bluuebunny/crossref_metadata_2025 huggingface dataset:
Pond Bottom Management at Commercial Shrimp Farms in Chantaburi Province, Thailand
Authors: Yuvanatemiya Vasin , Boyd Claude E. , Thavipoke Patana
Published: October 2011

Most shrimp farmers in Chantaburi Province, Thailand, use water jets to dislodge sediment from empty pond bottoms, and wastewater is held for sedimentation before discharge into natural waters. Other pond bottom management practices used by a few farmers are sediment excavation, leave sediment but till entire pond bottom, and no mechanical treatment. All four methods of pond bottom treatment are followed by sun drying for 30 d. Soil organic carbon concentration in ponds following dry‐out seldom exceeded 2%. Although shrimp production in 24 ponds supplied by the same source of water was negatively correlated with increasing soil organic carbon concentration (r = −0.582), this observation does not confirm a causative relationship. Moreover, in trials conducted at Burapha University, Chantaburi Campus, bottom soil organic matter concentration following dry‐out differed little irrespective of treatment method. Lower soil moisture concentration revealed that dry‐out was more complete with sediment removal than without, but better dry‐out resulted in lower soil pH. Removal of sediment by excavation or flushing is expensive, and natural dry‐out combined with liming and occasional sediment removal should be investigated as a less expensive and more environment‐friendly alternative to removing sediment after each crop.
Effect of Dietary pH Adjustment on the Utilization of Supplemental Methionine and Lysine by Juvenile Common Carp, Cyprinus carpio
Authors: Deng Junming , Kong Lingfu , An Qingcong , Bi Baoliang , Tao Linli , Zhang Xi
Published: October 2011

An 8‐wk feeding trial was conducted to compare the effect of dietary pH on the utilization of crystalline amino acid (CAA, 0.2% dl‐methionine and 0.4% l‐lysine·HCl) by juvenile common carp, Cyprinus carpio. A basal diet (diet C) with protein derived mostly from fish meal and soybean meal was supplemented with CAA without pH adjustment (diet CAA, pH 6.2) and with pH adjusted to 7.0 and 8.0 (diets CAA pH 7.0, CAA pH 8.0, respectively). Supplementation of CAA, regardless of dietary pH adjustment, significantly increased the feed intake and weight gain, and the latter was significantly higher in fish fed diets CAA pH 7.0 or CAA pH 8.0 compared to fish fed diet CAA. The intestinal protease activity was significantly higher in fish fed diets CAA pH 7.0 or CAA pH 8.0 compared to fish fed diet CAA. Apparent digestibility of dry matter and crude protein in diets CAA pH 7.0 and CAA pH 8.0 were significantly higher than those in diet C. Dietary supplementation of CAA generally decreased the plasma aspartate aminotransferase (AST) and alanine aminotransferase (ALT) activities, but markedly increased the hepatic AST and ALT activities. Compared to fish fed diet CAA, fish fed diets CAA pH 7.0 or CAA pH 8.0 showed higher hepatic AST activity but slightly lower plasma ammonia level. These results indicate that adjusting the pH of CAA‐supplemented diets to neutral or slightly alkaline resulted in improving the CAA utilization by common carp.
Jerusalem in Medieval Islamic Tradition
Authors: Khalek Nancy
Published: October 2011

The history of Islamic thought about Jerusalem has been hindered by a lack of comprehensive historical sources on the city in what is traditionally thought of as the Classical period of Islam, from the 6th to the mid‐13th centuries. As a result, scholars have relied on geographical works and texts in a genre known as ‘Religious Merits’ or faḍā’ il, as well as apocalyptic and prophetic tradition (ḥadīth) for insight into the role and importance of the city for early medieval Muslims. Jerusalem’s major Islamic monuments, including the Dome of the Rock and the Aqṣā Mosque, were early Muslim buildings whose meaning changed significantly over the course of the medieval period. The incorporation of towns and cities outside Mecca and Medina into a sacred landscape encompassing broad regions such as al‐Shām/Greater Syria was partly the by‐product of the effulgence of the faḍā’ il genre, a feature of the High Middle Ages. Like Damascus, Kufa and Baghdad, among others, Jerusalem became one of a constellation of pilgrimage centers in broader conceptions of the Islamic world’s actual and sacred territory.
The Invention of Japanese Religions
Authors: Josephson Jason Ānanda
Published: October 2011

In recent years, the academic study of religion has begun to challenge the usefulness of the concept of ‘religion’ itself. This article examines the extension of this critical turn to the issue of Japanese religion. It traces the history of the invention of Japanese religions as conceptual categories and discusses debates about the continuities and discontinuities of ‘religion’ (shūkyō) in Japan. Finally, it surveys the Japanese invention of ‘religion’ as a legal and political category.
Animals in Christian Theology
Authors: Grumett David
Published: October 2011

Animals appear to have been pushed to the margins of Christian theology. Andrew Linzey’s pioneering animal theology remedied this but now requires further development. Deeper readings are needed of historical theologians like Thomas Aquinas and Augustine on the topics of reason, rights and analogy. Physiologus and later Christian bestiaries must be mined in order to show how animals and other sentient beings, both real and mythical, image Christ and Christian virtues. Furthermore, present‐day forms of animal–human relationality, including pet ownership and meat‐eating, need to be appraised theologically. The result, achieved via close textual reading, constructive synthesis and interdisciplinary engagement, will be a theological re‐evaluation of animals and other sentient beings as moral agents and theological sources.
The Effects of Social Power on Goal Content and Goal Striving: A Situated Perspective
Authors: Willis Guillermo B. , Guinote Ana
Published: October 2011

