bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analyzing blocking to debug performance problems on multi-core systems
Authors: Fournier Pierre-Marc , Dagenais Michel R. 
Published: April 2010

Multi-core systems are rapidly becoming more prevalent. Consequently, developers frequently face performance bugs caused by unexpected interactions between parallel software components. The location of these bugs is difficult to identify with current tools. Indeed, the process exhibiting the slowness may be separated from the root cause of the problem by a blocking chain involving several other processes.
This article introduces a new approach for analyzing blocking on multi-core systems and reports on its implementation in the LTTV Delay Analyzer. It enables developers to quickly understand the dependencies among processes and see how the total elapsed time is divided into its main components. The LTTV Delay Analyzer was used to analyze and rapidly correct complex performance problems, something not possible with the existing tools. The Linux Trace Toolkit, LTTng, is used for most of the instrumentation and the trace recording, allowing the tracing of production systems with great accuracy and minimal impact. This approach uses solely kernel instrumentation and does not require the instrumentation or recompilation of processes. The analysis time is linear with respect to trace size.
Tainting is not pointless
Authors: Dalton Michael , Kannan Hari , Kozyrakis Christos 
Published: April 2010

Pointer tainting is a form of Dynamic Information Flow Tracking used primarily to prevent software security attacks such as buffer overflows. Researchers have also applied pointer tainting to malware and virus analysis.
A recent paper by Slowinska and Bos has criticized pointer tainting as a security mechanism, arguing that it is has serious, inherent false positive and false negative defects. We present a rebuttal that addresses the confusion due to the two uses of pointer tainting in security literature. We clarify that many of the arguments against pointer tainting apply only to its use as a malware and virus analysis platform, but do not apply to the application of pointer tainting to memory corruption protection. Hence, we argue that pointer tainting remains a useful and promising technique for robust protection against memory corruption attacks.
John Cassian and the Christology of Romans 8,3
Authors: Keech Dominic 
Published: April 2010

AbstractThis paper focuses on Cassian’s characterisation of Christ ‘in the likeness of sinful flesh’ (Romans 8,3) and argues that it forms a dual reception of the treatment of the same text found in the work of Origen and Augustine of Hippo. Inasmuch as Augustine’s exegesis constitutes a reception of Origen, Cassian’s reproduction of their shared thought forms a silent judgment on the impact and importance of the first Origenist Controversy in the Latin West. Further, whilst Origen and Augustine situate their Christological exegesis of the passage within a coherent account of the origin and transmission of sin, Cassian does not. Consequently, this paper questions recent scholarly attempts to re-evaluate Cassian’s capacities as a synthetic theologian, by arguing that he prioritised a distinct theological tradition and its authoritative representatives over a tight theological coherence in his work.
Variations in Subpixel Fire Properties with Season and Land Cover in Southern Africa
Authors: Eckmann Ted C. , Still Christopher J. , Roberts Dar A. , Michaelsen Joel C. 
Published: April 2010

AbstractSome of the most widely used datasets for monitoring the world’s fires come from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensors aboard NASA’s Terra and Aqua satellites. For virtually all remote sensing systems, including MODIS, pixels that contain fires comprise a mix of burning and nonburning components, each with sizes and temperatures that vary between pixels. Current remote sensing products provide little information about these subpixel components, severely limiting estimates of the gas and aerosol emissions and ecological impacts from the world’s fires. This study shows how multiple endmember spectral mixture analysis (MESMA) can estimate subpixel fire sizes and temperatures from MODIS and can overcome many limitations of existing methods for characterizing fire intensities from remotely sensed data, such as the fire radiative power (FRP) approach. This study used MESMA to estimate subpixel fire sizes and temperatures for MODIS scenes in southern Africa, analyzed how these sizes and temperatures varied with season and land cover, and compared these to analyses made with FRP. This study could be the first to analyze fire sizes and temperatures on a spatial scale as large as a MODIS scene and a temporal scale as large as a full fire season. The variations in MESMA estimates of fire temperature with season and land cover were more consistent than the FRP estimates. Based on these findings, MESMA appears to be more effective than FRP at capturing some variations in fire temperatures, which strongly influence the gas and aerosol emissions from fires, along with their effects on ecosystems.
Surface Pressure Features of Landfalling Typhoon Rainbands and Their Possible Causes
Authors: Yu Cheng-Ku , Tsai Chia-Lun 
Published: April 2010

