bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of Epidemiologically Unrelated
Acinetobacter baumannii
Isolates from Four Continents by Use of Multilocus Sequence Typing, Pulsed-Field Gel Electrophoresis, and Sequence-Based Typing of
bla
OXA-51-like
Genes
Authors: Hamouda Ahmed , Evans Benjamin A. , Towner Kevin J. , Amyes Sebastian G. B.
Published: April 2010

This study used a diverse collection of epidemiologically unrelated
Acinetobacter baumannii
isolates to compare the robustness of a multilocus sequence typing (MLST) scheme, based on conserved regions of seven housekeeping genes,
gltA
,
gdhB
,
recA
,
cpn60
,
rpoD
, g
yrB
, and
gpi
, with that of sequence-based typing of
bla
OXA-51-like
genes (SBT-
bla
OXA-51-like
genes). The data obtained by analysis of MLST and SBT-
bla
OXA-51-like
genes were compared to the data generated by pulsed-field gel electrophoresis (PFGE). The topologies of the phylogenetic trees generated for the
gyrB
and
gpi
genes showed evidence of recombination and were inconsistent with those of the trees generated for the other five genes. MLST identified 24 sequence types (STs), of which 19 were novel, and 5 novel alleles. Clonality was demonstrated by eBURST analysis and standardized index of association values of >1 (
P
< 0.001). MLST data revealed that all isolates harboring the major
bla
OXA-51-like
alleles OXA-66, OXA-69, and OXA-71 fell within the three major European clonal lineages. However, the MLST data were not always in concordance with the PFGE data, and some isolates containing the same
bla
OXA-51-like
allele demonstrated <50% relatedness by PFGE. It was concluded that the g
yrB
and
gpi
genes are not good candidates for use in MLST analysis and that a SBT-
bla
OXA-51-like
gene scheme produced results comparable to those produced by MLST for the identification of the major epidemic lineages, with the advantage of having a significantly reduced sequencing cost and time. It is proposed that studies of
A. baumannii
epidemiology could involve initial screening of
bla
OXA-51-like
alleles to identify isolates belonging to major epidemic lineages, followed by MLST analysis to categorize isolates from common lineages, with PFGE being reserved for fine-scale typing.
NON-CIRCULAR CHAIN RING ALLOWS A REDUCTION OF JOINT LOADING IN CYCLING
Authors: BISI MARIA CRISTINA , STAGNI RITA , GNUDI GIANNI , CAPPELLO ANGELO
Published: April 2010

Non-circular (NC) chain rings were primarily designed to improve the mechanical effectiveness of cycling. Their use can be investigated for application in rehabilitation: they could provide a solution to design an effective exercise reducing joint loading.

The aim of this study was to analyze the differences in kinematics, energy consumption, and joint moments between circular and NC chain rings, then to identify a profile that can reduce joint loads, maintaining equal mechanical and metabolic works.

Five young participants performed two tests on a cycloergometer; one with a circular chain ring and the other with an NC one. The test consisted in 15 min of cycling; during which they were asked to cycle at three different speeds and at two different powers. Stereophotogrammetric and metabolic data were acquired. Statistical analysis was applied on metabolic data. Joint angular velocities were obtained from kinematic data. A two-dimensional (2D) model of cycling was designed to estimate joint moments with both chain rings. A different ring profile was suggested to further reduce joint flexion peak moment.

NC chain ring allows a reduction of flexion joint moments with respect to the circular one without significant difference in metabolic and kinematic data. The new profile proposed further decreases maximum knee flexion moment maintaining equal mechanical work.
HIGH-SPEED AND SECURE ENCRYPTION SCHEMES BASED ON CHINESE REMAINDER THEOREM FOR STORAGE AND TRANSMISSION OF MEDICAL INFORMATION
Authors: AITHAL GANESH , HARI BHAT K. N. , ACHARYA U. SRIPATI
Published: April 2010

Medical records generated in hospitals often contain private and sensitive information. This privileged information must be prevented from falling into wrong hands. Thus, there is a strong need for developing a secure cryptographic scheme that can be adapted to use in conjunction with transmission and storage of medical information. Previous approaches have proposed the use of the advanced encryption standard (AES) algorithm for this purpose. In this article, we are proposing a new robust, high-speed, and secure cryptographic scheme that has the added advantage of being immune to side-channel attacks. In our article, we have shown that the performance of this scheme is superior in certain aspects to that of the A5/1 system used in global system for mobile (GSM) systems. The parallel architecture employed in this scheme makes it suitable to use in systems where the data-processing operations have to be carried out in real time.

