treatments and thus will make the management of stent biofilms more effective.
TEclass—a tool for automated classification of unknown eukaryotic transposable elements
Authors: Abrusán György , Grundmann Norbert , DeMester Luc , Makalowski Wojciech 
Published: April 2009

Abstract
Motivation: The large number of sequenced genomes required the development of software that reconstructs the consensus sequences of transposons and other repetitive elements. However, the available tools usually focus on the accurate identification of raw repeats and provide no information about the taxonomic position of the reconstructed consensi. TEclass is a tool to classify unknown transposable elements into their four main functional categories, which reflect their mode of transposition: DNA transposons, long terminal repeats (LTRs), long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs). TEclass uses machine learning support vector machine (SVM) for classification based on oligomer frequencies. It achieves 90–97% accuracy in the classification of novel DNA and LTR repeats, and 75% for LINEs and SINEs.
Availability: http://www.compgen.uni-muenster.de/teclass, stand alone program upon request.
Contact: abrusan@uni-muenster.de
CloudBurst: highly sensitive read mapping with MapReduce
Authors: Schatz Michael C. 
Published: April 2009

AbstractMotivation: Next-generation DNA sequencing machines are generating an enormous amount of sequence data, placing unprecedented demands on traditional single-processor read-mapping algorithms. CloudBurst is a new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping and personal genomics. It is modeled after the short read-mapping program RMAP, and reports either all alignments or the unambiguous best alignment for each read with any number of mismatches or differences. This level of sensitivity could be prohibitively time consuming, but CloudBurst uses the open-source Hadoop implementation of MapReduce to parallelize execution using multiple compute nodes.Results: CloudBurst's running time scales linearly with the number of reads mapped, and with near linear speedup as the number of processors increases. In a 24-processor core configuration, CloudBurst is up to 30 times faster than RMAP executing on a single core, while computing an identical set of alignments. Using a larger remote compute cloud with 96 cores, CloudBurst improved performance by &gt;100-fold, reducing the running time from hours to mere minutes for typical jobs involving mapping of millions of short reads to the human genome.Availability: CloudBurst is available open-source as a model for parallelizing algorithms with MapReduce at http://cloudburst-bio.sourceforge.net/.Contact: mschatz@umiacs.umd.edu
The influence of low-frequency variability and long-term trends in North Atlantic sea surface temperature on Irish waters
Authors: Cannaby Heather , Hüsrevoğlu Y. Sinan 
Published: April 2009

Abstract
Cannaby, H., and Hüsrevoğlu, Y. S. 2009. The influence of low-frequency variability and long-term trends in North Atlantic sea surface temperature on Irish waters. – ICES Journal of Marine Science, 66: 1480–1489. Sea surface temperature (SST) time-series collected in Irish waters between 1850 and 2007 exhibit a warming trend averaging 0.3°C. The strongest warming has occurred since 1994, with the warmest years in the record being 2005, 2006, and 2007. The warming trend is superimposed on significant interannual to multidecadal-scale variability, linked to basin-scale oscillations of the ocean–atmosphere system. The dominant modes of low-frequency variability in North Atlantic SST records, investigated using an empirical orthogonal function (EOF) analysis, correspond to the Atlantic Multidecadal Oscillation (AMO), the East Atlantic Pattern (EAP), and the North Atlantic Oscillation (NAO) index, respectively, accounting for 23, 16, and 9% of the total variance in the dataset. Interannual variability in Irish SST records is dominated by the AMO, which, currently in its warm phase, explains approximately half of the current warm anomaly in the record. The EAP and the NAO influence variability in Irish SST time-series on a smaller scale, with the EAP also contributing to the current warm anomaly. After resolving the prevalent oscillatory modes of variability in the SST record, the underlying warming trend compares well with the global greenhouse effect warming trend. The anthropogenic contribution to the current warm anomaly in Irish SSTs was estimated at 0.41°C for 2006, and this is predicted to increase annually.
Regulating a complex adaptive system via its wasp-waist: grappling with ecosystem-based management of the New England herring fishery
Authors: Bakun Andrew , Babcock Elizabeth A. , Santora Christine 
Published: April 2009