In this article, we integrate recent findings on the ways power affects goal pursuit. We review literature suggesting that power has two unique effects on goal pursuit: it affects the goals individuals choose to pursue, and the ways they pursue them. In short, we maintain that power‐holders prefer goals that suit their privileged positions – reward oriented and hierarchy‐maintenance goals – as well as goals that come easily to mind because they are chronically accessible or afforded in the situation. We go on to show that powerful individuals exhibit better self‐regulation during goal striving than powerless individuals, independently of goal content. Finally, we review conditions that reverse the effects of power on goal pursuit.
Data‐driven Methods for Modeling Social Perception
Authors: Todorov Alexander , Dotsch Ron , Wigboldus Daniel H. J. , Said Chris P.
Published: October 2011

How do we model the complexity of social perception? A major methodological problem is that the space of possible variables driving social perceptions is infinitely large, thus posing an insurmountable hurdle for conventional approaches. Here, we describe a set of data‐driven methods whose objective is to identify quantitative relationships between high‐dimensional variables (e.g., visual images) and behaviors (e.g., perceptual decisions) with as little bias as possible. We focus on social perception of faces, although the methods could be applied to other visual and nonvisual categories. We review two reverse correlation approaches: (a) psychophysical methods based on judgments of images altered with randomly generated noise, where the analysis relates the random variations of the images to judgments; and (b) methods based on judgments of randomly generated faces from a statistical, multidimensional face space model, where the analysis relates the dimensions of the face model to judgments.
How Stereotypes Stifle Performance Potential
Authors: Schmader Toni , Croft Alyssa
Published: October 2011

In academic and organizational domains, performance measures are often used to assess achievement or aptitude. When certain groups of people systematically underperform on such measures, a common interpretation is that the groups differ in inherent ability. However, social psychological research over the past 15 years has documented a phenomenon called stereotype threat whereby subtle situational reminders of negative stereotypes can stifle the performance of those who are targeted by them. In this article, we review research aimed at understanding the sequence of cognitive and affective processes that underlie these situationally‐induced performance impairments. We review evidence that being the target of negative stereotypes cues self‐uncertainty and a physiological stress response, engages more explicit monitoring of one’s performance, and efforts to regulate unwanted negative thoughts and feelings. Alone or in concert, these extra‐task processes hijack cognitive resources needed for successful performance. Armed with the knowledge of these mediating mechanisms, we then review evidence from both field and laboratory based research demonstrating that gender and racial gaps in achievement can be alleviated if not eliminated through creative and often subtle interventions that diffuse the pernicious effects that stereotypes can have.
Re‐examining Cultural Contradictions: Mothering Ideology and the Intersections of Class, Gender, and Race
Authors: Taylor Tiffany
Published: October 2011

Hays argues the dominant ideology of mothering in the United States is intensive mothering. Women embracing this ideology are completely devoted to their children and cultural contradictions of motherhood make it difficult to juggle work and family. Rothman argues further that ideologies of patriarchy, technology, and capitalism shape our notions of mothering. I explore these ideologies in this paper, paying careful attention to the labor performed by mothers – paid, childcare, and reproductive. Finally, using surrogacy as an example of how these ideologies interact, I argue that Rothman’s identifications of ideologies helps explain how the cultural contradictions of motherhood vary among mothers based on race and class.
Do Statins have a Role in Reduction/Prevention of Post‐PCI Restenosis?
Authors: Prasad Kailash
Published: October 2011

The pathophysiology of post‐PCI restenosis involves neointimal formation that consists of three phases: thrombosis (within 24 h), recruitment (3–8 days), and proliferation, which starts on day 8 of PCI. Various factors suggested to be predictors/risks for restenosis include C‐reactive protein (CRP), inflammatory mediators (cytokines and adhesion molecules), oxygen radicals, advanced glycation end products (AGEs) and their receptors (RAGE), and soluble RAGE (sRAGE). The earlier noted factors produce thrombogenesis, vascular smooth muscle cell proliferation, and extracellular matrix formation. Statins have pleiotropic effects. Besides lowering serum cholesterol, they have various other biological effects including antiinflammatory, antithrombotic, CRP‐lowering, antioxidant, antimitotic, and inhibition of smooth muscle cell proliferation. They inhibit matrix metalloproteinase and cyclooxygenase‐2, lower AGEs, decrease expression of RAGE and increase levels of serum sRAGE. They also increase the synthesis of nitric oxide (NO) by increasing endothelial NO synthase expression and activity. Preprocedural statin therapy is known to reduce peri‐ and post‐PCI myonecrosis and reduce the need for repeat revascularization. There is evidence that statin‐eluting stents inhibit in‐stent restenosis in animal models. It is concluded that because of the above attributes of statins, they are suitable candidates for reduction of post‐PCI restenosis and post‐PCI myonecrosis. The future directions for the use of statins in reduction of post‐PCI restenosis and myonecrosis have been discussed.
Lifecycle Pricing for Installed Base Management with Constrained Capacity and Remanufacturing
Authors: Robotis Andreas , Bhattacharya Shantanu , Van Wassenhove Luk N.
Published: October 2011