Residue number systems (RNS) based on Chinese remainder theorem (CRT) permits the representation of large integers in terms of combinations of smaller ones. The set of all CRT number system representation of an integer from 0 to M-1 with component wise modular addition and multiplication constitutes a direct sum of smaller commutative rings. An encryption and decryption algorithm based on the properties of direct sum of smaller rings offers distinct advantages over decimal or fixed radix arithmetic. We have utilized the representation of integers using CRT to successfully design additive, multiplicative, and affine stream cipher systems. The use of number system based on CRT allows speeding up the encryption/decryption algorithms, reduces the time complexity, and provides immunity to side-channel, algebraic, and known plain text attacks. In this article, the characteristics of additive, multiplicative, and affine stream cipher systems based on CRT number system representation have been studied and analyzed.
Reporting incentives and biases in online review forums
Authors: Jurca Radu , Garcin Florent , Talwar Arjun , Faltings Boi
Published: April 2010

Online reviews have become increasingly popular as a way to judge the quality of various products and services. However, recent work demonstrates that the absence of reporting incentives leads to a biased set of reviews that may not reflect the true quality. In this paper, we investigate underlying factors that influence users when reporting feedback. In particular, we study both reporting incentives and reporting biases observed in a widely used review forum, the Tripadvisor Web site. We consider three sources of information: first, the numerical ratings left by the user for different aspects of quality; second, the textual comment accompanying a review; third, the patterns in the time sequence of reports. We first show that groups of users who discuss a certain feature at length are more likely to agree in their ratings. Second, we show that users are more motivated to give feedback when they perceive a greater risk involved in a transaction. Third, a user's rating partly reflects the difference between true quality and prior expectation of quality, as inferred from previous reviews. We finally observe that because of these biases, when averaging review scores there are strong differences between the mean and the median. We speculate that the median may be a better way to summarize the ratings.
NSF funding advice
Authors: Wing Jeannette M. , Reed Daniel
Published: April 2010

The
Communications
Web site, http://cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of
Communications
, we'll publish selected posts or excerpts.

twitter

Follow us on Twitter at http://twitter.com/blogCACM

Jeannette M. Wing shares useful suggestions for department heads.

Daniel Reed discusses the importance of synergy among computing specialists and generalists.
Thacker wins Turing Award
Authors: Rosenberger Jack
Published: April 2010

Microsoft's Charles P. Thacker named 56th recipient of ACM's A.M. Turing Award.
Energy-efficient algorithms
Authors: Albers Susanne
Published: April 2010

Algorithmic solutions can help reduce energy consumption in computing environs.
Cassandra
Authors: Lakshman Avinash , Malik Prashant
Published: April 2010

Cassandra is a distributed storage system for managing very large amounts of structured data spread out across many commodity servers, while providing highly available service with no single point of failure. Cassandra aims to run on top of an infrastructure of hundreds of nodes (possibly spread across different data centers). At this scale, small and large components fail continuously. The way Cassandra manages the persistent state in the face of these failures drives the reliability and scalability of the software systems relying on this service. While in many ways Cassandra resembles a database and shares many design and implementation strategies therewith, Cassandra does not support a full relational data model; instead, it provides clients with a simple data model that supports dynamic control over data layout and format. Cassandra system was designed to run on cheap commodity hardware and handle high write throughput while not sacrificing read efficiency.
Decoupling storage and computation in Hadoop with SuperDataNodes
Authors: Porter George
Published: April 2010

The rise of ad-hoc data-intensive computing has led to the development of data-parallel programming systems such as Map/Reduce and Hadoop, which achieve scalability by tightly coupling storage and computation. This can be limiting when the ratio of computation to storage is not known in advance, or changes over time. In this work, we examine decoupling storage and computation in Hadoop through SuperDataNodes, which are servers that contain an order of magnitude more disks than traditional Hadoop nodes. We found that SuperDataNodes are not only capable of supporting workloads with high storage-to-processing workloads, but in some cases can outperform traditional Hadoop deployments through better management of a large centralized pool of disks.
Toward automatic policy refinement in repair services for large distributed systems
Authors: Goldszmidt Moises , Budiu Mihai , Zhang Yue , Pechuk Michael
Published: April 2010

In order to be economically feasible and to offer high levels of availability and performance, large scale distributed systems depend on the automation of repair services. While there has been considerable work on mechanisms for such automated services, a framework for evaluating and optimizing the policies governing such mechanisms has been lacking. In this paper we propose one such framework and report on our initial experience in applying the framework to analyze and optimize the operation a geo-distributed cloud storage system at Microsoft.
Bulletin board
Authors: Bortnikov Vita , Chockler Gregory , Roytman Alexey , Spreitzer Mike
Published: April 2010

We present the design and early experience with a completely new implementation of the Bulletin Board, a topicbased distributed shared memory service employed by commercial-grade application middleware, to achieve robustness and administrative simplicity with adequate latency and costs at the required throughput and scale. To facilitate scalability, only weak consistency is provided. For robustness and ease of use, the implementation is designed in a fully peer-to-peer fashion leveraging the weakly consistent group communication services provided by a semi-structured overlay network. We discuss issues in providing good (while not perfect) stability and reliability at tolerable cost. We address scalability issues, such as supporting large numbers of processes, large subscription spaces, and complex interest patterns. We also consider comprehensive API instrumentation.
Optimizing information flow in the gossip objects platform
Authors: Vigfusson Ymir , Birman Ken , Huang Qi , Nataraj Deepak P.
Published: April 2010