Abstract
This study uses temporally high-resolution surface observations, Doppler radar, and micro rain radar to document the finescale features of the two landfalling rainbands associated with Typhoon Longwang (2005) as they passed over northern Taiwan. The present case allows a unique opportunity to investigate well-defined, convectively active tropical cyclone rainbands over land. In particular, the surface pressure fluctuations observed during the passage of the two rainbands and their possible causes are explored. The rainbands were predominantly convective in nature, with embedded stratiform precipitation outside their inner/outer edge. Analyses of surface observations show similar surface pressure fluctuations during the rainband’s passage. Low (high) pressure with relatively strong (weak) cross-band flow and warmer (colder) temperature was located inside the outer (inner) edge. Maximum (minimum) pressure perturbations were observed to be ∼1.5 (∼−1) mb, with smaller magnitudes (&lt;∼0.4 mb) outside the outer/inner edge. In particular, the studied rainbands possess some wavelike characteristics such as outward propagation, undulations of surface pressure perturbations, and opposite phase relation between the surface pressure perturbations and the cross-band flow. Detailed analyses indicate that the combined effects of pressure perturbations produced by moist convection and those associated with wave activities initiated within the typhoon could explain the observed surface features. The present study provides observational evidence to support the importance of wave dynamics and their interactions with moist convection for the generation of surface pressure perturbations associated with the observed tropical cyclone rainbands.
Kullback–Leibler Divergence as a Forecast Skill Score with Classic Reliability–Resolution–Uncertainty Decomposition
Authors: Weijs Steven V. , van Nooijen Ronald , van de Giesen Nick 
Published: April 2010

AbstractThis paper presents a score that can be used for evaluating probabilistic forecasts of multicategory events. The score is a reinterpretation of the logarithmic score or ignorance score, now formulated as the relative entropy or Kullback–Leibler divergence of the forecast distribution from the observation distribution. Using the information–theoretical concepts of entropy and relative entropy, a decomposition into three components is presented, analogous to the classic decomposition of the Brier score. The information–theoretical twins of the components uncertainty, resolution, and reliability provide diagnostic information about the quality of forecasts. The overall score measures the information conveyed by the forecast. As was shown recently, information theory provides a sound framework for forecast verification. The new decomposition, which has proven to be very useful for the Brier score and is widely used, can help acceptance of the logarithmic score in meteorology.
Establishing a continuum of care between HIV prevention trials and public healthcare systems: The MIRA Standard of Care program
Authors: Clouse Kate , Montgomery Elizabeth T , Milford Cecilia , Watadzaushe Connie , Nkala Busi , Fancher Heidi , Lince Naomi , Cheng Helen , Thompson Marin , van der Straten Ariane 
Published: April 2010

