bluuebunny/crossref_metadata_2025 huggingface dataset:
Randomized Trial Comparing Intraoral Ultrasound to Landmark‐based Needle Aspiration in Patients with Suspected Peritonsillar Abscess
Authors: Costantino Thomas G. , Satz Wayne A. , Dehnkamp Wade , Goett Harry
Published: June 2012

ACADEMIC EMERGENCY MEDICINE 2012; 19:626–631 © 2012 by the Society for Academic Emergency Medicine

Objectives:  Traditionally, emergency physicians (EPs) have used anatomic landmark‐based needle aspiration to drain peritonsillar abscesses (PTAs). If this failed, an imaging study and/or consultation with another service to perform the drainage is obtained. Recently, some EPs have used ultrasound (US) to guide PTA drainage. This study seeks to determine which initial approach leads to greater successful drainage. The primary objective of this study was to compare the diagnostic accuracy of EPs for detecting PTA or peritonsillar cellulitis (PTC) using either intraoral US or initial needle aspiration after visual inspection (the landmark technique [LM]). Secondary objectives included the successful aspiration of purulent material in those patients with a PTA in each arm, the use of computed tomography (CT) scanning in each arm, and the otolaryngology (ENT) consultation rate in each arm.

Methods:  This was a prospective, randomized, controlled clinical trial of a convenience sample of adult patients who presented to a single, large, urban university hospital. Patients were enrolled if they presented with a constellation of signs and symptoms that were judged to be a PTA. These patients were randomized to receive intraoral US or to undergo LM drainage. The US was performed using an 8–5 MHz intracavitary transducer immediately prior to the procedure. The probe was then withdrawn and the provider who did the US also performed the needle aspiration. The LM was performed using visual landmarks in a superior to inferior approach until pus was obtained or at least two sticks were performed. Anesthesia was standardized. Patients returned for follow‐up in 2 days where a final diagnosis was rendered.

Results:  There were 28 patients enrolled, with 14 in each arm. US established the correct diagnosis more often than LM [(100%, 95% confidence interval [CI] = 75% to 100% vs. 64%, 95% CI = 39% to 84%; p = 0.04)]. US also led to more successful aspiration of purulent material by the EP than LM in patients with PTA [(100%, 95% CI = 63% to 100% vs. 50%, 95% CI = 24% to 76%; p = 0.04)]. The ENT consult rate was 7% (95% CI = 0% to 34%) for US versus 50% (95% CI = 27% to 73%) for LM (p = 0.03). The CT usage rate was 0% for US versus 35% for LM (p = 0.04).

Conclusions:  An initial intraoral US performed by EPs can reliably diagnose PTC and PTA. Additionally, using intraoral US to assist in the drainage of PTAs with needle aspiration leads to greater success compared to the traditional method of LM relying on physical exam alone.
From shoots to roots: transport and metabolic changes in tomato after simulated feeding by a specialist lepidopteran
Authors: Gómez Sara , Steinbrenner Adam D. , Osorio Sonia , Schueller Michael , Ferrieri Richard A. , Fernie Alisdair R. , Orians Colin M.
Published: June 2012

Upon herbivory, plants can swiftly reallocate newly acquired resources to different tissues within a plant. Although the herbivore‐induced movement of resources is apparent, the movement direction and the role of the remobilized resources are not well understood. Here, we used a two‐pronged approach combining radioisotope and metabolomic techniques to shed light on whole‐plant resource reallocation and changes in primary metabolism within the tomato, Solanum lycopersicum (L.) (Solanaceae), model in response to simulated herbivory by the specialist Manduca sexta (L.) (Lepidoptera: Sphingidae). Manduca sexta regurgitant applied to damaged leaves, but not mechanical damage alone, increased 11C‐photosynthate allocation to roots but did not affect 11CO2 fixation and leaf export. Changes in primary metabolite concentrations occurred mostly in sink tissues (apex and roots) as well as in damaged leaves. Both damage treatments (with and without M. sexta regurgitant application) resulted in increased concentrations of primary metabolites relative to undamaged plants in the apex and decreased concentrations in the roots, but there were also extensive changes specific to each damage treatment. Mechanical damage alone led to changes consistent with water stress caused by tissue damage. Manduca sexta led to metabolite increases in the apex consistent with an increase in glucose breakdown, metabolite increases in damaged leaves consistent with starch degradation, and metabolite decreases in roots suggesting a high use of metabolites. A possible explanation for the observed patterns in the aboveground tissues might be an increase in carbohydrate degradation to support defense production in attacked leaves and vulnerable developing leaves, and/or subsequent remobilization to belowground tissues to support high carbohydrate demand for respiration, enhanced nutrient uptake, and storage.
Inbreeding, herbivory, and the transcriptome of Solanum carolinense
Authors: Kariyat Rupesh R. , Mena‐Alí Jorge , Forry Brant , Mescher Mark C. , De Moraes Consuelo M. , Stephenson Andrew G.
Published: June 2012