AbstractBakun, A., Babcock, E. A., and Santora, C. 2009. Regulating a complex adaptive system via its wasp-waist: grappling with ecosystem-based management of the New England herring fishery. – ICES Journal of Marine Science, 66: 1768–1775. We use the New England herring fishery as an example of the unresolved scientific issues pertinent to ecosystem-based management of forage-fish fisheries. The biomass of herring off New England is currently well above maximum sustainable yield (BMSY), leading to pressure for expanded harvests. Associated concerns include: the maintenance of sufficiently abundant forage to meet the current needs of marine mammals and seabirds while supporting the rebuilding of overfished groundfish resources; the preservation of the service functions of a healthy population of pelagic zooplanktivorous fish to prevent possible outbreaks of pests, or hypoxia events; and the limitation of unintended bycatch of marine mammals, seabirds, and juvenile stages of groundfish. Perhaps a self-enhancing feedback loop, involving predation by herring on the early life stages of their groundfish predators, might result in regime shifts that could not be easily reversed. A plausible outcome of these ideas is a dichotomy in management choice between (i) promoting an ecosystem dominated by valuable groundfish resources and (ii) promoting the current ecosystem that features a large herring resource associated with abundant and energy-rich forage for marine mammals, seabirds, and continued high productivity of valuable shellfish resources.
Acoustic observations of micronekton fish on the scale of an ocean basin: potential and challenges
Authors: Kloser Rudy J. , Ryan Tim E. , Young Jock W. , Lewis Mark E. 
Published: April 2009

Abstract
Kloser, R. J., Ryan, T. E., Young, J. W., and Lewis, M. E. 2009. Acoustic observations of micronekton fish on the scale of an ocean basin: potential and challenges. – ICES Journal of Marine Science, 66: 998–1006. Acoustic methods of characterizing micronekton communities (∼2 to 20 cm length) on the scale of an ocean basin could provide valuable inputs to ecosystem-based fishery management, marine planning, and monitoring the effects of climate change. The micronekton fish are important forage for top predators (e.g. tunas), and information on their diversity, distribution, size-structure, and abundance is needed to increase accuracy of top-predator distribution and abundance predictions. At the scale of an ocean basin, four years of Tasman Sea transects using a fishing vessel provide fine-scale maps of acoustic backscatter at 38 kHz that reveal detailed spatial patterns and structure to depths of 1200 m. Research-vessel data provide detailed biodiversity, density, size structure, and acoustic-scattering information from depth-stratified net sampling and a lowered acoustic probe. Wet-weight biomass estimates of the micronekton fish in the region vary considerably by a factor of 5–58 between acoustics (16–29 g m−2), nets (1.6 g m−2), and large spatial-scale, ecological models (0.5–3 g m−2). We demonstrate the potential and challenges of an acoustic basin-scale, fishing-vessel monitoring programme, including optical and net sensing, which could assist in characterizing the biodiversity, distribution, and biomass of the micronekton fish.
Combination of peritumoral mast cells and T‐regulatory cells predicts prognosis of hepatocellular carcinoma
Authors: Ju Min‐Jie , Qiu Shuang‐Jian , Gao Qiang , Fan Jia , Cai Ming‐Yan , Li Yi‐Wei , Tang Zhao‐You 
Published: April 2009