Background The ability of researchers to provide sustainable care to individuals who acquire HIV during participation in HIV prevention trials has rapidly expanded along with national treatment options. The Methods for Improving Reproductive Health in Africa (MIRA) trial (2003—2006), a phase III multi-site randomized controlled trial, measured the effectiveness of the diaphragm used with Replens ® lubricant gel in preventing heterosexual acquisition of HIV among women in Zimbabwe and South Africa. The MIRA Standard of Care program, which started towards the end of the trial period and continued for 5 months after trial closeout, enabled women who acquired HIV during the trial to receive additional counseling and clinical care and facilitated links to long-term HIV-related care and treatment from public health facilities. Purpose To describe eligible participants’ uptake of these optional services and evaluate the program’s strengths and limitations. Methods All women who acquired HIV during their MIRA participation were re-contacted and invited to return to the study clinics for additional care and referrals. Sites reported monthly statistics of uptake of services. Results From start to end, 185 of 323 (57%) HIV-positive participants accepted additional care; 81 (25%) could not be relocated. 142 (44%) women received referrals to government healthcare facilities and 90 (28%) enrolled in wellness/ treatment programs. Fifty-seven (18%) declined further care, but reasons for doing so were not recorded systematically. Limitations The program began after most participants had exited from the MIRA trial and required re-contacting women, resulting in difficulty in locating some participants. Conclusions In the future, care for participants who seroconvert should be offered at the trial onset and fully integrated into clinical trials to avoid losing these participants for further care. More research is needed to identify and understand perceived barriers to establishing a continuum of care between clinical trials and public sector health facilities. Clinical Trials 2010; 7: 256—264. http:// ctj.sagepub.com
A disc with fivefold symmetry: the proposed fundamental seed structure for the formation of chrysotile asbestos fibres, polygonal serpentine fibres and polyhedral lizardite spheres
Authors: Cressey G. , Cressey B. A. , Wicks F. J. , Yada K. 
Published: April 2010

AbstractA chrysotile disc is proposed as the fundamental seed structure for the formation of chrysotile asbestos fibres, polygonal serpentine fibres and polyhedral lizardite spheres. The curvature, fivefold symmetry and hydrogen-bonding alignment of the layers in the seed disc control the formation of the 15 or 30 sectors in polygonal serpentine and the orientations of the planar arrays of 15 or 30 radial crystals in polyhedral serpentine. A polygonized disc precursor to polygonal fibre formation has been observed at an arrested stage of growth in a synthesis experiment.
Widenmannite, a rare uranyl lead carbonate: occurrence, formation and characterization
Authors: Plášil J. , Čejka J. , Sejkora J. , Škácha P. , Goliáš V. , Jarka P. , Laufek F. , Jehlička J. , Němec I. , Strnad L. 
Published: April 2010

AbstractThe rare uranyl lead carbonate widenmannite, Pb2(UO2)(CO3)3, was found at the Jánská vein, Příbram, Czech Republic, where two generations occur in several morphological types and mineral associations in hydrothermal veins. Alpha spectroscopy shows that these two generations have different ages, >220,000 and 118±12 y. ICP-MS analysis indicates that both widenmannites have a dominance of non-radiogenic Pb which originates from weathered galena. The older widenmannite I forms fine-grained, grey to beige aggregates in the highly altered supergene part of the hydrothermal ore vein in association with pyromorphite, cerussite and goethite. The younger widenmannite II occurs as white, yellow or greenish-yellow thin tabular crystals upto 0.5 mm long in association with cerussite, anglesite, limonite, kasolite and an unnamed Pb-U-O phase. Thermal analysis suggests that widenmannite decomposes in several steps, with Pb uranate as the final product. Infrared and Raman spectroscopy confirm the presence of non-equivalent (CO3)2– groups, bidentately coordinated in uranyl hexagonal polyhedra, forming the well known uranyl tricarbonate complex. Infrared spectroscopy shows conclusively that widenmannite does not contain molecular H2O.
Identification of an NK/T cell–restricted progenitor in adult bone marrow contributing to bone marrow– and thymic-dependent NK cells
Authors: Nozad Charoudeh Hojjatollah , Tang Yanjuan , Cheng Min , Cilio Corrado M. , Jacobsen Sten Eirik W. , Sitnicka Ewa 
Published: April 2010

AbstractAlthough bone marrow (BM) is the main site of natural killer (NK)–cell development in adult mice, recent studies have identified a distinct thymic-dependent NK pathway, implicating a possible close link between NK- and T-cell development in adult hematopoiesis. To investigate whether a potential NK-/T-lineage restriction of multipotent progenitors might take place already in the BM, we tested the full lineage potentials of NK-cell progenitors in adult BM. Notably, although Lin−CD122+NK1.1−DX5− NK-cell progenitors failed to commit to the B and myeloid lineages, they sustained a combined NK- and T-cell potential in vivo and in vitro at the single-cell level. Whereas T-cell development from NK/T progenitors is Notch-dependent, their contribution to thymic and BM NK cells remains Notch-independent. These findings demonstrate the existence of bipotent NK-/T-cell progenitors in adult BM.
The effect of deferasirox on cardiac iron in thalassemia major: impact of total body iron stores
Authors: Wood John C. , Kang Barinder P. , Thompson Alexis , Giardina Patricia , Harmatz Paul , Glynos Tara , Paley Carole , Coates Thomas D. 
Published: April 2010