Both inbreeding and herbivory are common in flowering plants, and both are known to reduce fitness. Although inbreeding might also be expected to impact inducible and constitutive plant defenses against herbivores in a variety of ways, investigators have only recently begun to examine the effects of inbreeding on resistance to herbivores. Here, we examined the effects of inbreeding in horsenettle, Solanum carolinense L. (Solanaceae), on herbivore damage and reproductive output under field conditions. In addition, we employed the commercially available Affymetrix tomato (Solanum esculentum L.) microarray to explore changes in S. carolinense gene expression associated with feeding by Manduca sexta) (L.) (Lepidoptera: Sphingidae) caterpillars on inbred and outbred horsenettle plants. We found that the inbred horsenettle plants experienced significantly greater herbivore damage in the field and exhibited only 11% of the seed production of outbred plants. Flea beetles and false potato beetles were the most abundant herbivores observed on the experimental plants, and both were observed significantly more often on inbred plants. The microarray‐generated transcriptomes of horsenettle revealed that the commercially available microarray chips can be reliably used with this important weed, that damage significantly up‐regulates many defense‐related genes, and that inbreeding depresses the expression of many genes especially those located in the jasmonic acid, ethylene, abscisic acid, and systemin‐mediated pathways that regulate the induction of defensive compounds and organic volatiles. Findings of the field study and the gene‐expression analysis are thus complementary, as the former demonstrates that inbreeding impacts plant resistance to herbivores, whereas the latter provides initial insights into the genetic mechanisms underlying these effects and their relationship to fitness.
C‐reactive protein, early life stress, and wellbeing in healthy adults
Authors: Carpenter L. L. , Gawuga C. E. , Tyrka A. R. , Price L. H.
Published: June 2012

Carpenter LL, Gawuga CE, Tyrka AR, Price LH. C‐reactive protein, early life stress, and wellbeing in healthy adults.

Objective:  To determine whether C‐reactive protein (CRP) can serve as a marker for alterations in immune function prior to the manifestation of significant psychiatric and medical disorders.

Method:  Ninety‐two healthy adults were recruited from the community and determined to be free of psychiatric or medical disorders. The concentration of plasma CRP from a single resting sample was examined in relation to current mental and physical health as well as to self‐reported history of early life adversity.

Results:  C‐reactive protein showed a significant positive correlation with body mass index (BMI; r = 0.477, P < 0.001). Non‐specific pain, fatigue, and lower overall quality of physical health were all associated with higher CRP concentrations (all P < 0.05 or P < 0.01), after controlling for effect of BMI and other relevant covariates. Subthreshold depression symptoms and other indices of mental/emotional wellbeing were not associated with CRP, nor was CRP significantly linked to any measures of early life adversity.

Conclusion:  Lower‐quality physical health and wellbeing, but not the presence of mood/anxiety symptoms or early life stress (ELS), were significantly related to plasma CRP. Elevated CRP does not appear to be a fundamental consequence of ELS among healthy adults.
Flexible dispersal strategies in native and non‐native ranges: environmental quality and the ‘good–stay, bad–disperse’ rule
Authors: Hui Cang , Roura‐Pascual Núria , Brotons Lluís , Robinson Robert A. , Evans Karl L.
Published: June 2012

Dispersal strategies are one of the most important determinants of range dynamics and a surrogate for invasiveness. We tested three inter‐related hypotheses derived from demographic and ecological models: (H1) short‐distance dispersal strategies arise at native range margins due to their demographic advantage; (H2) in non‐native areas a high diffusion rate is favoured at the advancing range front for niche filling; (H3) environmental deterioration can increase dispersal and lead to a ‘good–stay, bad–disperse’ strategy. Spatially and temporally explicit rates of spread and dispersal kernels of the European starling Sturnus vulgaris were generated for its native range (Britain) using ringing records from 1909 to 2008, and for a non‐native area (South Africa) using ringing data and distributional records since its introduction in 1897. There was a marked spatial and temporal variation in the rate of spread within both native and non‐native ranges. In the native range the rate of spread declined with increasing distance from the species’ European distribution (contradicting H1). In the non‐native range the rate of spread increased with distance from the introduction locality (supporting H2). The annual rate of spread in the native range also increased significantly when environmental conditions were deteriorating as indicated by marked population declines and relatively low abundance (H3), providing clear evidence for flexible dispersal strategies based on a ‘good–stay, bad–disperse’ rule. Starlings’ dispersal kernel followed an inverse power law and showed strong anisotropy and significant divergence between native and invasive populations, suggesting a flexible strategy comprising a dynamic response to spatial and temporal environmental variation with implications for predicting dispersal and range dynamics arising from environmental change.
Protein tyrosine phosphatase structure–function relationships in regulation and pathogenesis
Authors: Böhmer Frank , Szedlacsek Stefan , Tabernero Lydia , Östman Arne , den Hertog Jeroen
Published: June 2012

Protein phosphorylation on tyrosine residues is tightly controlled by protein tyrosine phosphatases (PTPs) at multiple levels: spatio‐temporal expression, subcellular localization and post‐translational modification. Structural and functional analysis of the PTP domains has provided insight into catalysis and regulatory mechanisms that control the enzymatic activity. Understanding the molecular basis of PTP regulation is of fundamental importance to dissect the pleiotropic effect of these enzymes in both health and disease. Here, we review recent insights into the regulation of receptor‐like PTPs by extracellular ligands and into regulation by reversible oxidation that impairs catalysis directly. The physiological roles of PTPs are essential in homeostasis in eukaryotic cells and pertubation of their functional attributes causes different disease states. As an example, we discuss recent findings indicating how inappropriate oxidation of PTPs in cancer cells may contribute to cell transformation. On the other hand, PTPs from many pathogens are key virulence factors and manipulate signalling pathways in the host cells to promote invasion and survival of the microorganisms. This research area has received relatively little attention but has advanced remarkably. We review the structural features of pathogenic PTPs, their similarities and differences with eukaryotic PTPs, and the possible exploitation of this knowledge for therapeutic intervention.
BaIn0.3Ti0.7O2.85/BaIn0.3Ti0.7O2.85‐Ni Electrolyte/Anode Half Cell for Solid Oxide Fuel Cell Prepared by Reactive Sintering
Authors: Letilly Marika , Joubert Olivier , Le Gal La Salle Annie
Published: June 2012