The peritumoral inflammatory environment is critical for the progression of intrahepatic recurrence of hepatocellular carcinoma (HCC) after curative resections. Here, we investigated the relevance of peritumoral mast cells (MCs) to HCC outcomes. Peritumoral tryptase+ MCs in addition to Foxp3+ T‐regulatory cells (Tregs) were evaluated using immunohistochemistry enumeration in tissue microarrays containing 207 randomly selected HCC patients. Clinicopathological factors and postoperative outcomes were compared between high and low subgroups of MCs or Tregs. Compared to low denstiy, higher peritumoral MCs were associated with poorer clinical outcomes, and independently related to elevated 5‐year recurrence incidence (54.1%vs 39.2%, P = 0.026). High‐dense MCs were especially related to increased probability of early recurrence (within 2 years) (P = 0.004). We also found that peritumoral Tregs were positively correlated with MCs in density (r = 0.353, P < 0.001) and reversely related to HCC outcomes. Notably, MCs in combination with Tregs displayed better prognostic performances than MCs alone (area under curve [AUC]survival = 0.629 vs 0.589, AUCrecurrence = 0.632 vs 0.591). Moreover, MCs were positively correlated to alanine aminotransferase, a serum inflammatory marker (P = 0.014). Therefore, peritumoral MCs are promising prognostic parameters for HCC mainly through inflammation response–related mechanisms, and we propose that MCs and Tregs may cooperate with each other and result in poorer prognosis. (Cancer Sci 2009; 100: 1267–1274)
Do the Transtheoretical Model processes of change, decisional balance and temptation predict stage movement? Evidence from smoking cessation in adolescents
Authors: Guo Boliang , Aveyard Paul , Fielding Antony , Sutton Stephen 
Published: April 2009

ABSTRACTAims  To examine the effects of processes of change (POC) on forward stage movement directly, indirectly through decisional balance and temptation, and total effects as a test of the key hypothesis of the Transtheoretical Model (TTM).Design  Prospective cohort study.Setting  United Kingdom.Participants  A total of 1160 adolescents aged 13–14 years who were current or former smokers at baseline.Measurements  Stage was assessed with the standard algorithm three times, once every 3 months. On each occasion the POC, decisional balance and temptation were measured with the standard questionnaires. Path analysis was used to examine the direct, indirectly mediated and total contribution of POC and the other constructs to stage movement 3 months later.Findings  Four of the 24 analyses showed evidence that the theoretically appropriate POC predicted stage transition, with statistically significant total effects. Effect sizes were small. When the POC were summarized to experiential and behavioural process means, one transition from pre‐contemplation was predicted by experiential processes and, contrary to the TTM, one transition predicted by behavioural processes. There was slightly more evidence that decisional balance (attitudes towards smoking) and temptation (ability to resist the urge to smoke) was associated with stage transition.Conclusions  POC use was not associated generally with stage transition and evidence that effects, if missed, must be modest, giving no support to the central tenet of the TTM.
Substance use and misuse in the aftermath of terrorism. A Bayesian meta‐analysis
Authors: DiMaggio Charles , Galea Sandro , Li Guohua 
Published: April 2009

ABSTRACTAim  To conduct a comprehensive analysis of the conflicting evidence on substance use and misuse following mass traumas such as terrorist incidents.Methods  We reviewed and synthesized evidence from 31 population‐based studies using Bayesian meta‐analysis and meta‐regression.Results  The majority of the studied were conducted in the aftermath of the terrorist attacks of 11 September 2001. Controlling for exposure, type of incident and time since the event occurred, 7.3% [95% credible interval (CrI) 1.1–32.5%] of a population can be expected to report increased alcohol consumption in the first 2 years following a terrorist event. There is, however, a 20% probability that the prevalence will be as high as 14%. The unadjusted prevalence of increased cigarette smoking following a terrorist event is 6.8% (95% Cr I 2.6–16.5%). Unadjusted reports of mixed drug use (including narcotics and prescription medications) was 16.3% (95% Cr I 1.3–72.5%).Conclusions  These results underscore the potentially pervasive behavioral health effects of mass terrorism, and suggest that public health interventions may usefully consider substance use as an area of focus after such events.
Prevalence and clinical relevance of corrected QT interval prolongation during methadone and buprenorphine treatment: a mortality assessment study
Authors: Anchersen Katinka , Clausen Thomas , Gossop Michael , Hansteen Viggo , Waal Helge 
Published: April 2009