Installed base management is the policy in which the manufacturer leases the product to consumers, and bundles repair and maintenance services along with the product. In this article, we investigate for the optimal leasing price and leasing duration decisions by a monopolist when the production and servicing capacity are constrained. The effect of diffusion of consumers in the installed base is considered, with the ownership of the product resting with the monopolist during the product lifecycle. The monopolist operating the installed base jointly optimizes the profits from leasing the product/service bundle along with maintenance revenues and remanufacturing savings. We formulate the manufacturer's problem as an optimal control problem and show that the optimal pricing strategy of the firm should be a skimming strategy. We also find that the effect of remanufacturing savings on the pricing decision and the length of the leasing duration changes significantly depending on the duration of the product's lifecycle. If the product lifecycle is long and remanufacturing savings are low, the firm should offer a shorter leasing duration, whereas if the remanufacturing savings are high, the firm should optimally offer a higher leasing duration. In contrast, if the time duration of the product lifecycle is low and remanufacturing savings are low, the firm prefers to offer a shorter leasing duration, whereas if the remanufacturing savings are high, the firm should optimally have a longer leasing duration. The article also shows that if the production capacity is small, the manufacturer increases the leasing duration. If the production capacity is very small, the manufacturer sets the leasing duration to be equal to the product lifecycle and does not use remanufacturing.
A “Coprolitic Vision” for Earth Science Education
Authors: Clary Renee M. , Wandersee James H.
Published: October 2011

William Buckland (1784–1846) first identified and scientifically studied coprolites in the early 1820s. Although some of his contemporaries did not look favorably upon him or his research, Buckland's early experiments advanced paleoecology and taphonomy. Because our informal presentations with coprolites resulted in students' spirited reactions, we investigated whether coprolite introduction, accompanied with its history of science, had potential for meaningful learning in K‐12 Earth Science classrooms. Practicing Earth Science teachers (N = 28) enrolled in an online paleontology course researched coprolites, identified potential student interest, and designed coprolite activities for their individual classrooms. Resulting projects were diverse and creative, and incorporated investigations into fossilization processes, paleoenvironments, food chains, and geologic time. In anonymous surveys, teachers indicated that their students' interest in coprolites is high. We propose inclusion of coprolites and their history in Earth Science classrooms as a portal to hook students' interest and as springboard to additional scientific topics.
Metabolism of sugars by genetically diverse species of oral Leptotrichia
Authors: Thompson J. , Pikis A.
Published: October 2011

Leptotrichia buccalis ATCC 14201 is a gram‐negative, anaerobic rod‐shaped bacterium resident in oral biofilm at the tooth surface. The sequenced genome of this organism reveals three contiguous genes at loci: Lebu_1525, Lebu_1526 and Lebu_1527. The translation products of these genes exhibit significant homology with phospho‐α‐glucosidase (Pagl), a regulatory protein (GntR) and a phosphoenol pyruvate‐dependent sugar transport protein (EIICB), respectively. In non‐oral bacterial species, these genes comprise the sim operon that facilitates sucrose isomer metabolism. Growth studies showed that L. buccalis fermented a wide variety of carbohydrates, including four of the five isomers of sucrose. Growth on the isomeric disaccharides elicited expression of a 50‐kDa polypeptide comparable in size to that encoded by Lebu_1525. The latter gene was cloned, and the expressed protein was purified to homogeneity from Escherichia coli TOP10 cells. In the presence of two cofactors, NAD+ and Mn2+ ions, the enzyme readily hydrolyzed p‐nitrophenyl‐α‐glucopyranoside 6‐phosphate (pNPαG6P), a chromogenic analogue of the phosphorylated isomers of sucrose. By comparative sequence alignment, immunoreactivity and signature motifs, the enzyme can be assigned to the phospho‐α‐glucosidase (Pagl) clade of Family 4 of the glycosyl hydrolase super family. We suggest that the products of Lebu_1527 and Lebu_1525, catalyze the phosphorylative translocation and hydrolysis of sucrose isomers in L. buccalis, respectively. Four genetically diverse, but 16S rDNA‐related, species of Leptotrichia have recently been described: L. goodfellowii, L. hofstadii, L. shahii and L. wadei. The phenotypic traits of these new species, with respect to carbohydrate utilization, have also been determined.
Initial evaluation of the effects of competitive memory training (COMET) on depression in schizophrenia‐spectrum patients with persistent auditory verbal hallucinations: A randomized controlled trial
Authors: van der Gaag Mark , van Oosterhout Bas , Daalman Kirstin , Sommer Iris E , Korrelboom Kees
Published: October 2011

Objectives.  This study investigates whether depression can be ameliorated by weakening the associations between auditory verbal hallucinations and easily activated networks with negative self‐evaluations, by strengthening the access to competing memories of positive self‐esteem.

Design.  A randomized controlled clinical trial comparing competitive memory training (COMET) with treatment as usual (TAU) in schizophrenia patients with persistent auditory hallucinations.