Gossip-based protocols are commonly used for diffusing information in large-scale distributed applications. GO (Gossip Objects) is a per-node gossip platform that we developed in support of this class of protocols. GO allows nodes to join multiple gossip groups without losing the appealing fixed bandwidth guarantee of gossip protocols, and the platform also optimizes latency in a principled manner. Our algorithm is based on the observations that multiple rumors can often be squeezed into a single IP packet, and that indirect routing of rumors can speed up delivery. We formalize these observations and develop a theoretical analysis of this algorithm. We have also implemented GO, and studied the effectiveness of the algorithm by comparing it to the more standard random dissemination gossip strategy.
IWCTS 2009 Workshop Report
Authors: Kim Sangho
Published: April 2010

IWCTS 2009 was the second international workshop that brings together researchers and practitioners from various domains to discuss the modeling, planning, and other computational aspects of transportation. The workshop provides not only paper sessions that cover the algorithms, modeling, and practice of transportation problems, but also panel discussions that cover the environmental issues, roles of computer scientists and future direction of transportation research.
Physiological modulation of circulating FGF21: relevance of free fatty acids and insulin
Authors: Mai Knut , Bobbert Thomas , Groth Christian , Assmann Anke , Meinus Sabine , Kraatz Jessica , Andres Janin , Arafat Ayman M. , Pfeiffer Andreas F. H. , Möhlig Matthias , Spranger Joachim
Published: April 2010

Fibroblast growth factor 21 (FGF-21), a novel metabolic factor in obesity and fasting metabolism, has been shown to be regulated by supraphysiological levels of free fatty acids (FFAs) under hyperinsulinemic conditions. Interestingly, it is still unclear whether the observed effects of FFAs on FGF-21 are relevant under physiological conditions, and the relative functions of FFAs and insulin within this context also need to be determined. Fourteen healthy men were studied in a randomized controlled crossover trial (RCT) using lipid heparin infusion (LHI) at a dose inducing physiological elevations of FFAs vs. saline heparin infusion. In a second randomized controlled trial, FGF-21 was analyzed in 14 patients with type 1 diabetes (6 men, 8 women) during continuous insulin supply vs. discontinued insulin infusion and subsequently increased lipolysis and ketosis. Circulating FGF-21 increased during physiologically elevated FFAs induced by LHI, which was accompanied by mild hyperinsulinemia. Interestingly, a mild elevation of FFAs resulting from complete insulin deficiency also increased FGF-21 levels. These results from two independent human RCTs suggest that FFAs increase circulating FGF-21, while insulin is only of minor importance under physiological conditions. This mechanism might explain the apparent paradox of increased FGF-21 levels in obesity, insulin resistance, and starvation.
Tropical Atlantic Hurricanes, Easterly Waves, and West African Mesoscale Convective Systems
Authors: Kouadio Yves K. , Machado Luiz A. T. , Servain Jacques
Published: April 2010

The relationship between tropical Atlantic hurricanes (Hs), atmospheric easterly waves (AEWs), and West African mesoscale convective systems (MCSs) is investigated. It points out atmospheric conditions over West Africa before hurricane formation. The analysis was performed for two periods, June–November in 2004 and 2005, during which 12 hurricanes (seven in 2004, five in 2005) were selected. Using the AEW signature in the 700 hPa vorticity, a backward trajectory was performed to the African coast, starting from the date and position of each hurricane, when and where it was catalogued as a tropical depression. At this step, using the Meteosat‐7 satellite dataset, we selected all the MCSs around this time and region, and tracked them from their initiation until their dissipation. This procedure allowed us to relate each of the selected Hs with AEWs and a succession of MCSs that occurred a few times over West Africa before initiation of the hurricane. Finally, a dipole in sea surface temperature (SST) was observed with a positive SST anomaly within the region of H generation and a negative SST anomaly within the Gulf of Guinea. This SST anomaly dipole could contribute to enhance the continental convergence associated with the monsoon that impacts on the West African MCSs formation.
Parameterized Hardware Design on Reconfigurable Computers: An Image Processing Case Study
Authors: Huang Miaoqing , Serres Olivier , El-Ghazawi Tarek , Newby Gregory
Published: April 2010

Reconfigurable Computers (RCs) with hardware (FPGA) co-processors can achieve significant performance improvement compared with traditional microprocessor (μP)-based computers for many scientific applications. The potential amount of speedup depends on the intrinsic parallelism of the target application as well as the characteristics of the target platform. In this work, we use image processing applications as a case study to demonstrate how hardware designs are parameterized by the co-processor architecture, particularly the data I/O, i.e., the local memory of the FPGA device and the interconnect between the FPGA and theμP. The local memory has to be used by applications that access data randomly. A typical case belonging to this category is image registration. On the other hand, an application such as edge detection can directly read data through the interconnect in a sequential fashion. Two different algorithms of image registration, the exhaustive search algorithm and the Discrete Wavelet Transform (DWT)-based search algorithm, are implemented on hardware, i.e., Xilinx Vertex-IIPro 50 on the Cray XD1 reconfigurable computer. The performance improvements of hardware implementations are10×and2×, respectively. Regarding the category of applications that directly access the interconnect, the hardware implementation of Canny edge detection can achieve544×speedup.
Multilevel Space‐Time Aggregation for Bright Field Cell Microscopy Segmentation and Tracking
Authors: Inglis Tiffany , De Sterck Hans , Sanders Geoffrey , Djambazian Haig , Sladek Robert , Sundararajan Saravanan , Hudson Thomas J.
Published: April 2010