BaIn

0.3

Ti

0.7

O

2.85 (
BIT07
)/
BIT07
‐Ni electrolyte/anode half cell was prepared by reactive sintering for solid oxide fuel cells. The precursors were
BaCO3

, In2O3

, and
TiO2

for electrolyte and
BaCO3

, In2O3

, TiO2

, NiO
, and carbon black for anode. The bi‐layers were prepared by a multilayer tape casting and co‐firing method. The compositions and microstructures of the phases were studied by X‐ray powder diffraction and scanning electron microscopy, respectively. The electrolytes were dense with pure perovskite phase with a thickness about 15 μm. The anodes were porous and no obvious reaction was found between
NiO
and the precursors of
BIT07
.
Low Vacuum Deposition of Aluminum Nitride Thin Films by Sputtering
Authors: Yao Li‐Ren , Lu Fu‐Hsing
Published: June 2012

Conventionally, sputtering deposition of thin films requires a low base pressure (high vacuum) to minimize influences of residual gases. Here, a high base pressure (low vacuum) was used, which can reduce significantly the overall processing time. Aluminum nitride (
AlN
) was selected as a model system of dielectric nitrides. All the analyses revealed that the obtained films under a low vacuum environment within specific processing windows exhibited characteristics similar to those of high‐vacuum made
AlN
films. Such a low vacuum deposition technique takes advantages of kinetically favorable formation of the nitride films and hence, has great potentials in many more technological applications.
Oxygen Consumption Response to Gradual Hypoxia in Spider Crab, Maja brachydactyla: Critical and Lethal Oxygen Saturations and Recovery Ability
Authors: Cerezo Valverde Jesús , Aguado‐Giménez Felipe , Dolores Hernández María , García García Benjamín
Published: June 2012

Spider crab, Maja brachydactyla, is a crustacean with interesting biological characteristics for intensive aquaculture. However, physiological studies are needed to establish the optimal conditions for its culture and maintenance. We analyzed the oxygen consumption response of spider crab to gradual hypoxia in relation to animal weight (W: 0.42–1.62 kg) and water temperature (T: 17.8–26.3 C), along with its ability to recover. Spider crab behaved as an oxygen regulator, maintaining its oxygen consumption constant until it reached critical oxygen saturation. This value varied between 24.1 and 53.3% oxygen saturation (42.4 ± 7.4% Sat.; 2.95 ± 0.43 mgO2/L), and significantly depended on the temperature (P < 0.01). The lethal oxygen saturation varied from 6.8 to 19.3% Sat. (12.57 ± 4.25% Sat.; 0.88 ± 0.29 mgO2/L) depending on temperature and body weight (P < 0.05). When oxygen levels were re‐established after exposure to acute hypoxia, the animals recovered, oxygen consumption remaining above the routine value for up to 15–20 h. We suggest survival oxygen saturation levels for spider crab of between 100 and 65% in the experimental conditions of this study.
Effects of Cryopreservation on Morphology and Viability of Sperm and Larvae of Atlantic Cod, Gadus morhua L.
Authors: Ottesen Oddvar H. , Marschhäuser Vegard , Babiak Igor
Published: June 2012

The effects of cryopreservation on the viability, morphology and capability of spermatozoa in Atlantic cod, Gadus morhua L., were studied. The sperm was cryopreserved in straws using Hanks' balanced salt solution, hens' egg yolks and glycerol in the vapor of liquid nitrogen. Straws of cryopreserved sperm were stored in liquid nitrogen and thawed in seawater (35 C) for 8 sec before use. The motility of cryopreserved sperm was low (range 8–19%) compared to motility before freezing (range 69–76%). The fertilization rate (range 94–95%) in control groups using fresh sperm was significantly higher (P < 0.05) than in test groups (range 48–72%). In cryopreserved sperm, a relatively high percentage (range 82–93%) of the spermatozoa had changes in morphology. Many spermatozoa had no mitochondria; when mitochondria were present, the observed number varied from one and five in cryopreserved spermatozoa, and from two and seven in noncryopreserved spermatozoa. In groups where cryopreserved sperm was used, the hatching rate was lower (range 18–38%) than in control groups (range 41–63%), indicating higher mortality during embryonic development. Paternal effects on progeny performance were noted in the proportion of abnormalities but no negative effects were identified in newly hatched larvae produced using cryopreserved sperm.
Economically important production relationships in channel catfish (Ictalurus punctatus) foodfish production
Authors: Bastola Umesh , Engle Carole R.
Published: June 2012

The catfish industry (Ictalurus punctatus), the largest segment of aquaculture in the USA, has declined in the number of operations, total yield and sales in recent years. This has led to a call for innovations to improve production efficiency and to lower the cost of production. This paper reviewed the literature on management parameters that affect economically important production parameters under the control of an individual catfish farmer. Stocking density, size of fish at stocking, duration of culture, cropping systems, feeding strategies and aeration were shown to significantly affect the economically important parameters of investment costs, yield and feed conversion ratio. Additional work is needed to quantitatively model the effects of multiple parameters and to develop user‐friendly versions to assist catfish farmers in decision making.
Interspecific fish hybrids in Brazil: management of genetic resources for sustainable use
Authors: Hashimoto Diogo T. , Senhorini José A. , Foresti Fausto , Porto‐Foresti Fábio
Published: June 2012