Methods.  Patients with schizophrenia‐spectrum disorders were randomized into COMET (n = 39) versus TAU (n = 38). COMET consisted of seven sessions with four stages: (1) identification of aspects of negative self‐esteem reinforced by the voice; (2) retrieval and re‐living of memories associated with positive self‐esteem; (3) positive self‐esteem is brought in to compete with the content of the voices to weaken the association between voice content and negative self‐evaluation; and (4) learning to disengage from the voices and to accept the voices as psychic phenomena.

Results.  Compared to TAU the COMET group improved on depression but there were no significant effects on auditory hallucinations. The effect of COMET on depression was fully mediated by self‐esteem and acceptance of voices, and partially mediated by social rank and attributed power to the voices.

Conclusions.  COMET can be helpful in reappraising the meaning and changing the emotional impact of auditory hallucinations. These findings are consistent with the results of comparable COMET protocols applied in other psychiatric diagnoses. The technique can be used within regular cognitive behavioural therapy.
Myocardial contractile and metabolic properties of familial hypertrophic cardiomyopathy caused by cardiac troponin I gene mutations: a simulation study
Authors: Wu Bo , Wang Longhui , Liu Qian , Luo Qingming
Published: October 2011

Familial hypertrophic cardiomyopathy (FHC) is an inherited disease that is caused by sarcomeric protein gene mutations. The mechanism by which these mutant proteins cause disease is uncertain. Experimentally, cardiac troponin I (CTnI) gene mutations mainly alter myocardial performance via increases in the Ca2+ sensitivity of cardiac contractility. In this study, we used an integrated simulation that links electrophysiology, contractile activity and energy metabolism of the myocardium to investigate alterations in myocardial contractile function and energy metabolism regulation as a result of increased Ca2+ sensitivity in CTnI mutations. Simulation results reproduced the following typical features of FHC: (1) slower relaxation (diastolic dysfunction) caused by prolonged [Ca2+]i and force transients; (2) higher energy consumption with the increase in Ca2+ sensitivity; and (3) reduced fatty acid oxidation and enhanced glucose utilization in hypertrophied heart metabolism. Furthermore, the simulation indicated that in conditions of high energy consumption (that is, more than an 18.3% increase in total energy consumption), the myocardial energetic metabolic network switched from a net consumer to a net producer of lactate, resulting in a low coupling of glucose oxidation to glycolysis, which is a common feature of hypertrophied hearts. This study provides a novel systematic myocardial contractile and metabolic analysis to help elucidate the pathogenesis of FHC and suggests that the alterations in resting heart energy supply and demand could contribute to disease progression.
Early postmyocardial infarction survival in Murphy Roths Large mice is mediated by attenuated apoptosis and inflammation but depends on genetic background
Authors: Hunt Darlene L. , Campbell Patrick H. , Zambon Alexander C. , Vranizan Karen , Evans Sylvia M. , Kuo Hai‐Chien , Yamaguchi Ken D. , Omens Jeffrey H. , McCulloch Andrew D.
Published: October 2011

The Murphy Roths Large (MRL) mouse, a strain capable of regenerating right ventricular myocardium, has a high postmyocardial infarction (post‐MI) survival rate compared with C57BL/6J (C57) mice. The biological processes responsible for this survival advantage are unknown. To assess the effect of genetic background, the LG/J strain, which harbours 75% of the MRL composite genome, was included in the study. The MRL survival advantage versus C57 mice (92 versus 68%, P < 0.05) occurred primarily in the first 5 days; LG/J survival was intermediate (P= n.s.). Microarray data analysis revealed an attenuation of apoptotic (P < 0.05) and stress response transcripts in MRL hearts compared with C57 hearts post‐MI. Supporting the microarray results, there were fewer TUNEL‐positive cells 1 day post‐MI in MRL infarcts compared with C57 infarcts (P= 0.001) and fewer CD45‐positive cells in the MRL infarct border zone 2 days post‐MI (P < 0.01); the LG/J results were intermediate (P= n.s.). The MRL hearts had smaller infarct scars and attenuated ventricular dilatation 30 days post‐MI compared with C57 hearts (P < 0.05). We conclude that the early post‐MI survival advantage of MRL mice over the C57 strain is mediated at least in part by reductions in apoptosis and inflammatory infiltration, and that these reductions may influence chronic remodelling. The intermediate survival, apoptosis and inflammation profile of LG/J mice suggests that this high tolerance for MI in the MRL mouse could be derived from its shared genetic background with the LG/J mouse.
Twelve weeks of treadmill exercise does not alter age‐dependent chronic kidney disease in the Fisher 344 male rat
Authors: Moningka Natasha C. , Sindler Amy L. , Muller‐Delp Judy M. , Baylis Chris
Published: October 2011

Non‐technical summary  In older people, the function of the kidney deteriorates, and one possible way to slow this process down is through exercise. Exercise increases the abundance of important enzymes that are needed for optimal vessel health and kidney function, for instance the nitric oxide synthase and superoxide dismutase (SOD) enzymes. It also reduces oxidative stress, a type of cellular injury caused by highly reactive molecules. When we compared young and old sedentary rats to young and old exercise‐trained (12 weeks treadmill) rats, we found that exercise was not effective in reversing the age‐related kidney changes. In old rats, renal function declined as did the abundance of the protective SOD enzymes, and oxidative stress increased; interestingly, exercise did not influence these changes. Our results suggest that the cardiovascular benefits of exercise do not necessarily extend to the kidney.
Defects in Ca2+ release associated with local expression of pathological ryanodine receptors in mouse muscle fibres
Authors: Lefebvre Romain , Legrand Claude , González‐Rodríguez Estela , Groom Linda , Dirksen Robert T. , Jacquemond Vincent
Published: October 2011