A multilevel aggregation method is applied to the problem of segmenting live cell bright field microscope images. The method employed is a variant of the so‐called “Segmentation by Weighted Aggregation” technique, which itself is based on Algebraic Multigrid methods. The variant of the method used is described in detail, and it is explained how it is tailored to the application at hand. In particular, a new scale‐invariant “saliency measure” is proposed for deciding when aggregates of pixels constitute salient segments that should not be grouped further. It is shown how segmentation based on multilevel intensity similarity alone does not lead to satisfactory results for bright field cells. However, the addition of multilevel intensity variance (as a measure of texture) to the feature vector of each aggregate leads to correct cell segmentation. Preliminary results are presented for applying the multilevel aggregation algorithm in space time to temporal sequences of microscope images, with the goal of obtaining space‐time segments (“object tunnels”) that track individual cells. The advantages and drawbacks of the space‐time aggregation approach for segmentation and tracking of live cells in sequences of bright field microscope images are presented, along with a discussion on how this approach may be used in the future work as a building block in a complete and robust segmentation and tracking system.
Immunogenic Tumor Cell Death for Optimal Anticancer Therapy: The Calreticulin Exposure Pathway
Authors: Zitvogel Laurence , Kepp Oliver , Senovilla Laura , Menger Laurie , Chaput Nathalie , Kroemer Guido
Published: April 2010

In response to some chemotherapeutic agents such as anthracyclines and oxaliplatin, cancer cells undergo immunogenic apoptosis, meaning that their corpses are engulfed by dendritic cells and that tumor cell antigens are presented to tumor-specific CD8+ T cells, which then control residual tumor cells. One of the peculiarities of immunogenic apoptosis is the early cell surface exposure of calreticulin (CRT), a protein that usually resides in the lumen of the endoplasmic reticulum (ER). When elicited by anthracyclines or oxaliplatin, the CRT exposure pathway is activated by pre-apoptotic ER stress and the phosphorylation of the eukaryotic translation initiation factor eIF2α by the kinase PERK, followed by caspase-8-mediated proteolysis of the ER-sessile protein BAP31, activation of the pro-apoptotic proteins Bax and Bak, anterograde transport of CRT from the ER to the Golgi apparatus and exocytosis of CRT-containing vesicles, finally resulting in CRT translocation onto the plasma membrane surface. Interruption of this complex pathway abolishes CRT exposure, annihilates the immunogenicity of apoptosis, and reduces the immune response elicited by anticancer chemotherapies. We speculate that human cancers that are incapable of activating the CRT exposure pathway are refractory to the immune-mediated component of anticancer therapies. Clin Cancer Res; 16(12); 3100–4. ©2010 AACR.
Cardiomyogenic Potential of C-Kit
+
–Expressing Cells Derived From Neonatal and Adult Mouse Hearts
Authors: Zaruba Marc-Michael , Soonpaa Mark , Reuter Sean , Field Loren J.
Published: April 2010

Background—

C-kit is a receptor tyrosine kinase family member expressed in hematopoietic stem cells. C-kit is also transiently expressed in cardiomyocyte precursors during development and in a rare cell population in the normal adult heart. In the present study, the cardiomyogenic potential of c-kit
+
cells isolated from normal neonatal, normal adult, and infarcted adult mouse hearts was evaluated.

Methods and Results—

Magnetic activated cell sorting was used to prepare c-kit
+
cells from the hearts of ACT-EGFP/MHC-nLAC double transgenic mice. These animals exhibit widespread enhanced green fluorescent protein (EGFP) expression and cardiomyocyte-restricted nuclear β-galactosidase activity, thus permitting simultaneous tracking of cell survival and differentiation. A subset of the c-kit
+
cells from double transgenic neonatal hearts acquired a cardiomyogenic phenotype when cocultured with fetal cardiomyocytes (2.4% of all EGFP
+
cells screened) but rarely when cultured alone or when cocultured with mouse fibroblasts (0.03% and 0.05% of the EGFP
+
cells screened, respectively). In contrast, c-kit
+
cells from normal adult double transgenic hearts failed to undergo cardiomyogenic differentiation when cocultured with nontransgenic fetal cardiomyocytes (>18 000 EGFP
+
cells screened) or when transplanted into normal or infarcted adult mouse hearts (14 EGFP
+
grafts examined). A single c-kit
+
cell from an infarcted double transgenic adult heart was observed to acquire a cardiomyogenic phenotype in coculture (>37 000 EGFP
+
cells screened).