AbstractWe present results from a prospective, multicenter, open-label, single-arm study evaluating response of cardiac and liver iron to deferasirox therapy for 18 months. Twenty-eight patients with abnormal T2* and normal left ventricular ejection fraction were enrolled from 4 US centers. All patients initially received deferasirox doses of 30 to 40 mg/kg per day. Patients were severely iron overloaded: mean liver iron concentration (LIC) 20.3 mg Fe/g dry weight, serum ferritin 4417 ng/mL, and cardiac T2* 8.6 ms. In the intent-to-treat population, 48% reached the primary endpoint (cardiac T2* improvement at 18 months, P = not significant). There were 2 deaths: 1 from congestive heart failure and 1 from sepsis. In the 22 patients completing the trial, LIC and cardiac T2* improvements were 16% (P = .06) and 14% (P = .07), respectively. Cardiac T2* improvement (13 patients) was predicted by initial LIC, final LIC, and percentage LIC change, but not initial cardiac T2*. Cardiac iron improved 24% in patients having LIC in the lower 2 quartiles and worsened 8.7% in patients having LIC in the upper 2 quartiles. Left ventricular ejection fraction was unchanged at all time points. Monotherapy with deferasirox was effective in patients with mild to moderate iron stores but failed to remove cardiac iron in patients with severe hepatic iron burdens. This study was registered at www.clinicaltrials.gov as #NCT00447694.
Evolution of the MAGUK protein gene family in premetazoan lineages
Authors: de Mendoza Alex , Suga Hiroshi , Ruiz-Trillo Iñaki 
Published: April 2010

Abstract

Background
Cell-to-cell communication is a key process in multicellular organisms. In multicellular animals, scaffolding proteins belonging to the family of membrane-associated guanylate kinases (MAGUK) are involved in the regulation and formation of cell junctions. These MAGUK proteins were believed to be exclusive to Metazoa. However, a MAGUK gene was recently identified in an EST survey of Capsaspora owczarzaki, an unicellular organism that branches off near the metazoan clade. To further investigate the evolutionary history of MAGUK, we have undertook a broader search for this gene family using available genomic sequences of different opisthokont taxa.

Results
Our survey and phylogenetic analyses show that MAGUK proteins are present not only in Metazoa, but also in the choanoflagellate Monosiga brevicollis and in the protist Capsaspora owczarzaki. However, MAGUKs are absent from fungi, amoebozoans or any other eukaryote. The repertoire of MAGUKs in Placozoa and eumetazoan taxa (Cnidaria + Bilateria) is quite similar, except for one class that is missing in Trichoplax, while Porifera have a simpler MAGUK repertoire. However, Vertebrata have undergone several independent duplications and exhibit two exclusive MAGUK classes. Three different MAGUK types are found in both M. brevicollis and C. owczarzaki: DLG, MPP and MAGI. Furthermore, M. brevicollis has suffered a lineage-specific diversification.

Conclusions
The diversification of the MAGUK protein gene family occurred, most probably, prior to the divergence between Metazoa+choanoflagellates and the Capsaspora+Ministeria clade. A MAGI-like, a DLG-like, and a MPP-like ancestral genes were already present in the unicellular ancestor of Metazoa, and new gene members have been incorporated through metazoan evolution within two major periods, one before the sponge-eumetazoan split and another within the vertebrate lineage. Moreover, choanoflagellates have suffered an independent MAGUK diversification. This study highlights the importance of generating enough genome data from the broadest possible taxonomic sampling, in order to fully understand the evolutionary history of major protein gene families.
Global transcriptome analysis of spore formation in Myxococcus xanthus reveals a locus necessary for cell differentiation
Authors: Müller Frank-Dietrich , Treuner-Lange Anke , Heider Johann , Huntley Stuart M , Higgs Penelope I 
Published: April 2010