Serrasalmid and pimelodid fish hybrids represent important advances for aquaculture in Brazil, but they also constitute serious genetic risks to cultivated and natural populations. Serrasalmid hybrids (‘tambacu’, ‘tambatinga’ and ‘patinga’) result from crosses between Colossoma macropomum, Piaractus mesopotamicus and Piaractus brachypomus. Pimelodid hybrids (‘ponto e vírgula’, ‘cachandiá’ and ‘cachapira’) arise from crosses between Pseudoplatystoma corruscans, Pseudoplatystoma reticulatum, Phractocephalus hemioliopterus and Leiarius marmoratus. The problems associated with hybrids mainly result from inappropriate use because these animals are reproductively compatible with their parental species. This review shows that monitoring of fish hybrids using genetic techniques is necessary for their sustainable development in aquaculture. The genetic technologies used to identify fish hybrids include cytogenetic methods, which are considered to be low cost, and polymerase chain reaction‐based molecular markers, which are associated with high throughput. Therefore, both types of genetic methodologies should be applied in monitoring programs aimed at brood stock management, wild stocks, the trade of hybrid juveniles and processed fish products in markets. Moreover, physical and genetic confinement of hybrids in aquaculture operations will be necessary to avoid the problems posed by these animals. The expected result of these measures will be the production of genetically improved animals by fish farms, allowing the sector to develop further and offering high‐quality animal protein.
Spontaneous non‐rdar mutations increase fitness of Salmonella in plants
Authors: Zaragoza William J. , Noel Jason T. , Teplitski Max
Published: June 2012

Proliferation of human enteric pathogens within alternate hosts, like plants, leads to temporal changes in gene expression and also selects for the phenotypic variants of the enterics that are presumed to be more fit within plants. Human enteric pathogens recovered from produce‐borne outbreaks exhibit peculiar phenotypes, for example many of them do not display the rdar (red dry and rough) phenotype. The non‐rdar phenotype results from mutations in cellulose and/or curli synthesis or regulation. How often these mutants arise, and whether they are more fit within plants is not entirely clear. We addressed this hypothesis by sequentially passaging the type strain of Salmonella enterica sv. Typhimurium ATCC14028 through tomatoes. Two spontaneous mutants defective in their ability to form red dry and rough colonies were further characterized. Even though attachment of the mutants to tomato surfaces was modestly reduced, they were 5‐ to 50‐fold more competitive than the wild‐type inside tomato fruits. Because the mutants were outcompeted by the wild‐type on common laboratory media, and not in tomatoes, the lack of the rdar phenotype is probably beneficial within tomatoes. Recombinase‐based in vivo expression tests indicate that the agfB and yihT genes were regulated differently in the mutants, although the corresponding mutations cannot fully account for the increased competitive fitness of the mutants. One of the variants has a mutated rpoS, which also reduced the expression of a SPI‐5 effector encoded by sopB. A survey of the Salmonella strains recovered from produce outbreaks revealed that some were similarly non‐rdar, likely containing rpoS mutations. This report indicates that the ‘perfect storm’ scenario, typically used to model outbreaks of produce‐borne gastroenteritis, needs to account for the ability of the pathogen to rapidly evolve and adapt to the crop production environments.
Congenital odontogenic keratocyst in a filly
Authors: Delaunois‐Vanderperren H.
Published: June 2012

This report describes a congenital odontogenic keratocyst in the left mandible of a filly. A definitive diagnosis was only made after histopathological examination. Mandibular cysts of odontogenic and osteogenic origin have been reported in the past but a case of a keratocyst has not been previously reported in the horse.
Pressure Drop for Fully Developed Turbulent Flow in Circular and Noncircular Ducts
Authors: Duan Zhipeng , Yovanovich M. M. , Muzychka Y. S.
Published: June 2012

The objective of this paper is to furnish the engineer with a simple and convenient means of estimating frictional pressure drop in ducts and the original physical behavior can be clearly reflected. Fully developed turbulent flow frictional pressure drop in noncircular ducts is examined. Simple models are proposed to predict the frictional pressure drop in smooth and rough noncircular channels. Through the selection of a novel characteristic length scale, the square root of the cross-sectional area, the effect of duct shape has been minimized. The proposed models have an accuracy of 6% for most common duct shapes of engineering practice and can be used to predict pressure drop of fully developed turbulent flow in noncircular ducts. It is found that the hydraulic diameter is not the appropriate length scale to use in defining the Reynolds number to ensure similarity between the circular and noncircular ducts. By using the Reynolds number based on the square root of the cross-sectional area, it is demonstrated that the circular tube relations may be applied to noncircular ducts eliminating large errors in estimation of pressure drop. The square root of the cross-sectional area is an appropriate characteristic dimension applicable to most duct geometries. The dimensionless mean wall shear stress is a desirable dimensionless parameter to describe fluid flow physical behavior so that fluid flow problems can be solved in the simple and direct manner. The dimensionless mean wall shear stress is presented graphically and appears more general and reasonable to reflect the fluid flow physical behavior than the traditional Moody diagram.
Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain Cp267, Isolated from a Llama
Authors: Lopes Thiago , Silva Artur , Thiago Rommel , Carneiro Adriana , Dorella Fernanda Alves , Rocha Flavia Souza , dos Santos Anderson Rodrigues , Lima Alex Ranieri Jerônimo , Guimarães Luis Carlos , Barbosa Eudes G. V. , Ribeiro Dayana , Fiaux Karina Kelly , Diniz Carlos Augusto Almeida , de Abreu Vinicius Augusto Carvalho , de Almeida Sintia Silva , Hassan Syed Shah , Ali Amjad , Bakhtiar Syeda Marriam , Aburjaile Flávia Figueira , Pinto Anne Cybelle , Soares Siomar de Castro , Pereira Ulisses de Padua , Schneider Maria Paula C. , Miyoshi Anderson , Edman Judy , Spier Sharon , Azevedo Vasco
Published: June 2012