Conclusions—

These data suggest that the ability of cardiac-resident c-kit
+
cells to acquire a cardiomyogenic phenotype is subject to temporal limitations or, alternatively, that the cardiomyogenic population is lost. Elucidation of the underlying molecular basis may permit robust cardiomyogenic induction in adult-derived cardiac c-kit
+
cells.
Storminess and Environmental Changes in the Mediterranean Central Area
Authors: Diodato Nazzareno , Bellocchi Gianni
Published: April 2010

Earth ecosystems are not static, and they respond to environmental changes, particularly climatic and anthropogenic. Precipitation varying in its extremeness, with shifts to greater or lesser intensity of individual storms and/or to change in the length and frequency of wet and dry periods, can adversely affect both urban and rural ecosystems. Here, the authors review long-term precipitation records of the central Mediterranean area and employ a Web geographical information system (GIS)-based analytical approach to compare current rainfall impact with historical data on different spatial and temporal scales. Autumn (September–November) was recognized as the most hazardous season that marks the evidence of a changing climate, with a shift toward more intense rainfalls in recent times. In the first decade of the third millennium, areas of peninsular and insular Italy have been especially affected by extreme rains. A focus was put on the island of Sicily, where extraordinary rain events occurred in September 2009, discussed in the context of upcoming trends and climate histories. An improved knowledge and understanding of the scale at which changes on extremes occur is essential for dealing with the forthcoming challenges regarding soil and water conservation practices. The characteristics of changes in natural rainfall, its role on terrestrial ecosystems, and its effect on surface water erosion dynamics are discussed. It is argued that understanding these issues are major priorities for future research to promote a better understanding of the Earth interaction with water resources and related hydrological issues.
The Necessity of Professional Disclosure and Informed Consent for Rehabilitation Counselors
Authors: Carlisle Jeffrey , Neulicht Ann T.
Published: April 2010

Within the rehabilitation counseling arena, professional disclosure and informed consent are critical concepts for the rehabilitation counselor to understand. Once understood, they become key components of a rehabilitation counselor’s daily practice. Counselors need to provide sufficient prior information about their evaluation and services to respect the individual’s right to make an informed choice about participating in the activities. This is one of the most important steps for the counselor to make at the outset of the relationship and thereafter. Yet, inconsistency abounds among rehabilitation counselors when it comes to providing a full and adequate disclosure, thereby ensuring the individual’s right to informed consent. This article addresses the history of these issues, the manner by which earlier versions of the Code of Professional Ethics for Rehabilitation Counselors addressed them, and the changes regarding disclosure and informed consent within the revised 2010 code. Because the code now requires written disclosure, this article provides guidance to rehabilitation counselors for incorporating proper professional disclosure and informed consent protocols into their daily professional activities.
Advances in the ecology, biogeography and conservation of seahorses (genus Hippocampus)
Authors: Scales Helen
Published: April 2010

Seahorses (genus Hippocampus) form a group of over 30 species of enigmatic and charismatic marine fish that are attracting increasing global concern for their threatened status. Particular issues include the overexploitation of seahorses in target and bycatch fisheries and their utilization for traditional Chinese medicines. Seahorses are also thought to be highly vulnerable to habitat loss and deterioration throughout their circumglobal range in temperate and tropical shallow seas. A suite of unusual biological characteristics, including male pregnancy, has not only stimulated research attention but also contributed to the seahorses’ apparently vulnerable nature. Key areas of advancement in recent years, as reviewed here, include the application of genetic tools to confirm the monogamous behaviour of many species both within and between breeding events, to elucidate their challenging taxonomy, to gain insight into their evolution, biogeography and origins, and to identify which species are being traded internationally. Efforts to conserve seahorses have included both ‘top-down’ and ‘bottom-up’ approaches, which together have highlighted the need for international regulation of seahorse exploitation and demonstrated that seahorses can stimulate local and regional action in protecting not only seahorses themselves but also a range of threatened habitats in which they live. Updating and extending the global assessment of individual seahorse species on the IUCN Red List of Threatened Species is urgently needed (currently only eight species have been fully assessed), as are a renewed survey of the global seahorse trade and further studies to assess how best to protect seahorses within marine reserves.
Carbon monoxide formation and emissions during waste incineration in a grate-circulating fluidized bed incinerator
Authors: Yanguo Zhang  , Qinghai Li  , Aihong Meng  , Changhe Chen
Published: April 2010

This paper presents an experimental study of carbon monoxide (CO) formation and emissions in both grate drying bed incinerators and circulating fluidized bed (CFB) incinerators to simulate the two key parts of a combined grate and circulating fluidized bed (grate-CFB) incinerator in order to investigate pollutant emission control in municipal solid waste (MSW) combustion that occurs in a grate-CFB incinerator utilizing a patented technology. Polyvinyl chloride, polystyrene, kitchen waste, paper, textile, etc. were chosen to simulate the MSW. The effects of temperature, air staging, and moisture on the CO formation and emissions were analysed for both the grate drying bed combustion and the CFB combustion. In the grate drying bed, the low temperatures increased the carbon to CO conversion rate which also increased slightly with the moisture content. Industrial field tests in a commercial grate-CFB incinerator showed that the CO concentration at the grate drying bed exit was very high and decreased along furnace height. The carbon to CO conversion rates were 0-20% for the grate drying bed which exceeded the range of 0.8-16% measured in a grate drying bed exit of the commercial grate-CFB incinerator tests. In the commercial grate-CFB incinerator tests, at excess air ratios ranging from 1.5-2.0 or more, the CO emissions decreased to a low and stable level, whose corresponding carbon to CO conversion rates were far lower than 0-10%. The low CO emission is one of the factors enabling the polychlorinated dibenzodioxin/polychlorinated dibenzofuran emissions to satisfy the Chinese national regulations.
Multi-Agent Simulations of the Evolution of Combinatorial Phonology
Authors: de Boer Bart , Zuidema Willem
Published: April 2010