Non‐Technical Summary  Calcium ions flowing through the type 1 ryanodine receptor (RyR1) calcium channel trigger contraction of skeletal muscle cells. Close to 300 mutations of the gene encoding RyR1 are responsible for several muscular diseases in human. Properties of pathological mutant RyR1s have so far been essentially assessed from studies in cultured cells and in differentiated native muscle fibres from a few available transgenic mouse models. We show that functional properties of mutant RyR1s can be reliably assessed following in vivo expression in adult mouse muscles. The Y523S, R615C and R2163H RyR1 mutants produce a similar over‐sensitive activation of the calcium flux whereas I4897T RyR1 mutants are responsible for a depressed Ca2+ flux. The alterations appear to result from inherent modifications of RyR1 channel function and not from indirect changes in the muscle fibre homeostasis. The present strategy will help understand the physio‐pathological defects underlying alterations of muscle function in affected patients.
Comparative Effectiveness of Aminoglycosides, Polymyxin B, and Tigecycline for Clearance of Carbapenem-Resistant Klebsiella pneumoniae from Urine
Authors: Satlin Michael J. , Kubin Christine J. , Blumenthal Jill S. , Cohen Andrew B. , Furuya E. Yoko , Wilson Stephen J. , Jenkins Stephen G. , Calfee David P.
Published: October 2011

Carbapenem-resistant
Klebsiella pneumoniae
(CRKP) is an increasingly common cause of health care-associated urinary tract infections. Antimicrobials with
in vitro
activity against CRKP are typically limited to polymyxins, tigecycline, and often, aminoglycosides. We conducted a retrospective cohort study of cases of CRKP bacteriuria at New York-Presbyterian Hospital from January 2005 through June 2010 to compare microbiologic clearance rates based on the use of polymyxin B, tigecycline, or an aminoglycoside. We constructed three active antimicrobial cohorts based on the active agent used and an untreated cohort of cases that did not receive antimicrobial therapy with Gram-negative activity. Microbiologic clearance was defined as having a follow-up urine culture that did not yield CRKP. Cases without an appropriate follow-up culture or that received multiple active agents or less than 3 days of the active agent were excluded. Eighty-seven cases were included in the active antimicrobial cohorts, and 69 were included in the untreated cohort. The microbiologic clearance rate was 88% in the aminoglycoside cohort (
n
= 41), compared to 64% in the polymyxin B (
P
= 0.02;
n
= 25), 43% in the tigecycline (
P
< 0.001;
n
= 21), and 36% in the untreated (
P
< 0.001;
n
= 69) cohorts. Using multivariate analysis, the odds of clearance were lower for the polymyxin B (odds ratio [OR], 0.10;
P
= 0.003), tigecycline (OR, 0.08;
P
= 0.001), and untreated (OR, 0.14;
P
= 0.003) cohorts than for the aminoglycoside cohort. Treatment with an aminoglycoside, when active
in vitro
, was associated with a significantly higher rate of microbiologic clearance of CRKP bacteriuria than treatment with either polymyxin B or tigecycline.
Candida albicans Infections in Renal Transplant Recipients: Effect of Caspofungin on Polymorphonuclear Cells
Authors: Allizond Valeria , Banche Giuliana , Giacchino Franca , Merlino Chiara , Scalas Daniela , Tullio Vivian , Garneri Giuseppe , Mandras Narcisa , Roana Janira , Cuffini Anna Maria
Published: October 2011

This study aimed to compare the caspofungin immunomodulating activities against
Candida albicans
on polymorphonuclear cells (PMNs) from renal transplant recipients (RTRs) and healthy subjects (HSs). RTR PMNs showed a significantly reduced fungicidal activity compared with that of HS PMNs. Addition of caspofungin to RTR PMNs significantly potentiated the yeast intracellular killing rate, achieving values similar to those observed for HS PMNs. These data show that caspofungin is suitable for invasive candidiasis treatment in patients with immune system-impaired components.
Cyclopropavir Susceptibility of Cytomegalovirus DNA Polymerase Mutants Selected after Antiviral Drug Exposure
Authors: Chou Sunwen , Marousek Gail , Bowlin Terry L.
Published: October 2011