In this work we report the genome of
Corynebacterium pseudotuberculosis
strain 267, isolated from a llama. This pathogen is of great veterinary and economic importance, as it is the cause of caseous lymphadenitis in several livestock species around the world and causes significant losses due to the high cost of treatment.
Genetic Fine Structure of a Salmonella enterica Serovar Typhi Strain Associated with the 2005 Outbreak of Typhoid Fever in Kelantan, Malaysia
Authors: Baddam Ramani , Kumar Narender , Thong Kwai-Lin , Ngoi Soo-Tein , Teh Cindy Shuan Ju , Yap Kien-Pong , Chai Lay-Ching , Avasthi Tiruvayipati Suma , Ahmed Niyaz
Published: June 2012

Among enteric pathogens,
Salmonella enterica
serovar Typhi is responsible for the largest number of food-borne outbreaks and fatalities. The ability of the pathogen to cause systemic infection for extended durations leads to a high cost of disease control. Chronic carriers play important roles in the evolution of
Salmonella
Typhi; therefore, identification and in-depth characterization of isolates from clinical cases and carriers, especially those from zones of endemicity where the pathogen has not been extensively studied, are necessary. Here, we describe the genome sequence of the highly virulent
Salmonella
Typhi strain BL196/05 isolated during the outbreak of typhoid in Kelantan, Malaysia, in 2005. The whole-genome sequence and comparative genomics of this strain should enable us to understand the virulence mechanisms and evolutionary dynamics of this pathogen in Malaysia and elsewhere.
Draft Genome Sequence of the Purple Photosynthetic Bacterium Phaeospirillum molischianum DSM120, a Particularly Versatile Bacterium
Authors: Duquesne K. , Prima V. , Ji B. , Rouy Z. , Médigue C. , Talla E. , Sturgis J. N.
Published: June 2012

Here we present the draft genome sequence of the versatile and adaptable purple photosynthetic bacterium
Phaeospirillum molischianum
DSM120. This study advances the understanding of the adaptability of this bacterium, as well as the differences between the
Phaeospirillum
and
Rhodospirillum
genera.
Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes
Authors: Müller Miklós , Mentel Marek , van Hellemond Jaap J. , Henze Katrin , Woehle Christian , Gould Sven B. , Yu Re-Young , van der Giezen Mark , Tielens Aloysius G. M. , Martin William F.
Published: June 2012

Major insights into the phylogenetic distribution, biochemistry, and evolutionary significance of organelles involved in ATP synthesis (energy metabolism) in eukaryotes that thrive in anaerobic environments for all or part of their life cycles have accrued in recent years. All known eukaryotic groups possess an organelle of mitochondrial origin, mapping the origin of mitochondria to the eukaryotic common ancestor, and genome sequence data are rapidly accumulating for eukaryotes that possess anaerobic mitochondria, hydrogenosomes, or mitosomes. Here we review the available biochemical data on the enzymes and pathways that eukaryotes use in anaerobic energy metabolism and summarize the metabolic end products that they generate in their anaerobic habitats, focusing on the biochemical roles that their mitochondria play in anaerobic ATP synthesis. We present metabolic maps of compartmentalized energy metabolism for 16 well-studied species. There are currently no enzymes of core anaerobic energy metabolism that are specific to any of the six eukaryotic supergroup lineages; genes present in one supergroup are also found in at least one other supergroup. The gene distribution across lineages thus reflects the presence of anaerobic energy metabolism in the eukaryote common ancestor and differential loss during the specialization of some lineages to oxic niches, just as oxphos capabilities have been differentially lost in specialization to anoxic niches and the parasitic life-style. Some facultative anaerobes have retained both aerobic and anaerobic pathways. Diversified eukaryotic lineages have retained the same enzymes of anaerobic ATP synthesis, in line with geochemical data indicating low environmental oxygen levels while eukaryotes arose and diversified.
How RecBCD Enzyme and Chi Promote DNA Break Repair and Recombination: a Molecular Biologist's View
Authors: Smith Gerald R.
Published: June 2012