A fundamental characteristic of human speech is that it uses a limited set of basic building blocks (phonemes, syllables), that are put to use in many different combinations to mark differences in meaning. This article investigates the evolution of such combinatorial phonology with a simulated population of agents. We first argue that it is a challenge to explain the transition from holistic to combinatorial phonology, as the first agent that has a mutation for using combinatorial speech does not benefit from this in a population of agents that use a holistic signaling system. We then present a solution for this evolutionary deadlock. We present experiments that show that when a repertoire of holistic signals is optimized for distinctiveness in a population of agents, it converges to a situation in which the signals can be analyzed as combinatorial, even though the agents are not aware of this structure. We argue that in this situation adaptations for productive combinatorial phonology can spread.
Transmission electron microscopy (TEM) of Earth and planetary materials: A review
Authors: Lee M. R.
Published: April 2010

Using high intensity beams of fast electrons, the transmission electron microscope (TEM) and scanning transmission electron microscope (STEM) enable comprehensive characterization of rocks and minerals at micrometre to sub-nanometre scales. This review outlines the ways in which samples of Earth and planetary materials can be rendered sufficiently thin for TEM and STEM work, and highlights the significant advances in site-specific preparation enabled by the focused ion beam (FIB) technique. Descriptions of the various modes of TEM and STEM imaging, electron diffraction and X-ray and electron spectroscopy are outlined, with an emphasis on new technologies that are of particular relevance to geoscientists. These include atomic-resolution Z-contrast imaging by high-angle annular dark-field STEM, electron crystallography by precession electron diffraction, spectrum mapping using X-rays and electrons, chemical imaging by energy-filtered TEM and true atomic-resolution imaging with the new generation of aberration-corrected microscopes. Despite the sophistication of modern instruments, the spatial resolution of imaging, diffraction and X-ray and electron spectroscopy work on many natural materials is likely to remain limited by structural and chemical damage to the thin samples during TEM and STEM.
Demicheleite-(I), BiSI, a new mineral from La Fossa Crater, Vulcano, Aeolian Islands, Italy
Authors: Demartin F. , Gramaccioli C. M. , Campostrini I.
Published: April 2010

Demicheleite-(I), ideally BiSI, is the iodine-dominant analogue of demicheleite-(Br) and demicheleite-(Cl). It was found in an active medium-temperature intracrateric fumarole at La Fossa crater, Vulcano Island, Aeolian archipelago, Sicily, Italy. The mineral is the first bismuth sulphoiodide so far discovered in a wholly natural environment, and corresponds to the already known synthetic compound. It occurs as acicular to stout, translucent crystals up to 0.25 mm long in an altered pyroclastic breccia, together with demicheleite-(Br), bismoclite, bismuthinite, godovikovite, panichiite, aiolosite, brontesite, adranosite and other new phases under study. The colour is dark red to black, the lustre submetallic. The unit cell is orthorhombic, space groupPnam, witha= 8.4501(7) Å,b= 10.1470(9) Å ,c= 4.1389(4) Å ,V= 354.88(4) Å3, andZ= 4. The crystal habit is prismatic, with the main forms {110} and {111} inferred from analogy with demicheleite-(Br). Twinning was not observed. The strongest 6 lines in the X-ray powder diffraction pattern [dobs.(Å) (I/I0) (hkl)] are: 6.490 (100) (110); 4.346 (94) (120); 3.896 (90) (210); 2.709 (60) (310); 2.161 (38) (330); 3.243 (22) (220). The chemical analysis obtained by WDS electron microprobe gave: Bi 58.32, S 9.43, I 23.69, Br 5.66, Cl 1.01, totalling 98.11 wt.%, corresponding to an empirical formula (based on 3 a.p.f.u.) of: Bi0.97S1.03(I0.65Br0.25Cl0.10)Σ1.00. The unit-cell data are close to those of the synthetic compound, whose crystal structure is already known. The calculated density is 6.411 g cm–3.
Heklaite, KNaSiF6, a new fumarolic mineral from Hekla volcano, Iceland
Authors: Garavelli A. , Balić-Žunić T. , Mitolo D. , Acquafredda P. , Leonardsen E. , Jakobsson S. P.
Published: April 2010

Heklaite, with the ideal formula KNaSiF6, was found among fumarolic encrustations collected in 1992 on the Hekla volcano, Iceland. Heklaite forms a fine-grained mass of micron- to sub-micron-sized crystals intimately associated with malladrite, hieratite and ralstonite. The mineral is colourless, transparent, non-fluorescent, has a vitreous lustre and a white streak. The calculated density is 2.69 g cm–3. An SEM-EDS quantitative chemical analysis shows the following range of concentrations (wt.%): Na 11.61–12.74 (average 11.98), K 17.02–18.97 (average 18.29), Si 13.48 –14.17 (average 13.91), F 54.88–56.19 (average 55.66). The empirical chemical formula, calculated on the basis of 9 a.p.f.u., is Na1.07K0.96Si1.01F5.97. X-ray powder diffraction indicates that heklaite is orthorhombic, space groupPnma, with the following unit-cell parameters:a= 9.3387(7) Å,b= 5.5032(4) Å,c= 9.7957(8) Å ,V= 503.43(7) Å3,Z= 4. The eight strongest reflections in the powder diffraction pattern [din Å (I/I0) (hkl)] are: 4.33 (53) (102); 4.26 (56) (111); 3.40 (49) (112); 3.37 (47) (202); 3.34 (100) (211); 2.251 (27) (303); 2.050 (52) (123); 2.016 (29) (321). On the basis of chemical analyses and X-ray data, heklaite corresponds to the synthetic compound KNaSiF6. The name is for the type locality, the Hekla volcano, Iceland.
The early publication of new mineral names: new procedures for the release of new mineral names and publication
Authors: Mills S.J.
Published: April 2010