Human cytomegalovirus (CMV) UL54 DNA polymerase (
pol
) mutants with known patterns of resistance to current antivirals ganciclovir (GCV), foscarnet (FOS), and cidofovir (CDV) were tested for cyclopropavir (CPV) susceptibility by a standardized reporter-based yield reduction assay. Exonuclease and A987G (region V) mutations at codons commonly associated with dual GCV-CDV resistance in clinical isolates paradoxically conferred increased CPV susceptibility. Various polymerase catalytic region mutations conferring FOS resistance with variable low-grade GCV and CDV cross-resistance also conferred CPV resistance, with 50% effective concentration (EC
50
) increases of 3- to 13-fold. CPV EC
50
values against several
pol
mutants were increased about 2-fold by adding UL97 mutation C592G. Propagation of a CMV exonuclease mutant under CPV selected for
pol
mutations less often than UL97 mutations. In 21 experiments, one instance each of mutations E756D and M844V, which were shown individually to confer 3- to 4-fold increases in CPV EC
50
, was detected. Unlike GCV and CDV, exonuclease mutations are not a preferred mechanism of CPV resistance, but mutations in and near
pol
region III may confer CPV resistance by affecting its recognition as an incoming base for DNA polymerization.
Chronological Aging Is Associated with Biophysical and Chemical Changes in the Capsule of Cryptococcus neoformans
Authors: Cordero Radames J. B. , Pontes Bruno , Guimarães Allan J. , Martinez Luis R. , Rivera Johanna , Fries Bettina C. , Nimrichter Leonardo , Rodrigues Marcio L. , Viana Nathan B. , Casadevall Arturo
Published: October 2011

Does the age of a microbial cell affect its virulence factors? To our knowledge, this question has not been addressed previously, but the answer is of great relevance for chronic infections where microbial cells persist and age in hosts.Cryptococcus neoformansis an encapsulated human-pathogenic fungus notorious for causing chronic infections where cells of variable age persist in tissue. The major virulence factor forC. neoformansis a polysaccharide (PS) capsule. To understand how chronological age could impact the cryptococcal capsule properties, we compared the elastic properties, permeabilities, zeta potentials, and glycosidic compositions of capsules from young and old cells and found significant differences in all parameters measured. Changes in capsular properties were paralleled by changes in PS molecular mass and density, as well as modified antigenic density and antiphagocytic properties. Remarkably, chronological aging under stationary-phase growth conditions was associated with the expression of α-1,3-glucans in the capsule, indicating a new structural capsular component. Our results establish that cryptococcal capsules are highly dynamic structures that change dramatically with chronological aging under prolonged stationary-phase growth conditions. Changes associated with cellular aging in chronic infections could contribute to the remarkable capacity of this fungus to persist in tissues by generating phenotypically and antigenically different capsules.
Setting up and maintaining differential insulators and boundaries for genomic imprinting
Authors: Murrell Adele
Published: October 2011

It is becoming increasingly clear that gene expression is strongly regulated by the surrounding chromatin and nuclear environment. Gene regulatory elements can influence expression over long distances and the genome needs mechanisms whereby transcription can be contained. Our current understanding of the mechanisms whereby insulator/boundary elements organise the genome into active and silent domains is based on chromatin looping models that separate genes and regulatory elements. Imprinted genes have parent-of-origin specific chromatin conformation that seems to be maintained in somatic tissues and reprogrammed in the germline. This review focuses on the proteins found to be present at insulator/boundary sequences at imprinted genes and examines the experimental evidence at the IGF2-H19 locus for a model in which CTCF or other proteins determine primary looping scaffolds that are maintained in most cell lineages and speculates how these loops may enable dynamic secondary associations that can activate or silence genes.
Genetic mating system and population history of the endangered Western Yellow-breasted Chat (Icteria virens auricollis) in British Columbia, Canada
Authors: Miño Carolina I. , Pollet Ingrid L. , Bishop Christine A. , Russello Michael A.
Published: October 2011

The Western Yellow-breasted Chat ( Icteria virens auricollis (Deppe, 1830)) is a Neotropical migrant, with a Canadian distribution restricted to breeding populations in southern British Columbia. Given its small population size and diminishing breeding habitat, Yellow-breasted Chats are federally endangered in Canada. We used genotypic data at eight microsatellite loci to assess genetic diversity, reconstruct population structure and demographic history, and characterize genetic mating system of Yellow-breasted Chats sampled across 60 nesting sites at five locations in the Okanagan Valley (n = 148). Microsatellite-based analyses indicated lack of significant genetic differentiation among breeding sites and no genetic evidence of population decline. Parentage assignments indicated moderate levels of extra-pair paternity, with 30.7% offspring not sired by attending males. Patterns of sibship among nestlings revealed 49.1% of the clutches were composed entirely of full-siblings, with half-siblings and unrelated nestlings present in some broods. These findings suggest that extra-pair paternity is common in Yellow-breasted Chats, similar to other avian species, and present the first evidence of conspecific brood parasitism in warblers. Our findings add to a growing body of research informing the need to establish a national park in the south Okanagan to preserve critical habitat and connect populations of species at risk.
Contender pressure versus resource dispersion as predictors of territory size of coyotes (Canis latrans)
Authors: Wilson R.R. , Shivik J.A.
Published: October 2011

Many studies have proposed resource dispersion as the main determinant of territory size in coyotes ( Canis latrans Say, 1823), but few have considered contender pressure as an alternative hypothesis. We tested for differences in rates of intra-territorial visitation, movement, and extra-territorial excursions between two populations of coyotes with large differences in territory sizes. We collected fine-scale (15 min) movement data of coyotes in southeastern Texas and south-central Idaho. Both populations were active for similar lengths of each day, but coyotes in Idaho had territories 10× larger, moved 2× faster, traveled 2× farther daily, and made extra-territorial excursions 3× less. Even with increased movement rates, coyotes in Idaho traversed territories slower than coyotes in Texas as predicted by the contender pressure hypothesis. We propose that in regions with high resource abundance, territory size of coyotes is determined by contender pressure and an inability to defend larger areas. Conversely, in low-resource areas, territory sizes are determined more by prey abundance and dispersion because intrusion rates are reduced given the lower density of conspecifics.
Can changes in provisioning by parent birds account for seasonally declining patterns of offspring recruitment?
Authors: Bortolotti L.E. , Harriman V.B. , Clark R.G. , Dawson R.D.
Published: October 2011