ABSTRACTAims  To determine the prevalence of corrected QT interval (QTc) prolongation among patients in opioid maintenance treatment (OMT) and to investigate mortality potentially attributable to QTc prolongation in the Norwegian OMT programme.Participants and setting  Two hundred OMT patients in Oslo were recruited to the QTc assessment study between October 2006 and August 2007. The Norwegian register of all patients receiving OMT in Norway (January 1997–December 2003) and the national death certificate register were used to assess mortality. Mortality records were examined for the 90 deaths that had occurred among 2382 patients with 6450 total years in OMT.Design and measures  The QTc interval was assessed by electrocardiography (ECG). All ECGs were examined by the same cardiologist, who was blind to patient history and medication. Mortality was calculated by cross‐matching the OMT register and the national death certificate register: deaths that were possibly attributable to QTc prolongation were divided by the number of patient‐years in OMT.Findings  In the QTc assessment sample (n = 200), 173 patients (86.5%) received methadone and 27 (13.5%) received buprenorphine. In the methadone group, 4.6% (n = 8) had a QTc above 500 milliseconds; 15% (n = 26) had a QTc interval above 470 milliseconds; and 28.9% (n = 50) had a QTc above 450 milliseconds. All patients receiving buprenorphine (n = 27) had QTc results <450 milliseconds. A positive dose‐dependent association was identified between QTc length and dose of methadone, and all patients with a QTc above 500 milliseconds were taking methadone doses of 120 mg or more. OMT patient mortality, where QTc prolongation could not be excluded as the cause of death, was 0.06/100 patient‐years. Only one death among 3850 OMT initiations occurred within the first month of treatment.Conclusion  Of the methadone patients, 4.6% had QTc intervals above 500 milliseconds. The maximum mortality attributable to QTc prolongation was low: 0.06 per 100 patient‐years.
Keratin 18 provides resistance to Fas‐mediated liver failure in mice
Authors: Leifeld L. , Kothe S. , Söhl G. , Hesse M. , Sauerbruch T. , Magin T. M. , Spengler U. 
Published: April 2009

AbstractBackground  Keratins are intermediate filament proteins of epithelial cells with pivotal functions for cell integrity. They comprise keratins 18 [K18] and 8 [K8] in hepatocytes. Keratins are of major importance for an intact cellular microarchitecture and have protective functions in human liver diseases. In mice, K8 has been demonstrated to protect against Fas‐antibody‐induced liver failure by direct interaction with apoptotic regulators, while the role of K18 remains unresolved.Materials and methods  We analysed effects of K18 deficiency on Fas‐induced liver failure in mice. We determined survival and analysed induction of apoptosis after injection of the agonistic Fas antibody Jo2 into K18−/− and wild‐type control mice by TUNEL assay and fluorometrically analysed caspase‐3, ‐8 and ‐9 activities 1, 2 and 3 h after Jo2 injection.Results  In K18−/− mice, survival of Fas‐antibody treated mice was significantly shorter than that of wild‐type controls (P = 0·02). However, shortened survival of K18−/− mice was caused by increased hepatic damage but was not correlated to enhanced induction of apoptotic pathways, as neither numbers of TUNEL positive apoptotic cells nor activities of caspases‐3, ‐8 and ‐9 differed between K18−/− and K18+/+ mice at any point of time.Conclusion  K18−/− mice are significantly more susceptible to Fas‐antibody‐induced liver failure. The cytoprotective effect of K18 is not explained by a differential activation of caspases‐3, ‐8 and ‐9, suggesting that K18 does not directly interfere with apoptotic regulators. Importantly, however, K18 exerts significant protective functions by other mechanisms.