New procedures are put in place in order to facilitate the dissemination of new mineral names into the public arena. Authors will get the opportunity to select whether the Commission will release the new mineral name upon successful approval in the Commission's monthly newsletter, which will be published in Mineralogical Magazine. Authors are also entitled to have the name not released until final publication, i.e. to retain the status quo. This will enable citations to be made using the new mineral name until the full description is published. Modifications to the existing rules, on the two-year time frame for new mineral publication, are also outlined.
The crystal structure and compositional range of mckinstryite
Authors: Kolitsch U.
Published: April 2010

The previously unknown crystal structure of mckinstryite, originally described as Ag1.18Cu0.82S or (Ag,Cu)2S, was solved and refined using single-crystal X-ray diffractometer data collected from a sample from the Clara mine, Black Forest (Mo-Kα radiation, CCD area detector, R1(F) = 3.85%). Mckinstryite has the refined formula Ag4.92Cu3.08S4 or Ag1.23Cu0.77S (idealized Ag5Cu3S4 or Ag1.25Cu0.75S) and crystallizes in space group Pnma (no. 62), with a = 14.047(3) Å, b = 7.805(2) Å , c = 15.691(3) Å, V = 1720.3(7) Å3, Z = 8. The structure contains five Ag, six Cu and eight S sites in the asymmetric unit. One of the Ag sites shows minor Cu-for-Ag substitution. The topology is based on flat, interrupted (010) layers of Cu and S atoms (all atoms on y = 0.25), in which the Cu atoms show triangular or two-coordination to S (interrupted {6,3} tiling). These layers alternate with uneven layers consisting of Ag atoms showing irregular three- to two-coordination to S. Some fairly short Ag–Cu contact distances (2.781–2.884 Å) strongly indicate that metal-metal interaction plays an important role in mckinstryite. The topology is related to that of stromeyerite (∼AgCuS) which contains complete flat layers of Cu atoms triangularly coordinated to S atoms, alternating with layers of loosely packed Ag atoms.

A critical evaluation of literature data on the chemical composition and unit-cell parameters of mckinstryite confirms the presence of a small compositional range of mckinstryite which extends approximately from Ag1.18Cu0.82S to Ag1.25Cu0.75S, with the presently studied sample being fairly Agrich. The accurate limits of this range at ambient temperature are still to be determined.
Senescence induction in human fibroblasts and hematopoietic progenitors by leukemogenic fusion proteins
Authors: Wajapeyee Narendra , Wang Shu-Zong , Serra Ryan W. , Solomon Peter D. , Nagarajan Arvindhan , Zhu Xiaochun , Green Michael R.
Published: April 2010

Hematologic malignancies are typically associated with leukemogenic fusion proteins, which are required to maintain the oncogenic state. Previous studies have shown that certain oncogenes that promote solid tumors, such as RAS and BRAF, can induce senescence in primary cells, which is thought to provide a barrier to tumorigenesis. In these cases, the activated oncogene elicits a DNA damage response (DDR), which is essential for the senescence program. Here we show that 3 leukemogenic fusion proteins, BCR-ABL, CBFB-MYH11, and RUNX1-ETO, can induce senescence in primary fibroblasts and hematopoietic progenitors. Unexpectedly, we find that senescence induction by BCR-ABL and CBFB-MYH11 occurs through a DDR-independent pathway, whereas RUNX1-ETO induces senescence in a DDR-dependent manner. All 3 fusion proteins activate the p38 MAPK pathway, which is required for senescence induction. Our results reveal diverse pathways for oncogene-induced senescence and further suggest that leukemias harbor genetic or epigenetic alterations that inactivate senescence induction genes.
Prognostic impact of IDH2 mutations in cytogenetically normal acute myeloid leukemia
Authors: Thol Felicitas , Damm Frederik , Wagner Katharina , Göhring Gudrun , Schlegelberger Brigitte , Hoelzer Dieter , Lübbert Michael , Heit Wolfgang , Kanz Lothar , Schlimok Günter , Raghavachar Aruna , Fiedler Walter , Kirchner Hartmut , Heil Gerhard , Heuser Michael , Krauter Jürgen , Ganser Arnold
Published: April 2010