Abstract

Background

Myxococcus xanthus is a Gram negative bacterium that can differentiate into metabolically quiescent, environmentally resistant spores. Little is known about the mechanisms involved in differentiation in part because sporulation is normally initiated at the culmination of a complex starvation-induced developmental program and only inside multicellular fruiting bodies. To obtain a broad overview of the sporulation process and to identify novel genes necessary for differentiation, we instead performed global transcriptome analysis of an artificial chemically-induced sporulation process in which addition of glycerol to vegetatively growing liquid cultures of M. xanthus leads to rapid and synchronized differentiation of nearly all cells into myxospore-like entities.

Results
Our analyses identified 1 486 genes whose expression was significantly regulated at least two-fold within four hours of chemical-induced differentiation. Most of the previously identified sporulation marker genes were significantly upregulated. In contrast, most genes that are required to build starvation-induced multicellular fruiting bodies, but which are not required for sporulation per se, were not significantly regulated in our analysis. Analysis of functional gene categories significantly over-represented in the regulated genes, suggested large rearrangements in core metabolic pathways, and in genes involved in protein synthesis and fate. We used the microarray data to identify a novel operon of eight genes that, when mutated, rendered cells unable to produce viable chemical- or starvation-induced spores. Importantly, these mutants displayed no defects in building fruiting bodies, suggesting these genes are necessary for the core sporulation process. Furthermore, during the starvation-induced developmental program, these genes were expressed in fruiting bodies but not in peripheral rods, a subpopulation of developing cells which do not sporulate.

Conclusions
These results suggest that microarray analysis of chemical-induced spore formation is an excellent system to specifically identify genes necessary for the core sporulation process of a Gram negative model organism for differentiation.
Pseudomonas aeruginosa inhibits in-vitro Candida biofilm development
Authors: Bandara HMHN , Yau JYY , Watt RM , Jin LJ , Samaranayake LP 
Published: April 2010

Abstract

Background
Elucidation of the communal behavior of microbes in mixed species biofilms may have a major impact on understanding infectious diseases and for the therapeutics. Although, the structure and the properties of monospecies biofilms and their role in disease have been extensively studied during the last decade, the interactions within mixed biofilms consisting of bacteria and fungi such as Candida spp. have not been illustrated in depth. Hence, the aim of this study was to evaluate the interspecies interactions of Pseudomonas aeruginosa and six different species of Candida comprising C. albicans, C. glabrata, C. krusei, C. tropicalis, C. parapsilosis, and C. dubliniensis in dual species biofilm development.

Results
A significant reduction in colony forming units (CFU) of C. parapsilosis (90 min), C. albicans and C. tropicalis (90 min, 24 h and 48 h), C. dubliniensis and C. glabrata, (24 h and 48 h) was noted when co-cultured with P. aeruginosa in comparison to their monospecies counterparts (P < 0.05). A simultaneous significant reduction in P. aeruginosa numbers grown with C. albicans (90 min and 48 h), C. krusei (90 min, 24 h and 48 h),C. glabrata, (24 h and 48 h), and an elevation of P. aeruginosa numbers co-cultured with C. tropicalis (48 h) was noted (P < 0.05). When data from all Candida spp. and P. aeruginosa were pooled, highly significant mutual inhibition of biofilm formation was noted (Candida P < 0.001, P. aeruginosa P < 0.01). Scanning Electron Microscopy (SEM) and Confocal Laser Scanning Microscopy (CLSM) analyses confirmed scanty architecture in dual species biofilm in spite of dense colonization in monospecies counterparts.

Conclusions

P. aeruginosa and Candida in a dual species environment mutually suppress biofilm development, both quantitatively and qualitatively. These findings provide a foundation to clarify the molecular basis of bacterial-fungal interactions, and to understand the pathobiology of mixed bacterial-fungal infections.