Declining reproductive success among individuals that breed later in the season occurs in numerous taxa and is particularly well-documented in birds. Principal ideas advanced to explain this pattern, the date and parental quality hypotheses, consider the ultimate causes of this phenomenon and have received much attention; however, proximate mechanisms have not been clearly elucidated. Parental provisioning could mediate a seasonal decline in nestling fitness. We delayed hatch dates and manipulated brood sizes of Tree Swallows ( Tachycineta bicolor (Vieillot, 1808)) to assess the ability of parents to compensate for deteriorating environmental conditions and increased demands of more chicks. We measured provisioning rates using audio recordings of nestlings begging. Brood size was the best predictor of provisioning frequency, with parents feeding larger broods more frequently than smaller ones. Delayed hatching did not reduce provisioning rate despite declining food abundance. Date and food abundance were unrelated to provisioning rate, suggesting no seasonal change in the quantity of food nestlings receive. However, provisioning frequency was informative about life-history strategies of Tree Swallows, showing that late breeders incurred the costs of deteriorating environmental conditions rather than passing these costs on to their offspring.
Enzymatic flux capacities in hummingbird flight muscles: a “one size fits all” hypothesis
Authors: Fernández M.J. , Bozinovic F. , Suarez R.K.
Published: October 2011

Hummingbirds (family Trochilidae) are among the smallest endothermic vertebrates representing an extreme, among birds, in their physiological design. They are unique in their ability to sustain hovering flight, one of the most energetically demanding forms of locomotion. Given that hovering metabolic rate (HMR) in hummingbirds scales allometrically as M0.78(M is mass), we tested the hypothesis that variation in HMR may be correlated with variation in maximal enzyme activities (Vmaxvalues) of key enzymes in glucose and fatty acid oxidation pathways in the flight muscles of four species of hummingbirds ranging in body mass from 4 to 20 g. We also estimated metabolic flux rates from respirometric data obtained during hovering flight. The data are striking in the lack of correlation between Vmaxvalues and flux rates at most steps in energy metabolism, particularly at the hexokinase and carnitine palmitoyltransferase reactions. In the context of hierarchical regulation analysis, this finding suggests that metabolic regulation (resulting from variation in substrate, product, or allosteric regulator concentrations) dominates as the proximate explanation for the interspecific variation in flux. On the other hand, we found no evidence of hierarchical regulation of flux, which results from variation in Vmaxand is based on variation in enzyme concentration [E]. The evolutionary conservation of pathways of energy metabolism suggests that “one size fits all” among hummingbirds.
Empowering End Users to Confine Their Own Applications
Authors: Schreuders Z. Cliffe , McGill Tanya , Payne Christian
Published: October 2011

Protecting end users from security threats is an extremely difficult, but increasingly critical, problem. Traditional security models that focused on separating users from each other have proven ineffective in an environment of widespread software vulnerabilities and rampant malware. However, alternative approaches that provide more finely grained security generally require greater expertise than typical end users can reasonably be expected to have, and consequently have had limited success.

The functionality-based application confinement (FBAC) model is designed to allow end users with limited expertise to assign applications hierarchical and parameterised policy abstractions based upon the functionalities each program is intended to perform. To validate the feasibility of this approach and assess the usability of existing mechanisms, a usability study was conducted comparing an implementation of the FBAC model with the widely used Linux-based SELinux and AppArmor security schemes. The results showed that the functionality-based mechanism enabled end users to effectively control the privileges of their applications with far greater success than widely used alternatives. In particular, policies created using FBAC were more likely to be enforced and exhibited significantly lower risk exposure, while not interfering with the ability of the application to perform its intended task. In addition to the success of the functionality-based approach, the usability study also highlighted a number of limitations and problems with existing mechanisms. These results indicate that a functionality-based approach has significant potential in terms of enabling end users with limited expertise to defend themselves against insecure and malicious software.
Practical Oblivious Outsourced Storage
Authors: Williams Peter , Sion Radu , Sotakova Miroslava
Published: October 2011

In this article we introduce a technique, guaranteeing access pattern privacy against a computationally bounded adversary, in outsourced data storage, with communication and computation overheads orders of magnitude better than existing approaches. In the presence of a small amount of temporary storage (enough to store
O
(√
n
log
n
) items and IDs, where
n
is the number of items in the database), we can achieve access pattern privacy with computational complexity of less than
O
(log
2
n
) per query (as compared to, for instance,
O
(log
4
n
) for existing approaches).