The repair of DNA double-strand breaks (DSBs) is essential for cell viability and important for homologous genetic recombination. In enteric bacteria such as
Escherichia coli
, the major pathway of DSB repair requires the RecBCD enzyme, a complex helicase-nuclease regulated by a simple unique DNA sequence called Chi. How Chi regulates RecBCD has been extensively studied by both genetics and biochemistry, and two contrasting mechanisms to generate a recombinogenic single-stranded DNA tail have been proposed: the nicking of one DNA strand at Chi versus the switching of degradation from one strand to the other at Chi. Which of these reactions occurs in cells has remained unproven because of the inability to detect intracellular DNA intermediates in bacterial recombination and DNA break repair. Here, I discuss evidence from a combination of genetics and biochemistry indicating that nicking at Chi is the intracellular (
in vivo
) reaction. This example illustrates the need for both types of analysis (i.e., molecular biology) to uncover the mechanism and control of complex processes in living cells.
INSTANTON REPRESENTATION OF PLEBANSKI GRAVITY: EUCLIDEAN SIGNATURE MINISUPERSPACE SOLUTION
Authors: ITA EYO EYO
Published: June 2012

Using the action for the instanton representation of Plebanski gravity (IRPG), we construct minisuperspace solutions restricted to diagonal variables. We have treated the Euclidean signature case with zero cosmological constant, depicting a gravitational analogy to free particle motion. This paper provides a testing ground for IRPG for a simple case, which will be extended to the full theory in future work.
REMARKS ON THE HARMONIC OSCILLATOR WITH A MINIMAL POSITION UNCERTAINTY
Authors: VALTANCOLI P.
Published: June 2012

We show that this problem gives rise to the same differential equation of a well known potential of ordinary quantum mechanics. However there is a subtle difference in the choice of the parameters of the hypergeometric function solving the differential equation which changes the physical discussion of the spectrum.
THE INTERACTION AND RELATIVE EFFECTIVENESS OF HARDWARE AND SOFTWARE DATA PREFETCH
Authors: VERMA SANTHOSH , KOPPELMAN DAVID M.
Published: June 2012

A major performance limiter in modern processors is the long latencies caused by data cache misses. Both compiler- and hardware-based prefetching schemes help hide these latencies and so improve performance. Compiler techniques infer memory access patterns through code analysis, and insert appropriate prefetch instructions. Hardware prefetching techniques work independently from the compiler by monitoring an access stream, detecting patterns in this stream and issuing prefetches based on these patterns. This paper looks at the interplay between compiler and hardware architecture-based prefetching techniques. Does either technique make the other one unnecessary? First, compilers' ability to achieve good results without extreme expertise is evaluated by preparing binaries with no prefetch, one-flag prefetch (no tuning), and expertly tuned prefetch. From runs of SPECcpu2006 binaries, we find that expertise avoids minor slowdown in a few benchmarks and provides substantial speedup in others. We compare software schemes to hardware prefetching schemes and our simulations show software alone substantially outperforms hardware alone on about half of a selection of benchmarks. While hardware matches or exceeds software in a few cases, software is better on average. Analysis reveals that in many cases hardware is not prefetching access patterns that it is capable of recognizing, due to some irregularities in the observed miss sequence. Hardware outperforms software on address sequences that the compiler would not guess. In general, while software is better at prefetching individual loads, hardware partly compensates for this by identifying more loads to prefetch. Using the two schemes together provides further benefits, but less than the sum of the contributions of each alone.
FINITE ELEMENT STUDY OF TRANSIENT PULSATILE MAGNETO-HEMODYNAMIC NON-NEWTONIAN FLOW AND DRUG DIFFUSION IN A POROUS MEDIUM CHANNEL
Authors: BÉG O. ANWAR , BÉG TASVEER A. , BHARGAVA R. , RAWAT S. , TRIPATHI D.
Published: June 2012

A numerical study of pulsatile hydromagnetic flow and mass transfer of a non-Newtonian biofluid through a porous channel containing a non-Darcian porous material is undertaken. An extensively-validated biofluid dynamics variational finite element code, BIOFLOW, is employed to obtain comprehensive computational solutions for the flow regime which is described using a spatially two-dimensional momentum equation and a spatially one-dimensional mass transport equation, under appropriate boundary conditions. The Nakamura-Sawada rheological model is employed which provides a higher yield stress than the Casson model. A non-Newtonian model is justified on the basis that blood exhibits deviation from Newtonian behavior at low shear rates. The conduit considered is rigid with a pulsatile pressure applied via an appropriate pressure gradient term. One hundred two-noded line elements have been employed in the computations. The influence of magnetic field on the flow is studied via the magnetohydrodynamic body force parameter (Nm), which defines the ratio of magnetic (Lorentz) retarding force to the viscous hydrodynamic force. Blood vessel blockage effects are simulated with a Darcy-Forchheimer nonlinear drag force model incorporating a Darcian linear impedance for low Reynolds numbers and a Forchheimer quadratic drag for higher Reynolds numbers. Transformed velocity and concentration profiles are plotted for the influence of Reynolds number (Re), Darcy parameter (λ), Forchheimer inertial drag parameter (NF), non-Newtonian parameter (β), and Schmidt number (Sc) and at various times (T). Three-dimensional profiles of velocity varying in space and time are also provided. Applications of the model include magnetic therapy, biomagnetic pharmaco-dynamics and the simulation of diseased arteries.
ADAMS-IWASAWA $\mathcal{N} = 8$ BLACK HOLES
Authors: CACCIATORI SERGIO LUIGI , CERCHIAI BIANCA LETIZIA , MARRANI ALESSIO
Published: June 2012

We study some of the properties of the geometry of the exceptional Lie group E7(7), which describes the U-duality of the [Formula: see text], d = 4 supergravity. In particular, based on a symplectic construction of the Lie algebra 𝔢7(7) due to Adams, we compute the Iwasawa decomposition of the symmetric space [Formula: see text], which gives the vector multiplets' scalar manifold of the corresponding supergravity theory.