Mutations in the nicotinamide adenine dinucleotide phosphate+–dependent isocitrate dehydrogenase gene 2 (IDH2) have recently been found in patients with acute myeloid leukemia (AML) as well as in patients with leukemic transformation of myeloproliferative neoplasms. We analyzed 272 adult patients with cytogenetically normal AML (CN-AML) for the presence of IDH2 mutations in codons R140 and R172. IDH2 mutations of amino acid 140 or 172 could be identified in 12.1% of CN-AML patients, with the majority of mutations (90%) occurring at position R140. The incidence of IDH2 mutations in AML patients with aberrant karyotypes (n = 130) was significantly lower (3.8%, P = .006). IDH2 mutations were mutually exclusive with mutations in IDH1. IDH2 mutation status alone or in combination with IDH1 mutations had no impact on response to therapy, overall survival, and relapse-free survival in patients with CN-AML. In conclusion, IDH2 mutations are frequently found in CN-AML, but in our analysis these mutations did not influence treatment outcome. This study was registered at www.clinicaltrials.gov as #NCT00209833.
Association between transforming growth factor β1 polymorphisms and atrial fibrillation in essential hypertensive subjects
Authors: Wang Yongzheng , Hou Xuwei , Li Yuliang
Published: April 2010

Background

The association of TGF β1 polymorphisms and atrial fibrillation (AF) in essential hypertensive (EH) subjects remains unknown. Methods EH subjects with AF (EH+AF+) and sinus rhythm (EH+AF-) were enrolled. The polymorphisms of +869 T → C at codon 10 and + 915 G → C at codon 25, were genotyped. The clinical characteristics including serum TGF β1 levels were detected.

Results

The GG genotypes of TGF β1 +915 G → C at codon 25 were more prevalent in subjects from EH+AF+ group than those from EH+AF- group (P = 0.009). The subjects with GG genotype from EH+AF+ group had the highest mean serum TGF β1 level, which was significantly higher than that of GG genotype subjects from EH+AF- group (3.18 ± 0.24 ng/dl vs.2.29 ± 0.14 ng/dl, P < 0.05). Multiple analyses revealed that the TGF β1 GG genotype of +915 G → C at codon 25 presented a 3.09 times higher risk in developing AF in the multivariate model after adjusting for age and gender.

Conclusion

The polymorphisms of TGF β1 +915 G → C at codon 25 were associated with occurrence of AF and serum TGF β1 level in EH subjects.
Predicting conserved protein motifs with Sub-HMMs
Authors: Horan Kevin , Shelton Christian R , Girke Thomas
Published: April 2010

Background

Profile HMMs (hidden Markov models) provide effective methods for modeling the conserved regions of protein families. A limitation of the resulting domain models is the difficulty to pinpoint their much shorter functional sub-features, such as catalytically relevant sequence motifs in enzymes or ligand binding signatures of receptor proteins.

Results

To identify these conserved motifs efficiently, we propose a method for extracting the most information-rich regions in protein families from their profile HMMs. The method was used here to predict a comprehensive set of sub-HMMs from the Pfam domain database. Cross-validations with the PROSITE and CSA databases confirmed the efficiency of the method in predicting most of the known functionally relevant motifs and residues. At the same time, 46,768 novel conserved regions could be predicted. The data set also allowed us to link at least 461 Pfam domains of known and unknown function by their common sub-HMMs. Finally, the sub-HMM method showed very promising results as an alternative search method for identifying proteins that share only short sequence similarities.

Conclusions

Sub-HMMs extend the application spectrum of profile HMMs to motif discovery. Their most interesting utility is the identification of the functionally relevant residues in proteins of known and unknown function. Additionally, sub-HMMs can be used for highly localized sequence similarity searches that focus on shorter conserved features rather than entire domains or global similarities. The motif data generated by this study is a valuable knowledge resource for characterizing protein functions in the future.
G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration
Authors: Fasold Mario , Stadler Peter F , Binder Hans
Published: April 2010

Background

The brightness of the probe spots on expression microarrays intends to measure the abundance of specific mRNA targets. Probes with runs of at least three guanines (G) in their sequence show abnormal high intensities which reflect rather probe effects than target concentrations. This G-bias requires correction prior to downstream expression analysis.

Results

Longer runs of three or more consecutive G along the probe sequence and in particular triple degenerated G at its solution end ((GGG)1-effect) are associated with exceptionally large probe intensities on GeneChip expression arrays. This intensity bias is related to non-specific hybridization and affects both perfect match and mismatch probes. The (GGG)1-effect tends to increase gradually for microarrays of later GeneChip generations. It was found for DNA/RNA as well as for DNA/DNA probe/target-hybridization chemistries. Amplification of sample RNA using T7-primers is associated with strong positive amplitudes of the G-bias whereas alternative amplification protocols using random primers give rise to much smaller and partly even negative amplitudes.

We applied positional dependent sensitivity models to analyze the specifics of probe intensities in the context of all possible short sequence motifs of one to four adjacent nucleotides along the 25meric probe sequence. Most of the longer motifs are adequately described using a nearest-neighbor (NN) model. In contrast, runs of degenerated guanines require explicit consideration of next nearest neighbors (GGG terms). Preprocessing methods such as vsn, RMA, dChip, MAS5 and gcRMA only insufficiently remove the G-bias from data.

Conclusions

Positional and motif dependent sensitivity models accounts for sequence effects of oligonucleotide probe intensities. We propose a positional dependent NN+GGG hybrid model to correct the intensity bias associated with probes containing poly-G motifs. It is implemented as a single-chip based calibration algorithm for GeneChips which can be applied in a pre-correction step prior to standard preprocessing.