We achieve these novel results by applying new insights based on probabilistic analyses of data shuffling algorithms to Oblivious RAM, allowing us to significantly improve its asymptotic complexity. This results in a protocol crossing the boundary between theory and practice and becoming generally applicable for access pattern privacy. We show that on off-the-shelf hardware, large data sets can be queried obliviously orders of magnitude faster than in existing work.
CANTINA+
Authors: Xiang Guang , Hong Jason , Rose Carolyn P. , Cranor Lorrie
Published: October 2011

Phishing is a plague in cyberspace. Typically, phish detection methods either use human-verified URL blacklists or exploit Web page features via machine learning techniques. However, the former is frail in terms of new phish, and the latter suffers from the scarcity of effective features and the high false positive rate (FP). To alleviate those problems, we propose a layered anti-phishing solution that aims at (1) exploiting the expressiveness of a rich set of features with machine learning to achieve a high true positive rate (TP) on novel phish, and (2) limiting the FP to a low level via filtering algorithms.

Specifically, we proposed CANTINA+, the most comprehensive feature-based approach in the literature including eight novel features, which exploits the HTML Document Object Model (DOM), search engines and third party services with machine learning techniques to detect phish. Moreover, we designed two filters to help reduce FP and achieve runtime speedup. The first is a near-duplicate phish detector that uses hashing to catch highly similar phish. The second is a login form filter, which directly classifies Web pages with no identified login form as legitimate.

We extensively evaluated CANTINA+ with two methods on a diverse spectrum of corpora with 8118 phish and 4883 legitimate Web pages. In the randomized evaluation, CANTINA+ achieved over 92% TP on unique testing phish and over 99% TP on near-duplicate testing phish, and about 0.4% FP with 10% training phish. In the time-based evaluation, CANTINA+ also achieved over 92% TP on unique testing phish, over 99% TP on near-duplicate testing phish, and about 1.4% FP under 20% training phish with a two-week sliding window. Capable of achieving 0.4% FP and over 92% TP, our CANTINA+ has been demonstrated to be a competitive anti-phishing solution.
Programming the cloud
Authors: Larus James R.
Published: October 2011

Client + cloud computing is a disruptive, new computing platform, combining diverse client devices -- PCs, smartphones, sensors, and single-function and embedded devices -- with the unlimited, on-demand computation and data storage offered by cloud computing services such as Amazon's AWS or Microsoft's Windows Azure. As with every advance in computing, programming is a fundamental challenge as client + cloud computing combines many difficult aspects of software development. Systems built for this world are inherently parallel and distributed, run on unreliable hardware, and must be continually available -- a challenging programming model for even the most skilled programmers. How then do ordinary programmers develop software for the Cloud? This talk presents one answer, Orleans, a software framework for building client + cloud applications. Orleans encourages use of simple concurrency patterns that are easy to understand and implement correctly, building on an actor-like model with declarative specification of persistence, replication, and consistency and using lightweight transactions to support the development of reliable and scalable client + cloud software.
Ordered vs. unordered
Authors: Hassaan Muhammad Amber , Burtscher Martin , Pingali Keshav
Published: October 2011

Outside of computational science, most problems are formulated in terms of irregular data structures such as graphs, trees and sets. Unfortunately, we understand relatively little about the structure of parallelism and locality in irregular algorithms. In this paper, we study multiple algorithms for four such problems: discrete-event simulation, single-source shortest path, breadth-first search, and minimal spanning trees. We show that the algorithms can be classified into two categories that we call unordered and ordered, and demonstrate experimentally that there is a trade-off between parallelism and work efficiency: unordered algorithms usually have more parallelism than their ordered counterparts for the same problem, but they may also perform more work. Nevertheless, our experimental results show that unordered algorithms typically lead to more scalable implementations, demonstrating that less work-efficient irregular algorithms may be better for parallel execution.
All-window profiling and composable models of cache sharing
Authors: Xiang Xiaoya , Bao Bin , Bai Tongxin , Ding Chen , Chilimbi Trishul
Published: October 2011

As multi-core processors become commonplace and cloud computing is gaining acceptance, more applications are run in a shared cache environment. Cache sharing depends on a concept called footprint, which depends on all cache accesses not just cache misses. Previous work has recognized the importance of footprint but has not provided a method for accurate measurement, mainly because the complete measurement requires counting data access in all execution windows, which takes time quadratic in the length of a trace. The paper first presents an algorithm efficient enough for off-line use to approximately measure the footprint with a guaranteed precision. The cost of the analysis can be adjusted by changing the precision. Then the paper presents a composable model. For a set of programs, the model uses the all-window footprint of each program to predict its cache interference with other programs without running these programs together. The paper evaluates the efficiency of all-window profiling using the SPEC 2000 benchmarks and compares the footprint interference model with a miss-rate based model and with exhaustive testing.
How's the parallel computing revolution going?
Authors: McKinley Kathryn S.
Published: October 2011

Two trends changed the computing landscape over the past decade: (1) hardware vendors started delivering chip multiprocessors (CMPs) instead of uniprocessors, and (2) software developers increasingly chose managed languages instead of native languages. Unfortunately, the former change is disrupting the virtuous-cycle between performance improvements and software innovation. Establishing a new parallel performance virtuous cycle for managed languages will require scalable applications executing on scalable Virtual Machine (VM) services, since the VM schedules, monitors, compiles, optimizes, garbage collects, and executes together with the application. This talk describes current progress, opportunities, and challenges for scalable VM services. The parallel computing revolution urgently needs more innovations.