The explicit expression of the Lie algebra is then used to analyze the origin of [Formula: see text] as scalar configuration of the "large" ⅛-BPS extremal black hole attractors. In this framework it turns out that the U(1) symmetry spanning such attractors is broken down to a discrete subgroup ℤ4, spoiling their dyonic nature near the origin of the scalar manifold.

This is a consequence of the fact that the maximal manifest off-shell symmetry of the Iwasawa parametrization is determined by a completely non-compact Cartan subalgebra of the maximal subgroup SL(8, ℝ) of E7(7), which breaks down the maximal possible covariance SL(8, ℝ) to a smaller SL(7, ℝ) subgroup. These results are compared with the ones obtained in other known bases, such as the Sezgin-van Nieuwenhuizen and the Cremmer-Julia /de Wit-Nicolai frames.
KRICHEVER-NOVIKOV TYPE ALGEBRAS — PERSONAL RECOLLECTIONS OF JULIUS WESS
Authors: SCHLICHENMAIER MARTIN
Published: June 2012

The author's research directions on Krichever-Novikov algebras was inspired by Julius Wess. After some recollections of Julius Wess, mainly from his Karlsruhe time, an overview over these (multi-point) algebras is given. They generalize the Witt, Virasoro, and related algebras to higher genus Riemann surfaces. Differential operator algebras, current algebras and their central extensions are discussed. For the two point situation some of these algebras were introduced by Krichever and Novikov in 1986. The multi-point generalization and the general setting is due to the author. References for further directions and applications are given.
PHONON DEPENDENCE ON THERMAL PROPERTIES OF RGaO3(R = La, Ce, Nd, Pr, Sm, Gd)
Authors: PARVEEN ATAHAR , GAUR N. K.
Published: June 2012

We have systematically investigated the effect of phonons on elastic, thermal and cohesive properties for rare earth gallates RGaO3 (R = La, Ce, Nd, Pr, Sm, Gd) by means of a Rigid Ion Model after modifying its framework to incorporate the van der Waals interactions. Besides that, we have calculated the temperature dependence of the specific heat for the present orthogallates. The results on bulk modulus, Debye temperature and specific heat reproduce well with the available experimental data.
MODELING OF FLOW FIELD AND SLAG/LIQUID INTERFACE IN THE CRYSTALLIZER SYSTEM OF A THIN SLAB STEEL CONTINUOUS CASTING
Authors: MAHMODI S. , MEISAMI A. H. , ATABAKI M. MAZAR , ABOUTALEBI M. R.
Published: June 2012

In the present investigation, a three dimensional steady flow field model inside crystallizer system of a thin slab steel continuous caster is presented using real geometrical dimension starting from the inlet port of the nozzle. The nozzle flow was modeled considering the minimum casting defects. In addition, a new numerical model is developed for a thin slab casting mold. The velocity of the liquid from the inlet and outlet of the nozzle was considered as the boundary condition. The liquid flow field was computed with main concern on the velocities exiting the nozzle ports for the flow in the liquid pool. It was shown that the fluid pattern in the liquid pool has four main fluid rings including two fluid rings provided by the outer fluid coming from the bottom outlets into the liquid pool and two small fluid rings prepared by the fluid coming from the upper inlets into the liquid pool. The flow pattern agrees well with real measurements obtained by water model. The pool simulation shows asymmetries between two sides of the flow, mainly in the lower recirculation zone. The predictions of slag/liquid interface at the top side of the nozzle and its fluctuations show good agreement with the experimental results. The maximum upward wave flow occurred because of the liquid contact to the upper ports. Hence, a maximum upward flow wave was defined to prevent any unsteady state at the highest casting speed and lowest submergence depth.
Integrated Code Generation for Loops
Authors: Eriksson Mattias , Kessler Christoph
Published: June 2012

Code generation in a compiler is commonly divided into several phases: instruction selection, scheduling, register allocation, spill code generation, and, in the case of clustered architectures, cluster assignment. These phases are interdependent; for instance, a decision in the instruction selection phase affects how an operation can be scheduled We examine the effect of this separation of phases on the quality of the generated code. To study this we have formulated optimal methods for code generation with integer linear programming; first for acyclic code and then we extend this method to modulo scheduling of loops. In our experiments we compare optimal modulo scheduling, where all phases are integrated, to modulo scheduling, where instruction selection and cluster assignment are done in a separate phase. The results show that, for an architecture with two clusters, the integrated method finds a better solution than the nonintegrated method for 27% of the instances.
A Nice Piece of Code
Authors: Neville-Neil George
Published: June 2012

In the last installment of Kode Vicious (A System is not a Product, ACM Queue 10 (4), April 2012), I mentioned that I had recently read two pieces of code that had actually lowered, rather than raised, my blood pressure. As promised, this edition’s KV covers that second piece of code.
Role of Serotonin Neurons in L-DOPA- and Graft-Induced Dyskinesia in a Rat Model of Parkinson's Disease
Authors: Shin Eunju , Tronci Elisabetta , Carta Manolo
Published: June 2012

L-DOPA, the most effective drug to treat motor symptoms of Parkinson's disease, causes abnormal involuntary movements, limiting its use in advanced stages of the disease. An increasing body of evidence points to the serotonin system as a key player in the appearance of L-DOPA-induced dyskinesia (LID). In fact, exogenously administered L-DOPA can be taken up by serotonin neurons, converted to dopamine and released as a false transmitter, contributing to pulsatile stimulation of striatal dopamine receptors. Accordingly, destruction of serotonin fibers or silencing serotonin neurons by serotonin agonists could counteract LID in animal models. Recent clinical work has also shown that serotonin neurons are present in the caudate/putamen of patients grafted with embryonic ventral mesencephalic cells, producing intense serotonin hyperinnervation. These patients experience graft-induced dyskinesia (GID), a type of dyskinesia phenotypically similar to the one induced by L-DOPA but independent from its administration. Interestingly, the 5-HT1Areceptor agonist buspirone has been shown to suppress GID in these patients, suggesting that serotonin neurons might be involved in the etiology of GID as for LID. In this paper we will discuss the experimental and clinical evidence supporting the involvement of the serotonin system in both LID and GID.
Cigarette Smoke Extract Stimulates Rat Pulmonary Artery Smooth Muscle Cell Proliferation via PKC-PDGFB Signaling
Authors: Xing Ai-ping , Du Yong-cheng , Hu Xiao-yun , Xu Jian-ying , Zhang Huan-ping , Li Yi , Nie Xin
Published: June 2012

Accumulating evidence suggests a direct role for cigarette smoke in pulmonary vascular remodeling, which contributes to the development of pulmonary hypertension. However, the molecular mechanisms underlying this process remain poorly understood. Platelet-derived growth factor (PDGF) is a potential mitogen and chemoattractant implicated in several biological processes, including cell survival, proliferation, and migration. In this study, we investigated the effect of cigarette smoke extract (CSE) on cell proliferation of rat pulmonary artery smooth muscle cells (rPASMCs). We found that stimulation of rPASMCs with CSE significantly increased cell proliferation and promoted cell cycle progression from G1 phase to the S and G2 phases. CSE treatment also significantly upregulated the mRNA and protein levels of PDGFB and PDGFRβ. Our study also revealed that Rottlerin, an inhibitor of PKCδsignaling, prevented CSE-induced cell proliferation, attenuated the increase of S and G2 phase populations induced by CSE treatment, and downregulated PDGFB and PDGFRβmRNA and protein levels in rPASMCs exposed to CSE. Collectively, our data demonstrated that CSE-induced cell proliferation of rPASMCs involved upregulation of the PKCδ-PDGFB pathway.
NUNS: A Nonuniform Network Split Method for Data-Centric Storage Sensor Networks
Authors: Lee Ki-Young , Kang Hong-Koo , Shin In-Su , Kim Jeong-Joon , Han Ki-Joon
Published: June 2012

If data have the same value frequently in a data-centric storage sensor network, then the load is concentrated on a specific sensor node and the node consumes energy rapidly. In addition, if the sensor network is expanded, the routing distance to the target sensor node becomes longer in data storing and query processing, and this increases the communication cost of the sensor network. This paper proposes a nonuniform network split(NUNS) method that distributes the load among sensor nodes in data-centric storage sensor networks and efficiently reduces the communication cost of expanding sensor networks. NUNS splits a sensor network into partitions of nonuniform sizes in a way of minimizing the difference in the number of sensor nodes and in the size of partitions, and it stores data occurring in each partition in the sensor nodes of the partition. In addition, NUNS splits each partition into zones of nonuniform sizes as many as the number of sensor nodes in the partition in a way of minimizing the difference in the size of the split zones and assigns each zone to the processing area of each sensor node. Finally, we performed various performance evaluations and proved the superiority of NUNS to existing methods.
Development of a Near-Field Bistatic Synthetic Aperture Radar for Complex Target Reconstruction
Authors: Johnson David G. , Brooker Graham M.
Published: June 2012

This paper begins with a description of the design, construction, and characterization of a small electromagnetic anechoic chamber, developed specifically to house a bistatic ISAR system for the analysis of rock samples. Particular emphasis is given to the practicalities of construction, with the intention of assisting those in a similar position, wishing to build an anechoic chamber on a tight budget. The second part of the paper outlines efficient algorithms that may be applied to the tomographic and topographic reconstruction of complex targets within the viewing geometry of this ISAR system.
Sleep Characteristics, Sleep Problems, and Associations to Quality of Life among Psychotherapists
Authors: Schlarb Angelika A. , Reis Dorota , Schröder Annette
Published: June 2012

Sleep problems, especially insomnia, are a common complaint among adults. International studies have shown prevalence rates between 4.7 and 36.2% for sleep difficulties in general, whereas 13.1–28.1% report insomnia symptoms. Sleep problems are associated with lower social and academic performance and can have a severe impact on psychological and physical health. Psychotherapists are suppliers within the public health system. The goal of this study was to outline sleep characteristics, prevalence of sleep problems, insomnia, and associations of quality of life among psychotherapists. A total of 774 psychotherapists (74.7% women; mean age 46 years) participated in the study. Sleep characteristics, sleep problems, well-being, life satisfaction and workload, as well as specific job demands, were assessed via a questionnaire. Analyses revealed that more than 4.2% of the surveyed psychotherapists have difficulties falling asleep, 12.7% often wake up in the night, and 26.6% feel tired, and 3.4% think that their interrupted sleep affects work performance. About 44.1% of them suffer from symptoms of insomnia. Path models showed that insomnia is significantly related to well-being and life satisfaction.